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3. The western redcedar genome reveals low genetic diversity in a self-compatible conifer

Author

Shalev, Tal J, El-Dien, Omnia Gamal, Yuen, Macaire MS, Shengqiang, Shu, Jackman, Shaun D, Warren, René L, Coombe, Lauren, van der Merwe, Lise, Stewart, Ada, Boston, Lori B, Plott, Christopher, Jenkins, Jerry, He, Guifen, Yan, Juying, Yan, Mi, Guo, Jie, Breinholt, Jesse W, Neves, Leandro G, Grimwood, Jane, Rieseberg, Loren H, Schmutz, Jeremy, Birol, Inanc, Kirst, Matias, Yanchuk, Alvin D, Ritland, Carol, Russell, John H, and Bohlmann, Joerg

Subjects
Biological Sciences, Ecology, Evolutionary Biology, Genetics, Human Genome, Tracheophyta, Self-Fertilization, Alleles, Heterozygote, Polymorphism, Genetic, Genetic Variation, Selection, Genetic, Medical and Health Sciences, Bioinformatics
Abstract

We assembled the 9.8-Gbp genome of western redcedar (WRC; Thuja plicata), an ecologically and economically important conifer species of the Cupressaceae. The genome assembly, derived from a uniquely inbred tree produced through five generations of self-fertilization (selfing), was determined to be 86% complete by BUSCO analysis, one of the most complete genome assemblies for a conifer. Population genomic analysis revealed WRC to be one of the most genetically depauperate wild plant species, with an effective population size of approximately 300 and no significant genetic differentiation across its geographic range. Nucleotide diversity, π, is low for a continuous tree species, with many loci showing zero diversity, and the ratio of π at zero- to fourfold degenerate sites is relatively high (approximately 0.33), suggestive of weak purifying selection. Using an array of genetic lines derived from up to five generations of selfing, we explored the relationship between genetic diversity and mating system. Although overall heterozygosity was found to decline faster than expected during selfing, heterozygosity persisted at many loci, and nearly 100 loci were found to deviate from expectations of genetic drift, suggestive of associative overdominance. Nonreference alleles at such loci often harbor deleterious mutations and are rare in natural populations, implying that balanced polymorphisms are maintained by linkage to dominant beneficial alleles. This may account for how WRC remains responsive to natural and artificial selection, despite low genetic diversity.

Published
2022

6. Shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants

Author

University of Florida, Kates, Heather [0000-0001-8490-2201], O'Meara, Brian C. [0000-0002-0337-5997], Stull, Gregory W. [0000-0002-2733-4823], James, Euan K. [0000-0001-7969-6570], Liu, Shui-Yin [0000-0002-8674-7097], Tian, Qin [0000-0002-7939-5329], Yi, Ting-Shuang [0000-0001-7093-9564], Conde, Daniel [0000-0001-8362-4190], Kirst, Matias [0000-0002-8186-3945], Ané, Jean-Michel [0000-0002-3128-9439], Soltis, Douglas [0000-0001-8638-4137], Guralnick, Robert [0000-0001-6682-1504], Soltis, Pamela [0000-0001-9310-8659], Folk, Ryan [0000-0002-5333-9273], Kates, Heather, O'Meara, Brian C., LaFrance, Raphael, Stull, Gregory W., James, Euan K., Liu, Shui-Yin, Tian, Qin, Yi, Ting-Shuang, Conde, Daniel, Kirst, Matias, Ané, Jean-Michel, Soltis, Douglas, Guralnick, Robert, Soltis, Pamela, Folk, Ryan, University of Florida, Kates, Heather [0000-0001-8490-2201], O'Meara, Brian C. [0000-0002-0337-5997], Stull, Gregory W. [0000-0002-2733-4823], James, Euan K. [0000-0001-7969-6570], Liu, Shui-Yin [0000-0002-8674-7097], Tian, Qin [0000-0002-7939-5329], Yi, Ting-Shuang [0000-0001-7093-9564], Conde, Daniel [0000-0001-8362-4190], Kirst, Matias [0000-0002-8186-3945], Ané, Jean-Michel [0000-0002-3128-9439], Soltis, Douglas [0000-0001-8638-4137], Guralnick, Robert [0000-0001-6682-1504], Soltis, Pamela [0000-0001-9310-8659], Folk, Ryan [0000-0002-5333-9273], Kates, Heather, O'Meara, Brian C., LaFrance, Raphael, Stull, Gregory W., James, Euan K., Liu, Shui-Yin, Tian, Qin, Yi, Ting-Shuang, Conde, Daniel, Kirst, Matias, Ané, Jean-Michel, Soltis, Douglas, Guralnick, Robert, Soltis, Pamela, and Folk, Ryan

Abstract

Root nodule symbiosis (RNS) is a complex trait that enables plants to access atmospheric nitrogen converted into usable forms through a mutualistic relationship with soil bacteria. Pinpointing the evolutionary origins of RNS is critical for understanding its genetic basis, but building this evolutionary context is complicated by data limitations and the intermittent presence of RNS in a single clade of ca. 30,000 species of flowering plants, i.e., the nitrogen-fixing clade (NFC). We developed the most extensive de novo phylogeny for the NFC and an RNS trait database to reconstruct the evolution of RNS. Our analysis identifies evolutionary rate heterogeneity associated with a two-step process: An ancestral precursor state transitioned to a more labile state from which RNS was rapidly gained at multiple points in the NFC. We illustrate how a two-step process could explain multiple independent gains and losses of RNS, contrary to recent hypotheses suggesting one gain and numerous losses, and suggest a broader phylogenetic and genetic scope may be required for genome-phenome mapping.

Published
2024

7. The single-cell transcriptome program of nodule development cellular lineages in Medicago truncatula

Author

Department of Energy (US), Biological and Environmental Research (US), Clemson University, Pereira, Wendell J. [0000-0003-1019-6281], Conde, Daniel [0000-0001-8362-4190], Triozzi, Paolo M. [0000-0003-0192-3336], Balmant, Kelly M. [0000-0001-5189-5121], Dervinis, Christopher [0000-0002-2176-4232], Schmidt, Henry W. [0000-0001-9465-9540], Boaventura-Novaes, Carolina [0000-0003-3674-4813], Chakraborty, Sanhita [0000-0001-7991-3977], Knaack, Sara A. [0000-0002-1178-2517], Gao, Yueyao [0000-0002-7607-2938], Feltus, Frank Alexander [0000-0002-2123-6114], Roy, Sushmita [0000-0001-7550-0542], Ané, Jean-Michel [0000-0002-3128-9439], Frugoli, Julia [0000-0003-1642-5911], Kirst, Matias [0000-0002-8186-3945], Pereira, Wendell J., Boyd, Jade, Conde, Daniel, Triozzi, Paolo M., Balmant, Kelly M., Dervinis, Christopher, Schmidt, Henry W., Boaventura-Novaes, Carolina, Chakraborty, Sanhita, Knaack, Sara A., Gao, Yueyao, Feltus, Frank Alexander, Roy, Sushmita, Ané, Jean-Michel, Frugoli, Julia, Kirst, Matias, Department of Energy (US), Biological and Environmental Research (US), Clemson University, Pereira, Wendell J. [0000-0003-1019-6281], Conde, Daniel [0000-0001-8362-4190], Triozzi, Paolo M. [0000-0003-0192-3336], Balmant, Kelly M. [0000-0001-5189-5121], Dervinis, Christopher [0000-0002-2176-4232], Schmidt, Henry W. [0000-0001-9465-9540], Boaventura-Novaes, Carolina [0000-0003-3674-4813], Chakraborty, Sanhita [0000-0001-7991-3977], Knaack, Sara A. [0000-0002-1178-2517], Gao, Yueyao [0000-0002-7607-2938], Feltus, Frank Alexander [0000-0002-2123-6114], Roy, Sushmita [0000-0001-7550-0542], Ané, Jean-Michel [0000-0002-3128-9439], Frugoli, Julia [0000-0003-1642-5911], Kirst, Matias [0000-0002-8186-3945], Pereira, Wendell J., Boyd, Jade, Conde, Daniel, Triozzi, Paolo M., Balmant, Kelly M., Dervinis, Christopher, Schmidt, Henry W., Boaventura-Novaes, Carolina, Chakraborty, Sanhita, Knaack, Sara A., Gao, Yueyao, Feltus, Frank Alexander, Roy, Sushmita, Ané, Jean-Michel, Frugoli, Julia, and Kirst, Matias

Abstract

Legumes establish a symbiotic relationship with nitrogen-fixing rhizobia by developing nodules. Nodules are modified lateral roots that undergo changes in their cellular development in response to bacteria, but the transcriptional reprogramming that occurs in these root cells remains largely uncharacterized. Here, we describe the cell-type-specific transcriptome response of Medicago truncatula roots to rhizobia during early nodule development in the wild-type genotype Jemalong A17, complemented with a hypernodulating mutant (sunn-4) to expand the cell population responding to infection and subsequent biological inferences. The analysis identifies epidermal root hair and stele sub-cell types associated with a symbiotic response to infection and regulation of nodule proliferation. Trajectory inference shows cortex-derived cell lineages differentiating to form the nodule primordia and, posteriorly, its meristem, while modulating the regulation of phytohormone-related genes. Gene regulatory analysis of the cell transcriptomes identifies new regulators of nodulation, including STYLISH 4, for which the function is validated.

Published
2024

9. Genomic selection in western redcedar: from proof of concept to operational application.

Author

Gamal El‐Dien, Omnia, Shalev, Tal J., Yuen, Macaire M. S., Van der Merwe, Lise, Kirst, Matias, Yanchuk, Alvin D., Ritland, Carol, Russell, John H., and Bohlmann, Joerg

Subjects
TREE breeding, JUNIPERS, WOOD quality, LINKAGE disequilibrium, PROOF of concept
Abstract

Summary: Forests face many threats. While traditional breeding may be too slow to deliver well‐adapted trees, genomic selection (GS) can accelerate the process. We describe a comprehensive study of GS from proof of concept to operational application in western redcedar (WRC, Thuja plicata).Using genomic data, we developed models on a training population (TrP) of trees to predict breeding values (BVs) in a target seedling population (TaP) for growth, heartwood chemistry, and foliar chemistry traits. We used cross‐validation to assess prediction accuracy (PACC) in the TrP; we also validated models for early‐expressed foliar traits in the TaP.Prediction accuracy was high across generations, environments, and ages. PACC was not reduced to zero among unrelated individuals in TrP and was only slightly reduced in the TaP, confirming strong linkage disequilibrium and the ability of the model to generate accurate predictions across breeding generations. Genomic BV predictions were correlated with those from pedigree but displayed a wider range of within‐family variation due to the ability of GS to capture the Mendelian sampling term.Using predicted TaP BVs in multi‐trait selection, we functionally implemented and integrated GS into an operational tree‐breeding program. [ABSTRACT FROM AUTHOR]

Published
2024
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10. The uncharacterized gene EVE contributes to vessel element dimensions in Populus

Author

Ribeiro, Cíntia L., Conde, Daniel, Balmant, Kelly M., Dervinis, Christopher, Johnson, Matthew G., McGrath, Aaron P., Szewczyk, Paul, Unda, Faride, Finegan, Christina A., Schmidt, Henry W., Miles, Brianna, Drost, Derek R., Novaes, Evandro, Gonzalez-Benecke, Carlos A., Peter, Gary F., Burleigh, J. Gordon, Martin, Timothy A., Mansfield, Shawn D., Chang, Geoffrey, Wicketti, Norman J., and Kirst, Matias

Published
2020

17. A chemical genetic roadmap to improved tomato flavor

Author

Tieman, Denise, Zhu, Guangtao, Resende, Marcio F. R., Lin, Tao, Nguyen, Cuong, Bies, Dawn, Rambla, Jose Luis, Beltran, Kristty Stephanie Ortiz, Taylor, Mark, Zhang, Bo, Ikeda, Hiroki, Liu, Zhongyuan, Fisher, Josef, Zemach, Itay, Monforte, Antonio, Zamir, Dani, Granell, Antonio, Kirst, Matias, Huang, Sanwen, and Klee, Harry

Published
2017

19. Single-nuclei transcriptome analysis of the shoot apex vascular system differentiation in Populus

Author

Federal Government of the United States, University of Florida, Conde, Daniel [0000-0001-8362-4190], Triozzi, Paolo M. [0000-0003-0192-3336], Pereira, Wendell J. [0000-0003-1019-6281], Schmidt, Henry W. [0000-0001-9465-9540], Balmant, Kelly M. [0000-0001-5189-5121], Knaack, Sara A.[0000-0002-1178-2517], Redondo-López, Arturo [0000-0003-2037-5400], Roy, Sushmita [0000-0002-3694-1705], Dervinis, Christopher [0000-0002-2176-4232], Kirst, Matias [0000-0002-8186-3945], Conde, Daniel, Triozzi, Paolo M., Pereira, Wendell J., Schmidt, Henry W., Balmant, Kelly M., Knaack, Sara A., Redondo-López, Arturo, Roy, Sushmita, Dervinis, Christopher, Kirst, Matias, Federal Government of the United States, University of Florida, Conde, Daniel [0000-0001-8362-4190], Triozzi, Paolo M. [0000-0003-0192-3336], Pereira, Wendell J. [0000-0003-1019-6281], Schmidt, Henry W. [0000-0001-9465-9540], Balmant, Kelly M. [0000-0001-5189-5121], Knaack, Sara A.[0000-0002-1178-2517], Redondo-López, Arturo [0000-0003-2037-5400], Roy, Sushmita [0000-0002-3694-1705], Dervinis, Christopher [0000-0002-2176-4232], Kirst, Matias [0000-0002-8186-3945], Conde, Daniel, Triozzi, Paolo M., Pereira, Wendell J., Schmidt, Henry W., Balmant, Kelly M., Knaack, Sara A., Redondo-López, Arturo, Roy, Sushmita, Dervinis, Christopher, and Kirst, Matias

Abstract

Differentiation of stem cells in the plant apex gives rise to aerial tissues and organs. Presently, we lack a lineage map of the shoot apex cells in woody perennials - a crucial gap considering their role in determining primary and secondary growth. Here, we used single-nuclei RNA-sequencing to determine cell type-specific transcriptomes of the Populus vegetative shoot apex. We identified highly heterogeneous cell populations clustered into seven broad groups represented by 18 transcriptionally distinct cell clusters. Next, we established the developmental trajectories of the epidermis, leaf mesophyll and vascular tissue. Motivated by the high similarities between Populus and Arabidopsis cell population in the vegetative apex, we applied a pipeline for interspecific single-cell gene expression data integration. We contrasted the developmental trajectories of primary phloem and xylem formation in both species, establishing the first comparison of vascular development between a model annual herbaceous and a woody perennial plant species. Our results offer a valuable resource for investigating the principles underlying cell division and differentiation conserved between herbaceous and perennial species while also allowing us to examine species-specific differences at single-cell resolution.

Published
2022

20. Decoding exceptional plant traits by comparative single-cell genomics

Author

Kirst, Matias [0000-0002-8186-3945], Conde, Daniel, Kirst, Matias, Kirst, Matias [0000-0002-8186-3945], Conde, Daniel, and Kirst, Matias

Abstract

Some plants have acquired traits of remarkable adaptive value to thrive under stress. Transferring these traits to crops could improve agriculture, but uncovering the toolkit required has remained largely elusive. We propose that single-cell genomics offers a framework to compare species with contrasting developmental traits and to identify the regulators of evolutionary innovations.

Published
2022

23. Transcriptome Analysis Reveals Putative Genes Involved in the Lipid Metabolism of Chaulmoogra Oil Biosynthesis in Carpotroche brasiliensis (Raddi) A.Gray, a Tropical Tree Species

Author

Vasconcelos, Letícia Maróstica de, primary, Bittencourt, Flora, additional, Vidal, Ramon Oliveira, additional, Silva, Edson Mario de Andrade, additional, Costa, Eduardo Almeida, additional, Micheli, Fabienne, additional, Kirst, Matias, additional, Pirovani, Carlos Priminho, additional, and Gaiotto, Fernanda Amato, additional

Published
2022
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25. Eucalypts

Author

Myburg, Alexander A., Potts, Brad M., Marques, Cristina M., Kirst, Matias, Gion, Jean-Marc, Grattapaglia, Dario, Grima-Pettenatti, Jacqueline, and Kole, Chittaranjan, editor

Published
2007
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28. The western redcedar genome reveals low genetic diversity in a self-compatible conifer

Author

Shalev, Tal J., primary, Gamal El-Dien, Omnia, additional, Yuen, Macaire M.S., additional, Shengqiang, Shu, additional, Jackman, Shaun D., additional, Warren, René L., additional, Coombe, Lauren, additional, van der Merwe, Lise, additional, Stewart, Ada, additional, Boston, Lori B., additional, Plott, Christopher, additional, Jenkins, Jerry, additional, He, Guifen, additional, Yan, Juying, additional, Yan, Mi, additional, Guo, Jie, additional, Breinholt, Jesse W., additional, Neves, Leandro G., additional, Grimwood, Jane, additional, Rieseberg, Loren H., additional, Schmutz, Jeremy, additional, Birol, Inanc, additional, Kirst, Matias, additional, Yanchuk, Alvin D., additional, Ritland, Carol, additional, Russell, John H., additional, and Bohlmann, Joerg, additional

Published
2022
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30. Two shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants

Author

Kates, Heather R., primary, O’Meara, Brian C., additional, LaFrance, Raphael, additional, Stull, Gregory W., additional, James, Euan K., additional, Conde, Daniel, additional, Liu, Shuiyin, additional, Tian, Qin, additional, Yi, Tingshuang, additional, Kirst, Matias, additional, Ané, Jean-Michel, additional, Soltis, Douglas E., additional, Guralnick, Robert P., additional, Soltis, Pamela S., additional, and Folk, Ryan A., additional

Published
2022
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31. Genomic selection reveals hidden relatedness and increased breeding efficiency in western redcedar polycross breeding

Author

Gamal El‐Dien, Omnia, primary, Shalev, Tal J., additional, Yuen, Macaire M. S., additional, Stirling, Rod, additional, Daniels, Lori D., additional, Breinholt, Jesse W., additional, Neves, Leandro G., additional, Kirst, Matias, additional, Van der Merwe, Lise, additional, Yanchuk, Alvin D., additional, Ritland, Carol, additional, Russell, John H., additional, and Bohlmann, Joerg, additional

Published
2022
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34. Aluminum tolerance in maize is associated with higher MATE1 gene copy number

Author

Maron, Lyza G., Guimarães, Claudia T., Kirst, Matias, Albert, Patrice S., Birchler, James A., Bradbury, Peter J., Buckler, Edward S., Coluccio, Alison E., Danilova, Tatiana V., Kudrna, David, Magalhaes, Jurandir V., Piñeros, Miguel A., Schatz, Michael C., Wing, Rod A., and Kochian, Leon V.

Published
2013

35. PLANT SCIENCE: A chemical genetic roadmap to improved tomato flavor

Author

Tieman, Denise, Zhu, Guangtao, Resende, Marcio F. R., Jr., Lin, Tao, Nguyen, Cuong, Bies, Dawn, Rambla, Jose Luis, Beltran, Kristty Stephanie Ortiz, Taylor, Mark, Zhang, Bo, Ikeda, Hiroki, Liu, Zhongyuan, Fisher, Josef, Zemach, Itay, Monforte, Antonio, Zamir, Dani, Granell, Antonio, Kirst, Matias, Huang, Sanwen, and Klee, Harry

Published
2017
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36. Additional file 1 of Temporal change in chromatin accessibility predicts regulators of nodulation in Medicago truncatula

Author

Knaack, Sara A., Conde, Daniel, Chakraborty, Sanhita, Balmant, Kelly M., Irving, Thomas B., Maia, Lucas Gontijo Silva, Triozzi, Paolo M., Dervinis, Christopher, Pereira, Wendell J., Maeda, Junko, Schmidt, Henry W., Ané, Jean-Michel, Kirst, Matias, and Roy, Sushmita

Abstract

Additional file 1: Table S1. Primers used in the RNAi validation study. Figure S1. Analysis workflow. Figure S2. Detailed DE gene statistics summary. Figure S3. Supplementary ESCAROLE clustering results. Figure S4. ATAC-seq data alignment statistics and fragment length distributions. Figure S5. ATAC-seq activity heatmaps and line plots for ±1 kb TSS regions in LCO-treatment data. Figure S6. ATAC-seq activity heatmaps and line plots for ±1 kb TSS regions in the comparable Maher et al. Medicago root sample data. Figure S7. Correlation of aggregated ATAC-seq activity for ±2 kb promoter regions. Figure S8. Supplementary ATAC-seq promoter analysis plots. Figure S9. Supplementary ATAC-seq peak-calling analysis plots. Figure S10. DRMN hyper-parameter tuning summary. Figure S11. DRMN module network edge-weight summary. Figure S12. DRMN module GO enrichment summary. Figure S13. Summary of ESCAROLE and DRMN transitioning gene set statistics and comparison. Figure S14. Summary of MTG-LASSO results and parameter tuning. Figure S15. Supplementary RNAi validation information.

Published
2022
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43. Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen‐fixing clade

Author

Pereira, Wendell J., primary, Knaack, Sara, additional, Chakraborty, Sanhita, additional, Conde, Daniel, additional, Folk, Ryan A., additional, Triozzi, Paolo M., additional, Balmant, Kelly M., additional, Dervinis, Christopher, additional, Schmidt, Henry W., additional, Ané, Jean‐Michel, additional, Roy, Sushmita, additional, and Kirst, Matias, additional

Published
2022
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49. Spatiotemporal cytokinin response imaging and ISOPENTENYLTRANSFERASE 3 function in Medicago nodule development

Author

Triozzi, Paolo M, primary, Irving, Thomas B, additional, Schmidt, Henry W, additional, Keyser, Zachary P, additional, Chakraborty, Sanhita, additional, Balmant, Kelly, additional, Pereira, Wendell J, additional, Dervinis, Christopher, additional, Mysore, Kirankumar S, additional, Wen, Jiangqi, additional, Ané, Jean-Michel, additional, Kirst, Matias, additional, and Conde, Daniel, additional

Published
2021
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50. Temporal change in chromatin accessibility predicts regulators of nodulation in Medicago truncatula

Author

Knaack, Sara A., primary, Conde, Daniel, additional, Chakraborty, Sanhita, additional, Balmant, Kelly M., additional, Irving, Thomas B., additional, Silva Maia, Lucas Gontijo, additional, Triozzi, Paolo M., additional, Dervinis, Christopher, additional, Pereira, Wendell J., additional, Maeda, Junko, additional, Schmidt, Henry W., additional, Ané, Jean-Michel, additional, Kirst, Matias, additional, and Roy, Sushmita, additional

Published
2021
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