Mao, Jian-Feng - Plant genomics

@article{shi_differential_2024,
	title = {Differential gene expression and potential regulatory network of fatty acid biosynthesis during fruit and leaf development in yellowhorn ({Xanthoceras} sorbifolium), an oil-producing tree with significant deployment values},
	volume = {14},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1297817},
	abstract = {Xanthoceras sorbifolium (yellowhorn) is a woody oil plant with super stress resistance and excellent oil characteristics. The yellowhorn oil can be used as biofuel and edible oil with high nutritional and medicinal value. However, genetic studies on yellowhorn are just in the beginning, and fundamental biological questions regarding its very long-chain fatty acid (VLCFA) biosynthesis pathway remain largely unknown. In this study, we reconstructed the VLCFA biosynthesis pathway and annotated 137 genes encoding relevant enzymes. We identified four oleosin genes that package triacylglycerols (TAGs) and are specifically expressed in fruits, likely playing key roles in yellowhorn oil production. Especially, by examining time-ordered gene co-expression network (TO-GCN) constructed from fruit and leaf developments, we identified key enzymatic genes and potential regulatory transcription factors involved in VLCFA synthesis. In fruits, we further inferred a hierarchical regulatory network with MYB-related (XS03G0296800) and B3 (XS02G0057600) transcription factors as top-tier regulators, providing clues into factors controlling carbon flux into fatty acids. Our results offer new insights into key genes and transcriptional regulators governing fatty acid production in yellowhorn, laying the foundation for efforts to optimize oil content and fatty acid composition. Moreover, the gene expression patterns and putative regulatory relationships identified here will inform metabolic engineering and molecular breeding approaches tailored to meet biofuel and bioproduct demands.},
	urldate = {2024-02-16},
	journal = {Frontiers in Plant Science},
	author = {Shi, Tian-Le and Ma, Hai-Yao and Wang, Xinrui and Liu, Hui and Yan, Xue-Mei and Tian, Xue-Chan and Li, Zhi-Chao and Bao, Yu-Tao and Chen, Zhao-Yang and Zhao, Shi-Wei and Xiang, Qiuhong and Jia, Kai-Hua and Nie, Shuai and Guan, Wenbin and Mao, Jian-Feng},
	month = jan,
	year = {2024},
	keywords = {⛔ No DOI found},
}

Xanthoceras sorbifolium (yellowhorn) is a woody oil plant with super stress resistance and excellent oil characteristics. The yellowhorn oil can be used as biofuel and edible oil with high nutritional and medicinal value. However, genetic studies on yellowhorn are just in the beginning, and fundamental biological questions regarding its very long-chain fatty acid (VLCFA) biosynthesis pathway remain largely unknown. In this study, we reconstructed the VLCFA biosynthesis pathway and annotated 137 genes encoding relevant enzymes. We identified four oleosin genes that package triacylglycerols (TAGs) and are specifically expressed in fruits, likely playing key roles in yellowhorn oil production. Especially, by examining time-ordered gene co-expression network (TO-GCN) constructed from fruit and leaf developments, we identified key enzymatic genes and potential regulatory transcription factors involved in VLCFA synthesis. In fruits, we further inferred a hierarchical regulatory network with MYB-related (XS03G0296800) and B3 (XS02G0057600) transcription factors as top-tier regulators, providing clues into factors controlling carbon flux into fatty acids. Our results offer new insights into key genes and transcriptional regulators governing fatty acid production in yellowhorn, laying the foundation for efforts to optimize oil content and fatty acid composition. Moreover, the gene expression patterns and putative regulatory relationships identified here will inform metabolic engineering and molecular breeding approaches tailored to meet biofuel and bioproduct demands.

@article{shi_high-quality_2024,
	title = {High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiae078},
	doi = {10.1093/plphys/kiae078},
	abstract = {Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio High-Fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the two parents of the well-studied F1 hybrid “84K” (Populus alba × P. tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from two small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the two subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77\% accuracy on the training set and 74\% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.},
	urldate = {2024-03-01},
	journal = {Plant Physiology},
	author = {Shi, Tian-Le and Jia, Kai-Hua and Bao, Yu-Tao and Nie, Shuai and Tian, Xue-Chan and Yan, Xue-Mei and Chen, Zhao-Yang and Li, Zhi-Chao and Zhao, Shi-Wei and Ma, Hai-Yao and Zhao, Ye and Li, Xiang and Zhang, Ren-Gang and Guo, Jing and Zhao, Wei and El-Kassaby, Yousry Aly and Müller, Niels and Van de Peer, Yves and Wang, Xiao-Ru and Street, Nathaniel Robert and Porth, Ilga and An, Xinmin and Mao, Jian-Feng},
	month = feb,
	year = {2024},
	pages = {kiae078},
}

Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio High-Fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the two parents of the well-studied F1 hybrid “84K” (Populus alba × P. tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from two small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the two subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.

@article{nie_progress_2024,
	title = {Progress in phylogenetics, multi-omics and flower coloration studies in \textit{{Rhododendron}}},
	volume = {4},
	copyright = {2024 The Author(s)},
	issn = {2769-2094},
	url = {https://www.maxapress.com/rticle/doi/10.48130/opr-0024-0001},
	doi = {10.48130/opr-0024-0001},
	abstract = {{\textless}p{\textgreater}The genus {\textless}italic{\textgreater}Rhododendron{\textless}/italic{\textgreater} exhibits an immense diversity of flower colors and represents one of the largest groups of woody plants, which is of great importance for ornamental plant research. This review summarizes recent progress in deciphering the genetic basis for flower coloration in {\textless}italic{\textgreater}Rhododendron{\textless}/italic{\textgreater}. We describe advances in phylogenetic reconstruction and genome sequencing of {\textless}italic{\textgreater}Rhododendron{\textless}/italic{\textgreater} species. The metabolic pathways of flower color are outlined, focusing on key structural and regulatory genes involved in pigment synthesis. Gene duplications and losses associated with color diversification are discussed. In addition, the application of multi-omics approaches and analysis of gene co-expression networks to elucidate complex gene regulatory mechanisms is emphasized. This synthesis of current knowledge provides a foundation for future research on the evolution of flower color diversity within the {\textless}italic{\textgreater}Rhododendron{\textless}/italic{\textgreater} lineage. Ultimately, these discoveries will support breeding endeavors aimed at harnessing the genetics of flower coloration and developing novel cultivars that exhibit desired floral traits.{\textless}/p{\textgreater}},
	language = {en},
	number = {1},
	urldate = {2024-02-23},
	journal = {Ornamental Plant Research},
	author = {Nie, Shuai and Ma, Hai-Yao and Shi, Tian-Le and Tian, Xue-Chan and El-Kassaby, Yousry A. and Porth, Ilga and Yang, Fu-Sheng and Mao, Jian-Feng and Nie, Shuai and Ma, Hai-Yao and Shi, Tian-Le and Tian, Xue-Chan and El-Kassaby, Yousry A. and Porth, Ilga and Yang, Fu-Sheng and Mao, Jian-Feng},
	month = jan,
	year = {2024},
	note = {Bandiera\_abtest: a
Cc\_license\_type: cc\_by
Cg\_type: Maximum Academic Press
Number: opr-0024-0001
Primary\_atype: Ornamental Plant Research
Publisher: Maximum Academic Press
Subject\_term: REVIEW
Subject\_term\_id: REVIEW},
}

\textlessp\textgreaterThe genus \textlessitalic\textgreaterRhododendron\textless/italic\textgreater exhibits an immense diversity of flower colors and represents one of the largest groups of woody plants, which is of great importance for ornamental plant research. This review summarizes recent progress in deciphering the genetic basis for flower coloration in \textlessitalic\textgreaterRhododendron\textless/italic\textgreater. We describe advances in phylogenetic reconstruction and genome sequencing of \textlessitalic\textgreaterRhododendron\textless/italic\textgreater species. The metabolic pathways of flower color are outlined, focusing on key structural and regulatory genes involved in pigment synthesis. Gene duplications and losses associated with color diversification are discussed. In addition, the application of multi-omics approaches and analysis of gene co-expression networks to elucidate complex gene regulatory mechanisms is emphasized. This synthesis of current knowledge provides a foundation for future research on the evolution of flower color diversity within the \textlessitalic\textgreaterRhododendron\textless/italic\textgreater lineage. Ultimately, these discoveries will support breeding endeavors aimed at harnessing the genetics of flower coloration and developing novel cultivars that exhibit desired floral traits.\textless/p\textgreater

@article{wang_chromosome-scale_2023,
	title = {Chromosome-scale genome assembly and insights into the metabolome and gene regulation of leaf color transition in an important oak species, {Quercus} dentata},
	volume = {238},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18814},
	doi = {10.1111/nph.18814},
	abstract = {Quercus dentata Thunb., a dominant forest tree species in northern China, has significant ecological and ornamental value due to its adaptability and beautiful autumn coloration, with color changes from green to yellow into red resulting from the autumnal shifts in leaf pigmentation. However, the key genes and molecular regulatory mechanisms for leaf color transition remain to be investigated. First, we presented a high-quality chromosome-scale assembly for Q. dentata. This 893.54 Mb sized genome (contig N50 = 4.21 Mb, scaffold N50 = 75.55 Mb; 2n = 24) harbors 31 584 protein-coding genes. Second, our metabolome analyses uncovered pelargonidin-3-O-glucoside, cyanidin-3-O-arabinoside, and cyanidin-3-O-glucoside as the main pigments involved in leaf color transition. Third, gene co-expression further identified the MYB-bHLH-WD40 (MBW) transcription activation complex as central to anthocyanin biosynthesis regulation. Notably, transcription factor (TF) QdNAC (QD08G038820) was highly co-expressed with this MBW complex and may regulate anthocyanin accumulation and chlorophyll degradation during leaf senescence through direct interaction with another TF, QdMYB (QD01G020890), as revealed by our further protein–protein and DNA–protein interaction assays. Our high-quality genome assembly, metabolome, and transcriptome resources further enrich Quercus genomics and will facilitate upcoming exploration of ornamental values and environmental adaptability in this important genus.},
	language = {en},
	number = {5},
	urldate = {2023-05-05},
	journal = {New Phytologist},
	author = {Wang, Wen-Bo and He, Xiang-Feng and Yan, Xue-Mei and Ma, Bo and Lu, Cun-Fu and Wu, Jing and Zheng, Yi and Wang, Wen-He and Xue, Wen-Bo and Tian, Xue-Chan and Guo, Jing-Fang and El-Kassaby, Yousry A. and Porth, Ilga and Leng, Ping-Sheng and Hu, Zeng-Hui and Mao, Jian-Feng},
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.18814},
	keywords = {Quercus, co-expression network, flavonoids, gene regulation, leaf color transition},
	pages = {2016--2032},
}

Quercus dentata Thunb., a dominant forest tree species in northern China, has significant ecological and ornamental value due to its adaptability and beautiful autumn coloration, with color changes from green to yellow into red resulting from the autumnal shifts in leaf pigmentation. However, the key genes and molecular regulatory mechanisms for leaf color transition remain to be investigated. First, we presented a high-quality chromosome-scale assembly for Q. dentata. This 893.54 Mb sized genome (contig N50 = 4.21 Mb, scaffold N50 = 75.55 Mb; 2n = 24) harbors 31 584 protein-coding genes. Second, our metabolome analyses uncovered pelargonidin-3-O-glucoside, cyanidin-3-O-arabinoside, and cyanidin-3-O-glucoside as the main pigments involved in leaf color transition. Third, gene co-expression further identified the MYB-bHLH-WD40 (MBW) transcription activation complex as central to anthocyanin biosynthesis regulation. Notably, transcription factor (TF) QdNAC (QD08G038820) was highly co-expressed with this MBW complex and may regulate anthocyanin accumulation and chlorophyll degradation during leaf senescence through direct interaction with another TF, QdMYB (QD01G020890), as revealed by our further protein–protein and DNA–protein interaction assays. Our high-quality genome assembly, metabolome, and transcriptome resources further enrich Quercus genomics and will facilitate upcoming exploration of ornamental values and environmental adaptability in this important genus.

@article{nie_gapless_2023,
	title = {Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color},
	volume = {10},
	issn = {2052-7276},
	url = {https://doi.org/10.1093/hr/uhac241},
	doi = {10.1093/hr/uhac241},
	abstract = {The genus Rhododendron (Ericaceae), with more than 1000 species highly diverse in flower color, is providing distinct ornamental values and a model system for flower color studies. Here, we investigated the divergence between two parental species with different flower color widely used for azalea breeding. Gapless genome assembly was generated for the yellow-flowered azalea, Rhododendron molle. Comparative genomics found recent proliferation of  long terminal repeat retrotransposons (LTR-RTs), especially Gypsy, has resulted in a 125 Mb (19\%) genome size increase in species-specific regions, and a significant amount of dispersed gene duplicates (13 402) and pseudogenes (17 437). Metabolomic assessment revealed that yellow flower coloration is attributed to the dynamic changes of carotenoids/flavonols biosynthesis and chlorophyll degradation. Time-ordered gene co-expression networks (TO-GCNs) and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct flower pigmentation. B3 and ERF TFs were found dominating the gene regulation of carotenoids/flavonols characterized pigmentation in R. molle, while WRKY, ERF, WD40, C2H2, and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-flowered R simsii. This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding.},
	number = {1},
	urldate = {2023-03-03},
	journal = {Horticulture Research},
	author = {Nie, Shuai and Zhao, Shi-Wei and Shi, Tian-Le and Zhao, Wei and Zhang, Ren-Gang and Tian, Xue-Chan and Guo, Jing-Fang and Yan, Xue-Mei and Bao, Yu-Tao and Li, Zhi-Chao and Kong, Lei and Ma, Hai-Yao and Chen, Zhao-Yang and Liu, Hui and El-Kassaby, Yousry A and Porth, Ilga and Yang, Fu-Sheng and Mao, Jian-Feng},
	month = jan,
	year = {2023},
	pages = {uhac241},
}

The genus Rhododendron (Ericaceae), with more than 1000 species highly diverse in flower color, is providing distinct ornamental values and a model system for flower color studies. Here, we investigated the divergence between two parental species with different flower color widely used for azalea breeding. Gapless genome assembly was generated for the yellow-flowered azalea, Rhododendron molle. Comparative genomics found recent proliferation of long terminal repeat retrotransposons (LTR-RTs), especially Gypsy, has resulted in a 125 Mb (19%) genome size increase in species-specific regions, and a significant amount of dispersed gene duplicates (13 402) and pseudogenes (17 437). Metabolomic assessment revealed that yellow flower coloration is attributed to the dynamic changes of carotenoids/flavonols biosynthesis and chlorophyll degradation. Time-ordered gene co-expression networks (TO-GCNs) and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct flower pigmentation. B3 and ERF TFs were found dominating the gene regulation of carotenoids/flavonols characterized pigmentation in R. molle, while WRKY, ERF, WD40, C2H2, and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-flowered R simsii. This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding.

@article{guo_genomic_2023,
	title = {Genomic clines across the species boundary between a hybrid pine and its progenitor in the eastern {Tibetan} {Plateau}},
	volume = {4},
	issn = {2590-3462},
	url = {https://www.sciencedirect.com/science/article/pii/S259034622300072X},
	doi = {10.1016/j.xplc.2023.100574},
	abstract = {Most species have clearly defined distribution ranges and ecological niches. The genetic and ecological causes of species differentiation and the mechanisms that maintain species boundaries between newly evolved taxa and their progenitors are, however, less clearly defined. This study investigated the genetic structure and clines in Pinus densata, a pine of hybrid origin on the southeastern Tibetan Plateau, to gain an understanding of the contemporary dynamics of species barriers. We analyzed genetic diversity in a range-wide collection of P. densata and representative populations of its progenitors, Pinus tabuliformis and Pinus yunnanensis, using exome capture sequencing. We detected four distinct genetic groups within P. densata that reflect its migration history and major gene-flow barriers across the landscape. The demographies of these genetic groups in the Pleistocene were associated with regional glaciation histories. Interestingly, population sizes rebounded rapidly during interglacial periods, suggesting persistence and resilience of the species during the Quaternary ice age. In the contact zone between P. densata and P. yunnanensis, 3.36\% of the analyzed loci (57 849) showed exceptional patterns of introgression, suggesting their potential roles in either adaptive introgression or reproductive isolation. These outliers showed strong clines along critical climate gradients and enrichment in a number of biological processes relevant to high-altitude adaptation. This indicates that ecological selection played an important role in generating genomic heterogeneity and a genetic barrier across a zone of species transition. Our study highlights the forces that operate to maintain species boundaries and promote speciation in the Qinghai-Tibetan Plateau and other mountain systems.},
	number = {4},
	urldate = {2023-08-24},
	journal = {Plant Communications},
	author = {Guo, Jing-Fang and Zhao, Wei and Andersson, Bea and Mao, Jian-Feng and Wang, Xiao-Ru},
	month = jul,
	year = {2023},
	keywords = {demographic history, ecological selection, genomic cline, introgression outliers, reproductive isolation, species boundary},
	pages = {100574},
}

Most species have clearly defined distribution ranges and ecological niches. The genetic and ecological causes of species differentiation and the mechanisms that maintain species boundaries between newly evolved taxa and their progenitors are, however, less clearly defined. This study investigated the genetic structure and clines in Pinus densata, a pine of hybrid origin on the southeastern Tibetan Plateau, to gain an understanding of the contemporary dynamics of species barriers. We analyzed genetic diversity in a range-wide collection of P. densata and representative populations of its progenitors, Pinus tabuliformis and Pinus yunnanensis, using exome capture sequencing. We detected four distinct genetic groups within P. densata that reflect its migration history and major gene-flow barriers across the landscape. The demographies of these genetic groups in the Pleistocene were associated with regional glaciation histories. Interestingly, population sizes rebounded rapidly during interglacial periods, suggesting persistence and resilience of the species during the Quaternary ice age. In the contact zone between P. densata and P. yunnanensis, 3.36% of the analyzed loci (57 849) showed exceptional patterns of introgression, suggesting their potential roles in either adaptive introgression or reproductive isolation. These outliers showed strong clines along critical climate gradients and enrichment in a number of biological processes relevant to high-altitude adaptation. This indicates that ecological selection played an important role in generating genomic heterogeneity and a genetic barrier across a zone of species transition. Our study highlights the forces that operate to maintain species boundaries and promote speciation in the Qinghai-Tibetan Plateau and other mountain systems.

@article{zhao_haplotype-resolved_2023,
	title = {Haplotype-resolved genome assembly of {Coriaria} nepalensis a non-legume nitrogen-fixing shrub},
	volume = {10},
	copyright = {2023 The Author(s)},
	issn = {2052-4463},
	url = {https://www.nature.com/articles/s41597-023-02171-6},
	doi = {10.1038/s41597-023-02171-6},
	abstract = {Coriaria nepalensis Wall. (Coriariaceae) is a nitrogen-fixing shrub which forms root nodules with the actinomycete Frankia. Oils and extracts of C. nepalensis have been reported to be bacteriostatic and insecticidal, and C. nepalensis bark provides a valuable tannin resource. Here, by combining PacBio HiFi sequencing and Hi-C scaffolding techniques, we generated a haplotype-resolved chromosome-scale genome assembly for C. nepalensis. This genome assembly is approximately 620 Mb in size with a contig N50 of 11 Mb, with 99.9\% of the total assembled sequences anchored to 40 pseudochromosomes. We predicted 60,862 protein-coding genes of which 99.5\% were annotated from databases. We further identified 939 tRNAs, 7,297 rRNAs, and 982 ncRNAs. The chromosome-scale genome of C. nepalensis is expected to be a significant resource for understanding the genetic basis of root nodulation with Frankia, toxicity, and tannin biosynthesis.},
	language = {en},
	number = {1},
	urldate = {2023-05-12},
	journal = {Scientific Data},
	author = {Zhao, Shi-Wei and Guo, Jing-Fang and Kong, Lei and Nie, Shuai and Yan, Xue-Mei and Shi, Tian-Le and Tian, Xue-Chan and Ma, Hai-Yao and Bao, Yu-Tao and Li, Zhi-Chao and Chen, Zhao-Yang and Zhang, Ren-Gang and Ma, Yong-Peng and El-Kassaby, Yousry A. and Porth, Ilga and Zhao, Wei and Mao, Jian-Feng},
	month = may,
	year = {2023},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Computational biology and bioinformatics, Plant sciences},
	pages = {259},
}

Coriaria nepalensis Wall. (Coriariaceae) is a nitrogen-fixing shrub which forms root nodules with the actinomycete Frankia. Oils and extracts of C. nepalensis have been reported to be bacteriostatic and insecticidal, and C. nepalensis bark provides a valuable tannin resource. Here, by combining PacBio HiFi sequencing and Hi-C scaffolding techniques, we generated a haplotype-resolved chromosome-scale genome assembly for C. nepalensis. This genome assembly is approximately 620 Mb in size with a contig N50 of 11 Mb, with 99.9% of the total assembled sequences anchored to 40 pseudochromosomes. We predicted 60,862 protein-coding genes of which 99.5% were annotated from databases. We further identified 939 tRNAs, 7,297 rRNAs, and 982 ncRNAs. The chromosome-scale genome of C. nepalensis is expected to be a significant resource for understanding the genetic basis of root nodulation with Frankia, toxicity, and tannin biosynthesis.

@article{yang_chromosome-level_2023,
	title = {The chromosome-level genome assembly and genes involved in biosynthesis of nervonic acid of {Malania} oleifera},
	volume = {10},
	copyright = {2023 The Author(s)},
	issn = {2052-4463},
	url = {https://www.nature.com/articles/s41597-023-02218-8},
	doi = {10.1038/s41597-023-02218-8},
	abstract = {Nervonic acid (C24:1 Δ15, NA) is a very long-chain monounsaturated fatty acid, a clinically indispensable resource in maintaining the brain and nerve cells development and regeneration. Till now, NA has been found in 38 plant species, among which the garlic-fruit tree (Malania oleifera) has been evaluated to be the best candidate for NA production. Here, we generated a high-quality chromosome-scale assembly of M. oleifera employing PacBio long-read, short-read Illumina as well as Hi-C sequencing data. The genome assembly consisted of 1.5 Gb with a contig N50 of {\textasciitilde}4.9 Mb and a scaffold N50 of {\textasciitilde}112.6 Mb. {\textasciitilde}98.2\% of the assembly was anchored into 13 pseudo-chromosomes. It contains {\textasciitilde}1123 Mb repeat sequences, and 27,638 protein-coding genes, 568 tRNAs, 230 rRNAs and 352 other non-coding RNAs. Additionally, we documented candidate genes involved in NA biosynthesis including 20 KCSs, 4 KCRs, 1 HCD and 1 ECR, and profiled the expression patterns of these genes in developing seeds. The high-quality assembly of the genome provides insights into the genome evolution of the M. oleifera genome and candidate genes involved in NA biosynthesis in the seeds of this important woody tree.},
	language = {en},
	number = {1},
	urldate = {2023-05-26},
	journal = {Scientific Data},
	author = {Yang, Tianquan and Zhang, Rengang and Tian, Xiaoling and Yao, Gang and Shen, Yuanting and Wang, Sihai and Mao, Jianfeng and Li, Guangyuan and Liu, Aizhong and Sun, Weibang and Ma, Yongpeng},
	month = may,
	year = {2023},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Genome, Genomics},
	pages = {298},
}

Nervonic acid (C24:1 Δ15, NA) is a very long-chain monounsaturated fatty acid, a clinically indispensable resource in maintaining the brain and nerve cells development and regeneration. Till now, NA has been found in 38 plant species, among which the garlic-fruit tree (Malania oleifera) has been evaluated to be the best candidate for NA production. Here, we generated a high-quality chromosome-scale assembly of M. oleifera employing PacBio long-read, short-read Illumina as well as Hi-C sequencing data. The genome assembly consisted of 1.5 Gb with a contig N50 of ~4.9 Mb and a scaffold N50 of ~112.6 Mb. ~98.2% of the assembly was anchored into 13 pseudo-chromosomes. It contains ~1123 Mb repeat sequences, and 27,638 protein-coding genes, 568 tRNAs, 230 rRNAs and 352 other non-coding RNAs. Additionally, we documented candidate genes involved in NA biosynthesis including 20 KCSs, 4 KCRs, 1 HCD and 1 ECR, and profiled the expression patterns of these genes in developing seeds. The high-quality assembly of the genome provides insights into the genome evolution of the M. oleifera genome and candidate genes involved in NA biosynthesis in the seeds of this important woody tree.

@article{tian_unique_2023,
	title = {Unique gene duplications and conserved microsynteny potentially associated with resistance to wood decay in the {Lauraceae}},
	volume = {14},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2023.1122549},
	abstract = {Wood decay resistance (WDR) is marking the value of wood utilization. Many trees of the Lauraceae have exceptional WDR, as evidenced by their use in ancient royal palace buildings in China. However, the genetics of WDR remain elusive. Here, through comparative genomics, we revealed the unique characteristics related to the high WDR in Lauraceae trees. We present a 1.27-Gb chromosome-level assembly for Lindera megaphylla (Lauraceae). Comparative genomics integrating major groups of angiosperm revealed Lauraceae species have extensively shared gene microsynteny associated with the biosynthesis of specialized metabolites such as isoquinoline alkaloids, flavonoid, lignins and terpenoid, which play significant roles in WDR. In Lauraceae genomes, tandem and proximal duplications (TD/PD) significantly expanded the coding space of key enzymes of biosynthesis pathways related to WDR, which may enhance the decay resistance of wood by increasing the accumulation of these compounds. Among Lauraceae species, genes of WDR-related biosynthesis pathways showed remarkable expansion by TD/PD and conveyed unique and conserved motifs in their promoter and protein sequences, suggesting conserved gene collinearity, gene expansion and gene regulation supporting the high WDR. Our study thus reveals genomic profiles related to biochemical transitions among major plant groups and the genomic basis of WDR in the Lauraceae.},
	urldate = {2023-03-31},
	journal = {Frontiers in Plant Science},
	author = {Tian, Xue-Chan and Guo, Jing-Fang and Yan, Xue-Mei and Shi, Tian-Le and Nie, Shuai and Zhao, Shi-Wei and Bao, Yu-Tao and Li, Zhi-Chao and Kong, Lei and Su, Guang-Ju and Mao, Jian-Feng and Lin, Jinxing},
	month = mar,
	year = {2023},
}

Wood decay resistance (WDR) is marking the value of wood utilization. Many trees of the Lauraceae have exceptional WDR, as evidenced by their use in ancient royal palace buildings in China. However, the genetics of WDR remain elusive. Here, through comparative genomics, we revealed the unique characteristics related to the high WDR in Lauraceae trees. We present a 1.27-Gb chromosome-level assembly for Lindera megaphylla (Lauraceae). Comparative genomics integrating major groups of angiosperm revealed Lauraceae species have extensively shared gene microsynteny associated with the biosynthesis of specialized metabolites such as isoquinoline alkaloids, flavonoid, lignins and terpenoid, which play significant roles in WDR. In Lauraceae genomes, tandem and proximal duplications (TD/PD) significantly expanded the coding space of key enzymes of biosynthesis pathways related to WDR, which may enhance the decay resistance of wood by increasing the accumulation of these compounds. Among Lauraceae species, genes of WDR-related biosynthesis pathways showed remarkable expansion by TD/PD and conveyed unique and conserved motifs in their promoter and protein sequences, suggesting conserved gene collinearity, gene expansion and gene regulation supporting the high WDR. Our study thus reveals genomic profiles related to biochemical transitions among major plant groups and the genomic basis of WDR in the Lauraceae.

@article{yan_unraveling_2023,
	title = {Unraveling the evolutionary dynamics of the {TPS} gene family in land plants},
	volume = {14},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2023.1273648},
	doi = {10.3389/fpls.2023.1273648},
	abstract = {Terpenes and terpenoids are key natural compounds for plant defense, development, and composition of plant oil. The synthesis and accumulation of a myriad of volatile terpenoid compounds in these plants may dramatically alter the quality and flavor of the oils, which provide great commercial utilization value for oil-producing plants. Terpene synthases (TPSs) are important enzymes responsible for terpenic diversity. Investigating the differentiation of the TPS gene family could provide valuable theoretical support for the genetic improvement of oil-producing plants. While the origin and function of TPS genes have been extensively studied, the exact origin of the initial gene fusion event - it occurred in plants or microbes - remains uncertain. Furthermore, a comprehensive exploration of the TPS gene differentiation is still pending. Here, phylogenetic analysis revealed that the fusion of the TPS gene likely occurred in the ancestor of land plants, following the acquisition of individual C- and N- terminal domains. Potential mutual transfer of TPS genes was observed among microbes and plants. Gene synteny analysis disclosed a differential divergence pattern between TPS-c and TPS-e/f subfamilies involved in primary metabolism and those (TPS-a/b/d/g/h subfamilies) crucial for secondary metabolites. Biosynthetic gene clusters (BGCs) analysis suggested a correlation between lineage divergence and potential natural selection in structuring terpene diversities. This study provides fresh perspectives on the origin and evolution of the TPS gene family.},
	urldate = {2023-11-03},
	journal = {Frontiers in Plant Science},
	author = {Yan, Xue-Mei and Zhou, Shan-Shan and Liu, Hui and Zhao, Shi-Wei and Tian, Xue-Chan and Shi, Tian-Le and Bao, Yu-Tao and Li, Zhi-Chao and Jia, Kai-Hua and Nie, Shuai and Guo, Jing-Fang and Kong, Lei and Porth, Ilga M. and Mao, Jian-Feng},
	month = oct,
	year = {2023},
	keywords = {⛔ No DOI found},
}

Terpenes and terpenoids are key natural compounds for plant defense, development, and composition of plant oil. The synthesis and accumulation of a myriad of volatile terpenoid compounds in these plants may dramatically alter the quality and flavor of the oils, which provide great commercial utilization value for oil-producing plants. Terpene synthases (TPSs) are important enzymes responsible for terpenic diversity. Investigating the differentiation of the TPS gene family could provide valuable theoretical support for the genetic improvement of oil-producing plants. While the origin and function of TPS genes have been extensively studied, the exact origin of the initial gene fusion event - it occurred in plants or microbes - remains uncertain. Furthermore, a comprehensive exploration of the TPS gene differentiation is still pending. Here, phylogenetic analysis revealed that the fusion of the TPS gene likely occurred in the ancestor of land plants, following the acquisition of individual C- and N- terminal domains. Potential mutual transfer of TPS genes was observed among microbes and plants. Gene synteny analysis disclosed a differential divergence pattern between TPS-c and TPS-e/f subfamilies involved in primary metabolism and those (TPS-a/b/d/g/h subfamilies) crucial for secondary metabolites. Biosynthetic gene clusters (BGCs) analysis suggested a correlation between lineage divergence and potential natural selection in structuring terpene diversities. This study provides fresh perspectives on the origin and evolution of the TPS gene family.

@article{an_high_2022,
	title = {High quality haplotype-resolved genome assemblies of {Populus} tomentosa {Carr}., a stabilized interspecific hybrid species widespread in {Asia}},
	volume = {22},
	issn = {1755-0998},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13507},
	doi = {10.1111/1755-0998.13507},
	abstract = {Populus has a wide ecogeographical range spanning the Northern Hemisphere, and interspecific hybrids are common. Populus tomentosa Carr. is widely distributed and cultivated in the eastern region of Asia, where it plays multiple important roles in forestry, agriculture, conservation, and urban horticulture. Reference genomes are available for several Populus species, however, our goals were to produce a very high quality de novo chromosome-level genome assembly in P. tomentosa genome that could serve as a reference for evolutionary and ecological studies of hybrid speciation throughout the genus. Here, combining long-read sequencing and Hi-C scaffolding, we present a high-quality, haplotype-resolved genome assembly. The genome size was 740.2 Mb, with a contig N50 size of 5.47 Mb and a scaffold N50 size of 46.68 Mb, consisting of 38 chromosomes, as expected with the known diploid chromosome number (2n = 2x = 38). A total of 59,124 protein-coding genes were identified. Phylogenomic analyses revealed that P. tomentosa is comprised of two distinct subgenomes, which we deomonstrate is likely to have resulted from hybridization between Populus adenopoda as the female parent and Populus alba var. pyramidalis as the male parent, with an origin of approximately 3.93 Ma. Although highly colinear, significant structural variation was found between the two subgenomes. Our study provides a valuable resource for ecological genetics and forest biotechnology.},
	language = {en},
	number = {2},
	urldate = {2023-04-27},
	journal = {Molecular Ecology Resources},
	author = {An, Xinmin and Gao, Kai and Chen, Zhong and Li, Juan and Yang, Xiong and Yang, Xiaoyu and Zhou, Jing and Guo, Ting and Zhao, Tianyun and Huang, Sai and Miao, Deyu and Ullah Khan, Wasif and Rao, Pian and Ye, Meixia and Lei, Bingqi and Liao, Weihua and Wang, Jia and Ji, Lexiang and Li, Ying and Guo, Bin and Siddig Mustafa, Nada and Li, Shanwen and Yun, Quanzheng and Keller, Stephen R. and Mao, Jian-Feng and Zhang, Ren-Gang and Strauss, Steven H.},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13507},
	keywords = {PacBio long-read sequencing, Populus tomentosa, forest biotechnology, haplotype-resolved genome assembly, hybridization},
	pages = {786--802},
}

Populus has a wide ecogeographical range spanning the Northern Hemisphere, and interspecific hybrids are common. Populus tomentosa Carr. is widely distributed and cultivated in the eastern region of Asia, where it plays multiple important roles in forestry, agriculture, conservation, and urban horticulture. Reference genomes are available for several Populus species, however, our goals were to produce a very high quality de novo chromosome-level genome assembly in P. tomentosa genome that could serve as a reference for evolutionary and ecological studies of hybrid speciation throughout the genus. Here, combining long-read sequencing and Hi-C scaffolding, we present a high-quality, haplotype-resolved genome assembly. The genome size was 740.2 Mb, with a contig N50 size of 5.47 Mb and a scaffold N50 size of 46.68 Mb, consisting of 38 chromosomes, as expected with the known diploid chromosome number (2n = 2x = 38). A total of 59,124 protein-coding genes were identified. Phylogenomic analyses revealed that P. tomentosa is comprised of two distinct subgenomes, which we deomonstrate is likely to have resulted from hybridization between Populus adenopoda as the female parent and Populus alba var. pyramidalis as the male parent, with an origin of approximately 3.93 Ma. Although highly colinear, significant structural variation was found between the two subgenomes. Our study provides a valuable resource for ecological genetics and forest biotechnology.

@article{ma_lilac_2022,
	title = {Lilac ({Syringa} oblata) genome provides insights into its evolution and molecular mechanism of petal color change},
	volume = {5},
	copyright = {2022 The Author(s)},
	issn = {2399-3642},
	url = {https://www.nature.com/articles/s42003-022-03646-9},
	doi = {10.1038/s42003-022-03646-9},
	abstract = {Color change during flower opening is common; however, little is understood on the biochemical and molecular basis related. Lilac (Syringa oblata), a well-known woody ornamental plant with obvious petal color changes, is an ideal model. Here, we presented chromosome-scale genome assembly for lilac, resolved the flavonoids metabolism, and identified key genes and potential regulatory networks related to petal color change. The genome assembly is 1.05 Gb anchored onto 23 chromosomes, with a BUSCO score of 96.6\%. Whole-genome duplication (WGD) event shared within Oleaceae was revealed. Metabolome quantification identified delphinidin-3-O-rutinoside (Dp3Ru) and cyanidin-3-O-rutinoside (Cy3Ru) as the major pigments; gene co-expression networks indicated WRKY an essential regulation factor at the early flowering stage, ERF more important in the color transition period (from violet to light nearly white), while the MBW complex participated in the entire process. Our results provide a foundation for functional study and molecular breeding in lilac.},
	language = {en},
	number = {1},
	urldate = {2023-04-27},
	journal = {Communications Biology},
	author = {Ma, Bo and Wu, Jing and Shi, Tian-Le and Yang, Yun-Yao and Wang, Wen-Bo and Zheng, Yi and Su, Shu-Chai and Yao, Yun-Cong and Xue, Wen-Bo and Porth, Ilga and El-Kassaby, Yousry A. and Leng, Ping-Sheng and Hu, Zeng-Hui and Mao, Jian-Feng},
	month = jul,
	year = {2022},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Gene regulatory networks, Genomics, Metabolomics, Secondary metabolism, Transcriptomics},
	pages = {1--13},
}

Color change during flower opening is common; however, little is understood on the biochemical and molecular basis related. Lilac (Syringa oblata), a well-known woody ornamental plant with obvious petal color changes, is an ideal model. Here, we presented chromosome-scale genome assembly for lilac, resolved the flavonoids metabolism, and identified key genes and potential regulatory networks related to petal color change. The genome assembly is 1.05 Gb anchored onto 23 chromosomes, with a BUSCO score of 96.6%. Whole-genome duplication (WGD) event shared within Oleaceae was revealed. Metabolome quantification identified delphinidin-3-O-rutinoside (Dp3Ru) and cyanidin-3-O-rutinoside (Cy3Ru) as the major pigments; gene co-expression networks indicated WRKY an essential regulation factor at the early flowering stage, ERF more important in the color transition period (from violet to light nearly white), while the MBW complex participated in the entire process. Our results provide a foundation for functional study and molecular breeding in lilac.

@article{nie_potential_2022,
	title = {Potential allopolyploid origin of {Ericales} revealed with gene-tree reconciliation},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2022.1006904},
	abstract = {Few incidents of ancient allopolyploidization (polyploidization by hybridization or merging diverged genomes) were previously revealed, although there is significant evidence for the accumulation of whole genome duplications (WGD) in plants. Here, we focused on Ericales, one of the largest and most diverse angiosperm orders with significant ornamental and economic value. Through integrating 24 high-quality whole genome data selected from {\textasciitilde} 200 Superasterids genomes/species and an algorithm of topology-based gene-tree reconciliation, we explored the evolutionary history of in Ericales with ancient complex. We unraveled the allopolyploid origin of Ericales and detected extensive lineage-specific gene loss following the polyploidization. Our study provided a new hypothesis regarding the origin of Ericales and revealed an instructive perspective of gene loss as a pervasive source of genetic variation and adaptive phenotypic diversity in Ericales.},
	urldate = {2023-03-27},
	journal = {Frontiers in Plant Science},
	author = {Nie, Shuai and Tian, Xue-Chan and Kong, Lei and Zhao, Shi-Wei and Chen, Zhao-Yang and Jiao, Si-Qian and El-Kassaby, Yousry A. and Porth, Ilga and Yang, Fu-Sheng and Zhao, Wei and Mao, Jian-Feng},
	month = nov,
	year = {2022},
	keywords = {⛔ No DOI found},
}

Few incidents of ancient allopolyploidization (polyploidization by hybridization or merging diverged genomes) were previously revealed, although there is significant evidence for the accumulation of whole genome duplications (WGD) in plants. Here, we focused on Ericales, one of the largest and most diverse angiosperm orders with significant ornamental and economic value. Through integrating 24 high-quality whole genome data selected from ~ 200 Superasterids genomes/species and an algorithm of topology-based gene-tree reconciliation, we explored the evolutionary history of in Ericales with ancient complex. We unraveled the allopolyploid origin of Ericales and detected extensive lineage-specific gene loss following the polyploidization. Our study provided a new hypothesis regarding the origin of Ericales and revealed an instructive perspective of gene loss as a pervasive source of genetic variation and adaptive phenotypic diversity in Ericales.

@article{liu_repetitive_2022,
	title = {Repetitive {Elements}, {Sequence} {Turnover} and {Cyto}-{Nuclear} {Gene} {Transfer} in {Gymnosperm} {Mitogenomes}},
	volume = {13},
	issn = {1664-8021},
	url = {https://www.frontiersin.org/articles/10.3389/fgene.2022.867736},
	abstract = {Among the three genomes in plant cells, the mitochondrial genome (mitogenome) is the least studied due to complex recombination and intergenomic transfer. In gymnosperms only ∼20 mitogenomes have been released thus far, which hinders a systematic investigation into the tempo and mode of mitochondrial DNA evolution in seed plants. Here, we report the complete mitogenome sequence of Platycladus orientalis (Cupressaceae). This mitogenome is assembled as two circular-mapping chromosomes with a size of ∼2.6 Mb and which contains 32 protein-coding genes, three rRNA and seven tRNA genes, and 1,068 RNA editing sites. Repetitive sequences, including dispersed repeats, transposable elements (TEs), and tandem repeats, made up 23\% of the genome. Comparative analyses with 17 other mitogenomes representing the five gymnosperm lineages revealed a 30-fold difference in genome size, 80-fold in repetitive content, and 230-fold in substitution rate. We found dispersed repeats are highly associated with mitogenome expansion (r = 0.99), and most of them were accumulated during recent duplication events. Syntenic blocks and shared sequences between mitogenomes decay rapidly with divergence time (r = 0.53), with the exceptions of Ginkgo and Cycads which retained conserved genome structure over long evolutionary time. Our phylogenetic analysis supports a sister group relationship of Cupressophytes and Gnetophytes; both groups are unique in that they lost 8–12 protein-coding genes, of which 4–7 intact genes are likely transferred to nucleus. These two clades also show accelerated and highly variable substitution rates relative to other gymnosperms. Our study highlights the dynamic and enigmatic evolution of gymnosperm mitogenomes.},
	urldate = {2023-04-27},
	journal = {Frontiers in Genetics},
	author = {Liu, Hui and Zhao, Wei and Zhang, Ren-Gang and Mao, Jian-Feng and Wang, Xiao-Ru},
	year = {2022},
	keywords = {⛔ No DOI found},
}

Among the three genomes in plant cells, the mitochondrial genome (mitogenome) is the least studied due to complex recombination and intergenomic transfer. In gymnosperms only ∼20 mitogenomes have been released thus far, which hinders a systematic investigation into the tempo and mode of mitochondrial DNA evolution in seed plants. Here, we report the complete mitogenome sequence of Platycladus orientalis (Cupressaceae). This mitogenome is assembled as two circular-mapping chromosomes with a size of ∼2.6 Mb and which contains 32 protein-coding genes, three rRNA and seven tRNA genes, and 1,068 RNA editing sites. Repetitive sequences, including dispersed repeats, transposable elements (TEs), and tandem repeats, made up 23% of the genome. Comparative analyses with 17 other mitogenomes representing the five gymnosperm lineages revealed a 30-fold difference in genome size, 80-fold in repetitive content, and 230-fold in substitution rate. We found dispersed repeats are highly associated with mitogenome expansion (r = 0.99), and most of them were accumulated during recent duplication events. Syntenic blocks and shared sequences between mitogenomes decay rapidly with divergence time (r = 0.53), with the exceptions of Ginkgo and Cycads which retained conserved genome structure over long evolutionary time. Our phylogenetic analysis supports a sister group relationship of Cupressophytes and Gnetophytes; both groups are unique in that they lost 8–12 protein-coding genes, of which 4–7 intact genes are likely transferred to nucleus. These two clades also show accelerated and highly variable substitution rates relative to other gymnosperms. Our study highlights the dynamic and enigmatic evolution of gymnosperm mitogenomes.

@article{jia_subphaser_2022,
	title = {{SubPhaser}: a robust allopolyploid subgenome phasing method based on subgenome-specific k-mers},
	volume = {235},
	issn = {1469-8137},
	shorttitle = {{SubPhaser}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18173},
	doi = {10.1111/nph.18173},
	abstract = {With advanced sequencing technology, dozens of complex polyploid plant genomes have been characterized. However, for many polyploid species, their diploid ancestors are unknown or extinct, making it impossible to unravel the subgenomes and genome evolution directly. We developed a novel subgenome-phasing algorithm, SubPhaser, specifically designed for a neoallopolyploid or a homoploid hybrid. SubPhaser first searches for the subgenome-specific sequence (k-mer), then assigns homoeologous chromosomes into subgenomes, and further provides tools to annotate and investigate specific sequences. SubPhaser works well on neoallopolyploids and homoploid hybrids containing subgenome-specific sequences like wheat, but fails on autopolyploids lacking subgenome-specific sequences like alfalfa, indicating that SubPhaser can phase neoallopolyploid/homoploid hybrids with high accuracy, sensitivity and performance. This highly accurate, highly sensitive, ancestral data free chromosome phasing algorithm, SubPhaser, offers significant application value for subgenome phasing in neoallopolyploids and homoploid hybrids, and for the subsequent exploration of genome evolution and related genetic/epigenetic mechanisms.},
	language = {en},
	number = {2},
	urldate = {2023-04-27},
	journal = {New Phytologist},
	author = {Jia, Kai-Hua and Wang, Zhao-Xuan and Wang, Longxin and Li, Guang-Yuan and Zhang, Wei and Wang, Xiao-Ling and Xu, Fang-Ji and Jiao, Si-Qian and Zhou, Shan-Shan and Liu, Hui and Ma, Yongpeng and Bi, Guiqi and Zhao, Wei and El-Kassaby, Yousry A. and Porth, Ilga and Li, Guowei and Zhang, Ren-Gang and Mao, Jian-Feng},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.18173},
	keywords = {SubPhaser, allopolyploids, k-mer, phasing, subgenome},
	pages = {801--809},
}

With advanced sequencing technology, dozens of complex polyploid plant genomes have been characterized. However, for many polyploid species, their diploid ancestors are unknown or extinct, making it impossible to unravel the subgenomes and genome evolution directly. We developed a novel subgenome-phasing algorithm, SubPhaser, specifically designed for a neoallopolyploid or a homoploid hybrid. SubPhaser first searches for the subgenome-specific sequence (k-mer), then assigns homoeologous chromosomes into subgenomes, and further provides tools to annotate and investigate specific sequences. SubPhaser works well on neoallopolyploids and homoploid hybrids containing subgenome-specific sequences like wheat, but fails on autopolyploids lacking subgenome-specific sequences like alfalfa, indicating that SubPhaser can phase neoallopolyploid/homoploid hybrids with high accuracy, sensitivity and performance. This highly accurate, highly sensitive, ancestral data free chromosome phasing algorithm, SubPhaser, offers significant application value for subgenome phasing in neoallopolyploids and homoploid hybrids, and for the subsequent exploration of genome evolution and related genetic/epigenetic mechanisms.

@article{xu_uv-b_2022,
	title = {{UV}-{B} and {UV}-{C} radiation trigger both common and distinctive signal perceptions and transmissions in {Pinus} tabuliformis {Carr}.},
	volume = {42},
	issn = {1758-4469},
	url = {https://doi.org/10.1093/treephys/tpac021},
	doi = {10.1093/treephys/tpac021},
	abstract = {In plants, ultraviolet (UV)-light is an important driver for growth and natural distribution, and is also a valuable tool for manipulating productivity as well as biotic interactions. Understanding of plant responses to different UV radiation is sparse, especially from a systems biology perspective and particularly for conifers. Here, we evaluated the physiological and transcriptomic responses to the short-term application of high-irradiance UV-B and UV-C waves on Pinus tabuliformis Carr., a major conifer in Northern China. By undertaking time-ordered gene coexpression network analyses and network comparisons incorporating physiological traits and gene expression variation, we uncovered communalities but also differences in P. tabuliformis responses to UV-B and UV-C. Both types of spectral bands caused a significant inhibition of photosynthesis, and conversely, the improvement of antioxidant capacity, flavonoid production and signaling pathways related to stress resistance, indicating a clear switch from predominantly primary metabolism to enhanced defensive metabolism in pine. We isolated distinct subnetworks for photoreceptor-mediated signal transduction, maximum quantum efficiency of photosystem II (Fv/Fm) regulation and flavonoid biosynthesis in response to UV-B and UV-C radiation. From these subnetworks, we further identified phototropins as potentially important elements in both UV-B and UV-C signaling and, for the first time, suggesting peptide hormones to be involved in promoting flavonoid biosynthesis against UV-B, while these hormones seem not to be implicated in the defense against UV-C exposure. The present study employed an effective strategy for disentangling the complex physiological and genetic regulatory mechanisms in a nonmodel plant species, and thus, provides a suitable reference for future functional evaluations and artificial UV-light mediated growing strategies in plant production.},
	number = {8},
	urldate = {2023-04-27},
	journal = {Tree Physiology},
	author = {Xu, Jie and Luo, Hang and Zhou, Shan-Shan and Jiao, Si-Qian and Jia, Kai-Hua and Nie, Shuai and Liu, Hui and Zhao, Wei and Wang, Xiao-Ru and El-Kassaby, Yousry A and Porth, Ilga and Mao, Jian-Feng},
	month = aug,
	year = {2022},
	pages = {1587--1600},
}

In plants, ultraviolet (UV)-light is an important driver for growth and natural distribution, and is also a valuable tool for manipulating productivity as well as biotic interactions. Understanding of plant responses to different UV radiation is sparse, especially from a systems biology perspective and particularly for conifers. Here, we evaluated the physiological and transcriptomic responses to the short-term application of high-irradiance UV-B and UV-C waves on Pinus tabuliformis Carr., a major conifer in Northern China. By undertaking time-ordered gene coexpression network analyses and network comparisons incorporating physiological traits and gene expression variation, we uncovered communalities but also differences in P. tabuliformis responses to UV-B and UV-C. Both types of spectral bands caused a significant inhibition of photosynthesis, and conversely, the improvement of antioxidant capacity, flavonoid production and signaling pathways related to stress resistance, indicating a clear switch from predominantly primary metabolism to enhanced defensive metabolism in pine. We isolated distinct subnetworks for photoreceptor-mediated signal transduction, maximum quantum efficiency of photosystem II (Fv/Fm) regulation and flavonoid biosynthesis in response to UV-B and UV-C radiation. From these subnetworks, we further identified phototropins as potentially important elements in both UV-B and UV-C signaling and, for the first time, suggesting peptide hormones to be involved in promoting flavonoid biosynthesis against UV-B, while these hormones seem not to be implicated in the defense against UV-C exposure. The present study employed an effective strategy for disentangling the complex physiological and genetic regulatory mechanisms in a nonmodel plant species, and thus, provides a suitable reference for future functional evaluations and artificial UV-light mediated growing strategies in plant production.

@article{zhou_comprehensive_2021,
	title = {A comprehensive annotation dataset of intact {LTR} retrotransposons of 300 plant genomes},
	volume = {8},
	copyright = {2021 The Author(s)},
	issn = {2052-4463},
	url = {https://www.nature.com/articles/s41597-021-00968-x},
	doi = {10.1038/s41597-021-00968-x},
	abstract = {LTR retrotransposons (LTR-RTs) are ubiquitous and represent the dominant repeat element in plant genomes, playing important roles in functional variation, genome plasticity and evolution. With the advent of new sequencing technologies, a growing number of whole-genome sequences have been made publicly available, making it possible to carry out systematic analyses of LTR-RTs. However, a comprehensive and unified annotation of LTR-RTs in plant groups is still lacking. Here, we constructed a plant intact LTR-RTs dataset, which is designed to classify and annotate intact LTR-RTs with a standardized procedure. The dataset currently comprises a total of 2,593,685 intact LTR-RTs from genomes of 300 plant species representing 93 families of 46 orders. The dataset is accompanied by sequence, diverse structural and functional annotation, age determination and classification information associated with the LTR-RTs. This dataset will contribute valuable resources for investigating the evolutionary dynamics and functional implications of LTR-RTs in plant genomes.},
	language = {en},
	number = {1},
	urldate = {2023-04-27},
	journal = {Scientific Data},
	author = {Zhou, Shan-Shan and Yan, Xue-Mei and Zhang, Kai-Fu and Liu, Hui and Xu, Jie and Nie, Shuai and Jia, Kai-Hua and Jiao, Si-Qian and Zhao, Wei and Zhao, You-Jie and Porth, Ilga and El Kassaby, Yousry A. and Wang, Tongli and Mao, Jian-Feng},
	month = jul,
	year = {2021},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Data mining, Mobile elements},
	pages = {174},
}

LTR retrotransposons (LTR-RTs) are ubiquitous and represent the dominant repeat element in plant genomes, playing important roles in functional variation, genome plasticity and evolution. With the advent of new sequencing technologies, a growing number of whole-genome sequences have been made publicly available, making it possible to carry out systematic analyses of LTR-RTs. However, a comprehensive and unified annotation of LTR-RTs in plant groups is still lacking. Here, we constructed a plant intact LTR-RTs dataset, which is designed to classify and annotate intact LTR-RTs with a standardized procedure. The dataset currently comprises a total of 2,593,685 intact LTR-RTs from genomes of 300 plant species representing 93 families of 46 orders. The dataset is accompanied by sequence, diverse structural and functional annotation, age determination and classification information associated with the LTR-RTs. This dataset will contribute valuable resources for investigating the evolutionary dynamics and functional implications of LTR-RTs in plant genomes.

@article{liu_centromere-specific_2021,
	title = {Centromere-{Specific} {Retrotransposons} and {Very}-{Long}-{Chain} {Fatty} {Acid} {Biosynthesis} in the {Genome} of {Yellowhorn} ({Xanthoceras} sorbifolium, {Sapindaceae}), an {Oil}-{Producing} {Tree} {With} {Significant} {Drought} {Resistance}},
	volume = {12},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2021.766389},
	doi = {10/gnsqvv},
	abstract = {In-depth genome characterization is still lacking for most of biofuel crops, especially for centromeres, which play a fundamental role during nuclear division and in the maintenance of genome stability. This study applied long-read sequencing technologies to assemble a highly contiguous genome for yellowhorn (Xanthoceras sorbifolium), an oil-producing tree, and conducted extensive comparative analyses to understand centromere structure and evolution, and fatty acid biosynthesis. We produced a reference-level genome of yellowhorn, ∼470 Mb in length with ∼95\% of contigs anchored onto 15 chromosomes. Genome annotation identified 22,049 protein-coding genes and 65.7\% of the genome sequence as repetitive elements. Long terminal repeat retrotransposons (LTR-RTs) account for ∼30\% of the yellowhorn genome, which is maintained by a moderate birth rate and a low removal rate. We identified the centromeric regions on each chromosome and found enrichment of centromere-specific retrotransposons of LINE1 and Gypsy in these regions, which have evolved recently (∼0.7 MYA). We compared the genomes of three cultivars and found frequent inversions. We analyzed the transcriptomes from different tissues and identified the candidate genes involved in very-long-chain fatty acid biosynthesis and their expression profiles. Collinear block analysis showed that yellowhorn shared the gamma (γ) hexaploidy event with Vitis vinifera but did not undergo any further whole-genome duplication. This study provides excellent genomic resources for understanding centromere structure and evolution and for functional studies in this important oil-producing plant.},
	urldate = {2021-12-16},
	journal = {Frontiers in Plant Science},
	author = {Liu, Hui and Yan, Xue-Mei and Wang, Xin-rui and Zhang, Dong-Xu and Zhou, Qingyuan and Shi, Tian-Le and Jia, Kai-Hua and Tian, Xue-Chan and Zhou, Shan-Shan and Zhang, Ren-Gang and Yun, Quan-Zheng and Wang, Qing and Xiang, Qiuhong and Mannapperuma, Chanaka and Van Zalen, Elena and Street, Nathaniel R. and Porth, Ilga and El-Kassaby, Yousry A. and Zhao, Wei and Wang, Xiao-Ru and Guan, Wenbin and Mao, Jian-Feng},
	year = {2021},
	pages = {2546},
}

In-depth genome characterization is still lacking for most of biofuel crops, especially for centromeres, which play a fundamental role during nuclear division and in the maintenance of genome stability. This study applied long-read sequencing technologies to assemble a highly contiguous genome for yellowhorn (Xanthoceras sorbifolium), an oil-producing tree, and conducted extensive comparative analyses to understand centromere structure and evolution, and fatty acid biosynthesis. We produced a reference-level genome of yellowhorn, ∼470 Mb in length with ∼95% of contigs anchored onto 15 chromosomes. Genome annotation identified 22,049 protein-coding genes and 65.7% of the genome sequence as repetitive elements. Long terminal repeat retrotransposons (LTR-RTs) account for ∼30% of the yellowhorn genome, which is maintained by a moderate birth rate and a low removal rate. We identified the centromeric regions on each chromosome and found enrichment of centromere-specific retrotransposons of LINE1 and Gypsy in these regions, which have evolved recently (∼0.7 MYA). We compared the genomes of three cultivars and found frequent inversions. We analyzed the transcriptomes from different tissues and identified the candidate genes involved in very-long-chain fatty acid biosynthesis and their expression profiles. Collinear block analysis showed that yellowhorn shared the gamma (γ) hexaploidy event with Vitis vinifera but did not undergo any further whole-genome duplication. This study provides excellent genomic resources for understanding centromere structure and evolution and for functional studies in this important oil-producing plant.

@article{shen_chromosome-scale_2021,
	title = {Chromosome-{Scale} {Genome} {Assembly} for {Chinese} {Sour} {Jujube} and {Insights} {Into} {Its} {Genome} {Evolution} and {Domestication} {Signature}},
	volume = {12},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2021.773090},
	doi = {10.3389/fpls.2021.773090},
	abstract = {Sour or wild jujube fruits and dried seeds are popular food all over the world. In this study, we reported a high-quality genome assembly of sour jujube (Ziziphus jujuba Mill. var. spinosa), with a size of 406 Mbp and scaffold N50 of 30.3 Mbp, which experienced only γ hexaploidization event, without recent genome duplication. Population structure analysis identified four jujube subgroups (two domesticated ones, i.e., D1 in West China and D2 in East/SouthEast China, semi-wild, and wild), which underwent an evolutionary history of a significant decline of effective population size during the Last Glacial Period. The respective selection signatures of three subgroups were discovered, such as strong peaks on chromosomes \#3 in D1, \#1 in D2, and \#4 in wild. Genes under the most significant selection on chromosomes \#4 in wild were confirmed to be involved in fruit variations among jujube accessions, in transcriptomic analysis. Our study offered novel insights into the jujube population structure and domestication and provided valuable genomic resources for jujube improvement in stress response and fruit flavor in the future.},
	urldate = {2023-04-27},
	journal = {Frontiers in Plant Science},
	author = {Shen, Lian-Ying and Luo, Hang and Wang, Xiao-Ling and Wang, Xue-Meng and Qiu, Xiao-Jing and Liu, Hui and Zhou, Shan-Shan and Jia, Kai-Hua and Nie, Shuai and Bao, Yu-Tao and Zhang, Ren-Gang and Yun, Quan-Zheng and Chai, Ying-Hui and Lu, Jin-Ying and Li, Yu and Zhao, Shu-Wei and Mao, Jian-Feng and Jia, Shan-Gang and Mao, Yong-Min},
	year = {2021},
}

Sour or wild jujube fruits and dried seeds are popular food all over the world. In this study, we reported a high-quality genome assembly of sour jujube (Ziziphus jujuba Mill. var. spinosa), with a size of 406 Mbp and scaffold N50 of 30.3 Mbp, which experienced only γ hexaploidization event, without recent genome duplication. Population structure analysis identified four jujube subgroups (two domesticated ones, i.e., D1 in West China and D2 in East/SouthEast China, semi-wild, and wild), which underwent an evolutionary history of a significant decline of effective population size during the Last Glacial Period. The respective selection signatures of three subgroups were discovered, such as strong peaks on chromosomes #3 in D1, #1 in D2, and #4 in wild. Genes under the most significant selection on chromosomes #4 in wild were confirmed to be involved in fruit variations among jujube accessions, in transcriptomic analysis. Our study offered novel insights into the jujube population structure and domestication and provided valuable genomic resources for jujube improvement in stress response and fruit flavor in the future.

@article{jia_chromosome-scale_2021,
	title = {Chromosome-scale assembly and evolution of the tetraploid {Salvia} splendens ({Lamiaceae}) genome},
	volume = {8},
	copyright = {2021 The Author(s)},
	issn = {2052-7276},
	url = {https://www.nature.com/articles/s41438-021-00614-y},
	doi = {10/gmskmf},
	abstract = {Polyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chromosome-scale genome assembly of tetraploid scarlet sage (Salvia splendens), one of the most diverse ornamental plants. We found evidence for three WGD events following an older WGD event shared by most eudicots (the γ event). A comprehensive, spatiotemporal, genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries, which could be associated with genomic rearrangements, transposable element proximity discrepancies, coding sequence variation, selection pressure, and transcription factor binding site differences. The observed differences between homoeologs may reflect the first step toward sub- and/or neofunctionalization. This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.},
	language = {en},
	number = {1},
	urldate = {2021-09-02},
	journal = {Horticulture Research},
	author = {Jia, Kai-Hua and Liu, Hui and Zhang, Ren-Gang and Xu, Jie and Zhou, Shan-Shan and Jiao, Si-Qian and Yan, Xue-Mei and Tian, Xue-Chan and Shi, Tian-Le and Luo, Hang and Li, Zhi-Chao and Bao, Yu-Tao and Nie, Shuai and Guo, Jing-Fang and Porth, Ilga and El-Kassaby, Yousry A. and Wang, Xiao-Ru and Chen, Charles and Van de Peer, Yves and Zhao, Wei and Mao, Jian-Feng},
	month = sep,
	year = {2021},
	pages = {1--15},
}

Polyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chromosome-scale genome assembly of tetraploid scarlet sage (Salvia splendens), one of the most diverse ornamental plants. We found evidence for three WGD events following an older WGD event shared by most eudicots (the γ event). A comprehensive, spatiotemporal, genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries, which could be associated with genomic rearrangements, transposable element proximity discrepancies, coding sequence variation, selection pressure, and transcription factor binding site differences. The observed differences between homoeologs may reflect the first step toward sub- and/or neofunctionalization. This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.

@article{he_chromosome-scale_2021,
	title = {Chromosome-scale assembly of the genome of {Salix} dunnii reveals a male-heterogametic sex determination system on chromosome 7},
	volume = {21},
	issn = {1755-0998},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13362},
	doi = {10.1111/1755-0998.13362},
	abstract = {Sex determination systems in plants can involve either female or male heterogamety (ZW or XY, respectively). Here we used Illumina short reads, Oxford Nanopore Technologies (ONT) long reads and Hi-C reads to assemble the first chromosome-scale genome of a female willow tree (Salix dunnii), and to predict genes using transcriptome sequences and available databases. The final genome sequence of 328 Mb in total was assembled in 29 scaffolds, and includes 31,501 predicted genes. Analyses of short-read sequence data that included female and male plants suggested a male heterogametic sex-determining factor on chromosome 7, implying that, unlike the female heterogamety of most species in the genus Salix, male heterogamety evolved in the subgenus Salix. The S. dunnii sex-linked region occupies about 3.21 Mb of chromosome 7 in females (representing its position in the X chromosome), probably within a pericentromeric region. Our data suggest that this region is enriched for transposable element insertions, and about one-third of its 124 protein-coding genes were gained via duplications from other genome regions. We detect purifying selection on the genes that were ancestrally present in the region, though some have been lost. Transcriptome data from female and male individuals show more male- than female-biased genes in catkin and leaf tissues, and indicate enrichment for male-biased genes in the pseudo-autosomal regions. Our study provides valuable genomic resources for further studies of sex-determining regions in the family Salicaceae, and sex chromosome evolution.},
	language = {en},
	number = {6},
	urldate = {2023-04-27},
	journal = {Molecular Ecology Resources},
	author = {He, Li and Jia, Kai-Hua and Zhang, Ren-Gang and Wang, Yuan and Shi, Tian-Le and Li, Zhi-Chao and Zeng, Si-Wen and Cai, Xin-Jie and Wagner, Natascha Dorothea and Hörandl, Elvira and Muyle, Aline and Yang, Ke and Charlesworth, Deborah and Mao, Jian-Feng},
	year = {2021},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13362},
	keywords = {XX/XY, gene expression, genome-wide association, long terminal repeat-retrotransposons, sex-linked region},
	pages = {1966--1982},
}

Sex determination systems in plants can involve either female or male heterogamety (ZW or XY, respectively). Here we used Illumina short reads, Oxford Nanopore Technologies (ONT) long reads and Hi-C reads to assemble the first chromosome-scale genome of a female willow tree (Salix dunnii), and to predict genes using transcriptome sequences and available databases. The final genome sequence of 328 Mb in total was assembled in 29 scaffolds, and includes 31,501 predicted genes. Analyses of short-read sequence data that included female and male plants suggested a male heterogametic sex-determining factor on chromosome 7, implying that, unlike the female heterogamety of most species in the genus Salix, male heterogamety evolved in the subgenus Salix. The S. dunnii sex-linked region occupies about 3.21 Mb of chromosome 7 in females (representing its position in the X chromosome), probably within a pericentromeric region. Our data suggest that this region is enriched for transposable element insertions, and about one-third of its 124 protein-coding genes were gained via duplications from other genome regions. We detect purifying selection on the genes that were ancestrally present in the region, though some have been lost. Transcriptome data from female and male individuals show more male- than female-biased genes in catkin and leaf tissues, and indicate enrichment for male-biased genes in the pseudo-autosomal regions. Our study provides valuable genomic resources for further studies of sex-determining regions in the family Salicaceae, and sex chromosome evolution.

@article{cheng_haplotype-resolved_2021,
	title = {Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger},
	volume = {8},
	issn = {2662-6810},
	doi = {10/gmhq7d},
	abstract = {Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.},
	language = {eng},
	number = {1},
	journal = {Horticulture Research},
	author = {Cheng, Shi-Ping and Jia, Kai-Hua and Liu, Hui and Zhang, Ren-Gang and Li, Zhi-Chao and Zhou, Shan-Shan and Shi, Tian-Le and Ma, Ai-Chu and Yu, Cong-Wen and Gao, Chan and Cao, Guang-Lei and Zhao, Wei and Nie, Shuai and Guo, Jing-Fang and Jiao, Si-Qian and Tian, Xue-Chan and Yan, Xue-Mei and Bao, Yu-Tao and Yun, Quan-Zheng and Wang, Xin-Zhu and Porth, Ilga and El-Kassaby, Yousry A. and Wang, Xiao-Ru and Li, Zhen and Van de Peer, Yves and Mao, Jian-Feng},
	month = aug,
	year = {2021},
	pages = {188},
}

Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.

@article{guo_low_2021,
	title = {Low genetic diversity and population connectivity fuel vulnerability to climate change for the {Tertiary} relict pine {Pinus} bungeana},
	volume = {61},
	issn = {1759-6831},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jse.12821},
	doi = {10.1111/jse.12821},
	abstract = {Endemic species are important components of regional biodiversity and hold the key to understanding local adaptation and evolutionary processes that shape species distributions. This study investigated the biogeographic history of a relict conifer Pinus bungeana Zucc. ex Endl. confined to central China. We examined genetic diversity in P. bungeana using genotyping-by-sequencing and chloroplast and mitochondrial DNA markers. We performed spatial and temporal inference of recent genetic and demographic changes, and dissected the impacts of geography and environmental gradients on population differentiation. We then projected P. bungeana's risk of decline under future climates. We found extremely low nucleotide diversity (average π 0.0014), and strong population structure (global FST 0.234) even at regional scales, reflecting long-term isolation in small populations. The species experienced severe bottlenecks in the early Pliocene and continued to decline in the Pleistocene in the western distribution, whereas the east expanded recently. Local adaptation played a small (8\%) but significant role in population diversity. Low genetic diversity in fragmented populations makes the species highly vulnerable to climate change, particularly in marginal and relict populations. We suggest that conservation efforts should focus on enhancing gene pool and population growth through assisted migration within each genetic cluster to reduce the risk of further genetic drift and extinction.},
	language = {en},
	number = {1},
	urldate = {2023-04-27},
	journal = {Journal of Systematics and Evolution},
	author = {Guo, Jing-Fang and Wang, Baosheng and Liu, Zhan-Lin and Mao, Jian-Feng and Wang, Xiao-Ru and Zhao, Wei},
	month = dec,
	year = {2021},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jse.12821},
	keywords = {Pinus bungeana, climate relict, genetic diversity, genomic offset, migration barrier, population bottleneck},
	pages = {143--156},
}

Endemic species are important components of regional biodiversity and hold the key to understanding local adaptation and evolutionary processes that shape species distributions. This study investigated the biogeographic history of a relict conifer Pinus bungeana Zucc. ex Endl. confined to central China. We examined genetic diversity in P. bungeana using genotyping-by-sequencing and chloroplast and mitochondrial DNA markers. We performed spatial and temporal inference of recent genetic and demographic changes, and dissected the impacts of geography and environmental gradients on population differentiation. We then projected P. bungeana's risk of decline under future climates. We found extremely low nucleotide diversity (average π 0.0014), and strong population structure (global FST 0.234) even at regional scales, reflecting long-term isolation in small populations. The species experienced severe bottlenecks in the early Pliocene and continued to decline in the Pleistocene in the western distribution, whereas the east expanded recently. Local adaptation played a small (8%) but significant role in population diversity. Low genetic diversity in fragmented populations makes the species highly vulnerable to climate change, particularly in marginal and relict populations. We suggest that conservation efforts should focus on enhancing gene pool and population growth through assisted migration within each genetic cluster to reduce the risk of further genetic drift and extinction.

@article{xu_uv-b-induced_2021,
	title = {{UV}-{B}-induced molecular mechanisms of stress physiology responses in the major northern {Chinese} conifer {Pinus} tabuliformis {Carr}.},
	volume = {41},
	issn = {1758-4469},
	url = {https://doi.org/10.1093/treephys/tpaa180},
	doi = {10.1093/treephys/tpaa180},
	abstract = {During their lifetimes, plants are exposed to different abiotic stress factors eliciting various physiological responses and triggering important defense processes. For UV-B radiation responses in forest trees, the genetics and molecular regulation remain to be elucidated. Here, we exposed Pinus tabuliformis Carr., a major conifer from northern China, to short-term high-intensity UV-B and employed a systems biology approach to characterize the early physiological processes and the hierarchical gene regulation, which revealed a temporal transition from primary to secondary metabolism, the buildup of enhanced antioxidant capacity and stress-signaling activation. Our findings showed that photosynthesis and biosynthesis of photosynthetic pigments were inhibited, while flavonoids and their related derivates biosynthesis, as well as glutathione and glutathione S-transferase mediated antioxidant processes, were enhanced. Likewise, stress-related phytohormones (jasmonic acid, salicylic acid and ethylene), kinase and reactive oxygen species signal transduction pathways were activated. Biological processes regulated by auxin and karrikin were, for the first time, found to be involved in plant defense against UV-B by promoting the biosynthesis of flavonoids and the improvement of antioxidant capacity in our research system. Our work evaluated the physiological and transcriptome perturbations in a conifer’s response to UV-B, and generally, highlighted the necessity of a systems biology approach in addressing plant stress biology.},
	number = {7},
	urldate = {2021-11-04},
	journal = {Tree Physiology},
	author = {Xu, Jie and Nie, Shuai and Xu, Chao-Qun and Liu, Hui and Jia, Kai-Hua and Zhou, Shan-Shan and Zhao, Wei and Zhou, Xian-Qing and El-Kassaby, Yousry A and Wang, Xiao-Ru and Porth, Ilga and Mao, Jian-Feng},
	month = jul,
	year = {2021},
	keywords = {China, Chinese red pine, Gene Expression Regulation, Plant, Pinus, RNA-seq, Stress, Physiological, Tracheophyta, Ultraviolet Rays, high energy UV-B, physiological reprogramming, time-ordered gene regulatory network},
	pages = {1247--1263},
}

During their lifetimes, plants are exposed to different abiotic stress factors eliciting various physiological responses and triggering important defense processes. For UV-B radiation responses in forest trees, the genetics and molecular regulation remain to be elucidated. Here, we exposed Pinus tabuliformis Carr., a major conifer from northern China, to short-term high-intensity UV-B and employed a systems biology approach to characterize the early physiological processes and the hierarchical gene regulation, which revealed a temporal transition from primary to secondary metabolism, the buildup of enhanced antioxidant capacity and stress-signaling activation. Our findings showed that photosynthesis and biosynthesis of photosynthetic pigments were inhibited, while flavonoids and their related derivates biosynthesis, as well as glutathione and glutathione S-transferase mediated antioxidant processes, were enhanced. Likewise, stress-related phytohormones (jasmonic acid, salicylic acid and ethylene), kinase and reactive oxygen species signal transduction pathways were activated. Biological processes regulated by auxin and karrikin were, for the first time, found to be involved in plant defense against UV-B by promoting the biosynthesis of flavonoids and the improvement of antioxidant capacity in our research system. Our work evaluated the physiological and transcriptome perturbations in a conifer’s response to UV-B, and generally, highlighted the necessity of a systems biology approach in addressing plant stress biology.

@article{jiao_variation_2021,
	title = {Variation in {Platycladus} orientalis ({Cupressaceae}) {Reproductive} {Output} and {Its} {Effect} on {Seed} {Orchard} {Crops}’ {Genetic} {Diversity}},
	volume = {12},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {1999-4907},
	url = {https://www.mdpi.com/1999-4907/12/11/1429},
	doi = {10.3390/f12111429},
	abstract = {The genetic efficiency of seed orchards is crucial for determining seed crops’ genetic gain and diversity. Platycladus orientalis is a conifer tree of important ecological value in China. Here, we assessed the reproductive output (fertility) variation for 166 clones in a first-generation P. orientalis seed orchard over five years and across three years for each gender (female: 2017, 2018, and 2020 and male: 2017, 2019, and 2021). Fertility variation and genetic diversity parameters were estimated for each gender-year combination. The reproductive output (fertility) variation differed among years, provinces, clones nested within provinces, and ramets within clones. We observed asymmetry in the gender reproductive output and parental imbalance and determined their profound effects on the genetic diversity of these seed crops. The maleness index revealed the existence of female-biased or male-biased clones. When seeds from multiple individuals and years were blended, we found an increase in the effective number of parents (Np) and in genetic diversity (GD), and a reduced fertility variation (Ψ) in the seed orchard. When we set the effective number of parents (Np) to 30, the GD of the seed orchard could be maintained at more than 95\%. Thus, achieving genetic diversity balance in seed production can be accomplished through monitoring the fertility variation of orchards and through the utilization of the thereby generated information for the advanced generation of seed orchards.},
	language = {en},
	number = {11},
	urldate = {2023-04-27},
	journal = {Forests},
	author = {Jiao, Si-Qian and Li, Meiyu and Zhu, Yuan-Jiao and Zhou, Shan-Shan and Zhao, Shi-Wei and Li, Zhi-Chao and Bao, Yu-Tao and Shi, Tian-Le and Zhang, Hui-Jin and Yang, Xiao-Lei and Zhu, Ji-Jun and Porth, Ilga and El-Kassaby, Yousry A. and Cheng, Shi-Ping and Li, Yue and Mao, Jian-Feng},
	month = nov,
	year = {2021},
	note = {Number: 11
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {\textit{Platycladus orientalis}, effective parent number, fertility variation, parental balance, reproductive strobili production},
	pages = {1429},
}

The genetic efficiency of seed orchards is crucial for determining seed crops’ genetic gain and diversity. Platycladus orientalis is a conifer tree of important ecological value in China. Here, we assessed the reproductive output (fertility) variation for 166 clones in a first-generation P. orientalis seed orchard over five years and across three years for each gender (female: 2017, 2018, and 2020 and male: 2017, 2019, and 2021). Fertility variation and genetic diversity parameters were estimated for each gender-year combination. The reproductive output (fertility) variation differed among years, provinces, clones nested within provinces, and ramets within clones. We observed asymmetry in the gender reproductive output and parental imbalance and determined their profound effects on the genetic diversity of these seed crops. The maleness index revealed the existence of female-biased or male-biased clones. When seeds from multiple individuals and years were blended, we found an increase in the effective number of parents (Np) and in genetic diversity (GD), and a reduced fertility variation (Ψ) in the seed orchard. When we set the effective number of parents (Np) to 30, the GD of the seed orchard could be maintained at more than 95%. Thus, achieving genetic diversity balance in seed production can be accomplished through monitoring the fertility variation of orchards and through the utilization of the thereby generated information for the advanced generation of seed orchards.

@article{yang_chromosome-level_2020,
	title = {Chromosome-level genome assembly of a parent species of widely cultivated azaleas},
	volume = {11},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/s41467-020-18771-4},
	doi = {10.1038/s41467-020-18771-4},
	abstract = {Abstract
            
              Azaleas (Ericaceae) comprise one of the most diverse ornamental plants, renowned for their cultural and economic importance. We present a chromosome-scale genome assembly for
              Rhododendron simsii
              , the primary ancestor of azalea cultivars. Genome analyses unveil the remnants of an ancient whole-genome duplication preceding the radiation of most Ericaceae, likely contributing to the genomic architecture of flowering time. Small-scale gene duplications contribute to the expansion of gene families involved in azalea pigment biosynthesis. We reconstruct entire metabolic pathways for anthocyanins and carotenoids and their potential regulatory networks by detailed analysis of time-ordered gene co-expression networks. MYB, bHLH, and WD40 transcription factors may collectively regulate anthocyanin accumulation in
              R. simsii
              , particularly at the initial stages of flower coloration, and with WRKY transcription factors controlling progressive flower coloring at later stages. This work provides a cornerstone for understanding the underlying genetics governing flower timing and coloration and could accelerate selective breeding in azalea.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Yang, Fu-Sheng and Nie, Shuai and Liu, Hui and Shi, Tian-Le and Tian, Xue-Chan and Zhou, Shan-Shan and Bao, Yu-Tao and Jia, Kai-Hua and Guo, Jing-Fang and Zhao, Wei and An, Na and Zhang, Ren-Gang and Yun, Quan-Zheng and Wang, Xin-Zhu and Mannapperuma, Chanaka and Porth, Ilga and El-Kassaby, Yousry Aly and Street, Nathaniel Robert and Wang, Xiao-Ru and Van de Peer, Yves and Mao, Jian-Feng},
	month = dec,
	year = {2020},
	pages = {5269},
}

Abstract Azaleas (Ericaceae) comprise one of the most diverse ornamental plants, renowned for their cultural and economic importance. We present a chromosome-scale genome assembly for Rhododendron simsii , the primary ancestor of azalea cultivars. Genome analyses unveil the remnants of an ancient whole-genome duplication preceding the radiation of most Ericaceae, likely contributing to the genomic architecture of flowering time. Small-scale gene duplications contribute to the expansion of gene families involved in azalea pigment biosynthesis. We reconstruct entire metabolic pathways for anthocyanins and carotenoids and their potential regulatory networks by detailed analysis of time-ordered gene co-expression networks. MYB, bHLH, and WD40 transcription factors may collectively regulate anthocyanin accumulation in R. simsii , particularly at the initial stages of flower coloration, and with WRKY transcription factors controlling progressive flower coloring at later stages. This work provides a cornerstone for understanding the underlying genetics governing flower timing and coloration and could accelerate selective breeding in azalea.

@article{jiao_development_2020,
	title = {Development of a {Large} {Gene}-{Associated} {SSR} {Marker} {Set} and in-{Depth} {Genetic} {Characterization} in {Scarlet} {Sage}},
	volume = {11},
	issn = {1664-8021},
	url = {https://www.frontiersin.org/articles/10.3389/fgene.2020.00504},
	doi = {10.3389/fgene.2020.00504},
	abstract = {Salvia splendens, scarlet or tropical sage, is a tender perennial herbaceous flowering plant popularly grown in public and private gardens all over the world. In this study, we developed a set of simple sequence repeats (SSRs) from genome-wide sequences to assess the genetic diversity and population structure among 112 cultivars. We obtained 364,379 SSRs by mining scarlet sage’s recently published whole genome sequence; 14,545 gene-associated SSR loci were identified in 2 kb gene flanking regions. Among the 768 gene-associated SSR primer sets we screened, 576 loci successfully amplified in DNA pools of 3–4 different cultivars, of which 271 remained polymorphic when tested across eight individual plants. We searched for the related gene functions attributable to these gene-associated SSRs using diverse databases, resulting in 259 Non-redundant matching sequences, 205 individual Gene Ontology (GO) terms, 236 assigned to eukaryotic orthologous groups, and 67 KEGG-annotated (Kyoto Encyclopedia of Genes and Genomes) sequences. We finally selected 41 polymorphic SSR loci to infer genetic diversity and population structure among 112 S. splendens accessions. Based on the developed gene-associated SSRs, clustering analyses consistently revealed two distinct genetic groups within the core collection of S. splendens cultivars. This work developed and characterized an exhaustive set of genome-wide gene-associated SSR markers for scarlet sage. These SSRs can provide species identification, genetic diversity and population structure information for S. splendens, and will therefore be important tools for the management and protection of S. splendens germplasm.},
	urldate = {2023-04-27},
	journal = {Frontiers in Genetics},
	author = {Jiao, Si-Qian and Dong, Ai-Xiang and Shi, Tian-Le and Liu, Hui and Porth, Ilga and Xin, Hai-Bo and Mao, Jian-Feng},
	year = {2020},
}

Salvia splendens, scarlet or tropical sage, is a tender perennial herbaceous flowering plant popularly grown in public and private gardens all over the world. In this study, we developed a set of simple sequence repeats (SSRs) from genome-wide sequences to assess the genetic diversity and population structure among 112 cultivars. We obtained 364,379 SSRs by mining scarlet sage’s recently published whole genome sequence; 14,545 gene-associated SSR loci were identified in 2 kb gene flanking regions. Among the 768 gene-associated SSR primer sets we screened, 576 loci successfully amplified in DNA pools of 3–4 different cultivars, of which 271 remained polymorphic when tested across eight individual plants. We searched for the related gene functions attributable to these gene-associated SSRs using diverse databases, resulting in 259 Non-redundant matching sequences, 205 individual Gene Ontology (GO) terms, 236 assigned to eukaryotic orthologous groups, and 67 KEGG-annotated (Kyoto Encyclopedia of Genes and Genomes) sequences. We finally selected 41 polymorphic SSR loci to infer genetic diversity and population structure among 112 S. splendens accessions. Based on the developed gene-associated SSRs, clustering analyses consistently revealed two distinct genetic groups within the core collection of S. splendens cultivars. This work developed and characterized an exhaustive set of genome-wide gene-associated SSR markers for scarlet sage. These SSRs can provide species identification, genetic diversity and population structure information for S. splendens, and will therefore be important tools for the management and protection of S. splendens germplasm.

@article{zhao_effects_2020,
	title = {Effects of landscapes and range expansion on population structure and local adaptation},
	volume = {228},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.16619},
	doi = {10.1111/nph.16619},
	abstract = {Understanding the origin and distribution of genetic diversity across landscapes is critical for predicting the future of organisms in changing climates. This study investigated how adaptive and demographic forces have shaped diversity and population structure in Pinus densata, a keystone species on Qinghai-Tibetan Plateau (QTP). We examined the distribution of genomic diversity across the range of P. densata using exome capture sequencing. We applied spatially explicit tests to dissect the impacts of allele surfing, geographic isolation and environmental gradients on population differentiation and forecasted how this genetic legacy may limit the persistence of P. densata in future climates. We found that allele surfing from range expansion could explain the distribution of 39\% of the c. 48 000 genotyped single nucleotide polymorphisms (SNPs). Uncorrected, these allele frequency clines severely confounded inferences of selection. After controlling for demographic processes, isolation-by-environment explained 9.2–19.5\% of the genetic structure, with c. 4.0\% of loci being affected by selection. Allele surfing and genotype–environment associations resulted in genomic mismatch under projected climate scenarios. We illustrate that significant local adaptation, when coupled with reduced diversity as a result of demographic history, constrains potential evolutionary response to climate change. The strong signal of genomic vulnerability in P. densata may be representative for other QTP endemics.},
	language = {en},
	number = {1},
	urldate = {2023-04-27},
	journal = {New Phytologist},
	author = {Zhao, Wei and Sun, Yan-Qiang and Pan, Jin and Sullivan, Alexis R. and Arnold, Michael L. and Mao, Jian-Feng and Wang, Xiao-Ru},
	year = {2020},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.16619},
	keywords = {Pinus densata, Qinghai-Tibetan Plateau, allele frequency cline, exome sequences, genomic mismatch, local adaptation, nucleotide diversity},
	pages = {330--343},
}

Understanding the origin and distribution of genetic diversity across landscapes is critical for predicting the future of organisms in changing climates. This study investigated how adaptive and demographic forces have shaped diversity and population structure in Pinus densata, a keystone species on Qinghai-Tibetan Plateau (QTP). We examined the distribution of genomic diversity across the range of P. densata using exome capture sequencing. We applied spatially explicit tests to dissect the impacts of allele surfing, geographic isolation and environmental gradients on population differentiation and forecasted how this genetic legacy may limit the persistence of P. densata in future climates. We found that allele surfing from range expansion could explain the distribution of 39% of the c. 48 000 genotyped single nucleotide polymorphisms (SNPs). Uncorrected, these allele frequency clines severely confounded inferences of selection. After controlling for demographic processes, isolation-by-environment explained 9.2–19.5% of the genetic structure, with c. 4.0% of loci being affected by selection. Allele surfing and genotype–environment associations resulted in genomic mismatch under projected climate scenarios. We illustrate that significant local adaptation, when coupled with reduced diversity as a result of demographic history, constrains potential evolutionary response to climate change. The strong signal of genomic vulnerability in P. densata may be representative for other QTP endemics.

@article{sun_genetic_2020,
	title = {Genetic {Variation} {Related} to {High} {Elevation} {Adaptation} {Revealed} by {Common} {Garden} {Experiments} in {Pinus} yunnanensis},
	volume = {10},
	issn = {1664-8021},
	url = {https://www.frontiersin.org/articles/10.3389/fgene.2019.01405},
	doi = {10.3389/fgene.2019.01405},
	abstract = {Local adaptation, adaptation to specialized niches and environmental clines have been extensively reported for forest trees. Investigation of the adaptive genetic variation is crucial for forest resource management and breeding, especially in the context of global climate change. Here, we utilized a Pinus yunnanensis common garden experiments established at high and low elevation sites to assess the differences in growth and survival among populations and between the two common garden sites. The studied traits showed significant variation between the two test sites and among populations, suggesting adaptive divergence. To detect genetic variation related to environment, we captured 103,608 high quality SNPs based on RNA sequencing, and used them to assess the genetic diversity and population structure. We identified 321 outlier SNPs from 131 genes showing significant divergence in allelic frequency between survival populations of two sites. Functional categories associated with adaptation to high elevation were found to be related to flavonoid biosynthesis, response to UV, DNA repair, response to reactive oxygen species, and membrane lipid metabolic process. Further investigation of the outlier genes showed overrepresentation of the flavonoid biosynthesis pathway, suggesting that this pathway may play a key role in P. yunnanensis adaptation to high elevation environments. The outlier genes identified, and their variants, provide a basic reference for advanced investigations.},
	urldate = {2023-04-27},
	journal = {Frontiers in Genetics},
	author = {Sun, Yan-Qiang and Zhao, Wei and Xu, Chao-Qun and Xu, Yulan and El-Kassaby, Yousry A. and De La Torre, Amanda R. and Mao, Jian-Feng},
	year = {2020},
}

Local adaptation, adaptation to specialized niches and environmental clines have been extensively reported for forest trees. Investigation of the adaptive genetic variation is crucial for forest resource management and breeding, especially in the context of global climate change. Here, we utilized a Pinus yunnanensis common garden experiments established at high and low elevation sites to assess the differences in growth and survival among populations and between the two common garden sites. The studied traits showed significant variation between the two test sites and among populations, suggesting adaptive divergence. To detect genetic variation related to environment, we captured 103,608 high quality SNPs based on RNA sequencing, and used them to assess the genetic diversity and population structure. We identified 321 outlier SNPs from 131 genes showing significant divergence in allelic frequency between survival populations of two sites. Functional categories associated with adaptation to high elevation were found to be related to flavonoid biosynthesis, response to UV, DNA repair, response to reactive oxygen species, and membrane lipid metabolic process. Further investigation of the outlier genes showed overrepresentation of the flavonoid biosynthesis pathway, suggesting that this pathway may play a key role in P. yunnanensis adaptation to high elevation environments. The outlier genes identified, and their variants, provide a basic reference for advanced investigations.

@article{jia_landscape_2020,
	title = {Landscape genomics predicts climate change-related genetic offset for the widespread {Platycladus} orientalis ({Cupressaceae})},
	volume = {13},
	issn = {1752-4571},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/eva.12891},
	doi = {10.1111/eva.12891},
	abstract = {Understanding and quantifying populations' adaptive genetic variation and their response to climate change are critical to reforestation's seed source selection, forest management decisions, and gene conservation. Landscape genomics combined with geographic and environmental information provide an opportunity to interrogate forest populations' genome-wide variation for understanding the extent to which evolutionary forces shape past and contemporary populations' genetic structure, and identify those populations that may be most at risk under future climate change. Here, we used genotyping by sequencing to generate over 11,000 high-quality variants from Platycladus orientalis range-wide collection to evaluate its diversity and to predict genetic offset under future climate scenarios. Platycladus orientalis is a widespread conifer in China with significant ecological, timber, and medicinal values. We found population structure and evidences of isolation by environment, indicative of adaptation to local conditions. Gradient forest modeling identified temperature-related variables as the most important environmental factors influencing genetic variation and predicted areas with higher risk under future climate change. This study provides an important reference for forest resource management and conservation for P. orientalis.},
	language = {en},
	number = {4},
	urldate = {2023-04-27},
	journal = {Evolutionary Applications},
	author = {Jia, Kai-Hua and Zhao, Wei and Maier, Paul Andrew and Hu, Xian-Ge and Jin, Yuqing and Zhou, Shan-Shan and Jiao, Si-Qian and El-Kassaby, Yousry A and Wang, Tongli and Wang, Xiao-Ru and Mao, Jian-Feng},
	year = {2020},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.12891},
	keywords = {Platycladus orientalis, adaptation, climate change, genetic offset, genotyping by sequencing, population structure},
	pages = {665--676},
}

Understanding and quantifying populations' adaptive genetic variation and their response to climate change are critical to reforestation's seed source selection, forest management decisions, and gene conservation. Landscape genomics combined with geographic and environmental information provide an opportunity to interrogate forest populations' genome-wide variation for understanding the extent to which evolutionary forces shape past and contemporary populations' genetic structure, and identify those populations that may be most at risk under future climate change. Here, we used genotyping by sequencing to generate over 11,000 high-quality variants from Platycladus orientalis range-wide collection to evaluate its diversity and to predict genetic offset under future climate scenarios. Platycladus orientalis is a widespread conifer in China with significant ecological, timber, and medicinal values. We found population structure and evidences of isolation by environment, indicative of adaptation to local conditions. Gradient forest modeling identified temperature-related variables as the most important environmental factors influencing genetic variation and predicted areas with higher risk under future climate change. This study provides an important reference for forest resource management and conservation for P. orientalis.

@article{wang_monomer_2020,
	title = {Monomer {Structural} {Stability} of a {Tau} {Class} {Glutathione} {Transferase} ({PtGSTU1}) from \textit{{Pinus} tabulaeformis}},
	volume = {33},
	issn = {1001-1498},
	url = {http://www.lykxyj.com/en/article/doi/10.13275/j.cnki.lykxyj.2020.02.001},
	doi = {10.13275/j.cnki.lykxyj.2020.02.001},
	number = {2},
	urldate = {2023-04-27},
	journal = {林业科学研究},
	author = {Wang, Xiao-Xia and Yang, Hai-Ling and Mao, Jian-Feng and Wang, Xiao-Ru},
	month = mar,
	year = {2020},
	note = {Publisher: 林业科学研究},
	pages = {1--8},
}

@article{ma_acer_2020,
	title = {The {Acer} truncatum genome provides insights into nervonic acid biosynthesis},
	volume = {104},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.14954},
	doi = {10.1111/tpj.14954},
	abstract = {Acer truncatum (purpleblow maple) is a woody tree species that produces seeds with high levels of valuable fatty acids (especially nervonic acid). However, the lack of a complete genome sequence has limited both basic and applied research on A. truncatum. We describe a high-quality draft genome assembly comprising 633.28 Mb (contig N50 = 773.17 kb; scaffold N50 = 46.36 Mb) with at least 28 438 predicted genes. The genome underwent an ancient triplication, similar to the core eudicots, but there have been no recent whole-genome duplication events. Acer yangbiense and A. truncatum are estimated to have diverged about 9.4 million years ago. A combined genomic, transcriptomic, metabonomic, and cell ultrastructural analysis provided new insights into the biosynthesis of very long-chain monounsaturated fatty acids. In addition, three KCS genes were found that may contribute to regulating nervonic acid biosynthesis. The KCS paralogous gene family expanded to 28 members, with 10 genes clustered together and distributed in the 0.27-Mb region of pseudochromosome 4. Our chromosome-scale genomic characterization may facilitate the discovery of agronomically important genes and stimulate functional genetic research on A. truncatum. Furthermore, the data presented also offer important foundations from which to study the molecular mechanisms influencing the production of nervonic acids.},
	language = {en},
	number = {3},
	urldate = {2023-04-27},
	journal = {The Plant Journal},
	author = {Ma, Qiuyue and Sun, Tianlin and Li, Shushun and Wen, Jing and Zhu, Lu and Yin, Tongming and Yan, Kunyuan and Xu, Xiao and Li, Shuxian and Mao, Jianfeng and Wang, Ya-nan and Jin, Shuangxia and Zhao, Xing and Li, Qianzhong},
	year = {2020},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.14954},
	keywords = {Acer truncatum, KCS, de novo assembly, nervonic acid, very long-chain monounsaturated fatty acid},
	pages = {662--678},
}

Acer truncatum (purpleblow maple) is a woody tree species that produces seeds with high levels of valuable fatty acids (especially nervonic acid). However, the lack of a complete genome sequence has limited both basic and applied research on A. truncatum. We describe a high-quality draft genome assembly comprising 633.28 Mb (contig N50 = 773.17 kb; scaffold N50 = 46.36 Mb) with at least 28 438 predicted genes. The genome underwent an ancient triplication, similar to the core eudicots, but there have been no recent whole-genome duplication events. Acer yangbiense and A. truncatum are estimated to have diverged about 9.4 million years ago. A combined genomic, transcriptomic, metabonomic, and cell ultrastructural analysis provided new insights into the biosynthesis of very long-chain monounsaturated fatty acids. In addition, three KCS genes were found that may contribute to regulating nervonic acid biosynthesis. The KCS paralogous gene family expanded to 28 members, with 10 genes clustered together and distributed in the 0.27-Mb region of pseudochromosome 4. Our chromosome-scale genomic characterization may facilitate the discovery of agronomically important genes and stimulate functional genetic research on A. truncatum. Furthermore, the data presented also offer important foundations from which to study the molecular mechanisms influencing the production of nervonic acids.

@incollection{yan_terpene_2020,
	address = {Cham},
	series = {Compendium of {Plant} {Genomes}},
	title = {The {Terpene} {Synthase} {Gene} {Family} in {Norway} {Spruce}},
	isbn = {978-3-030-21001-4},
	url = {https://doi.org/10.1007/978-3-030-21001-4_11},
	abstract = {Terpenes (isoprenes) represent a diverse group of chemical compounds that plants produce during normal development (e.g., phytohormones), and mostly as secondary metabolites with important roles in defense responses against diverse environmental stressors, either abiotic or biotic in nature. Studies with an aspect on conifer-derived terpenes have highlighted some of the underlying metabolic and molecular mechanisms in the implicated defense processes. Terpene synthases (TPSs), being the core enzymes for terpenes’ functional diversity, therefore, gained attention as the key elements for molecular terpene studies. Norway spruce (Picea abies) is arguably Europe’s native conifer with the most substantial economic and ecological value given its vast geographic distribution throughout the continent as an indigenous species and, introduced, as an important plantation species outside its natural range. In this study, we aimed at retrieving TPS genes from the genomes of Norway spruce and, in addition, of representative land plant lineages in order to resolve their phylogenetic relationship. We show that the majority of TPS genes from gymnosperms are distributed within the TPS-d subfamily. As expected, the “DDXXD” and the “RXR” motifs are highly conserved for TPS in general, and the structural characteristics of closely related TPS genes are highly similar. Concrete subfamily membership along with shared structural molecular properties was the main driver of gene expression variation among Norway spruce TPSs, indicating important functional divergence. In this study, the two key factors within TPS gene structure that were related to differential TPS gene expression were found to be motif composition and intron size. Our study is valuable for further in-depth functional evaluation of these additionally uncovered spruce TPSs and will support future efforts in metabolic engineering involving terpenes.},
	language = {en},
	urldate = {2023-04-27},
	booktitle = {The {Spruce} {Genome}},
	publisher = {Springer International Publishing},
	author = {Yan, Xue-Mei and Zhou, Shan-Shan and Porth, Ilga M. and Mao, Jian-Feng},
	editor = {Porth, Ilga M. and De la Torre, Amanda R.},
	year = {2020},
	doi = {10.1007/978-3-030-21001-4_11},
	keywords = {Conserved motif, Functional divergence, Gene expression, Gene structure, Picea abies, Terpene synthase},
	pages = {177--192},
}

Terpenes (isoprenes) represent a diverse group of chemical compounds that plants produce during normal development (e.g., phytohormones), and mostly as secondary metabolites with important roles in defense responses against diverse environmental stressors, either abiotic or biotic in nature. Studies with an aspect on conifer-derived terpenes have highlighted some of the underlying metabolic and molecular mechanisms in the implicated defense processes. Terpene synthases (TPSs), being the core enzymes for terpenes’ functional diversity, therefore, gained attention as the key elements for molecular terpene studies. Norway spruce (Picea abies) is arguably Europe’s native conifer with the most substantial economic and ecological value given its vast geographic distribution throughout the continent as an indigenous species and, introduced, as an important plantation species outside its natural range. In this study, we aimed at retrieving TPS genes from the genomes of Norway spruce and, in addition, of representative land plant lineages in order to resolve their phylogenetic relationship. We show that the majority of TPS genes from gymnosperms are distributed within the TPS-d subfamily. As expected, the “DDXXD” and the “RXR” motifs are highly conserved for TPS in general, and the structural characteristics of closely related TPS genes are highly similar. Concrete subfamily membership along with shared structural molecular properties was the main driver of gene expression variation among Norway spruce TPSs, indicating important functional divergence. In this study, the two key factors within TPS gene structure that were related to differential TPS gene expression were found to be motif composition and intron size. Our study is valuable for further in-depth functional evaluation of these additionally uncovered spruce TPSs and will support future efforts in metabolic engineering involving terpenes.

@article{liu_tetracentron_2020,
	title = {The {Tetracentron} genome provides insight into the early evolution of eudicots and the formation of vessel elements},
	volume = {21},
	issn = {1474-760X},
	url = {https://doi.org/10.1186/s13059-020-02198-7},
	doi = {10.1186/s13059-020-02198-7},
	abstract = {Tetracentron sinense is an endemic and endangered deciduous tree. It belongs to the Trochodendrales, one of four early diverging lineages of eudicots known for having vesselless secondary wood. Sequencing and resequencing of the T. sinense genome will help us understand eudicot evolution, the genetic basis of tracheary element development, and the genetic diversity of this relict species.},
	number = {1},
	urldate = {2023-04-27},
	journal = {Genome Biology},
	author = {Liu, Ping-Li and Zhang, Xi and Mao, Jian-Feng and Hong, Yan-Ming and Zhang, Ren-Gang and E, Yilan and Nie, Shuai and Jia, Kaihua and Jiang, Chen-Kun and He, Jian and Shen, Weiwei and He, Qizouhong and Zheng, Wenqing and Abbas, Samar and Jewaria, Pawan Kumar and Tian, Xuechan and Liu, Chang-jun and Jiang, Xiaomei and Yin, Yafang and Liu, Bo and Wang, Li and Jin, Biao and Ma, Yongpeng and Qiu, Zongbo and Baluška, František and Šamaj, Jozef and He, Xinqiang and Niu, Shihui and Xie, Jianbo and Xie, Lei and Xu, Huimin and Kong, Hongzhi and Ge, Song and Dixon, Richard A. and Jiao, Yuannian and Lin, Jinxing},
	month = dec,
	year = {2020},
	keywords = {Genetic diversity, Phylogenomic, Resequencing, Tetracentron sinense, VND7, Vessel, Whole genome duplication},
	pages = {291},
}

Tetracentron sinense is an endemic and endangered deciduous tree. It belongs to the Trochodendrales, one of four early diverging lineages of eudicots known for having vesselless secondary wood. Sequencing and resequencing of the T. sinense genome will help us understand eudicot evolution, the genetic basis of tracheary element development, and the genetic diversity of this relict species.

@article{luo_complete_2020,
	title = {The complete mitochondrial genome of an endangered tree: {Malania} oleifera},
	volume = {5},
	issn = {null},
	shorttitle = {The complete mitochondrial genome of an endangered tree},
	url = {https://doi.org/10.1080/23802359.2020.1841583},
	doi = {10.1080/23802359.2020.1841583},
	abstract = {Malania oleifera is an endangered species found in restricted areas in Karst areas in Southwestern China and is also with significant economic and ecological values. Here, complete mitochondrial genome of M. oleifera was characterized, which is the first for the Olacaceae family. The mitogenome is 527,575 bp in length with a GC content of 45.65\%, including one pseudogene, and 38 protein-coding, 32 tRNA, three rRNA genes. Eleven genes have two copies in the mitogenome, and 3 genes are trans-spliced. Phylogenetic tree found that M. oleifera is making a sister branch to that of species from Rosids and Asterids.},
	number = {4},
	urldate = {2023-04-27},
	journal = {Mitochondrial DNA Part B},
	author = {Luo, Hang and Xu, Jie and Jiao, Si-Qian and Zhang, Ren-Gang and Mao, Jian-Feng},
	month = oct,
	year = {2020},
	pmid = {33426292},
	note = {Publisher: Taylor \& Francis
\_eprint: https://doi.org/10.1080/23802359.2020.1841583},
	keywords = {Malania oleifera, endangered species, mitochondrial genome},
	pages = {3829--3830},
}

Malania oleifera is an endangered species found in restricted areas in Karst areas in Southwestern China and is also with significant economic and ecological values. Here, complete mitochondrial genome of M. oleifera was characterized, which is the first for the Olacaceae family. The mitogenome is 527,575 bp in length with a GC content of 45.65%, including one pseudogene, and 38 protein-coding, 32 tRNA, three rRNA genes. Eleven genes have two copies in the mitogenome, and 3 genes are trans-spliced. Phylogenetic tree found that M. oleifera is making a sister branch to that of species from Rosids and Asterids.

@article{hu_transcriptome-wide_2020,
	title = {Transcriptome-wide identification and profiling of {miRNAs} in a stress-tolerant conifer {Sabina} chinensis},
	volume = {45},
	issn = {0973-7138},
	url = {https://doi.org/10.1007/s12038-020-0002-4},
	doi = {10.1007/s12038-020-0002-4},
	abstract = {miRNAs are important regulatory components involving in many biological processes, including plant development, vegetative and reproductive growth, and stress response. However, identification and characterization of miRNAs still remain limited for conifer species. In this study, with deep sequencing, we obtained 1,314,450 unique reads with 18–30 nt length from a stress-tolerant conifer, Sabina chinensis. We identified 37 conserved and 103 novel miRNAs, their unique characteristics were further analyzed, and 10 randomly selected were validated by qRT-PCR. Through miRNA target predictions and annotations, we found miRNA may have several targets as well a target could be regulated by several miRNAs, and a total of 2,397 mRNAs were predicted to be targets of the 140 miRNAs. These targets included not only important transcription factors such as auxin response factors, but also indispensable non-transcriptional factor proteins. Pathway-based analysis showed that S. chinensis miRNAs are involved in 172 metabolic pathways, of which 3 were discovered in adaptation-related pathways, indicating their possible relevance to the species’ stress-tolerance characteristics. This study is expected to lay the foundation for exploring the regulative roles of miRNAs in development, growth, and response to environmental stresses of S. chinensis.},
	language = {en},
	number = {1},
	urldate = {2023-04-27},
	journal = {Journal of Biosciences},
	author = {Hu, Xian-Ge and Zhou, Shan-Shan and Yang, Ying and Liu, Hui and Anil, Shrestha and Wang, Qing and Zhao, Wei and Gao, Qiong and El-Kassaby, Yousry A. and Wang, Tongli and Li, Yue and Mao, Jian-Feng},
	month = feb,
	year = {2020},
	keywords = {Sabina chinensis, miRNA, miRNA target, pathway},
	pages = {41},
}

miRNAs are important regulatory components involving in many biological processes, including plant development, vegetative and reproductive growth, and stress response. However, identification and characterization of miRNAs still remain limited for conifer species. In this study, with deep sequencing, we obtained 1,314,450 unique reads with 18–30 nt length from a stress-tolerant conifer, Sabina chinensis. We identified 37 conserved and 103 novel miRNAs, their unique characteristics were further analyzed, and 10 randomly selected were validated by qRT-PCR. Through miRNA target predictions and annotations, we found miRNA may have several targets as well a target could be regulated by several miRNAs, and a total of 2,397 mRNAs were predicted to be targets of the 140 miRNAs. These targets included not only important transcription factors such as auxin response factors, but also indispensable non-transcriptional factor proteins. Pathway-based analysis showed that S. chinensis miRNAs are involved in 172 metabolic pathways, of which 3 were discovered in adaptation-related pathways, indicating their possible relevance to the species’ stress-tolerance characteristics. This study is expected to lay the foundation for exploring the regulative roles of miRNAs in development, growth, and response to environmental stresses of S. chinensis.

@article{ouyang_complete_2019,
	title = {Complete plastome sequences of {Picea} asperata and {P}. crassifolia and comparative analyses with {P}. abies and {P}. morrisonicola},
	volume = {62},
	issn = {0831-2796},
	url = {https://cdnsciencepub.com/doi/10.1139/gen-2018-0195},
	doi = {10.1139/gen-2018-0195},
	abstract = {Picea asperata and P. crassifolia have sympatric ranges and are closely related, but the differences between these species at the plastome level are unknown. To better understand the patterns of variation among Picea plastomes, the complete plastomes of P. asperata and P. crassifolia were sequenced. Then, the plastomes were compared with the complete plastomes of P. abies and P. morrisonicola, which are closely and distantly related to the focal species, respectively. We also used these sequences to construct phylogenetic trees to determine the relationships among and between the four species as well as additional taxa from Pinaceae and other gymnosperms. Analysis of our sequencing data allowed us to identify 438 single nucleotide polymorphism (SNPs) point mutation events, 95 indel events, four inversion events, and seven highly variable regions, including six gene spacer regions (psbJ-petA, trnT-psaM, trnS-trnD, trnL-rps4, psaC-ccsA, and rps7-trnL) and one gene (ycf1). The highly variable regions are appropriate targets for future use in the phylogenetic reconstructions of closely related, sympatric species of Picea as well as Pinaceae in general.},
	number = {5},
	urldate = {2023-04-27},
	journal = {Genome},
	author = {Ouyang, Fangqun and Hu, Jiwen and Wang, Junchen and Ling, Juanjuan and Wang, Zhi and Wang, Nan and Ma, Jianwei and Zhang, Hanguo and Mao, Jian-Feng and Wang, Junhui},
	month = may,
	year = {2019},
	note = {Publisher: NRC Research Press},
	pages = {317--328},
}

Picea asperata and P. crassifolia have sympatric ranges and are closely related, but the differences between these species at the plastome level are unknown. To better understand the patterns of variation among Picea plastomes, the complete plastomes of P. asperata and P. crassifolia were sequenced. Then, the plastomes were compared with the complete plastomes of P. abies and P. morrisonicola, which are closely and distantly related to the focal species, respectively. We also used these sequences to construct phylogenetic trees to determine the relationships among and between the four species as well as additional taxa from Pinaceae and other gymnosperms. Analysis of our sequencing data allowed us to identify 438 single nucleotide polymorphism (SNPs) point mutation events, 95 indel events, four inversion events, and seven highly variable regions, including six gene spacer regions (psbJ-petA, trnT-psaM, trnS-trnD, trnL-rps4, psaC-ccsA, and rps7-trnL) and one gene (ycf1). The highly variable regions are appropriate targets for future use in the phylogenetic reconstructions of closely related, sympatric species of Picea as well as Pinaceae in general.

@article{el-kassaby_concept_2019,
	title = {Concept for gene conservation strategy for the endangered {Chinese} yellowhorn, {Xanthoceras} sorbifolium, based on simulation of pairwise kinship coefficients},
	volume = {432},
	issn = {0378-1127},
	url = {https://www.sciencedirect.com/science/article/pii/S0378112718314543},
	doi = {10.1016/j.foreco.2018.10.045},
	abstract = {A molecular markers-based conservation strategy framework for the endemic endangered Chinese yellowhorn, Xanthoceras sorbifolium, is developed. The method utilizes pairwise kinship coefficients, a measure of genetic similarity/dissimilarity, between individuals and contrasts two simulated mating schemes that either promote “no co-ancestry” or “co-ancestry” through multiple matings of particular individuals as well as a “hybrid” scenario involving both “no co-ancestry” and “co-ancestry” mating schemes. Selection of mating individuals is focused on maximizing genetic dissimilarity, hence capturing maximum genetic diversity. These approaches were compared on a population of 79 ancient yellowhorn trees scattered across 13 populations. Simulated matings were evaluated based on their average pairwise kinship, effective population size, and average number of alleles/locus. In this regard, no co-ancestry has been proven to be superior to co-ancestry mating scheme; however, co-ancestry offered opportunities for increasing effective population size, a desirable attribute for combating the detrimental effect of genetic drift. The hybrid approach, with reduced number of crosses, produced acceptable condition with maximum genetic diversity and high effective population size and genetic dissimilarity among the produced offspring. The advantages and disadvantages of marker-based gene conservation are highlighted and discussed. Subject area: Conservation genetics and biodiversity.},
	language = {en},
	urldate = {2023-04-27},
	journal = {Forest Ecology and Management},
	author = {El-Kassaby, Yousry A. and Wang, Qing and Wang, Tongli and Ratcliffe, Blaise and Bi, Quan-Xin and Wang, Zhou and Mao, Jian-Feng and Guan, Wenbin},
	month = jan,
	year = {2019},
	keywords = {Conservation, Genetic diversity, Microsatellites, Pairwise kinship relationship, Yellowhorn},
	pages = {976--982},
}

A molecular markers-based conservation strategy framework for the endemic endangered Chinese yellowhorn, Xanthoceras sorbifolium, is developed. The method utilizes pairwise kinship coefficients, a measure of genetic similarity/dissimilarity, between individuals and contrasts two simulated mating schemes that either promote “no co-ancestry” or “co-ancestry” through multiple matings of particular individuals as well as a “hybrid” scenario involving both “no co-ancestry” and “co-ancestry” mating schemes. Selection of mating individuals is focused on maximizing genetic dissimilarity, hence capturing maximum genetic diversity. These approaches were compared on a population of 79 ancient yellowhorn trees scattered across 13 populations. Simulated matings were evaluated based on their average pairwise kinship, effective population size, and average number of alleles/locus. In this regard, no co-ancestry has been proven to be superior to co-ancestry mating scheme; however, co-ancestry offered opportunities for increasing effective population size, a desirable attribute for combating the detrimental effect of genetic drift. The hybrid approach, with reduced number of crosses, produced acceptable condition with maximum genetic diversity and high effective population size and genetic dissimilarity among the produced offspring. The advantages and disadvantages of marker-based gene conservation are highlighted and discussed. Subject area: Conservation genetics and biodiversity.

@article{jiao_development_2019,
	title = {Development of novel {EST}-{SSR} markers for {Ephedra} sinica ({Ephedraceae}) by transcriptome database mining},
	volume = {7},
	issn = {2168-0450},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/aps3.1212},
	doi = {10.1002/aps3.1212},
	abstract = {Premise of the Study Ephedra sinica (Ephedraceae) is a gymnosperm shrub with a wide distribution across Central and Eastern Asia. It is widely cultivated as a medicinal plant, but its wild populations are monitored to determine whether protection is needed. Methods and Results Thirty-six microsatellite markers, including 11 polymorphic markers, were developed from E. distachya RNA-Seq data deposited in the National Center for Biotechology Information dbEST database. Among 100 genotyped E. sinica individuals originating from five different population groups, the allele number ranged from three to 22 per locus. Levels of observed and expected heterozygosity ranged from 0 to 0.866 (average 0.176) and 0 to 0.876 (average 0.491), respectively. Allelic polymorphism information content ranged from 0.000 to 0.847 (average 0.333). Cross-species amplifications were successfully conducted with two related Ephedra species for all 11 di- or trinucleotide simple sequence repeats. Conclusions This study provides the first set of microsatellite markers for genetic monitoring and surveying of this medicinal plant.},
	language = {en},
	number = {1},
	urldate = {2023-04-27},
	journal = {Applications in Plant Sciences},
	author = {Jiao, Si-Qian and Sun, Yan-Qiang and Zhang, Dong-Xu and Gao, Qiong and Jin, Yuqing and Liu, Hui and Ma, Yongpeng and Yang, Yong and Porth, Ilga and Mao, Jian-Feng},
	year = {2019},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/aps3.1212},
	keywords = {Ephedra sinica, Ephedraceae, expressed sequence tag–simple sequence repeat (EST-SSR) marker, genetic diversity, gymnosperm, medicinal plant},
	pages = {e01212},
}

Premise of the Study Ephedra sinica (Ephedraceae) is a gymnosperm shrub with a wide distribution across Central and Eastern Asia. It is widely cultivated as a medicinal plant, but its wild populations are monitored to determine whether protection is needed. Methods and Results Thirty-six microsatellite markers, including 11 polymorphic markers, were developed from E. distachya RNA-Seq data deposited in the National Center for Biotechology Information dbEST database. Among 100 genotyped E. sinica individuals originating from five different population groups, the allele number ranged from three to 22 per locus. Levels of observed and expected heterozygosity ranged from 0 to 0.866 (average 0.176) and 0 to 0.876 (average 0.491), respectively. Allelic polymorphism information content ranged from 0.000 to 0.847 (average 0.333). Cross-species amplifications were successfully conducted with two related Ephedra species for all 11 di- or trinucleotide simple sequence repeats. Conclusions This study provides the first set of microsatellite markers for genetic monitoring and surveying of this medicinal plant.

@article{zhou_floral_2019,
	title = {Floral development and the formation of functionally unisexual flowers in {Xanthoceras} sorbifolium ({Sapindaceae}), a morphologically andromonoecious tree endemic to northern {China}},
	volume = {33},
	issn = {1432-2285},
	url = {https://doi.org/10.1007/s00468-019-01879-6},
	doi = {10.1007/s00468-019-01879-6},
	abstract = {Xanthoceras sorbifolium is apparently andromonoecious but exhibits a cryptically monoecious breeding system. Sexual differentiation in male and functional female flowers occurs 2 weeks before flowering.},
	language = {en},
	number = {6},
	urldate = {2023-04-27},
	journal = {Trees},
	author = {Zhou, Qingyuan and Cai, Qing and Zheng, Yuanrun and Wu, Zhiyan and Mao, Jianfeng},
	month = dec,
	year = {2019},
	keywords = {Andromonoecy, Floral development, Monoecy, Systematic relationship, Xanthoceras sorbifolium},
	pages = {1571--1582},
}

Xanthoceras sorbifolium is apparently andromonoecious but exhibits a cryptically monoecious breeding system. Sexual differentiation in male and functional female flowers occurs 2 weeks before flowering.

@article{xu_genome_2019,
	title = {Genome sequence of {Malania} oleifera, a tree with great value for nervonic acid production},
	volume = {8},
	issn = {2047-217X},
	url = {https://doi.org/10.1093/gigascience/giy164},
	doi = {10.1093/gigascience/giy164},
	abstract = {Malania oleifera, a member of the Olacaceae family, is an IUCN red listed tree, endemic and restricted to the Karst region of southwest China. This tree's seed is valued for its high content of precious fatty acids (especially nervonic acid). However, studies on its genetic makeup and fatty acid biogenesis are severely hampered by a lack of molecular and genetic tools.We generated 51 Gb and 135 Gb of raw DNA sequences, using Pacific Biosciences (PacBio) single-molecule real-time and 10× Genomics sequencing, respectively. A final genome assembly, with a scaffold N50 size of 4.65 Mb and a total length of 1.51 Gb, was obtained by primary assembly based on PacBio long reads plus scaffolding with 10× Genomics reads. Identified repeats constituted ∼82\% of the genome, and 24,064 protein-coding genes were predicted with high support. The genome has low heterozygosity and shows no evidence for recent whole genome duplication. Metabolic pathway genes relating to the accumulation of long-chain fatty acid were identified and studied in detail.Here, we provide the first genome assembly and gene annotation for M. oleifera. The availability of these resources will be of great importance for conservation biology and for the functional genomics of nervonic acid biosynthesis.},
	number = {2},
	urldate = {2023-04-27},
	journal = {GigaScience},
	author = {Xu, Chao-Qun and Liu, Hui and Zhou, Shan-Shan and Zhang, Dong-Xu and Zhao, Wei and Wang, Sihai and Chen, Fu and Sun, Yan-Qiang and Nie, Shuai and Jia, Kai-Hua and Jiao, Si-Qian and Zhang, Ren-Gang and Yun, Quan-Zheng and Guan, Wenbin and Wang, Xuewen and Gao, Qiong and Bennetzen, Jeffrey L and Maghuly, Fatemeh and Porth, Ilga and Van de Peer, Yves and Wang, Xiao-Ru and Ma, Yongpeng and Mao, Jian-Feng},
	month = feb,
	year = {2019},
	pages = {giy164},
}

Malania oleifera, a member of the Olacaceae family, is an IUCN red listed tree, endemic and restricted to the Karst region of southwest China. This tree's seed is valued for its high content of precious fatty acids (especially nervonic acid). However, studies on its genetic makeup and fatty acid biogenesis are severely hampered by a lack of molecular and genetic tools.We generated 51 Gb and 135 Gb of raw DNA sequences, using Pacific Biosciences (PacBio) single-molecule real-time and 10× Genomics sequencing, respectively. A final genome assembly, with a scaffold N50 size of 4.65 Mb and a total length of 1.51 Gb, was obtained by primary assembly based on PacBio long reads plus scaffolding with 10× Genomics reads. Identified repeats constituted ∼82% of the genome, and 24,064 protein-coding genes were predicted with high support. The genome has low heterozygosity and shows no evidence for recent whole genome duplication. Metabolic pathway genes relating to the accumulation of long-chain fatty acid were identified and studied in detail.Here, we provide the first genome assembly and gene annotation for M. oleifera. The availability of these resources will be of great importance for conservation biology and for the functional genomics of nervonic acid biosynthesis.

@article{jin_genome-wide_2019,
	title = {Genome-{Wide} {Variant} {Identification} and {High}-{Density} {Genetic} {Map} {Construction} {Using} {RADseq} for {Platycladus} orientalis ({Cupressaceae})},
	volume = {9},
	issn = {2160-1836},
	url = {https://doi.org/10.1534/g3.119.400684},
	doi = {10.1534/g3.119.400684},
	abstract = {Platycladus orientalis is an ecologically important native conifer in Northern China and exotic species in many parts of the world; however, knowledge about the species’ genetics and genome are very limited. The availability of well-developed battery of genetic markers, with large genome coverage, is a prerequisite for the species genetic dissection of adaptive attributes and efficient selective breeding. Here, we present a genome-wide genotyping method with double-digestion restriction site associated DNA sequencing (ddRAD-seq) that is effective in generating large number of Mendelian markers for genome mapping and other genetic applications. Using 139 megagametophytes collected from a single mother tree, we assembled 397,226 loci, of which 108,683 (27.4\%) were polymorphic. After stringent filtering for 1:1 segregation ratio and missing rate of \<20\%, the remaining 23,926 loci (22\% of the polymorphic loci) were ordered into 11 linkage groups (LGs) and distributed across 7,559 unique positions, with a total map length of 1,443 cM and an average spacing of 0.2 cM between adjacent unique positions. The 11 LGs correspond to the species’ 11 haploid genome chromosome number. This genetic map is among few high-density maps available for conifers to date, and represents the first genetic map for P. orientalis. The information generated serves as a solid foundation not only for marker-assisted breeding efforts, but also for comparative conifer genomic studies.},
	number = {11},
	urldate = {2023-04-27},
	journal = {G3 Genes/Genomes/Genetics},
	author = {Jin, Yuqing and Zhao, Wei and Nie, Shuai and Liu, Si-Si and El-Kassaby, Yousry A and Wang, Xiao-Ru and Mao, Jian-Feng},
	month = nov,
	year = {2019},
	pages = {3663--3672},
}

Platycladus orientalis is an ecologically important native conifer in Northern China and exotic species in many parts of the world; however, knowledge about the species’ genetics and genome are very limited. The availability of well-developed battery of genetic markers, with large genome coverage, is a prerequisite for the species genetic dissection of adaptive attributes and efficient selective breeding. Here, we present a genome-wide genotyping method with double-digestion restriction site associated DNA sequencing (ddRAD-seq) that is effective in generating large number of Mendelian markers for genome mapping and other genetic applications. Using 139 megagametophytes collected from a single mother tree, we assembled 397,226 loci, of which 108,683 (27.4%) were polymorphic. After stringent filtering for 1:1 segregation ratio and missing rate of <20%, the remaining 23,926 loci (22% of the polymorphic loci) were ordered into 11 linkage groups (LGs) and distributed across 7,559 unique positions, with a total map length of 1,443 cM and an average spacing of 0.2 cM between adjacent unique positions. The 11 LGs correspond to the species’ 11 haploid genome chromosome number. This genetic map is among few high-density maps available for conifers to date, and represents the first genetic map for P. orientalis. The information generated serves as a solid foundation not only for marker-assisted breeding efforts, but also for comparative conifer genomic studies.

@article{zhou_-depth_2019,
	title = {In-depth transcriptome characterization uncovers distinct gene family expansions for {Cupressus} gigantea important to this long-lived species’ adaptability to environmental cues},
	volume = {20},
	issn = {1471-2164},
	url = {https://doi.org/10.1186/s12864-019-5584-6},
	doi = {10.1186/s12864-019-5584-6},
	abstract = {Cupressus gigantea, a rare and endangered tree species with remarkable medicinal value, is endemic to the Tibetan Plateau. Yet, little is known about the underlying genetics of the unique ecological adaptability of this extremely long-lived conifer with a large genome size. Here, we present its first de novo and multi-tissue transcriptome in-depth characterization.},
	number = {1},
	urldate = {2023-04-27},
	journal = {BMC Genomics},
	author = {Zhou, Shan-Shan and Xing, Zhen and Liu, Hui and Hu, Xian-Ge and Gao, Qiong and Xu, Jie and Jiao, Si-Qian and Jia, Kai-Hua and Jin, Yu Qing and Zhao, Wei and Porth, Ilga and El-Kassaby, Yousry A. and Mao, Jian-Feng},
	month = mar,
	year = {2019},
	keywords = {Cupressus gigantea, De novo transcriptome assembly, Ecology, Gene family evolution, Gene functional annotation},
	pages = {213},
}

Cupressus gigantea, a rare and endangered tree species with remarkable medicinal value, is endemic to the Tibetan Plateau. Yet, little is known about the underlying genetics of the unique ecological adaptability of this extremely long-lived conifer with a large genome size. Here, we present its first de novo and multi-tissue transcriptome in-depth characterization.

@article{xu_late_2019,
	title = {Late {Pleistocene} speciation of three closely related tree peonies endemic to the {Qinling}–{Daba} {Mountains}, a major glacial refugium in {Central} {China}},
	volume = {9},
	issn = {2045-7758},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.5284},
	doi = {10.1002/ece3.5284},
	abstract = {Determining the factors promoting speciation is a major task in ecological and evolutionary research and can be aided by phylogeographic analysis. The Qinling–Daba Mountains (QDM) located in central China form an important geographic barrier between southern subtropical and northern temperate regions, and exhibit complex topography, climatic, and ecological diversity. Surprisingly, few phylogeographic analyses and studies of plant speciation in this region have been conducted. To address this issue, we investigated the genetic divergence and evolutionary histories of three closely related tree peony species (Paeonia qiui, P. jishanensis, and P. rockii) endemic to the QDM. Forty populations of the three tree peony species were genotyped using 22 nuclear simple sequence repeat markers (nSSRs) and three chloroplast DNA sequences to assess genetic structure and phylogenetic relationships, supplemented by morphological characterization and ecological niche modeling (ENM). Morphological and molecular genetic analyses showed the three species to be clearly differentiated from each other. In addition, coalescent analyses using DIYABC conducted on nSSR variation indicated that the species diverged from each other in the late Pleistocene, while ecological niche modeling (ENM) suggested they occupied a larger area during the Last Glacial Maximum (LGM) than at present. The combined genetic evidence from nuclear and chloroplast DNA and the results of ENM indicate that each species persisted through the late Pleistocene in multiple refugia in the Qinling, Daba, and Taihang Mountains with divergence favored by restricted gene flow caused by geographic isolation, ecological divergence, and limited pollen and seed dispersal. Our study contributes to a growing understanding of the origin and population structure of tree peonies and provides insights into the high level of plant endemism present in the Qinling–Daba Mountains of Central China.},
	language = {en},
	number = {13},
	urldate = {2023-04-27},
	journal = {Ecology and Evolution},
	author = {Xu, Xing-Xing and Cheng, Fang-Yun and Peng, Li-Ping and Sun, Yan-Qiang and Hu, Xian-Ge and Li, San-Yuan and Xian, Hong-Li and Jia, Kai-Hua and Abbott, Richard J. and Mao, Jian-Feng},
	year = {2019},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.5284},
	keywords = {ecological niche modeling, genetic divergence, multiple refugia, niche divergence, phylogeography, speciation, tree peony},
	pages = {7528--7548},
}

Determining the factors promoting speciation is a major task in ecological and evolutionary research and can be aided by phylogeographic analysis. The Qinling–Daba Mountains (QDM) located in central China form an important geographic barrier between southern subtropical and northern temperate regions, and exhibit complex topography, climatic, and ecological diversity. Surprisingly, few phylogeographic analyses and studies of plant speciation in this region have been conducted. To address this issue, we investigated the genetic divergence and evolutionary histories of three closely related tree peony species (Paeonia qiui, P. jishanensis, and P. rockii) endemic to the QDM. Forty populations of the three tree peony species were genotyped using 22 nuclear simple sequence repeat markers (nSSRs) and three chloroplast DNA sequences to assess genetic structure and phylogenetic relationships, supplemented by morphological characterization and ecological niche modeling (ENM). Morphological and molecular genetic analyses showed the three species to be clearly differentiated from each other. In addition, coalescent analyses using DIYABC conducted on nSSR variation indicated that the species diverged from each other in the late Pleistocene, while ecological niche modeling (ENM) suggested they occupied a larger area during the Last Glacial Maximum (LGM) than at present. The combined genetic evidence from nuclear and chloroplast DNA and the results of ENM indicate that each species persisted through the late Pleistocene in multiple refugia in the Qinling, Daba, and Taihang Mountains with divergence favored by restricted gene flow caused by geographic isolation, ecological divergence, and limited pollen and seed dispersal. Our study contributes to a growing understanding of the origin and population structure of tree peonies and provides insights into the high level of plant endemism present in the Qinling–Daba Mountains of Central China.

@article{hu_local_2019,
	title = {Local {Adaptation} and {Response} of {Platycladus} orientalis ({L}.) {Franco} {Populations} to {Climate} {Change}},
	volume = {10},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {1999-4907},
	url = {https://www.mdpi.com/1999-4907/10/8/622},
	doi = {10.3390/f10080622},
	abstract = {Knowledge about the local adaptation and response of forest tree populations to the climate is important for assessing the impact of climate change and developing adaptive genetic resource management strategies. However, such information is not available for most plant species. Here, based on 69 provenances tested at 19 common garden experimental sites, we developed a universal response function (URF) for tree height at seven years of age for the important and wide-spread native Chinese tree species Platycladus orientalis (L.) Franco. URF was recently used to predict the potential growth response of a population originating from any climate and growing in any climate conditions. The developed model integrated both genetic and environmental effects, and explained 55\% of the total variation in tree height observed among provenances and test sites in China. We found that local provenances performed better than non-local counterparts in habitats located in central, eastern, and southwestern China, showing the evidence of local adaptation as compared to other regions. In contrast, non-local provenances outperformed local ones in peripheral areas in northern and northwestern China, suggesting an adaptational lag in these areas. Future projections suggest that the suitable habitat areas of P. orientalis would expand by 15\%–39\% and shift northward by 0.8–3 degrees in latitude; however, the projected tree height of this species would decline by 4\%–8\% if local provenances were used. If optimal provenances were used, tree height growth could be improved by 13\%–15\%, along with 59\%–71\% suitable habitat expansion. Thus, assisted migration with properly selected seed sources would be effective in avoiding maladaptation in new plantations under a changing climate for P. orientalis.},
	language = {en},
	number = {8},
	urldate = {2023-04-27},
	journal = {Forests},
	author = {Hu, Xian-Ge and Mao, Jian-Feng and El-Kassaby, Yousry A. and Jia, Kai-Hua and Jiao, Si-Qian and Zhou, Shan-Shan and Li, Yue and Coops, Nicholas C. and Wang, Tongli},
	month = aug,
	year = {2019},
	note = {Number: 8
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {\textit{Platycladus orientalis}, adaptation, assisted migration, climate change, provenance test, universal response function},
	pages = {622},
}

Knowledge about the local adaptation and response of forest tree populations to the climate is important for assessing the impact of climate change and developing adaptive genetic resource management strategies. However, such information is not available for most plant species. Here, based on 69 provenances tested at 19 common garden experimental sites, we developed a universal response function (URF) for tree height at seven years of age for the important and wide-spread native Chinese tree species Platycladus orientalis (L.) Franco. URF was recently used to predict the potential growth response of a population originating from any climate and growing in any climate conditions. The developed model integrated both genetic and environmental effects, and explained 55% of the total variation in tree height observed among provenances and test sites in China. We found that local provenances performed better than non-local counterparts in habitats located in central, eastern, and southwestern China, showing the evidence of local adaptation as compared to other regions. In contrast, non-local provenances outperformed local ones in peripheral areas in northern and northwestern China, suggesting an adaptational lag in these areas. Future projections suggest that the suitable habitat areas of P. orientalis would expand by 15%–39% and shift northward by 0.8–3 degrees in latitude; however, the projected tree height of this species would decline by 4%–8% if local provenances were used. If optimal provenances were used, tree height growth could be improved by 13%–15%, along with 59%–71% suitable habitat expansion. Thus, assisted migration with properly selected seed sources would be effective in avoiding maladaptation in new plantations under a changing climate for P. orientalis.

@article{peng_modelling_2019,
	title = {Modelling environmentally suitable areas for the potential introduction and cultivation of the emerging oil crop {Paeonia} ostii in {China}},
	volume = {9},
	copyright = {2019 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-019-39449-y},
	doi = {10.1038/s41598-019-39449-y},
	abstract = {Paeonia ostii is a traditional ornamental and medicinal species that has attracted considerable interest for its high oil value. To facilitate the effective and rational cultivation and application of P. ostii in China, it is necessary to determine its potential spatial habitat distribution and environmental requirements. Using high-resolution environmental data for current and future climate scenarios, the potential suitable area and climatic requirements of P. ostii were modelled. Among the 11 environmental variables investigated, growing degree days, precipitation of the wettest month, mean temperature of the coldest quarter, global UV-B radiation, annual precipitation, and soil pH played major roles in determining the suitability of a habitat for the cultivation of P. ostii. Under the current environmental conditions in China, a total area of 20.31 × 105 km2 is suitable for growing P. ostii, accounting for 21.16\% of the country’s total land area. Under the two future climate scenario/year combinations (i.e., representative concentration pathways [RCPs], RCP2.6 and RCP8.5 in 2050), this species would increase its suitable area at high latitudes while decrease at low latitudes. These results present valuable information and a theoretical reference point for identifying the suitable cultivation areas of P. ostii.},
	language = {en},
	number = {1},
	urldate = {2023-04-27},
	journal = {Scientific Reports},
	author = {Peng, Li-Ping and Cheng, Fang-Yun and Hu, Xian-Ge and Mao, Jian-Feng and Xu, Xing-Xing and Zhong, Yuan and Li, San-Yuan and Xian, Hong-Li},
	month = mar,
	year = {2019},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Biogeography, Ecological modelling},
	pages = {3213},
}

Paeonia ostii is a traditional ornamental and medicinal species that has attracted considerable interest for its high oil value. To facilitate the effective and rational cultivation and application of P. ostii in China, it is necessary to determine its potential spatial habitat distribution and environmental requirements. Using high-resolution environmental data for current and future climate scenarios, the potential suitable area and climatic requirements of P. ostii were modelled. Among the 11 environmental variables investigated, growing degree days, precipitation of the wettest month, mean temperature of the coldest quarter, global UV-B radiation, annual precipitation, and soil pH played major roles in determining the suitability of a habitat for the cultivation of P. ostii. Under the current environmental conditions in China, a total area of 20.31 × 105 km2 is suitable for growing P. ostii, accounting for 21.16% of the country’s total land area. Under the two future climate scenario/year combinations (i.e., representative concentration pathways [RCPs], RCP2.6 and RCP8.5 in 2050), this species would increase its suitable area at high latitudes while decrease at low latitudes. These results present valuable information and a theoretical reference point for identifying the suitable cultivation areas of P. ostii.

@article{liu_complete_2019,
	title = {The complete chloroplast genome sequence annotation for {Malania} oleifera, a critically endangered and important bioresource tree},
	volume = {11},
	issn = {1877-7260},
	url = {https://doi.org/10.1007/s12686-018-1005-4},
	doi = {10.1007/s12686-018-1005-4},
	abstract = {In this study, we characterize the chloroplast genome of Malania oleifera Chun et S. Lee, the only species of this genus and member of the Olacaceae family. M. oleifera is an interesting seed oil plant for medicinal purposes. It is also a critically endangered species, which is currently recorded on the International Union for Conservation of Nature (IUCN) Red List and in the “Red Data Book of Chinese Plants: the Rare and Endangered Plants”. Its total chloroplast genome length is 125,050 bp, including a large single copy region of 76,387 bp, a short single copy gene region of 15 bp, and a pair of inverted repeats (IRs) of 24,324 bp. We annotated 80 genes in this chloroplast genome, including 51 protein-coding genes, 4 ribosomal RNAs, 4 pseudogenes and 21 tRNA genes. We found 15 genes duplicated in the IR regions, and the overall GC content was found to be 38.17\%. Phylogenetic analysis showed that M. oleifera is closely related to Erythropalum scandens comparing nine chloroplast genomes from Santalales.},
	language = {en},
	number = {3},
	urldate = {2023-04-27},
	journal = {Conservation Genetics Resources},
	author = {Liu, Si-Si and Hu, Yi-Heng and Maghuly, Fatemeh and Porth, Ilga Mercedes and Mao, Jian-Feng},
	month = sep,
	year = {2019},
	keywords = {Chloroplast genome, Malania oleifera, Phylogenetic analysis},
	pages = {271--274},
}

In this study, we characterize the chloroplast genome of Malania oleifera Chun et S. Lee, the only species of this genus and member of the Olacaceae family. M. oleifera is an interesting seed oil plant for medicinal purposes. It is also a critically endangered species, which is currently recorded on the International Union for Conservation of Nature (IUCN) Red List and in the “Red Data Book of Chinese Plants: the Rare and Endangered Plants”. Its total chloroplast genome length is 125,050 bp, including a large single copy region of 76,387 bp, a short single copy gene region of 15 bp, and a pair of inverted repeats (IRs) of 24,324 bp. We annotated 80 genes in this chloroplast genome, including 51 protein-coding genes, 4 ribosomal RNAs, 4 pseudogenes and 21 tRNA genes. We found 15 genes duplicated in the IR regions, and the overall GC content was found to be 38.17%. Phylogenetic analysis showed that M. oleifera is closely related to Erythropalum scandens comparing nine chloroplast genomes from Santalales.

@article{xia_combining_2018,
	title = {Combining mitochondrial and nuclear genome analyses to dissect the effects of colonization, environment, and geography on population structure in {Pinus} tabuliformis},
	volume = {11},
	issn = {1752-4571},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/eva.12697},
	doi = {10.1111/eva.12697},
	abstract = {The phylogeographic histories of plants in East Asia are complex and shaped by both past large-scale climatic oscillations and dramatic tectonic events. The impact of these historic events, as well as ecological adaptation, on the distribution of biodiversity remains to be elucidated. Pinus tabuliformis is the dominant coniferous tree in northern China, with a large distribution across wide environmental gradients. We examined genetic variation in this species using genotyping-by-sequencing and mitochondrial (mt) DNA markers. We found population structure on both nuclear and mt genomes with a geographic pattern that corresponds well with the landscape of northern China. To understand the contributions of environment, geography, and colonization history to the observed population structure, we performed ecological niche modeling and partitioned the among-population genomic variance into isolation by environment (IBE), isolation by distance (IBD), and isolation by colonization (IBC). We used mtDNA, which is transmitted by seeds in pine, to reflect colonization. We found little impact of IBE, IBD, and IBC on variation in neutral SNPs, but significant impact of IBE on a group of outlier loci. The lack of IBC illustrates that the maternal history can be quickly eroded from the nuclear genome by high rates of gene flow. Our results suggest that genomic variation in P. tabuliformis is largely affected by neutral and stochastic processes, and the signature of local adaptation is visible only at robust outlier loci. This study enriches our understanding on the complex evolutionary forces that shape the distribution of genetic variation in plant taxa in northern China, and guides breeding, conservation, and reforestation programs for P. tabuliformis.},
	language = {en},
	number = {10},
	urldate = {2023-04-27},
	journal = {Evolutionary Applications},
	author = {Xia, Hanhan and Wang, Baosheng and Zhao, Wei and Pan, Jin and Mao, Jian-Feng and Wang, Xiao-Ru},
	year = {2018},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.12697},
	keywords = {demographic history, genotyping-by-sequencing, local adaptation, niche modeling, population structure},
	pages = {1931--1945},
}

The phylogeographic histories of plants in East Asia are complex and shaped by both past large-scale climatic oscillations and dramatic tectonic events. The impact of these historic events, as well as ecological adaptation, on the distribution of biodiversity remains to be elucidated. Pinus tabuliformis is the dominant coniferous tree in northern China, with a large distribution across wide environmental gradients. We examined genetic variation in this species using genotyping-by-sequencing and mitochondrial (mt) DNA markers. We found population structure on both nuclear and mt genomes with a geographic pattern that corresponds well with the landscape of northern China. To understand the contributions of environment, geography, and colonization history to the observed population structure, we performed ecological niche modeling and partitioned the among-population genomic variance into isolation by environment (IBE), isolation by distance (IBD), and isolation by colonization (IBC). We used mtDNA, which is transmitted by seeds in pine, to reflect colonization. We found little impact of IBE, IBD, and IBC on variation in neutral SNPs, but significant impact of IBE on a group of outlier loci. The lack of IBC illustrates that the maternal history can be quickly eroded from the nuclear genome by high rates of gene flow. Our results suggest that genomic variation in P. tabuliformis is largely affected by neutral and stochastic processes, and the signature of local adaptation is visible only at robust outlier loci. This study enriches our understanding on the complex evolutionary forces that shape the distribution of genetic variation in plant taxa in northern China, and guides breeding, conservation, and reforestation programs for P. tabuliformis.

@article{huang_development_2018,
	title = {Development of high transferability {cpSSR} markers for individual identification and genetic investigation in {Cupressaceae} species},
	volume = {8},
	issn = {2045-7758},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.4053},
	doi = {10.1002/ece3.4053},
	abstract = {Given the low substitution rate in plastomes, the polymorphic and codominant nature of chloroplast SSRs (cpSSRs) makes them ideal markers, complementing their nuclear counterpart. In Cupressaceae, cpSSRs are mostly paternally inherited, thus, they are useful in mating systems and pollen flow studies. Using e-PCR, 92 SSR loci were identified across six Cupressaceae plastomes, and primers were designed for 26 loci with potential interspecific transferability. The 26 developed cpSSRs were polymorphic in four genera, Platycladus, Sabina, Juniperus, and Cupressus and are suitable for Cupressaceae molecular genetic studies and utilization. We genotyped 192 Platycladus orientalis samples from a core breeding population using 10 of the developed cpSSRs and 10 nuclear SSRs, and these individuals were identified with high confidence. The developed cpSSRs can be used in (1) a marker-assisted breeding scheme, specifically when paternity identification is required, (2) population genetics investigations, and (3) biogeography of Cupressaceae and unraveling the genetic relationships between related species.},
	language = {en},
	number = {10},
	urldate = {2023-04-27},
	journal = {Ecology and Evolution},
	author = {Huang, Li-Sha and Sun, Yan-Qiang and Jin, Yuqing and Gao, Qiong and Hu, Xian-Ge and Gao, Fu-Ling and Yang, Xiao-Lei and Zhu, Ji-Jun and El-Kassaby, Yousry A. and Mao, Jian-Feng},
	year = {2018},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.4053},
	keywords = {Cupressaceae, chloroplast SSRs, genetic diversity, haplotype, mating system, paternity test},
	pages = {4967--4977},
}

Given the low substitution rate in plastomes, the polymorphic and codominant nature of chloroplast SSRs (cpSSRs) makes them ideal markers, complementing their nuclear counterpart. In Cupressaceae, cpSSRs are mostly paternally inherited, thus, they are useful in mating systems and pollen flow studies. Using e-PCR, 92 SSR loci were identified across six Cupressaceae plastomes, and primers were designed for 26 loci with potential interspecific transferability. The 26 developed cpSSRs were polymorphic in four genera, Platycladus, Sabina, Juniperus, and Cupressus and are suitable for Cupressaceae molecular genetic studies and utilization. We genotyped 192 Platycladus orientalis samples from a core breeding population using 10 of the developed cpSSRs and 10 nuclear SSRs, and these individuals were identified with high confidence. The developed cpSSRs can be used in (1) a marker-assisted breeding scheme, specifically when paternity identification is required, (2) population genetics investigations, and (3) biogeography of Cupressaceae and unraveling the genetic relationships between related species.

@article{dong_high-quality_2018,
	title = {High-quality assembly of the reference genome for scarlet sage, {Salvia} splendens, an economically important ornamental plant},
	volume = {7},
	issn = {2047-217X},
	url = {https://doi.org/10.1093/gigascience/giy068},
	doi = {10.1093/gigascience/giy068},
	abstract = {Salvia splendens Ker-Gawler, scarlet or tropical sage, is a tender herbaceous perennial widely introduced and seen in public gardens all over the world. With few molecular resources, breeding is still restricted to traditional phenotypic selection, and the genetic mechanisms underlying phenotypic variation remain unknown. Hence, a high-quality reference genome will be very valuable for marker-assisted breeding, genome editing, and molecular genetics.We generated 66 Gb and 37 Gb of raw DNA sequences, respectively, from whole-genome sequencing of a largely homozygous scarlet sage inbred line using Pacific Biosciences (PacBio) single-molecule real-time and Illumina HiSeq sequencing platforms. The PacBio de novo assembly yielded a final genome with a scaffold N50 size of 3.12 Mb and a total length of 808 Mb. The repetitive sequences identified accounted for 57.52\% of the genome sequence, and  54,008 protein-coding genes were predicted collectively with ab initio and homology-based gene prediction from the masked genome. The divergence time between S. splendens and Salvia miltiorrhiza was estimated at 28.21 million years ago (Mya). Moreover, 3,797 species-specific genes and 1,187 expanded gene families were identified for the scarlet sage genome.We provide the first genome sequence and gene annotation for the scarlet sage. The availability of these resources will be of great importance for further breeding strategies, genome editing, and comparative genomics among related species.},
	number = {7},
	urldate = {2023-04-27},
	journal = {GigaScience},
	author = {Dong, Ai-Xiang and Xin, Hai-Bo and Li, Zi-Jing and Liu, Hui and Sun, Yan-Qiang and Nie, Shuai and Zhao, Zheng-Nan and Cui, Rong-Feng and Zhang, Ren-Gang and Yun, Quan-Zheng and Wang, Xin-Ning and Maghuly, Fatemeh and Porth, Ilga and Cong, Ri-Chen and Mao, Jian-Feng},
	month = jul,
	year = {2018},
	pages = {giy068},
}

Salvia splendens Ker-Gawler, scarlet or tropical sage, is a tender herbaceous perennial widely introduced and seen in public gardens all over the world. With few molecular resources, breeding is still restricted to traditional phenotypic selection, and the genetic mechanisms underlying phenotypic variation remain unknown. Hence, a high-quality reference genome will be very valuable for marker-assisted breeding, genome editing, and molecular genetics.We generated 66 Gb and 37 Gb of raw DNA sequences, respectively, from whole-genome sequencing of a largely homozygous scarlet sage inbred line using Pacific Biosciences (PacBio) single-molecule real-time and Illumina HiSeq sequencing platforms. The PacBio de novo assembly yielded a final genome with a scaffold N50 size of 3.12 Mb and a total length of 808 Mb. The repetitive sequences identified accounted for 57.52% of the genome sequence, and  54,008 protein-coding genes were predicted collectively with ab initio and homology-based gene prediction from the masked genome. The divergence time between S. splendens and Salvia miltiorrhiza was estimated at 28.21 million years ago (Mya). Moreover, 3,797 species-specific genes and 1,187 expanded gene families were identified for the scarlet sage genome.We provide the first genome sequence and gene annotation for the scarlet sage. The availability of these resources will be of great importance for further breeding strategies, genome editing, and comparative genomics among related species.

@article{huang_pollination_2018,
	title = {Pollination dynamics in a {Platycladus} orientalis seed orchard as revealed by partial pedigree reconstruction},
	volume = {48},
	issn = {0045-5067},
	url = {https://cdnsciencepub.com/doi/10.1139/cjfr-2018-0077},
	doi = {10.1139/cjfr-2018-0077},
	abstract = {Pollination dynamics was studied in a first-generation Platycladus orientalis (L.) Franco seed orchard with pedigree reconstruction using eight nuclear and four chloroplast SSRs. The pedigree reconstruction assigned 371 of 448 studied seeds to one of the orchard’s 192 candidate male parents and showed a high level of outcrossing and pollen contamination in the orchard’s seed crop. While the orchard’s seed population showed greater allelic richness compared with the parental population, a few alleles present in the parental population were missing in the seed crop. Additionally, we detected no significant correlation between male reproductive energy (pollen yield) and male reproductive success; however, uneven parental contribution was also observed. Pollen management practices were recommended to ensure the maintenance of genetic diversity in the seed crops and increase in genetic gain.},
	number = {8},
	urldate = {2023-04-27},
	journal = {Canadian Journal of Forest Research},
	author = {Huang, Li-Sha and Song, Jiayin and Sun, Yan-Qiang and Gao, Qiong and Jiao, Si-Qian and Zhou, Shan-Shan and Jin, Yuqing and Yang, Xiao-Lei and Zhu, Ji-Jun and Gao, Fu-Ling and El-Kassaby, Yousry A. and Mao, Jian-Feng},
	month = aug,
	year = {2018},
	note = {Publisher: NRC Research Press},
	pages = {952--957},
}

Pollination dynamics was studied in a first-generation Platycladus orientalis (L.) Franco seed orchard with pedigree reconstruction using eight nuclear and four chloroplast SSRs. The pedigree reconstruction assigned 371 of 448 studied seeds to one of the orchard’s 192 candidate male parents and showed a high level of outcrossing and pollen contamination in the orchard’s seed crop. While the orchard’s seed population showed greater allelic richness compared with the parental population, a few alleles present in the parental population were missing in the seed crop. Additionally, we detected no significant correlation between male reproductive energy (pollen yield) and male reproductive success; however, uneven parental contribution was also observed. Pollen management practices were recommended to ensure the maintenance of genetic diversity in the seed crops and increase in genetic gain.

@article{mao_approaches_2017,
	title = {Approaches used to detect and test hybridization: combining phylogenetic and population genetic analyses},
	volume = {25},
	issn = {1005-0094},
	shorttitle = {Approaches used to detect and test hybridization},
	url = {https://www.biodiversity-science.net/EN/10.17520/biods.2017097},
	doi = {10.17520/biods.2017097},
	abstract = {Hybridization among diverging (interspecific or intraspecific) groups ...},
	language = {en},
	number = {6},
	urldate = {2023-04-27},
	journal = {Biodiversity Science},
	author = {Mao, Jian-Feng and Ma, Yongpeng and Zhou, Renchao},
	month = jun,
	year = {2017},
	pages = {577},
}

Hybridization among diverging (interspecific or intraspecific) groups ...

@article{peng_genetic_2017,
	title = {Genetic analyses reveal independent domestication origins of the emerging oil crop {Paeonia} ostii, a tree peony with a long-term cultivation history},
	volume = {7},
	copyright = {2017 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-017-04744-z},
	doi = {10.1038/s41598-017-04744-z},
	abstract = {Paeonia ostii, a member of tree peony, is an emerging oil crop with important medical and oil uses and widely cultivated in China. Dissolving the genetic diversity and domestication history of this species is important for further genetic improvements and deployments. We firstly selected 29 simple sequence repeats (SSRs) via transcriptome mining, segregation analyses and polymorphism characterizations; then, 901 individuals from the range-wide samples were genotyped using well-characterized SSR markers. We observed moderate genetic diversity among individuals, and Shaanxi Province was identified as the center of genetic diversity for our cultivated plants. Five well-separated gene pools were detected by STRUCTURE analyses, and the results suggested that multiple independent domestication origins occurred in Shaanxi Province and Tongling City (Anhui Province). Taken together, the genetic evidence and the historical records suggest multiple long-distance introductions after the plant was domesticated in Shandong, Henan and Hunan provinces. The present study provides the first genetic evaluation of the domestication history of P. ostii, and our results provide an important reference for further genetic improvements and deployments of this important crop.},
	language = {en},
	number = {1},
	urldate = {2023-04-27},
	journal = {Scientific Reports},
	author = {Peng, Li-Ping and Cai, Chang-Fu and Zhong, Yuan and Xu, Xing-Xing and Xian, Hong-Li and Cheng, Fang-Yun and Mao, Jian-Feng},
	month = jul,
	year = {2017},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Structural variation},
	pages = {5340},
}

Paeonia ostii, a member of tree peony, is an emerging oil crop with important medical and oil uses and widely cultivated in China. Dissolving the genetic diversity and domestication history of this species is important for further genetic improvements and deployments. We firstly selected 29 simple sequence repeats (SSRs) via transcriptome mining, segregation analyses and polymorphism characterizations; then, 901 individuals from the range-wide samples were genotyped using well-characterized SSR markers. We observed moderate genetic diversity among individuals, and Shaanxi Province was identified as the center of genetic diversity for our cultivated plants. Five well-separated gene pools were detected by STRUCTURE analyses, and the results suggested that multiple independent domestication origins occurred in Shaanxi Province and Tongling City (Anhui Province). Taken together, the genetic evidence and the historical records suggest multiple long-distance introductions after the plant was domesticated in Shandong, Henan and Hunan provinces. The present study provides the first genetic evaluation of the domestication history of P. ostii, and our results provide an important reference for further genetic improvements and deployments of this important crop.

@article{metcalfe_informing_2017,
	title = {Informing climate models with rapid chamber measurements of forest carbon uptake},
	volume = {23},
	issn = {13541013},
	url = {http://doi.wiley.com/10.1111/gcb.13451},
	doi = {10/f3vbr8},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Global Change Biology},
	author = {Metcalfe, Daniel B. and Ricciuto, Daniel and Palmroth, Sari and Campbell, Catherine and Hurry, Vaughan and Mao, Jiafu and Keel, Sonja G. and Linder, Sune and Shi, Xiaoying and Näsholm, Torgny and Ohlsson, Klas E. A. and Blackburn, M. and Thornton, Peter E. and Oren, Ram},
	month = may,
	year = {2017},
	pages = {2130--2139},
}

@article{hu_predicting_2017,
	title = {Predicting {Future} {Seed} {Sourcing} of {Platycladus} orientalis ({L}.) for {Future} {Climates} {Using} {Climate} {Niche} {Models}},
	volume = {8},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {1999-4907},
	url = {https://www.mdpi.com/1999-4907/8/12/471},
	doi = {10.3390/f8120471},
	abstract = {Climate niche modeling has been widely used to assess the impact of climate change on forest trees at the species level. However, geographically divergent tree populations are expected to respond differently to climate change. Considering intraspecific local adaptation in modeling species responses to climate change will thus improve the credibility and usefulness of climate niche models, particularly for genetic resources management. In this study, we used five Platycladus orientalis (L.) seed zones (Northwestern; Northern; Central; Southern; and Subtropical) covering the entire species range in China. A climate niche model was developed and used to project the suitable climatic conditions for each of the five seed zones for current and various future climate scenarios (Representative Concentration Pathways: RCP2.6, RCP4.5, RCP6.0, and RCP8.5). Our results indicated that the Subtropical seed zone would show consistent reduction for all climate change scenarios. The remaining seed zones, however, would experience various degrees of expansion in suitable habitat relative to their current geographic distributions. Most of the seed zones would gain suitable habitats at their northern distribution margins and higher latitudes. Thus, we recommend adjusting the current forest management strategies to mitigate the negative impacts of climate change.},
	language = {en},
	number = {12},
	urldate = {2023-04-27},
	journal = {Forests},
	author = {Hu, Xian-Ge and Wang, Tongli and Liu, Si-Si and Jiao, Si-Qian and Jia, Kai-Hua and Zhou, Shan-Shan and Jin, Yuqing and Li, Yue and El-Kassaby, Yousry A. and Mao, Jian-Feng},
	month = dec,
	year = {2017},
	note = {Number: 12
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {climate change, conifer, local adaptation, seed zone, spatial shifts},
	pages = {471},
}

Climate niche modeling has been widely used to assess the impact of climate change on forest trees at the species level. However, geographically divergent tree populations are expected to respond differently to climate change. Considering intraspecific local adaptation in modeling species responses to climate change will thus improve the credibility and usefulness of climate niche models, particularly for genetic resources management. In this study, we used five Platycladus orientalis (L.) seed zones (Northwestern; Northern; Central; Southern; and Subtropical) covering the entire species range in China. A climate niche model was developed and used to project the suitable climatic conditions for each of the five seed zones for current and various future climate scenarios (Representative Concentration Pathways: RCP2.6, RCP4.5, RCP6.0, and RCP8.5). Our results indicated that the Subtropical seed zone would show consistent reduction for all climate change scenarios. The remaining seed zones, however, would experience various degrees of expansion in suitable habitat relative to their current geographic distributions. Most of the seed zones would gain suitable habitats at their northern distribution margins and higher latitudes. Thus, we recommend adjusting the current forest management strategies to mitigate the negative impacts of climate change.

@article{hu_novo_2016,
	title = {De {Novo} {Transcriptome} {Assembly} and {Characterization} for the {Widespread} and {Stress}-{Tolerant} {Conifer} {Platycladus} orientalis},
	volume = {11},
	issn = {1932-6203},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0148985},
	doi = {10.1371/journal.pone.0148985},
	abstract = {Platycladus orientalis, of the family Cupressaceae, is a widespread conifer throughout China and is extensively used for ecological reforestation, horticulture, and in medicine. Transcriptome assemblies are required for this ecologically important conifer for understanding genes underpinning adaptation and complex traits for breeding programs. To enrich the species’ genomic resources, a de novo transcriptome sequencing was performed using Illumina paired-end sequencing. In total, 104,073,506 high quality sequence reads (approximately 10.3 Gbp) were obtained, which were assembled into 228,948 transcripts and 148,867 unigenes that were longer than 200 nt. Quality assessment using CEGMA showed that the transcriptomes obtained were mostly complete for highly conserved core eukaryotic genes. Based on similarity searches with known proteins, 62,938 (42.28\% of all unigenes), 42,158 (28.32\%), and 23,179 (15.57\%) had homologs in the Nr, GO, and KOG databases, 25,625 (17.21\%) unigenes were mapped to 322 pathways by BLASTX comparison against the KEGG database and 1,941 unigenes involved in environmental signaling and stress response were identified. We also identified 43 putative terpene synthase (TPS) functional genes loci and compared them with TPSs from other species. Additionally, 5,296 simple sequence repeats (SSRs) were identified in 4,715 unigenes, which were assigned to 142 motif types. This is the first report of a complete transcriptome analysis of P. orientalis. These resources provide a foundation for further studies of adaptation mechanisms and molecular-based breeding programs.},
	language = {en},
	number = {2},
	urldate = {2023-04-27},
	journal = {PLOS ONE},
	author = {Hu, Xian-Ge and Liu, Hui and Jin, YuQing and Sun, Yan-Qiang and Li, Yue and Zhao, Wei and El-Kassaby, Yousry A. and Wang, Xiao-Ru and Mao, Jian-Feng},
	month = feb,
	year = {2016},
	note = {Publisher: Public Library of Science},
	keywords = {Genome annotation, Genomic databases, Genomics, Microsatellite loci, Pines, RNA sequencing, Terpenes, Transcriptome analysis},
	pages = {e0148985},
}

Platycladus orientalis, of the family Cupressaceae, is a widespread conifer throughout China and is extensively used for ecological reforestation, horticulture, and in medicine. Transcriptome assemblies are required for this ecologically important conifer for understanding genes underpinning adaptation and complex traits for breeding programs. To enrich the species’ genomic resources, a de novo transcriptome sequencing was performed using Illumina paired-end sequencing. In total, 104,073,506 high quality sequence reads (approximately 10.3 Gbp) were obtained, which were assembled into 228,948 transcripts and 148,867 unigenes that were longer than 200 nt. Quality assessment using CEGMA showed that the transcriptomes obtained were mostly complete for highly conserved core eukaryotic genes. Based on similarity searches with known proteins, 62,938 (42.28% of all unigenes), 42,158 (28.32%), and 23,179 (15.57%) had homologs in the Nr, GO, and KOG databases, 25,625 (17.21%) unigenes were mapped to 322 pathways by BLASTX comparison against the KEGG database and 1,941 unigenes involved in environmental signaling and stress response were identified. We also identified 43 putative terpene synthase (TPS) functional genes loci and compared them with TPSs from other species. Additionally, 5,296 simple sequence repeats (SSRs) were identified in 4,715 unigenes, which were assigned to 142 motif types. This is the first report of a complete transcriptome analysis of P. orientalis. These resources provide a foundation for further studies of adaptation mechanisms and molecular-based breeding programs.

@article{jin_genetic_2016,
	title = {Genetic evaluation of the breeding population of a valuable reforestation conifer {Platycladus} orientalis ({Cupressaceae})},
	volume = {6},
	copyright = {2016 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/srep34821},
	doi = {10.1038/srep34821},
	abstract = {Platycladus orientalis, a widespread conifer with long lifespan and significant adaptability. It is much used in reforestation in north China and commonly planted in central Asia. With the increasing demand for plantation forest in central to north China, breeding programs are progressively established for this species. Efficient use of breeding resources requires good understanding of the genetic value of the founder breeding materials. This study investigated the distribution of genetic variation in 192 elite trees collected for the breeding program for the central range of the species. We developed first set of 27 polymorphic EST-derived SSR loci for the species from transcriptome/genome data. After examination of amplification quality, 10 loci were used to evaluate the genetic variation in the breeding population. We found moderate genetic diversity (average He = 0.348) and low population differentiation (Fst = 0.011). Extensive admixture and no significant geographic population structure characterized this set of collections. Our analyses of the diversity and population structure are important steps toward a long-term sustainable deployment of the species and provide valuable genetic information for conservation and breeding applications.},
	language = {en},
	number = {1},
	urldate = {2023-04-27},
	journal = {Scientific Reports},
	author = {Jin, Yuqing and Ma, Yongpeng and Wang, Shun and Hu, Xian-Ge and Huang, Li-Sha and Li, Yue and Wang, Xiao-Ru and Mao, Jian-Feng},
	month = oct,
	year = {2016},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Forestry, Plant breeding},
	pages = {34821},
}

Platycladus orientalis, a widespread conifer with long lifespan and significant adaptability. It is much used in reforestation in north China and commonly planted in central Asia. With the increasing demand for plantation forest in central to north China, breeding programs are progressively established for this species. Efficient use of breeding resources requires good understanding of the genetic value of the founder breeding materials. This study investigated the distribution of genetic variation in 192 elite trees collected for the breeding program for the central range of the species. We developed first set of 27 polymorphic EST-derived SSR loci for the species from transcriptome/genome data. After examination of amplification quality, 10 loci were used to evaluate the genetic variation in the breeding population. We found moderate genetic diversity (average He = 0.348) and low population differentiation (Fst = 0.011). Extensive admixture and no significant geographic population structure characterized this set of collections. Our analyses of the diversity and population structure are important steps toward a long-term sustainable deployment of the species and provide valuable genetic information for conservation and breeding applications.

@article{huang_genetic_2016,
	title = {Genetic structure of needle morphological and anatomical traits of {Pinus} yunnanensis},
	volume = {27},
	issn = {1993-0607},
	url = {https://doi.org/10.1007/s11676-015-0133-x},
	doi = {10.1007/s11676-015-0133-x},
	abstract = {Pinus yunnanensis Franch. is an particular conifer tree species in Yunnan–Guizhou plateau in southwest China. The morphological and anatomical traits of needles are important to evaluate geographic variation and population dynamics of conifer species. Seedlings from seven populations of P. yunnanensis were analyzed, looking at 22 morphological and anatomical needle traits. The results showed that variations among and within populations were significantly different for all traits and the variance components within populations were generally higher than that among populations in the most tested needle traits. The proportions of three-needle fascicle were significantly different among populations. The traits related to needle size in both morphology and anatomy were positive with latitude and negative with annual temperature and precipitation. Ratio indices, including mesophyll area/vascular bundle area, mesophyll area/resin canals area, vascular bundle area/resin canals area and mesophyll area/(resin canals area and vascular bundle area), were negatively correlated with elevation and positively correlated with the annual mean temperature, showing some fitness feature for the populations. Needle traits were more significantly correlated with longitude than with other four environmental factors. Needle length was significantly correlated with almost all environmental factors. First four principal components accounted for 81.596 \% of the variation with eigenvalues {\textgreater}1; the differences among populations were mainly dependent on needle width, stomatal density, section areas of vascular bundle, total resin canals, and mesophyll, as well as area ratio traits. Seven populations were divided into three categories by Euclidean distance. Variations in needle traits among the populations have shown systematic microevolution in terms of geographic impact on P. yunnanensis. This study would provide empirical data to characterize adaptation and genetic variation of P. yunnanensis, which would be helpful for management of genetic resources and reasonable utilization of them in future.},
	language = {en},
	number = {1},
	urldate = {2023-04-27},
	journal = {Journal of Forestry Research},
	author = {Huang, Yujie and Mao, Jianfeng and Chen, Zhiqiang and Meng, Jingxiang and Xu, Yulan and Duan, Anan and Li, Yue},
	month = feb,
	year = {2016},
	keywords = {Genetic structure, Geographic population, Morphological and anatomical traits, Needle, Pinus yunnanensis},
	pages = {13--25},
}

Pinus yunnanensis Franch. is an particular conifer tree species in Yunnan–Guizhou plateau in southwest China. The morphological and anatomical traits of needles are important to evaluate geographic variation and population dynamics of conifer species. Seedlings from seven populations of P. yunnanensis were analyzed, looking at 22 morphological and anatomical needle traits. The results showed that variations among and within populations were significantly different for all traits and the variance components within populations were generally higher than that among populations in the most tested needle traits. The proportions of three-needle fascicle were significantly different among populations. The traits related to needle size in both morphology and anatomy were positive with latitude and negative with annual temperature and precipitation. Ratio indices, including mesophyll area/vascular bundle area, mesophyll area/resin canals area, vascular bundle area/resin canals area and mesophyll area/(resin canals area and vascular bundle area), were negatively correlated with elevation and positively correlated with the annual mean temperature, showing some fitness feature for the populations. Needle traits were more significantly correlated with longitude than with other four environmental factors. Needle length was significantly correlated with almost all environmental factors. First four principal components accounted for 81.596 % of the variation with eigenvalues \textgreater1; the differences among populations were mainly dependent on needle width, stomatal density, section areas of vascular bundle, total resin canals, and mesophyll, as well as area ratio traits. Seven populations were divided into three categories by Euclidean distance. Variations in needle traits among the populations have shown systematic microevolution in terms of geographic impact on P. yunnanensis. This study would provide empirical data to characterize adaptation and genetic variation of P. yunnanensis, which would be helpful for management of genetic resources and reasonable utilization of them in future.

@article{xu_germination_2016,
	title = {Germination and early seedling growth of {Pinus} densata {Mast}. provenances},
	volume = {27},
	issn = {1993-0607},
	url = {https://doi.org/10.1007/s11676-015-0186-x},
	doi = {10.1007/s11676-015-0186-x},
	abstract = {We studied seed germination and early seedling growth of Pinus densata to explore the range of variability within the species and to inform afforestation practices. Phenotypes were evaluated at a forest tree nursery under conditions that support Pinus yunnanensis, one of the presumed parental species of P. densata. Seeds were collected from 20 open-pollinated trees within each of eight autochthonous populations representing the natural distribution of P. densata in China to assess variation in germination traits and early seedling growth, and to examine the relationships among these traits. Results showed that seeds from all populations germinated and seedlings established successfully. There were significant differences among populations in 13 of 14 traits evaluated. Seed germination and early seedling growth were strongly related to seed size and seed weight. Bigger seeds germinated earlier and faster than small seeds, and seedling size was positively correlated with seed size. Some germination traits were strongly and significantly correlated with climatic variables associated with the provenance of the studied populations. Based on these observations, we conclude there were large, significant, and biologically important differences among P. densata populations in seed germination and seedling growth traits. The observed variability probably reflects a high degree of adaptive differentiation among populations that is likely to be relevant for future afforestation.},
	language = {en},
	number = {2},
	urldate = {2023-04-27},
	journal = {Journal of Forestry Research},
	author = {Xu, Yulan and Cai, Nianhui and He, Bin and Zhang, Ruili and Zhao, Wei and Mao, Jianfeng and Duan, Anan and Li, Yue and Woeste, Keith},
	month = apr,
	year = {2016},
	keywords = {Afforestation, Conifer, Gaoshan pine, Provenance, Seed germination, Seed size, Seedling vigor},
	pages = {283--294},
}

We studied seed germination and early seedling growth of Pinus densata to explore the range of variability within the species and to inform afforestation practices. Phenotypes were evaluated at a forest tree nursery under conditions that support Pinus yunnanensis, one of the presumed parental species of P. densata. Seeds were collected from 20 open-pollinated trees within each of eight autochthonous populations representing the natural distribution of P. densata in China to assess variation in germination traits and early seedling growth, and to examine the relationships among these traits. Results showed that seeds from all populations germinated and seedlings established successfully. There were significant differences among populations in 13 of 14 traits evaluated. Seed germination and early seedling growth were strongly related to seed size and seed weight. Bigger seeds germinated earlier and faster than small seeds, and seedling size was positively correlated with seed size. Some germination traits were strongly and significantly correlated with climatic variables associated with the provenance of the studied populations. Based on these observations, we conclude there were large, significant, and biologically important differences among P. densata populations in seed germination and seedling growth traits. The observed variability probably reflects a high degree of adaptive differentiation among populations that is likely to be relevant for future afforestation.

@article{hu_global_2016,
	title = {Global transcriptome analysis of {Sabina} chinensis ({Cupressaceae}), a valuable reforestation conifer},
	volume = {36},
	issn = {1572-9788},
	url = {https://doi.org/10.1007/s11032-016-0526-3},
	doi = {10.1007/s11032-016-0526-3},
	abstract = {Sabina chinensis has broad distribution in China and is widely used in the reforestation and as an urban tree. The species is frost resistant and grows well on contaminated soils and is becoming valuable for soil remediation and protection against air pollution. Breeding programs aimed at exploiting the species’ unique properties were handicapped by the lack of basic genetic information. Here, we established a transcriptomic profiling study from five different tissues using RNA-Seq to gain insight on the functional genes and the development of molecular markers for breeding and conservation purposes. In total 90,382,108 high-quality sequence reads ({\textasciitilde}9.0 bp) were obtained, and 116,814 unigenes (≥200 nt) were assembled. Of which, 45,026 and 15,589 unigenes were mapped to the Nr and KOG databases, 31,288 (26.78 \%) and 17,596 (15.06 \%) were annotated to GO and KEGG database, respectively. Additionally, 28,843 (24.68 \%) and 43,033 (36.84 \%) S. chinensis unigenes were aligned to the Pinus taeda draft genome and PLAZA2.5 database, respectively. A total of 4570 simple sequence repeat (SSR) motifs were identified in the unigenes. Furthermore, we obtained 6 (12.5 \%) polymorphic and 21 (43.75 \%) monomorphic loci in the verification of 48 randomly selected SSR loci. This study represents the first transcriptome data of S. chinensis and confirms that the transcriptome assembly data of S. chinensis are a useful resource for EST-SSR loci development. The substantial number of transcripts obtained will aid our understanding of the species adaptation mechanisms and provide valuable genomic information for conservation and breeding applications.},
	language = {en},
	number = {7},
	urldate = {2023-04-27},
	journal = {Molecular Breeding},
	author = {Hu, Xian-Ge and Liu, Hui and Zhang, Jia-Qing and Sun, Yan-Qiang and Jin, YuQing and Zhao, Wei and El-Kassaby, Yousry A. and Wang, Xiao-Ru and Mao, Jian-Feng},
	month = jul,
	year = {2016},
	keywords = {De novo assembly, EST-SSR, Gene discovery, RNA-Seq, Sabina chinensis},
	pages = {99},
}

Sabina chinensis has broad distribution in China and is widely used in the reforestation and as an urban tree. The species is frost resistant and grows well on contaminated soils and is becoming valuable for soil remediation and protection against air pollution. Breeding programs aimed at exploiting the species’ unique properties were handicapped by the lack of basic genetic information. Here, we established a transcriptomic profiling study from five different tissues using RNA-Seq to gain insight on the functional genes and the development of molecular markers for breeding and conservation purposes. In total 90,382,108 high-quality sequence reads (~9.0 bp) were obtained, and 116,814 unigenes (≥200 nt) were assembled. Of which, 45,026 and 15,589 unigenes were mapped to the Nr and KOG databases, 31,288 (26.78 %) and 17,596 (15.06 %) were annotated to GO and KEGG database, respectively. Additionally, 28,843 (24.68 %) and 43,033 (36.84 %) S. chinensis unigenes were aligned to the Pinus taeda draft genome and PLAZA2.5 database, respectively. A total of 4570 simple sequence repeat (SSR) motifs were identified in the unigenes. Furthermore, we obtained 6 (12.5 %) polymorphic and 21 (43.75 %) monomorphic loci in the verification of 48 randomly selected SSR loci. This study represents the first transcriptome data of S. chinensis and confirms that the transcriptome assembly data of S. chinensis are a useful resource for EST-SSR loci development. The substantial number of transcripts obtained will aid our understanding of the species adaptation mechanisms and provide valuable genomic information for conservation and breeding applications.

@article{bi_characterisation_2015,
	title = {Characterisation of {EST}-based {SSR} loci in the endangered tree {Manchurian} fir {Abies} holophylla: a transcriptomic approach},
	volume = {7},
	issn = {1877-7260},
	shorttitle = {Characterisation of {EST}-based {SSR} loci in the endangered tree {Manchurian} fir {Abies} holophylla},
	url = {https://doi.org/10.1007/s12686-014-0384-4},
	doi = {10.1007/s12686-014-0384-4},
	abstract = {The International Union for the Conservation of Nature has declared Abies holophylla maxim an endangered species. In the study described herein, 171 novel microsatellite markers were identified by mining the transcriptomic database of Abies balsamea to develop a practical and realistic conservation strategy. Among these markers, fragments of expected sizes were amplified from 86 loci of which 14 exhibited polymorphism and 34 monomorphism in eight individuals of A. holophylla. The number of alleles in these 14 expressed sequence tag-simple sequence repeats (EST-SSRs) ranged from two to three per locus, and the observed (Ho) and expected heterozygosity (He) values ranged from 0 to 1.0 and 0.117 to 0.594, respectively. Polymorphic information content respectively ranged from 0.110 to 0.511. These polymorphic markers will be useful for evaluating genetic biodiversity and aid in the development of a conservation strategy for this relict species.},
	language = {en},
	number = {2},
	urldate = {2023-04-27},
	journal = {Conservation Genetics Resources},
	author = {Bi, Quanxin and Jin, Yuqing and Guan, Wenbin and Mao, Jian-Feng},
	month = jun,
	year = {2015},
	keywords = {Abies holophylla, EST-SSR, Endangered tree},
	pages = {415--418},
}

The International Union for the Conservation of Nature has declared Abies holophylla maxim an endangered species. In the study described herein, 171 novel microsatellite markers were identified by mining the transcriptomic database of Abies balsamea to develop a practical and realistic conservation strategy. Among these markers, fragments of expected sizes were amplified from 86 loci of which 14 exhibited polymorphism and 34 monomorphism in eight individuals of A. holophylla. The number of alleles in these 14 expressed sequence tag-simple sequence repeats (EST-SSRs) ranged from two to three per locus, and the observed (Ho) and expected heterozygosity (He) values ranged from 0 to 1.0 and 0.117 to 0.594, respectively. Polymorphic information content respectively ranged from 0.110 to 0.511. These polymorphic markers will be useful for evaluating genetic biodiversity and aid in the development of a conservation strategy for this relict species.

@article{jin_development_2015,
	title = {Development of 23 novel polymorphic {EST}-{SSR} markers for the endangered relict conifer {Metasequoia} glyptostroboides},
	volume = {3},
	issn = {2168-0450},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.3732/apps.1500038},
	doi = {10.3732/apps.1500038},
	abstract = {Premise of the study: Metasequoia glyptostroboides is an endangered relict conifer species endemic to China. In this study, expressed sequence tag–simple sequence repeat (EST-SSR) markers were developed using transcriptome mining for future genetic and functional studies. Methods and Results: We collected 97,565 unigene sequences generated by 454 pyrosequencing. A bioinformatics analysis identified 2087 unique and putative microsatellites, from which 96 novel microsatellite markers were developed. Fifty-three of the 96 primer sets successfully amplified clear fragments of the expected sizes; 23 of those loci were polymorphic. The number of alleles per locus ranged from two to eight, with an average of three, and the observed and expected heterozygosity values ranged from 0 to 1.0 and 0.117 to 0.813, respectively. Conclusions: These microsatellite loci will enrich the genetic resources to develop functional studies and conservation strategies for this endangered relict species.},
	language = {en},
	number = {9},
	urldate = {2023-04-27},
	journal = {Applications in Plant Sciences},
	author = {Jin, Yuqing and Bi, Quanxin and Guan, Wenbin and Mao, Jian-Feng},
	year = {2015},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.3732/apps.1500038},
	keywords = {454 pyrosequencing, Cupressaceae, EST-SSR, Metasequoia glyptostroboides, microsatellite, relict plant},
	pages = {1500038},
}

Premise of the study: Metasequoia glyptostroboides is an endangered relict conifer species endemic to China. In this study, expressed sequence tag–simple sequence repeat (EST-SSR) markers were developed using transcriptome mining for future genetic and functional studies. Methods and Results: We collected 97,565 unigene sequences generated by 454 pyrosequencing. A bioinformatics analysis identified 2087 unique and putative microsatellites, from which 96 novel microsatellite markers were developed. Fifty-three of the 96 primer sets successfully amplified clear fragments of the expected sizes; 23 of those loci were polymorphic. The number of alleles per locus ranged from two to eight, with an average of three, and the observed and expected heterozygosity values ranged from 0 to 1.0 and 0.117 to 0.813, respectively. Conclusions: These microsatellite loci will enrich the genetic resources to develop functional studies and conservation strategies for this endangered relict species.

@article{mao_development_2015,
	title = {Development of 36 novel polymorphic microsatellites for the critically endangered tree {Pinus} squamaia, by transcriptome database mining},
	volume = {7},
	issn = {1877-7260},
	url = {https://doi.org/10.1007/s12686-014-0300-y},
	doi = {10.1007/s12686-014-0300-y},
	abstract = {Pinus squamaia X. W. Li is a critically endangered five-needle pine species, with only 35 wild individuals left. To understand its genetic variability, 506 novel microsatellite markers were developed by mining the transcriptome database of P. lambertiana. 196 loci were able to amplify a fragment of expected size in P. squamaia, of which 36 were polymorphic. The number of alleles of these 36 EST-SSRs in 16 individuals varied from 2 to 4, with an average of 2.2. The observed (Ho) and expected (He) heterozygosity values ranged from 0.000 to 1.000 (averaging 0.564) and 0.061 to 0.500 (averaging 0.356), respectively. Twenty-four loci showed significant departure from HWE after Bonferroni correction. This was the first report of candidate molecular markers on P. squamaia, which will facilitate future analyses of genetic diversity and population structure.},
	language = {en},
	number = {1},
	urldate = {2023-04-27},
	journal = {Conservation Genetics Resources},
	author = {Mao, Jian-Feng and Cui, Bin-Bin and Zhang, Zhi-Yong and Liu, Hui and Li, Ying-Yue},
	month = mar,
	year = {2015},
	keywords = {Expressed sequence tag (EST), Microstallites, Pinus lambertiana, Pinus squamaia, Transcriptome},
	pages = {93--94},
}

Pinus squamaia X. W. Li is a critically endangered five-needle pine species, with only 35 wild individuals left. To understand its genetic variability, 506 novel microsatellite markers were developed by mining the transcriptome database of P. lambertiana. 196 loci were able to amplify a fragment of expected size in P. squamaia, of which 36 were polymorphic. The number of alleles of these 36 EST-SSRs in 16 individuals varied from 2 to 4, with an average of 2.2. The observed (Ho) and expected (He) heterozygosity values ranged from 0.000 to 1.000 (averaging 0.564) and 0.061 to 0.500 (averaging 0.356), respectively. Twenty-four loci showed significant departure from HWE after Bonferroni correction. This was the first report of candidate molecular markers on P. squamaia, which will facilitate future analyses of genetic diversity and population structure.

@article{bi_efficiently_2015,
	title = {Efficiently developing a large set of polymorphic {EST}-{SSR} markers for {Xanthoceras} sorbifolium by mining raw reads from high-throughput sequencing},
	volume = {7},
	issn = {1877-7260},
	url = {https://doi.org/10.1007/s12686-014-0386-2},
	doi = {10.1007/s12686-014-0386-2},
	abstract = {Yellow-horn (Xanthoceras sorbifolium Bunge) is an economically and ecologically important tree in northern China that is facing severe stress from human activity and the changing climate. Transcriptome-wide or genome-wide genetic markers are required for functional studies and development of conservation strategies based on genetic variation within the species. In this report, using an in silico microsatellite detection and primer design strategy implemented in the computer program QDD, we detected and designed primers for 477 candidate polymorphic EST-SSR (simple sequences repeat in expressed sequence tags) loci by mining raw reads from high-throughput transcriptome sequencing of pooled samples. A total of 48 primer loci were selected randomly and evaluated, of which 29 (60.42 \%) were polymorphic in eight individuals. Based on these results, this development strategy can be used for the development of EST-SSR markers. This large set of marker resources can be used for mining, performing functional studies, and developing conservation strategies for this endangered species.},
	language = {en},
	number = {2},
	urldate = {2023-04-27},
	journal = {Conservation Genetics Resources},
	author = {Bi, Quanxin and Mao, Jian-Feng and Guan, Wenbin},
	month = jun,
	year = {2015},
	keywords = {EST-SSR, Endangered tree, QDD, Xanthoceras sorbifolium},
	pages = {423--425},
}

Yellow-horn (Xanthoceras sorbifolium Bunge) is an economically and ecologically important tree in northern China that is facing severe stress from human activity and the changing climate. Transcriptome-wide or genome-wide genetic markers are required for functional studies and development of conservation strategies based on genetic variation within the species. In this report, using an in silico microsatellite detection and primer design strategy implemented in the computer program QDD, we detected and designed primers for 477 candidate polymorphic EST-SSR (simple sequences repeat in expressed sequence tags) loci by mining raw reads from high-throughput transcriptome sequencing of pooled samples. A total of 48 primer loci were selected randomly and evaluated, of which 29 (60.42 %) were polymorphic in eight individuals. Based on these results, this development strategy can be used for the development of EST-SSR markers. This large set of marker resources can be used for mining, performing functional studies, and developing conservation strategies for this endangered species.

@article{zhang_isolation_2015,
	title = {Isolation and characterization of thirty-eight microsatellite loci for the {Pinus} wangii, an endangered species},
	volume = {7},
	issn = {1877-7260},
	url = {https://doi.org/10.1007/s12686-014-0379-1},
	doi = {10.1007/s12686-014-0379-1},
	abstract = {Piuns wangii Hu et Cheng is an endangered five-needle pine species, with scattered populations and scare individuals. To study its genetic diversity and better address conservation programs, 506 novel microsatellite markers were developed by mining the transcriptome database of P. lambertiana. 117 loci were able to amplify a fragment of expected size in P. wangii, of which 38 were polymorphic. The number of alleles of these 38 EST-SSRs in 16 individuals varied from 2 to 6, with an average of 2.6. The observed (Ho) and expected (He) heterozygosity values ranged from 0.000 to 1.000 (averaging 0.532) and 0.117–0.693 (averaging 0.394), respectively. Twenty-three loci showed significant departure from HWE after Bonferroni correction. This was the first report of candidate molecular markers on P. wangii, which will facilitate future analyses of genetic diversity and population structure.},
	language = {en},
	number = {2},
	urldate = {2023-04-27},
	journal = {Conservation Genetics Resources},
	author = {Zhang, Zhi-Yong and Cui, Binbin and Mao, Jian-Feng and Pang, Xiao-Ming and Li, Ying-Yue},
	month = jun,
	year = {2015},
	keywords = {Conservation genetics, Expressed sequence tag (EST), Microsatellites, Pinus wangii},
	pages = {397--398},
}

Piuns wangii Hu et Cheng is an endangered five-needle pine species, with scattered populations and scare individuals. To study its genetic diversity and better address conservation programs, 506 novel microsatellite markers were developed by mining the transcriptome database of P. lambertiana. 117 loci were able to amplify a fragment of expected size in P. wangii, of which 38 were polymorphic. The number of alleles of these 38 EST-SSRs in 16 individuals varied from 2 to 6, with an average of 2.6. The observed (Ho) and expected (He) heterozygosity values ranged from 0.000 to 1.000 (averaging 0.532) and 0.117–0.693 (averaging 0.394), respectively. Twenty-three loci showed significant departure from HWE after Bonferroni correction. This was the first report of candidate molecular markers on P. wangii, which will facilitate future analyses of genetic diversity and population structure.

@article{zhang_novel_2015,
	title = {Novel polymorphic {EST}-derived microsatellite markers for the red-listed five needle pine, {Pinus} dabeshanensis},
	volume = {7},
	issn = {1877-7260},
	url = {https://doi.org/10.1007/s12686-014-0329-y},
	doi = {10.1007/s12686-014-0329-y},
	abstract = {Pinus dabeshanensis is an endangered five needle pine endemic to mid-South of China. This pine finds its very limited natural occurrence in the Dabie mountains area with altitudes ranging 900–1400 m. We identified 3,516 SSR loci from the transcriptome assembly of the congeneric species P. lambertiana, and evaluated 671 loci we found. Finally, 28 novel polymorphic microsatellite markers were developed for P. dabeshanensis. Markers were characterized using 36 individuals, representing all existing populations from across the species geographic range. Species level analysis of these 28 polymorphic markers revealed the mean number per locus was 2.786 (range 2–6) and mean observed and expected heterozygosities were 0.332 (range 0.000–1.000) and 0.316 (range 0.033–0.691), respectively. This study provides the first set of microsatellite markers for the conservation genetics which in turn will facilitate conservation management for this pine.},
	language = {en},
	number = {1},
	urldate = {2023-04-27},
	journal = {Conservation Genetics Resources},
	author = {Zhang, Zhi-Yong and Cui, Bin-Bin and Mao, Jian-Feng and Pang, Xiao-Ming and Liu, Hui and Li, Ying-Yue},
	month = mar,
	year = {2015},
	keywords = {Conservation genetics, Five needle pine, Microsatellite, Pinus dabeshanensis},
	pages = {191--192},
}

Pinus dabeshanensis is an endangered five needle pine endemic to mid-South of China. This pine finds its very limited natural occurrence in the Dabie mountains area with altitudes ranging 900–1400 m. We identified 3,516 SSR loci from the transcriptome assembly of the congeneric species P. lambertiana, and evaluated 671 loci we found. Finally, 28 novel polymorphic microsatellite markers were developed for P. dabeshanensis. Markers were characterized using 36 individuals, representing all existing populations from across the species geographic range. Species level analysis of these 28 polymorphic markers revealed the mean number per locus was 2.786 (range 2–6) and mean observed and expected heterozygosities were 0.332 (range 0.000–1.000) and 0.316 (range 0.033–0.691), respectively. This study provides the first set of microsatellite markers for the conservation genetics which in turn will facilitate conservation management for this pine.

@article{pan_optimization_2015,
	title = {Optimization of the genotyping-by-sequencing strategy for population genomic analysis in conifers},
	volume = {15},
	issn = {1755-0998},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.12342},
	doi = {10.1111/1755-0998.12342},
	abstract = {Flexibility and low cost make genotyping-by-sequencing (GBS) an ideal tool for population genomic studies of nonmodel species. However, to utilize the potential of the method fully, many parameters affecting library quality and single nucleotide polymorphism (SNP) discovery require optimization, especially for conifer genomes with a high repetitive DNA content. In this study, we explored strategies for effective GBS analysis in pine species. We constructed GBS libraries using HpaII, PstI and EcoRI-MseI digestions with different multiplexing levels and examined the effect of restriction enzymes on library complexity and the impact of sequencing depth and size selection of restriction fragments on sequence coverage bias. We tested and compared UNEAK, Stacks and GATK pipelines for the GBS data, and then developed a reference-free SNP calling strategy for haploid pine genomes. Our GBS procedure proved to be effective in SNP discovery, producing 7000–11 000 and 14 751 SNPs within and among three pine species, respectively, from a PstI library. This investigation provides guidance for the design and analysis of GBS experiments, particularly for organisms for which genomic information is lacking.},
	language = {en},
	number = {4},
	urldate = {2023-04-27},
	journal = {Molecular Ecology Resources},
	author = {Pan, Jin and Wang, Baosheng and Pei, Zhi-Yong and Zhao, Wei and Gao, Jie and Mao, Jian-Feng and Wang, Xiao-Ru},
	year = {2015},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.12342},
	keywords = {SNP validation, conifer genome, genotyping-by-sequencing, library preparation parameters, sequencing depth},
	pages = {711--722},
}

Flexibility and low cost make genotyping-by-sequencing (GBS) an ideal tool for population genomic studies of nonmodel species. However, to utilize the potential of the method fully, many parameters affecting library quality and single nucleotide polymorphism (SNP) discovery require optimization, especially for conifer genomes with a high repetitive DNA content. In this study, we explored strategies for effective GBS analysis in pine species. We constructed GBS libraries using HpaII, PstI and EcoRI-MseI digestions with different multiplexing levels and examined the effect of restriction enzymes on library complexity and the impact of sequencing depth and size selection of restriction fragments on sequence coverage bias. We tested and compared UNEAK, Stacks and GATK pipelines for the GBS data, and then developed a reference-free SNP calling strategy for haploid pine genomes. Our GBS procedure proved to be effective in SNP discovery, producing 7000–11 000 and 14 751 SNPs within and among three pine species, respectively, from a PstI library. This investigation provides guidance for the design and analysis of GBS experiments, particularly for organisms for which genomic information is lacking.

@article{hu_predicting_2015,
	title = {Predicting {Impacts} of {Future} {Climate} {Change} on the {Distribution} of the {Widespread} {Conifer} {Platycladus} orientalis},
	volume = {10},
	issn = {1932-6203},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0132326},
	doi = {10.1371/journal.pone.0132326},
	abstract = {Chinese thuja (Platycladus orientalis) has a wide but fragmented distribution in China. It is an important conifer tree in reforestation and plays important roles in ecological restoration in the arid mountains of northern China. Based on high-resolution environmental data for current and future scenarios, we modeled the present and future suitable habitat for P. orientalis, evaluated the importance of environmental factors in shaping the species´ distribution, and identified regions of high risk under climate change scenarios. The niche models showed that P. orientalis has suitable habitat of ca. 4.2×106 km2 across most of eastern China and identified annual temperature, monthly minimum and maximum ultraviolet-B radiation and wet-day frequency as the critical factors shaping habitat availability for P. orientalis. Under the low concentration greenhouse gas emissions scenario, the range of the species may increase as global warming intensifies; however, under the higher concentrations of emissions scenario, we predicted a slight expansion followed by contraction in distribution. Overall, the range shift to higher latitudes and elevations would become gradually more significant. The information gained from this study should be an useful reference for implementing long-term conservation and management strategies for the species.},
	language = {en},
	number = {7},
	urldate = {2023-04-27},
	journal = {PLOS ONE},
	author = {Hu, Xian-Ge and Jin, Yuqing and Wang, Xiao-Ru and Mao, Jian-Feng and Li, Yue},
	month = jul,
	year = {2015},
	note = {Publisher: Public Library of Science},
	keywords = {Anthropogenic climate change, China, Climate change, Conifers, Forests, Habitats, Latitude, Ultraviolet B},
	pages = {e0132326},
}

Chinese thuja (Platycladus orientalis) has a wide but fragmented distribution in China. It is an important conifer tree in reforestation and plays important roles in ecological restoration in the arid mountains of northern China. Based on high-resolution environmental data for current and future scenarios, we modeled the present and future suitable habitat for P. orientalis, evaluated the importance of environmental factors in shaping the species´ distribution, and identified regions of high risk under climate change scenarios. The niche models showed that P. orientalis has suitable habitat of ca. 4.2×106 km2 across most of eastern China and identified annual temperature, monthly minimum and maximum ultraviolet-B radiation and wet-day frequency as the critical factors shaping habitat availability for P. orientalis. Under the low concentration greenhouse gas emissions scenario, the range of the species may increase as global warming intensifies; however, under the higher concentrations of emissions scenario, we predicted a slight expansion followed by contraction in distribution. Overall, the range shift to higher latitudes and elevations would become gradually more significant. The information gained from this study should be an useful reference for implementing long-term conservation and management strategies for the species.

@article{ouyang_transcriptome_2015,
	title = {Transcriptome {Analysis} {Reveals} that {Red} and {Blue} {Light} {Regulate} {Growth} and {Phytohormone} {Metabolism} in {Norway} {Spruce} [{Picea} abies ({L}.) {Karst}.]},
	volume = {10},
	issn = {1932-6203},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0127896},
	doi = {10.1371/journal.pone.0127896},
	abstract = {The mechanisms by which different light spectra regulate plant shoot elongation vary, and phytohormones respond differently to such spectrum-associated regulatory effects. Light supplementation can effectively control seedling growth in Norway spruce. However, knowledge of the effective spectrum for promoting growth and phytohormone metabolism in this species is lacking. In this study, 3-year-old Norway spruce clones were illuminated for 12 h after sunset under blue or red light-emitting diode (LED) light for 90 d, and stem increments and other growth traits were determined. Endogenous hormone levels and transcriptome differences in the current needles were assessed to identify genes related to the red and blue light regulatory responses. The results showed that the stem increment and gibberellin (GA) levels of the seedlings illuminated by red light were 8.6\% and 29.0\% higher, respectively, than those of the seedlings illuminated by blue light. The indoleacetic acid (IAA) level of the seedlings illuminated by red light was 54.6\% lower than that of the seedlings illuminated by blue light, and there were no significant differences in abscisic acid (ABA) or zeatin riboside [ZR] between the two groups of seedlings. The transcriptome results revealed 58,736,166 and 60,555,192 clean reads for the blue-light- and red-light-illuminated samples, respectively. Illumina sequencing revealed 21,923 unigenes, and 2744 (approximately 93.8\%) out of 2926 differentially expressed genes (DEGs) were found to be upregulated under blue light. The main KEGG classifications of the DEGs were metabolic pathway (29\%), biosynthesis of secondary metabolites (20.49\%) and hormone signal transduction (8.39\%). With regard to hormone signal transduction, AUXIN-RESISTANT1 (AUX1), AUX/IAA genes, auxin-inducible genes, and early auxin-responsive genes [(auxin response factor (ARF) and small auxin-up RNA (SAUR)] were all upregulated under blue light compared with red light, which might have yielded the higher IAA level. DELLA and phytochrome-interacting factor 3 (PIF3), involved in negative GA signaling, were also upregulated under blue light, which may be related to the lower GA level. Light quality also affects endogenous hormones by influencing secondary metabolism. Blue light promoted phenylpropanoid biosynthesis, phenylalanine metabolism, flavonoid biosynthesis and flavone and flavonol biosynthesis, accompanied by upregulation of most of the genes in their pathways. In conclusion, red light may promote stem growth by regulating biosynthesis of GAs, and blue light may promote flavonoid, lignin, phenylpropanoid and some hormones (such as jasmonic acid) which were related to plant defense in Norway spruce, which might reduce the primary metabolites available for plant growth.},
	language = {en},
	number = {8},
	urldate = {2023-04-27},
	journal = {PLOS ONE},
	author = {OuYang, Fangqun and Mao, Jian-Feng and Wang, Junhui and Zhang, Shougong and Li, Yue},
	month = aug,
	year = {2015},
	note = {Publisher: Public Library of Science},
	keywords = {Biosynthesis, Gene expression, Gibberellins, Light, Metabolic pathways, Plant hormones, Seedlings, Signal transduction},
	pages = {e0127896},
}

The mechanisms by which different light spectra regulate plant shoot elongation vary, and phytohormones respond differently to such spectrum-associated regulatory effects. Light supplementation can effectively control seedling growth in Norway spruce. However, knowledge of the effective spectrum for promoting growth and phytohormone metabolism in this species is lacking. In this study, 3-year-old Norway spruce clones were illuminated for 12 h after sunset under blue or red light-emitting diode (LED) light for 90 d, and stem increments and other growth traits were determined. Endogenous hormone levels and transcriptome differences in the current needles were assessed to identify genes related to the red and blue light regulatory responses. The results showed that the stem increment and gibberellin (GA) levels of the seedlings illuminated by red light were 8.6% and 29.0% higher, respectively, than those of the seedlings illuminated by blue light. The indoleacetic acid (IAA) level of the seedlings illuminated by red light was 54.6% lower than that of the seedlings illuminated by blue light, and there were no significant differences in abscisic acid (ABA) or zeatin riboside [ZR] between the two groups of seedlings. The transcriptome results revealed 58,736,166 and 60,555,192 clean reads for the blue-light- and red-light-illuminated samples, respectively. Illumina sequencing revealed 21,923 unigenes, and 2744 (approximately 93.8%) out of 2926 differentially expressed genes (DEGs) were found to be upregulated under blue light. The main KEGG classifications of the DEGs were metabolic pathway (29%), biosynthesis of secondary metabolites (20.49%) and hormone signal transduction (8.39%). With regard to hormone signal transduction, AUXIN-RESISTANT1 (AUX1), AUX/IAA genes, auxin-inducible genes, and early auxin-responsive genes [(auxin response factor (ARF) and small auxin-up RNA (SAUR)] were all upregulated under blue light compared with red light, which might have yielded the higher IAA level. DELLA and phytochrome-interacting factor 3 (PIF3), involved in negative GA signaling, were also upregulated under blue light, which may be related to the lower GA level. Light quality also affects endogenous hormones by influencing secondary metabolism. Blue light promoted phenylpropanoid biosynthesis, phenylalanine metabolism, flavonoid biosynthesis and flavone and flavonol biosynthesis, accompanied by upregulation of most of the genes in their pathways. In conclusion, red light may promote stem growth by regulating biosynthesis of GAs, and blue light may promote flavonoid, lignin, phenylpropanoid and some hormones (such as jasmonic acid) which were related to plant defense in Norway spruce, which might reduce the primary metabolites available for plant growth.

@article{dong_strategy_2014,
	title = {A strategy for characterization of persistent heteroduplex {DNA} in higher plants},
	volume = {80},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.12631},
	doi = {10.1111/tpj.12631},
	abstract = {Heteroduplex DNA (hDNA) generated during homologous recombination (HR) is an important component that shapes genetic diversity in sexually reproducing organisms. However, studies of this process in higher plants are limited. This is because hDNAs are difficult to capture in higher plants as their reproductive developmental model only produces normal gametes and does not preserve the mitotic products of the post-meiotic segregation (PMS) process which is crucial for studying hDNAs. In this study, using the model system for tree and woody perennial plant biology (Populus), we propose a strategy for characterizing hDNAs in higher plants. We captured hDNAs by constructing triploid hybrids originating from a cross between unreduced 2n eggs (containing hDNA information as a result of inhibition chromosome segregation at the PMS stage) with normal male gametes. These triploid hybrids allowed us to detect the frequency and location of persistent hDNAs resulting from HR at the molecular level. We found that the frequency of persistent hDNAs, which ranged from 5.3 to 76.6\%, was related to locations of the simple sequence repeat markers at the chromosomes, such as the locus–centromere distance, the surrounding DNA sequence and epigenetic information, and the richness of protein-coding transcripts at these loci. In summary, this study provides a method for characterizing persistent hDNAs in higher plants. When high-throughput sequencing techniques can be incorporated, genome-wide persistent hDNA assays for higher plants can be easily carried out using the strategy presented in this study.},
	language = {en},
	number = {2},
	urldate = {2023-04-27},
	journal = {The Plant Journal},
	author = {Dong, Chun-Bo and Mao, Jian-Feng and Suo, Yu-Jing and Shi, Le and Wang, Jun and Zhang, Ping-Dong and Kang, Xiang-Yang},
	year = {2014},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.12631},
	keywords = {Populus pseudo-simonii × Populus nigra ‘Zheyin3\#’, Populus × beijingensis, heteroduplex DNA, post-meiotic segregation, triploid},
	pages = {282--291},
}

Heteroduplex DNA (hDNA) generated during homologous recombination (HR) is an important component that shapes genetic diversity in sexually reproducing organisms. However, studies of this process in higher plants are limited. This is because hDNAs are difficult to capture in higher plants as their reproductive developmental model only produces normal gametes and does not preserve the mitotic products of the post-meiotic segregation (PMS) process which is crucial for studying hDNAs. In this study, using the model system for tree and woody perennial plant biology (Populus), we propose a strategy for characterizing hDNAs in higher plants. We captured hDNAs by constructing triploid hybrids originating from a cross between unreduced 2n eggs (containing hDNA information as a result of inhibition chromosome segregation at the PMS stage) with normal male gametes. These triploid hybrids allowed us to detect the frequency and location of persistent hDNAs resulting from HR at the molecular level. We found that the frequency of persistent hDNAs, which ranged from 5.3 to 76.6%, was related to locations of the simple sequence repeat markers at the chromosomes, such as the locus–centromere distance, the surrounding DNA sequence and epigenetic information, and the richness of protein-coding transcripts at these loci. In summary, this study provides a method for characterizing persistent hDNAs in higher plants. When high-throughput sequencing techniques can be incorporated, genome-wide persistent hDNA assays for higher plants can be easily carried out using the strategy presented in this study.

@article{xing_needle_2014,
	title = {Needle morphological evidence of the homoploid hybrid origin of {Pinus} densata based on analysis of artificial hybrids and the putative parents, {Pinus} tabuliformis and {Pinus} yunnanensis},
	volume = {4},
	issn = {2045-7758},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.1062},
	doi = {10.1002/ece3.1062},
	abstract = {Genetic analyses indicate that Pinus densata is a natural homoploid hybrid originating from Pinus tabuliformis and Pinus yunnanensis. Needle morphological and anatomical features show relative species stability and can be used to identify coniferous species. Comparative analyses of these needle characteristics and phenotypic differences between the artificial hybrids, P. densata, and parental species can be used to determine the genetic and phenotypic evolutionary consequences of natural hybridization. Twelve artificial hybrid families, the two parental species, and P. densata were seeded in a high-altitude habitat in Linzhi, Tibet. The needles of artificial hybrids and the three pine species were collected, and 24 needle morphological and anatomical traits were analyzed. Based on these results, variations in 10 needle traits among artificial hybrid families and 22 traits among species and artificial hybrids were predicted and found to be under moderate genetic control. Nineteen needle traits in artificial hybrids were similar to those in P. densata and between the two parental species, P. tabuliformis and P. yunnanensis. The ratio of plants with three needle clusters in artificial hybrids was 22.92\%, which was very similar to P. densata. The eight needle traits (needle length, the mean number of stomata in sections 2 mm in length of the convex and flat sides of the needle, mean stomatal density, mesophyll/vascular bundle area ratio, mesophyll/resin canal area ratio, mesophyll/(resin canals and vascular bundles) area ratio, vascular bundle/resin canal area ratio) relative to physiological adaptability were similar to the artificial hybrids and P. densata. The similar needle features between the artificial hybrids and P. densata could be used to verify the homoploid hybrid origin of P. densata and helps to better understand of the hybridization roles in adaptation and speciation in plants.},
	language = {en},
	number = {10},
	urldate = {2023-04-27},
	journal = {Ecology and Evolution},
	author = {Xing, Fangqian and Mao, Jian-Feng and Meng, Jingxiang and Dai, Jianfeng and Zhao, Wei and Liu, Hao and Xing, Zhen and Zhang, Hua and Wang, Xiao-Ru and Li, Yue},
	year = {2014},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.1062},
	keywords = {Anatomy, Pinus densata, Pinus tabuliformis, Pinus yunnanensis, artificial hybrid, morphology},
	pages = {1890--1902},
}

Genetic analyses indicate that Pinus densata is a natural homoploid hybrid originating from Pinus tabuliformis and Pinus yunnanensis. Needle morphological and anatomical features show relative species stability and can be used to identify coniferous species. Comparative analyses of these needle characteristics and phenotypic differences between the artificial hybrids, P. densata, and parental species can be used to determine the genetic and phenotypic evolutionary consequences of natural hybridization. Twelve artificial hybrid families, the two parental species, and P. densata were seeded in a high-altitude habitat in Linzhi, Tibet. The needles of artificial hybrids and the three pine species were collected, and 24 needle morphological and anatomical traits were analyzed. Based on these results, variations in 10 needle traits among artificial hybrid families and 22 traits among species and artificial hybrids were predicted and found to be under moderate genetic control. Nineteen needle traits in artificial hybrids were similar to those in P. densata and between the two parental species, P. tabuliformis and P. yunnanensis. The ratio of plants with three needle clusters in artificial hybrids was 22.92%, which was very similar to P. densata. The eight needle traits (needle length, the mean number of stomata in sections 2 mm in length of the convex and flat sides of the needle, mean stomatal density, mesophyll/vascular bundle area ratio, mesophyll/resin canal area ratio, mesophyll/(resin canals and vascular bundles) area ratio, vascular bundle/resin canal area ratio) relative to physiological adaptability were similar to the artificial hybrids and P. densata. The similar needle features between the artificial hybrids and P. densata could be used to verify the homoploid hybrid origin of P. densata and helps to better understand of the hybridization roles in adaptation and speciation in plants.

@article{zhao_weak_2014,
	title = {Weak crossability barrier but strong juvenile selection supports ecological speciation of the hybrid pine {Pinus} {Densata} on the tibetan plateau},
	volume = {68},
	issn = {0014-3820},
	url = {https://doi.org/10.1111/evo.12496},
	doi = {10.1111/evo.12496},
	abstract = {Determining how a new hybrid lineage can achieve reproductive isolation is a key to understanding the process and mechanisms of homoploid hybrid speciation. Here, we evaluated the degree and nature of reproductive isolation between the ecologically successful hybrid species Pinus densata and its parental species P. tabuliformis and P. yunnanensis. We performed interspecific crosses among the three species to assess their crossability. We then conducted reciprocal transplantation experiments to evaluate their fitness differentiation, and to examine how natural populations representing different directions of introgression differ in adaptation. The crossing experiments revealed weak genetic barriers among the species. The transplantation trials showed manifest evidence of local adaptation as the three species all performed best in their native habitats. Pinus densata populations from the western edge of its distribution have evolved a strong local adaptation to the specific habitat in that range; populations representing different directions of introgressants with the two parental species all showed fitness disadvantages in this P. densata habitat. These observations illustrate that premating isolation through selection against immigrants from other habitat types or postzygotic isolation through selection against backcrosses between the three species is strong. Thus, ecological selection in combination with endogenous components and geographic isolation has likely played a significant role in the speciation of P. densata.},
	number = {11},
	urldate = {2023-04-27},
	journal = {Evolution},
	author = {Zhao, Wei and Meng, Jingxiang and Wang, Baosheng and Zhang, Lisha and Xu, Yulan and Zeng, Qing-Yin and Li, Yue and Mao, Jian-Feng and Wang, Xiao-Ru},
	month = nov,
	year = {2014},
	pages = {3120--3133},
}

Determining how a new hybrid lineage can achieve reproductive isolation is a key to understanding the process and mechanisms of homoploid hybrid speciation. Here, we evaluated the degree and nature of reproductive isolation between the ecologically successful hybrid species Pinus densata and its parental species P. tabuliformis and P. yunnanensis. We performed interspecific crosses among the three species to assess their crossability. We then conducted reciprocal transplantation experiments to evaluate their fitness differentiation, and to examine how natural populations representing different directions of introgression differ in adaptation. The crossing experiments revealed weak genetic barriers among the species. The transplantation trials showed manifest evidence of local adaptation as the three species all performed best in their native habitats. Pinus densata populations from the western edge of its distribution have evolved a strong local adaptation to the specific habitat in that range; populations representing different directions of introgressants with the two parental species all showed fitness disadvantages in this P. densata habitat. These observations illustrate that premating isolation through selection against immigrants from other habitat types or postzygotic isolation through selection against backcrosses between the three species is strong. Thus, ecological selection in combination with endogenous components and geographic isolation has likely played a significant role in the speciation of P. densata.

@article{wang_impact_2013,
	title = {Impact of {Geography} and {Climate} on the {Genetic} {Differentiation} of the {Subtropical} {Pine} {Pinus} yunnanensis},
	volume = {8},
	issn = {1932-6203},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0067345},
	doi = {10.1371/journal.pone.0067345},
	abstract = {Southwest China is a biodiversity hotspot characterized by complex topography, heterogeneous regional climates and rich flora. The processes and driving factors underlying this hotspot remain to be explicitly tested across taxa to gain a general understanding of the evolution of biodiversity and speciation in the region. In this study, we examined the role played by historically neutral processes, geography and environment in producing the current genetic diversity of the subtropical pine Pinus yunnanensis. We used genetic and ecological methods to investigate the patterns of genetic differentiation and ecological niche divergence across the distribution range of this species. We found both continuous genetic differentiation over the majority of its range, and discrete isolated local clusters. The discrete differentiation between two genetic groups in the west and east peripheries is consistent with niche divergence and geographical isolation of these groups. In the central area of the species’ range, population structure was shaped mainly by neutral processes and geography rather than by ecological selection. These results show that geographical and environmental factors together created stronger and more discrete genetic differentiation than isolation by distance alone, and illustrate the importance of ecological factors in forming or maintaining genetic divergence across a complex landscape. Our findings differ from other phylogenetic studies that identified the historical drainage system in the region as the primary factor shaping population structure, and highlight the heterogeneous contributions that geography and environment have made to genetic diversity among taxa in southwest China.},
	language = {en},
	number = {6},
	urldate = {2023-04-27},
	journal = {PLOS ONE},
	author = {Wang, Baosheng and Mao, Jian-Feng and Zhao, Wei and Wang, Xiao-Ru},
	month = jun,
	year = {2013},
	note = {Publisher: Public Library of Science},
	keywords = {Biogeography, Ecological niches, Environmental geography, Mitochondrial DNA, Paleogenetics, Phylogeography, Population genetics, Rivers},
	pages = {e67345},
}

Southwest China is a biodiversity hotspot characterized by complex topography, heterogeneous regional climates and rich flora. The processes and driving factors underlying this hotspot remain to be explicitly tested across taxa to gain a general understanding of the evolution of biodiversity and speciation in the region. In this study, we examined the role played by historically neutral processes, geography and environment in producing the current genetic diversity of the subtropical pine Pinus yunnanensis. We used genetic and ecological methods to investigate the patterns of genetic differentiation and ecological niche divergence across the distribution range of this species. We found both continuous genetic differentiation over the majority of its range, and discrete isolated local clusters. The discrete differentiation between two genetic groups in the west and east peripheries is consistent with niche divergence and geographical isolation of these groups. In the central area of the species’ range, population structure was shaped mainly by neutral processes and geography rather than by ecological selection. These results show that geographical and environmental factors together created stronger and more discrete genetic differentiation than isolation by distance alone, and illustrate the importance of ecological factors in forming or maintaining genetic divergence across a complex landscape. Our findings differ from other phylogenetic studies that identified the historical drainage system in the region as the primary factor shaping population structure, and highlight the heterogeneous contributions that geography and environment have made to genetic diversity among taxa in southwest China.

@article{liang_seedling_2013,
	title = {Seedling performance of {Pinus} densata and its parental population in the habitat of {P}. tabuliformis},
	volume = {37},
	issn = {1005-264X},
	url = {https://www.plant-ecology.com/EN/10.3724/SP.J.1258.2013.00016},
	doi = {10.3724/SP.J.1258.2013.00016},
	abstract = {Aims Pinus densata is the natural diploid hybrid of P. tabuliformis an...},
	language = {en},
	number = {2},
	urldate = {2023-04-27},
	journal = {Chinese Journal of Plant Ecology},
	author = {Liang, Dong and Mao, Jian-Feng and Zhao, Wei and Zhou, Xian-Qing and Yuan, Yuan and Wang, Li-Ming and Xing, Fang-Qian and Wang, Xiao-Ru and Li, Yue},
	month = aug,
	year = {2013},
	pages = {150},
}

Aims Pinus densata is the natural diploid hybrid of P. tabuliformis an...

@article{gao_demography_2012,
	title = {Demography and speciation history of the homoploid hybrid pine {Pinus} densata on the {Tibetan} {Plateau}},
	volume = {21},
	issn = {1365-294X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-294X.2012.05712.x},
	doi = {10.1111/j.1365-294X.2012.05712.x},
	abstract = {Pinus densata is an ecologically successful homoploid hybrid that inhabits vast areas of heterogeneous terrain on the south-eastern Tibetan Plateau as a result of multiple waves of colonization. Its region of origin, route of colonization onto the plateau and the directions of introgression with its parental species have previously been defined, but little is known about the isolation and divergence history of its populations. In this study, we surveyed nucleotide polymorphism over eight nuclear loci in 19 representative populations of P. densata and its parental species. Using this information and coalescence simulations, we assessed the historical changes in its population size, gene flow and divergence in time and space. The results indicate a late Miocene origin for P. densata associated with the recent uplift of south-eastern Tibet. The subsequent differentiation between geographical regions of this species began in the late Pliocene and was induced by regional topographical changes and Pleistocene glaciations. The ancestral P. densata population had a large effective population size but the central and western populations were established by limited founders, suggesting that there were severe bottlenecks during the westward migration out of the ancestral hybrid zone. After separating from their ancestral populations, population expansion occurred in all geographical regions especially in the western range. Gene flow in P. densata was restricted to geographically neighbouring populations, resulting in significant differentiation between regional groups. The new information on the divergence and demographic history of P. densata reported herein enhances our understanding of its speciation process on the Tibetan Plateau.},
	language = {en},
	number = {19},
	urldate = {2023-04-27},
	journal = {Molecular Ecology},
	author = {Gao, Jie and Wang, Baosheng and Mao, Jian-Feng and Ingvarsson, Pär and Zeng, Qing-Yin and Wang, Xiao-Ru},
	year = {2012},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-294X.2012.05712.x},
	keywords = {coalescent simulation, effective population size, gene flow, hybrid speciation, isolation history, nucleotide diversity},
	pages = {4811--4827},
}

Pinus densata is an ecologically successful homoploid hybrid that inhabits vast areas of heterogeneous terrain on the south-eastern Tibetan Plateau as a result of multiple waves of colonization. Its region of origin, route of colonization onto the plateau and the directions of introgression with its parental species have previously been defined, but little is known about the isolation and divergence history of its populations. In this study, we surveyed nucleotide polymorphism over eight nuclear loci in 19 representative populations of P. densata and its parental species. Using this information and coalescence simulations, we assessed the historical changes in its population size, gene flow and divergence in time and space. The results indicate a late Miocene origin for P. densata associated with the recent uplift of south-eastern Tibet. The subsequent differentiation between geographical regions of this species began in the late Pliocene and was induced by regional topographical changes and Pleistocene glaciations. The ancestral P. densata population had a large effective population size but the central and western populations were established by limited founders, suggesting that there were severe bottlenecks during the westward migration out of the ancestral hybrid zone. After separating from their ancestral populations, population expansion occurred in all geographical regions especially in the western range. Gene flow in P. densata was restricted to geographically neighbouring populations, resulting in significant differentiation between regional groups. The new information on the divergence and demographic history of P. densata reported herein enhances our understanding of its speciation process on the Tibetan Plateau.

@article{wang_colonization_2011,
	title = {Colonization of the {Tibetan} {Plateau} by the homoploid hybrid pine {Pinus} densata},
	volume = {20},
	issn = {1365-294X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-294X.2011.05157.x},
	doi = {10.1111/j.1365-294X.2011.05157.x},
	abstract = {Pinus densata is an intriguingly successful homoploid hybrid species that occupies vast areas of the southeastern Tibetan Plateau in which neither of its parental species are present, but the colonization processes involved are poorly understood. To shed light on how this species colonized and became established on the plateau, we surveyed paternally inherited chloroplast (cp) and maternally inherited mitochondrial (mt) DNA variation within and among 54 populations of P. densata and its putative parental species throughout their respective ranges. Strong spatial genetic structure of both cp and mtDNA were detected in P. densata populations. Mitotypes specific to P. densata were likely generated by complex recombination events. A putative ancestral hybrid zone in the northeastern periphery of P. densata was identified, and we propose that the species then colonized the plateau by migrating westwards. Along the colonization route, consecutive bottlenecks and surfing of rare alleles caused a significant reduction in genetic diversity and strong population differentiation. The direction and intensity of introgression from parental species varied among geographic regions. In western parts of its range, the species seems to have been isolated from seed and pollen flow from its parent species for a long time. The observed spatial distribution of genetic diversity in P. densata also appears to reflect the persistence of this species on the plateau during the last glaciation. Our results indicate that both ancient and contemporary population dynamics have contributed to the spatial distribution of genetic diversity in P. densata, which accordingly reflects its evolutionary history.},
	language = {en},
	number = {18},
	urldate = {2023-04-27},
	journal = {Molecular Ecology},
	author = {Wang, Baosheng and Mao, Jian-Feng and Gao, Jie and Zhao, Wei and Wang, Xiao-Ru},
	year = {2011},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-294X.2011.05157.x},
	keywords = {bottleneck, colonization history, hybrid speciation, mtDNA recombination, population structure},
	pages = {3796--3811},
}

Pinus densata is an intriguingly successful homoploid hybrid species that occupies vast areas of the southeastern Tibetan Plateau in which neither of its parental species are present, but the colonization processes involved are poorly understood. To shed light on how this species colonized and became established on the plateau, we surveyed paternally inherited chloroplast (cp) and maternally inherited mitochondrial (mt) DNA variation within and among 54 populations of P. densata and its putative parental species throughout their respective ranges. Strong spatial genetic structure of both cp and mtDNA were detected in P. densata populations. Mitotypes specific to P. densata were likely generated by complex recombination events. A putative ancestral hybrid zone in the northeastern periphery of P. densata was identified, and we propose that the species then colonized the plateau by migrating westwards. Along the colonization route, consecutive bottlenecks and surfing of rare alleles caused a significant reduction in genetic diversity and strong population differentiation. The direction and intensity of introgression from parental species varied among geographic regions. In western parts of its range, the species seems to have been isolated from seed and pollen flow from its parent species for a long time. The observed spatial distribution of genetic diversity in P. densata also appears to reflect the persistence of this species on the plateau during the last glaciation. Our results indicate that both ancient and contemporary population dynamics have contributed to the spatial distribution of genetic diversity in P. densata, which accordingly reflects its evolutionary history.

@article{mao_distinct_2011,
	title = {Distinct {Niche} {Divergence} {Characterizes} the {Homoploid} {Hybrid} {Speciation} of {Pinus} densata on the {Tibetan} {Plateau}.},
	volume = {177},
	issn = {0003-0147},
	url = {https://www.journals.uchicago.edu/doi/10.1086/658905},
	doi = {10.1086/658905},
	abstract = {Ecological divergence and selection for novel adaptations to new habitats have been theoretically proposed to play important roles in promoting homoploid hybrid speciation (HHS). The successful establishment of Pinus densata on the Tibetan Plateau is one of the few known examples of HHS. In this study, we carried out extensive field expeditions to obtain representative coverage of occurrence sites of P. densata and its two putative parents. We then applied a series of geographic information system–based analyses to define the patterns of environmental variation within and among the three pine species, to remove potentially confounding effects of spatial autocorrelation in the environmental data due to allopatric ranges, and to build species distribution models. All results consistently indicated that the ecological preferences of P. densata and its parental species have diverged, and they identified candidate ecological factors associated with habitat-specific adaptation. Projections from niche modeling indicated that P. densata could extend across a vast range along the parallel valley systems of the southeastern Tibetan Plateau. Our findings provide evidence of a distinct niche shift in P. densata and support the hypothesis that local adaptation and geographic isolation help maintain and reinforce between-species differences and reproductive isolation in the species complex.},
	number = {4},
	urldate = {2023-04-27},
	journal = {The American Naturalist},
	author = {Mao, Jian-Feng and Wang, Xiao-Ru},
	month = apr,
	year = {2011},
	note = {Publisher: The University of Chicago Press},
	keywords = {ecological differentiation, hybrid speciation, local adaptation, reproductive isolation},
	pages = {424--439},
}

Ecological divergence and selection for novel adaptations to new habitats have been theoretically proposed to play important roles in promoting homoploid hybrid speciation (HHS). The successful establishment of Pinus densata on the Tibetan Plateau is one of the few known examples of HHS. In this study, we carried out extensive field expeditions to obtain representative coverage of occurrence sites of P. densata and its two putative parents. We then applied a series of geographic information system–based analyses to define the patterns of environmental variation within and among the three pine species, to remove potentially confounding effects of spatial autocorrelation in the environmental data due to allopatric ranges, and to build species distribution models. All results consistently indicated that the ecological preferences of P. densata and its parental species have diverged, and they identified candidate ecological factors associated with habitat-specific adaptation. Projections from niche modeling indicated that P. densata could extend across a vast range along the parallel valley systems of the southeastern Tibetan Plateau. Our findings provide evidence of a distinct niche shift in P. densata and support the hypothesis that local adaptation and geographic isolation help maintain and reinforce between-species differences and reproductive isolation in the species complex.

@article{liu_geographic_2011,
	title = {Geographic {Isolation} between the {Homoploid} {Hybrid} {Pinus} densata and {Its} {Parental} {Pinus} yunnanensis},
	volume = {33},
	issn = {2096-2703},
	url = {https://journal.kib.ac.cn/EN/10.3724/SP.J.1143.2011.10227},
	doi = {10.3724/SP.J.1143.2011.10227},
	abstract = {In order to elucidate the geographic isolation mechanisms between the ...},
	language = {en},
	number = {3},
	urldate = {2023-04-27},
	journal = {Plant Diversity and Resources},
	author = {Liu, Yong-Liang and Mao, Jian-Feng and Wang, Xiao-Ru and Li, Yue},
	month = jun,
	year = {2011},
	keywords = {⚠️ Invalid DOI},
	pages = {269},
}

In order to elucidate the geographic isolation mechanisms between the ...

@article{mao_empirical_2009,
	title = {Empirical assessment of the reproductive fitness components of the hybrid pine {Pinus} densata on the {Tibetan} {Plateau}},
	volume = {23},
	issn = {1573-8477},
	url = {https://doi.org/10.1007/s10682-008-9244-6},
	doi = {10.1007/s10682-008-9244-6},
	abstract = {Pinus densata is distributed on the Tibetan Plateau, where it forms extensive forests at high elevations. Genetic studies have provided evidence that P. densata originated through hybridization between P. yunnanensis and P. tabuliformis. To clarify the relationships among these pines, and assess their reproductive fitness in their respective habitats, we conducted a comparative analysis of eight cone and seed morphometric traits and six reproductive traits in them. Among the eight morphometric traits examined, six appeared to be intermediate in P. densata between those of P. yunnanensis and P. tabuliformis. There were significant differences among the three pines in all of the morphometric traits, and P. densata showed greater variability in these traits than the other two pines. In contrast to the morphometric traits, the reproductive traits (including the proportions of filled and empty seeds, ovule abortion rate, seed efficiency, meiotic abnormalities during microsporogenesis and pollen viability) differed little among the three pines, indicating that they have similar overall rates of effective pollination and fertilization in their respective natural environments. Despite their location on the high plateau, natural populations of P. densata appeared to have normal levels of reproductive success, comparable to those of the two parental species in their natural habitats. This study provides empirical data characterizing the reproductive success and adaptation of a stabilized homoploid hybrid in a novel habitat that is ecologically and spatially inaccessible to its parental species.},
	language = {en},
	number = {3},
	urldate = {2023-04-27},
	journal = {Evolutionary Ecology},
	author = {Mao, Jian-Feng and Li, Yue and Wang, Xiao-Ru},
	month = may,
	year = {2009},
	keywords = {Cone and seed traits, Fertilization, Hybrid speciation, Microsporogenesis, Ovule abortion, Reproductive success},
	pages = {447--462},
}

Pinus densata is distributed on the Tibetan Plateau, where it forms extensive forests at high elevations. Genetic studies have provided evidence that P. densata originated through hybridization between P. yunnanensis and P. tabuliformis. To clarify the relationships among these pines, and assess their reproductive fitness in their respective habitats, we conducted a comparative analysis of eight cone and seed morphometric traits and six reproductive traits in them. Among the eight morphometric traits examined, six appeared to be intermediate in P. densata between those of P. yunnanensis and P. tabuliformis. There were significant differences among the three pines in all of the morphometric traits, and P. densata showed greater variability in these traits than the other two pines. In contrast to the morphometric traits, the reproductive traits (including the proportions of filled and empty seeds, ovule abortion rate, seed efficiency, meiotic abnormalities during microsporogenesis and pollen viability) differed little among the three pines, indicating that they have similar overall rates of effective pollination and fertilization in their respective natural environments. Despite their location on the high plateau, natural populations of P. densata appeared to have normal levels of reproductive success, comparable to those of the two parental species in their natural habitats. This study provides empirical data characterizing the reproductive success and adaptation of a stabilized homoploid hybrid in a novel habitat that is ecologically and spatially inaccessible to its parental species.

@article{mao_cone_2007,
	title = {Cone and seed characteristics of {Pinus} {Densata} and their adaptive fitness implications},
	volume = {31},
	issn = {1005-264X},
	url = {https://www.plant-ecology.com/EN/10.17521/cjpe.2007.0033},
	doi = {10.17521/cjpe.2007.0033},
	abstract = {Aims Pinus densata is an important forest species in the high mountain...},
	language = {en},
	number = {2},
	urldate = {2023-04-27},
	journal = {Chinese Journal of Plant Ecology},
	author = {Mao, Jian-Feng and Li, Yue and Liu, Yu-Jun and Liu, Hao and Wang, Xiao-Ru},
	month = oct,
	year = {2007},
	pages = {291},
}

Aims Pinus densata is an important forest species in the high mountain...

@article{funamoto_comparative_2003,
	title = {A comparative chromosomal study of three {Rhodiola} species ({Crassulaceae}) collected in central {Tianshan} {Mountains}, {Xinjiang}, {China}},
	volume = {7},
	shorttitle = {A comparative chromosomal study of three {Rhodiola} species ({Crassulaceae}) collected in central {Tianshan} {Mountains}, {Xinjiang}, {China}},
	url = {https://cir.nii.ac.jp/crid/1521417755499686144},
	abstract = {Chromosomal characters of three Rhodiola species (R. gelida, R. quadrifida and R. aff. litwinowii) collected in central Tianshan Mountains in Xinjiang, China, had commonly the simple chromocenter type in the resting chromosomes and the proximal type in the mitotic prophase chromosomes. Rhodiola gelida and R. quadrifida showed the chromosome number of 2n=20 and R. aff. litwinowii showed the chromosome number of 2n=16. The chromosome numbers of R. gelida and R. aff. litwinowii were reported here for the first time, and the chromosome number of R. quadrifida verified the previous report. Rhodiola gelida and R. quadrifida had monomodal (gradual) decrease in chromosome length from the largest to the smallest chromosomes in alighment and R. aff. litwinowii had bimodal decrease in chromosome length.},
	language = {en},
	number = {2},
	urldate = {2023-04-27},
	journal = {Chromosome Science},
	author = {Funamoto, Tsuneo and Kondo, Katsuhiko and Hong, De-yuan and Mao, Jian-Feng and Ogura, Hisakazu},
	year = {2003},
	note = {Publisher: The Society of Chromosome Research},
	keywords = {⛔ No DOI found},
	pages = {55--60},
}

Chromosomal characters of three Rhodiola species (R. gelida, R. quadrifida and R. aff. litwinowii) collected in central Tianshan Mountains in Xinjiang, China, had commonly the simple chromocenter type in the resting chromosomes and the proximal type in the mitotic prophase chromosomes. Rhodiola gelida and R. quadrifida showed the chromosome number of 2n=20 and R. aff. litwinowii showed the chromosome number of 2n=16. The chromosome numbers of R. gelida and R. aff. litwinowii were reported here for the first time, and the chromosome number of R. quadrifida verified the previous report. Rhodiola gelida and R. quadrifida had monomodal (gradual) decrease in chromosome length from the largest to the smallest chromosomes in alighment and R. aff. litwinowii had bimodal decrease in chromosome length.

@article{ogura_chromosome_2003,
	title = {Chromosome constitution of seven wild {Allium} species in the {Tianshan} {Mountains} ({Abstracts} of the oral and poster presentations, {Abstracts} of the 54th {Annual} {Meeting} of the {Society} of {Chromosome} {Research})},
	volume = {7},
	shorttitle = {Chromosome constitution of seven wild {Allium} species in the {Tianshan} {Mountains}({Abstracts} of the oral and poster presentations, {Abstracts} of the 54th {Annual} {Meeting} of the {Society} of {Chromosome} {Research})},
	url = {https://cir.nii.ac.jp/crid/1540854195286041984},
	language = {en},
	number = {4},
	urldate = {2023-04-27},
	journal = {Chromosome science},
	author = {Ogura, Hisakazu and Kondo, Katsuhiko and Mao, Jian-Feng and Funamoto, Tsuneo and Tan, Dun-yan and Ge, Song and Hong, De-yuan},
	year = {2003},
	note = {Publisher: Society of Chromosome Research},
	keywords = {⛔ No DOI found},
	pages = {128},
}

@article{funamoto_somatic_2002,
	title = {Somatic chromosomes of three {Parnassia} species({Saxifragaceae}) in {Xinjiang}, {China}},
	volume = {6},
	url = {https://cir.nii.ac.jp/crid/1520573331025517696},
	abstract = {Somatic chromosomes of three Parnassia species collected in Xinjiang, China were observed. They had commonly the simple chromocenter type of resting chromosomes and the proximal type of mitotic prophase chromosomes. The chromosome numbers of 2n=36 and 2n=36+1～8 supernumerary chromosomes for P. bifolia were reported here for the first time. The chromosome number of 2n=18 for P. laxmannii and P. palustris var. palustris was verified the previous reports. Three Parnassia species had similar small size chromosomes and the basic chromosome number of x=9. The karyotype of Parnassia laxmannii consisted of 18 mediancentromeric chromosomes, while that of the other two species consisted commonly of median- and submedian-centromeric chromosomes.},
	language = {en},
	number = {1},
	urldate = {2023-04-27},
	journal = {Chromosome Science},
	author = {Funamoto, Tsuneo and Kondo, Katsuhiko and Hong, De-yuan and Ge, Song and Mao, Jian-Feng and Ogura, Hisakazu},
	year = {2002},
	note = {Publisher: The Society of Chromosome Research},
	pages = {27--34},
}

Somatic chromosomes of three Parnassia species collected in Xinjiang, China were observed. They had commonly the simple chromocenter type of resting chromosomes and the proximal type of mitotic prophase chromosomes. The chromosome numbers of 2n=36 and 2n=36+1～8 supernumerary chromosomes for P. bifolia were reported here for the first time. The chromosome number of 2n=18 for P. laxmannii and P. palustris var. palustris was verified the previous reports. Three Parnassia species had similar small size chromosomes and the basic chromosome number of x=9. The karyotype of Parnassia laxmannii consisted of 18 mediancentromeric chromosomes, while that of the other two species consisted commonly of median- and submedian-centromeric chromosomes.

@article{kang_x-y_and_j-f_mao_gamete_2001,
	title = {Gamete fertility morphological variations in offsprings of triploid clones of {Populus} tomentosa},
	volume = {23},
	shorttitle = {Gamete fertility morphological variations in offsprings of triploid clones of {Populus} tomentosa},
	author = {Kang, X.-Y. {and} J.-F. Mao},
	year = {2001},
	pages = {20--23},
}