Automation of tree-ring detection and measurements using deep learning.
Poláček, M., Arizpe, A., Hüther, P., Weidlich, L., Steindl, S., & Swarts, K.
Methods in Ecology and Evolution, 14(9): 2233–2242. 2023.
_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.14183
Paper
doi
link
bibtex
abstract
@article{polacek_automation_2023,
title = {Automation of tree-ring detection and measurements using deep learning},
volume = {14},
copyright = {© 2023 GMI - Gregor Mendel Institute of Molecular Plant Biology. Methods in Ecology and Evolution published by John Wiley \& Sons Ltd on behalf of British Ecological Society.},
issn = {2041-210X},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.14183},
doi = {10.1111/2041-210X.14183},
abstract = {Core samples from trees are a critical reservoir of ecological information, informing our understanding of past climates, as well as contemporary ecosystem responses to global change. Manual measurements of annual growth rings in trees are slow, labour-intensive and subject to human bias, hindering the generation of big datasets. We present an alternative, neural network-based implementation that automates detection and measurement of tree-ring boundaries from coniferous species. We trained our Mask R-CNN extensively on over 8000 manually annotated ring boundaries from microscope-imaged Norway Spruce Picea abies increment cores. We assessed the performance of the trained model after post-processing on real-world data generated from our core processing pipeline. The CNN after post-processing performed well, with recognition of over 98\% of ring boundaries (recall) with a precision in detection of 96\% when tested on real-world data. Additionally, we have implemented automatic measurements based on minimum distance between rings. With minimal editing for missed ring detections, these measurements were 98\% correlated with human measurements of the same samples. Tests on other three conifer species demonstrate that the CNN generalizes well to other species with similar structure. We demonstrate the efficacy of automating the measurement of growth increment in tree core samples. Our CNN-based system provides high predictive performance in terms of both tree-ring detection and growth rate determination. Our application is readily deployable as a Docker container and requires only basic command line skills. Additionally, an easy re-training option allows users to expand capabilities to other wood types. Application outputs include both editable annotations of predictions as well as ring-width measurements in a commonly used .pos format, facilitating the efficient generation of large ring-width measurement datasets from increment core samples, an important source of environmental data.},
language = {en},
number = {9},
urldate = {2024-03-22},
journal = {Methods in Ecology and Evolution},
author = {Poláček, Miroslav and Arizpe, Alexis and Hüther, Patrick and Weidlich, Lisa and Steindl, Sonja and Swarts, Kelly},
year = {2023},
note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.14183},
keywords = {automation, computer vision, mask R-CNN, phenotyping, tree rings},
pages = {2233--2242},
}
Core samples from trees are a critical reservoir of ecological information, informing our understanding of past climates, as well as contemporary ecosystem responses to global change. Manual measurements of annual growth rings in trees are slow, labour-intensive and subject to human bias, hindering the generation of big datasets. We present an alternative, neural network-based implementation that automates detection and measurement of tree-ring boundaries from coniferous species. We trained our Mask R-CNN extensively on over 8000 manually annotated ring boundaries from microscope-imaged Norway Spruce Picea abies increment cores. We assessed the performance of the trained model after post-processing on real-world data generated from our core processing pipeline. The CNN after post-processing performed well, with recognition of over 98% of ring boundaries (recall) with a precision in detection of 96% when tested on real-world data. Additionally, we have implemented automatic measurements based on minimum distance between rings. With minimal editing for missed ring detections, these measurements were 98% correlated with human measurements of the same samples. Tests on other three conifer species demonstrate that the CNN generalizes well to other species with similar structure. We demonstrate the efficacy of automating the measurement of growth increment in tree core samples. Our CNN-based system provides high predictive performance in terms of both tree-ring detection and growth rate determination. Our application is readily deployable as a Docker container and requires only basic command line skills. Additionally, an easy re-training option allows users to expand capabilities to other wood types. Application outputs include both editable annotations of predictions as well as ring-width measurements in a commonly used .pos format, facilitating the efficient generation of large ring-width measurement datasets from increment core samples, an important source of environmental data.
Domestication and lowland adaptation of coastal preceramic maize from Paredones, Peru.
Vallebueno-Estrada, M., Hernández-Robles, G. G, González-Orozco, E., Lopez-Valdivia, I., Rosales Tham, T., Vásquez Sánchez, V., Swarts, K., Dillehay, T. D, Vielle-Calzada, J., & Montiel, R.
eLife, 12: e83149. April 2023.
Publisher: eLife Sciences Publications, Ltd
Paper
doi
link
bibtex
abstract
@article{vallebueno-estrada_domestication_2023,
title = {Domestication and lowland adaptation of coastal preceramic maize from {Paredones}, {Peru}},
volume = {12},
issn = {2050-084X},
url = {https://doi.org/10.7554/eLife.83149},
doi = {10.7554/eLife.83149},
abstract = {Archaeological cobs from Paredones and Huaca Prieta (Peru) represent some of the oldest maize known to date, yet they present relevant phenotypic traits corresponding to domesticated maize. This contrasts with the earliest Mexican macro-specimens from Guila Naquitz and San Marcos, which are phenotypically intermediate for these traits, even though they date more recently in time. To gain insights into the origins of ancient Peruvian maize, we sequenced DNA from three Paredones specimens dating {\textasciitilde}6700–5000 calibrated years before present (BP), conducting comparative analyses with two teosinte subspecies (Zea mays ssp. mexicana and parviglumis) and extant maize, that include highland and lowland landraces from Mesoamerica and South America. We show that Paredones maize originated from the same domestication event as Mexican maize and was domesticated by {\textasciitilde}6700 BP, implying rapid dispersal followed by improvement. Paredones maize shows no relevant gene flow from mexicana, smaller than that observed in teosinte parviglumis. Thus, Paredones samples represent the only maize without confounding mexicana variation found to date. It also harbors significantly fewer alleles previously found to be adaptive to highlands, but not of alleles adaptive to lowlands, supporting a lowland migration route. Our overall results imply that Paredones maize originated in Mesoamerica, arrived in Peru without mexicana introgression through a rapid lowland migration route, and underwent improvements in both Mesoamerica and South America.},
urldate = {2024-03-22},
journal = {eLife},
author = {Vallebueno-Estrada, Miguel and Hernández-Robles, Guillermo G and González-Orozco, Eduardo and Lopez-Valdivia, Ivan and Rosales Tham, Teresa and Vásquez Sánchez, Víctor and Swarts, Kelly and Dillehay, Tom D and Vielle-Calzada, Jean-Philippe and Montiel, Rafael},
editor = {Weigel, Detlef},
month = apr,
year = {2023},
note = {Publisher: eLife Sciences Publications, Ltd},
keywords = {domestication, lowlands, paleogenomics, paredones},
pages = {e83149},
}
Archaeological cobs from Paredones and Huaca Prieta (Peru) represent some of the oldest maize known to date, yet they present relevant phenotypic traits corresponding to domesticated maize. This contrasts with the earliest Mexican macro-specimens from Guila Naquitz and San Marcos, which are phenotypically intermediate for these traits, even though they date more recently in time. To gain insights into the origins of ancient Peruvian maize, we sequenced DNA from three Paredones specimens dating ~6700–5000 calibrated years before present (BP), conducting comparative analyses with two teosinte subspecies (Zea mays ssp. mexicana and parviglumis) and extant maize, that include highland and lowland landraces from Mesoamerica and South America. We show that Paredones maize originated from the same domestication event as Mexican maize and was domesticated by ~6700 BP, implying rapid dispersal followed by improvement. Paredones maize shows no relevant gene flow from mexicana, smaller than that observed in teosinte parviglumis. Thus, Paredones samples represent the only maize without confounding mexicana variation found to date. It also harbors significantly fewer alleles previously found to be adaptive to highlands, but not of alleles adaptive to lowlands, supporting a lowland migration route. Our overall results imply that Paredones maize originated in Mesoamerica, arrived in Peru without mexicana introgression through a rapid lowland migration route, and underwent improvements in both Mesoamerica and South America.
‘Seeing’ the electromagnetic spectrum: spotlight on the cryptochrome photocycle.
Aguida, B., Babo, J., Baouz, S., Jourdan, N., Procopio, M., El-Esawi, M. A., Engle, D., Mills, S., Wenkel, S., Huck, A., Berg-Sørensen, K., Kampranis, S. C., Link, J., & Ahmad, M.
Frontiers in Plant Science, 15. March 2024.
Paper
link
bibtex
abstract
@article{aguida_seeing_2024,
title = {‘{Seeing}’ the electromagnetic spectrum: spotlight on the cryptochrome photocycle},
volume = {15},
issn = {1664-462X},
shorttitle = {‘{Seeing}’ the electromagnetic spectrum},
url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1340304},
abstract = {Cryptochromes are widely dispersed flavoprotein photoreceptors that regulate numerous developmental responses to light in plants, as well as to stress and entrainment of the circadian clock in animals and humans. All cryptochromes are closely related to an ancient family of light-absorbing flavoenzymes known as photolyases, which use light as an energy source for DNA repair but themselves have no light sensing role. Here we review the means by which plant cryptochromes acquired a light sensing function. This transition involved subtle changes within the flavin binding pocket which gave rise to a visual photocycle consisting of light-inducible and dark-reversible flavin redox state transitions. In this photocycle, light first triggers flavin reduction from an initial dark-adapted resting state (FADox). The reduced state is the biologically active or ‘lit’ state, correlating with biological activity. Subsequently, the photoreduced flavin reoxidises back to the dark adapted or ‘resting’ state. Because the rate of reoxidation determines the lifetime of the signaling state, it significantly modulates biological activity. As a consequence of this redox photocycle Crys respond to both the wavelength and the intensity of light, but are in addition regulated by factors such as temperature, oxygen concentration, and cellular metabolites that alter rates of flavin reoxidation even independently of light. Mechanistically, flavin reduction is correlated with conformational change in the protein, which is thought to mediate biological activity through interaction with biological signaling partners. In addition, a second, entirely independent signaling mechanism arises from the cryptochrome photocycle in the form of reactive oxygen species (ROS). These are synthesized during flavin reoxidation, are known mediators of biotic and abiotic stress responses, and have been linked to Cry biological activity in plants and animals. Additional special properties arising from the cryptochrome photocycle include responsivity to electromagnetic fields and their applications in optogenetics. Finally, innovations in methodology such as the use of Nitrogen Vacancy (NV) diamond centers to follow cryptochrome magnetic field sensitivity in vivo are discussed, as well as the potential for a whole new technology of ‘magneto-genetics’ for future applications in synthetic biology and medicine.},
urldate = {2024-03-22},
journal = {Frontiers in Plant Science},
author = {Aguida, Blanche and Babo, Jonathan and Baouz, Soria and Jourdan, Nathalie and Procopio, Maria and El-Esawi, Mohamed A. and Engle, Dorothy and Mills, Stephen and Wenkel, Stephan and Huck, Alexander and Berg-Sørensen, Kirstine and Kampranis, Sotirios C. and Link, Justin and Ahmad, Margaret},
month = mar,
year = {2024},
keywords = {⛔ No DOI found},
}
Cryptochromes are widely dispersed flavoprotein photoreceptors that regulate numerous developmental responses to light in plants, as well as to stress and entrainment of the circadian clock in animals and humans. All cryptochromes are closely related to an ancient family of light-absorbing flavoenzymes known as photolyases, which use light as an energy source for DNA repair but themselves have no light sensing role. Here we review the means by which plant cryptochromes acquired a light sensing function. This transition involved subtle changes within the flavin binding pocket which gave rise to a visual photocycle consisting of light-inducible and dark-reversible flavin redox state transitions. In this photocycle, light first triggers flavin reduction from an initial dark-adapted resting state (FADox). The reduced state is the biologically active or ‘lit’ state, correlating with biological activity. Subsequently, the photoreduced flavin reoxidises back to the dark adapted or ‘resting’ state. Because the rate of reoxidation determines the lifetime of the signaling state, it significantly modulates biological activity. As a consequence of this redox photocycle Crys respond to both the wavelength and the intensity of light, but are in addition regulated by factors such as temperature, oxygen concentration, and cellular metabolites that alter rates of flavin reoxidation even independently of light. Mechanistically, flavin reduction is correlated with conformational change in the protein, which is thought to mediate biological activity through interaction with biological signaling partners. In addition, a second, entirely independent signaling mechanism arises from the cryptochrome photocycle in the form of reactive oxygen species (ROS). These are synthesized during flavin reoxidation, are known mediators of biotic and abiotic stress responses, and have been linked to Cry biological activity in plants and animals. Additional special properties arising from the cryptochrome photocycle include responsivity to electromagnetic fields and their applications in optogenetics. Finally, innovations in methodology such as the use of Nitrogen Vacancy (NV) diamond centers to follow cryptochrome magnetic field sensitivity in vivo are discussed, as well as the potential for a whole new technology of ‘magneto-genetics’ for future applications in synthetic biology and medicine.
The super-pangenome of Populus unveil genomic facets for its adaptation and diversification in widespread forest trees.
Shi, T., Zhang, X., Hou, Y., Jia, C., Dan, X., Zhang, Y., Jiang, Y., Lai, Q., Feng, J., Feng, J., Ma, T., Wu, J., Liu, S., Zhang, L., Long, Z., Chen, L., Street, N. R., Ingvarsson, P. K., Liu, J., Yin, T., & Wang, J.
Molecular Plant. March 2024.
Paper
doi
link
bibtex
abstract
@article{shi_super-pangenome_2024,
title = {The super-pangenome of \textit{{Populus}} unveil genomic facets for its adaptation and diversification in widespread forest trees},
issn = {1674-2052},
url = {https://www.sciencedirect.com/science/article/pii/S1674205224000820},
doi = {10.1016/j.molp.2024.03.009},
abstract = {Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world’s most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pan-genomes with transcriptomes, methylomes and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pan-genes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142,202 structural variants (SVs) across species, which intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180 bp presence/absence variant impacting the expression of the CUC2 gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome (http://www.populus-superpangenome.com/). Together, the present pioneering super-pangenome resource in forest trees not only aid in the advancement of breeding efforts of this globally important tree genus but also offer valuable insights into potential avenues for comprehending tree biology.},
urldate = {2024-03-22},
journal = {Molecular Plant},
author = {Shi, Tingting and Zhang, Xinxin and Hou, Yukang and Jia, Changfu and Dan, Xuming and Zhang, Yulin and Jiang, Yuanzhong and Lai, Qiang and Feng, Jiajun and Feng, Jianju and Ma, Tao and Wu, Jiali and Liu, Shuyu and Zhang, Lei and Long, Zhiqin and Chen, Liyang and Street, Nathaniel R. and Ingvarsson, Pär K. and Liu, Jianquan and Yin, Tongming and Wang, Jing},
month = mar,
year = {2024},
keywords = {genome evolution, pan-genomes, structural variation, whole genome duplication},
}
Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world’s most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pan-genomes with transcriptomes, methylomes and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pan-genes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142,202 structural variants (SVs) across species, which intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180 bp presence/absence variant impacting the expression of the CUC2 gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome (http://www.populus-superpangenome.com/). Together, the present pioneering super-pangenome resource in forest trees not only aid in the advancement of breeding efforts of this globally important tree genus but also offer valuable insights into potential avenues for comprehending tree biology.
Profiling of 1-aminocyclopropane-1-carboxylic acid and selected phytohormones in Arabidopsis using liquid chromatography-tandem mass spectrometry.
Karady, M., Hladík, P., Cermanová, K., Jiroutová, P., Antoniadi, I., Casanova-Sáez, R., Ljung, K., & Novák, O.
Plant Methods, 20(1): 41. March 2024.
Paper
doi
link
bibtex
abstract
@article{karady_profiling_2024,
title = {Profiling of 1-aminocyclopropane-1-carboxylic acid and selected phytohormones in {Arabidopsis} using liquid chromatography-tandem mass spectrometry},
volume = {20},
issn = {1746-4811},
url = {https://doi.org/10.1186/s13007-024-01165-8},
doi = {10.1186/s13007-024-01165-8},
abstract = {Gaseous phytohormone ethylene levels are directly influenced by the production of its immediate non-volatile precursor 1-aminocyclopropane-1-carboxylic acid (ACC). Owing to the strongly acidic character of the ACC molecule, its quantification has been difficult to perform. Here, we present a simple and straightforward validated method for accurate quantification of not only ACC levels, but also major members of other important phytohormonal classes – auxins, cytokinins, jasmonic acid, abscisic acid and salicylic acid from the same biological sample.},
number = {1},
urldate = {2024-03-22},
journal = {Plant Methods},
author = {Karady, Michal and Hladík, Pavel and Cermanová, Kateřina and Jiroutová, Petra and Antoniadi, Ioanna and Casanova-Sáez, Rubén and Ljung, Karin and Novák, Ondřej},
month = mar,
year = {2024},
keywords = {1-aminocyclopropane-1-carboxylic acid, ACC, Abscisic acid, Arabidopsis, Auxin, Cytokinin, Ethylene, Jasmonic acid, Liquid chromatography, Mass spectrometry, Plant hormones, Salicylic acid},
pages = {41},
}
Gaseous phytohormone ethylene levels are directly influenced by the production of its immediate non-volatile precursor 1-aminocyclopropane-1-carboxylic acid (ACC). Owing to the strongly acidic character of the ACC molecule, its quantification has been difficult to perform. Here, we present a simple and straightforward validated method for accurate quantification of not only ACC levels, but also major members of other important phytohormonal classes – auxins, cytokinins, jasmonic acid, abscisic acid and salicylic acid from the same biological sample.