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1. Extraordinary preservation of gene collinearity over three hundred million years revealed in homosporous lycophytes

Author

Li, Cheng, Wickell, David, Kuo, Li-Yaung, Chen, Xueqing, Nie, Bao, Liao, Xuezhu, Peng, Dan, Ji, Jiaojiao, Jenkins, Jerry, Williams, Mellissa, Shu, Shengqiang, Plott, Christopher, Barry, Kerrie, Rajasekar, Shanmugam, Grimwood, Jane, Han, Xiaoxu, Sun, Shichao, Hou, Zhuangwei, He, Weijun, Dai, Guanhua, Sun, Cheng, Schmutz, Jeremy, Leebens-Mack, James H, Li, Fay-Wei, and Wang, Li

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Evolutionary Biology, Genetics, Human Genome, Genome, Plant, Genomics, Genome Size, Phylogeny, Evolution, Molecular, homosporous lycophytes, genome evolution, whole genome duplication, gene collinearity, subgenome dominance
Abstract

Homosporous lycophytes (Lycopodiaceae) are a deeply diverged lineage in the plant tree of life, having split from heterosporous lycophytes (Selaginella and Isoetes) ~400 Mya. Compared to the heterosporous lineage, Lycopodiaceae has markedly larger genome sizes and remains the last major plant clade for which no chromosome-level assembly has been available. Here, we present chromosomal genome assemblies for two homosporous lycophyte species, the allotetraploid Huperzia asiatica and the diploid Diphasiastrum complanatum. Remarkably, despite that the two species diverged ~350 Mya, around 30% of the genes are still in syntenic blocks. Furthermore, both genomes had undergone independent whole genome duplications, and the resulting intragenomic syntenies have likewise been preserved relatively well. Such slow genome evolution over deep time is in stark contrast to heterosporous lycophytes and is correlated with a decelerated rate of nucleotide substitution. Together, the genomes of H. asiatica and D. complanatum not only fill a crucial gap in the plant genomic landscape but also highlight a potentially meaningful genomic contrast between homosporous and heterosporous species.

Published
2024

2. Phylogenomics and the rise of the angiosperms

Author

Zuntini, Alexandre R., Carruthers, Tom, Maurin, Olivier, Bailey, Paul C., Leempoel, Kevin, Brewer, Grace E., Epitawalage, Niroshini, Françoso, Elaine, Gallego-Paramo, Berta, McGinnie, Catherine, Negrão, Raquel, Roy, Shyamali R., Simpson, Lalita, Toledo Romero, Eduardo, Barber, Vanessa M. A., Botigué, Laura, Clarkson, James J., Cowan, Robyn S., Dodsworth, Steven, Johnson, Matthew G., Kim, Jan T., Pokorny, Lisa, Wickett, Norman J., Antar, Guilherme M., DeBolt, Lucinda, Gutierrez, Karime, Hendriks, Kasper P., Hoewener, Alina, Hu, Ai-Qun, Joyce, Elizabeth M., Kikuchi, Izai A. B. S., Larridon, Isabel, Larson, Drew A., de Lírio, Elton John, Liu, Jing-Xia, Malakasi, Panagiota, Przelomska, Natalia A. S., Shah, Toral, Viruel, Juan, Allnutt, Theodore R., Ameka, Gabriel K., Andrew, Rose L., Appelhans, Marc S., Arista, Montserrat, Ariza, María Jesús, Arroyo, Juan, Arthan, Watchara, Bachelier, Julien B., Bailey, C. Donovan, Barnes, Helen F., Barrett, Matthew D., Barrett, Russell L., Bayer, Randall J., Bayly, Michael J., Biffin, Ed, Biggs, Nicky, Birch, Joanne L., Bogarín, Diego, Borosova, Renata, Bowles, Alexander M. C., Boyce, Peter C., Bramley, Gemma L. C., Briggs, Marie, Broadhurst, Linda, Brown, Gillian K., Bruhl, Jeremy J., Bruneau, Anne, Buerki, Sven, Burns, Edie, Byrne, Margaret, Cable, Stuart, Calladine, Ainsley, Callmander, Martin W., Cano, Ángela, Cantrill, David J., Cardinal-McTeague, Warren M., Carlsen, Mónica M., Carruthers, Abigail J. A., de Castro Mateo, Alejandra, Chase, Mark W., Chatrou, Lars W., Cheek, Martin, Chen, Shilin, Christenhusz, Maarten J. M., Christin, Pascal-Antoine, Clements, Mark A., Coffey, Skye C., Conran, John G., Cornejo, Xavier, Couvreur, Thomas L. P., Cowie, Ian D., Csiba, Laszlo, Darbyshire, Iain, Davidse, Gerrit, Davies, Nina M. J., Davis, Aaron P., van Dijk, Kor-jent, Downie, Stephen R., Duretto, Marco F., Duvall, Melvin R., Edwards, Sara L., Eggli, Urs, Erkens, Roy H. J., Escudero, Marcial, de la Estrella, Manuel, Fabriani, Federico, Fay, Michael F., Ferreira, Paola de L., Ficinski, Sarah Z., Fowler, Rachael M., Frisby, Sue, Fu, Lin, Fulcher, Tim, Galbany-Casals, Mercè, Gardner, Elliot M., German, Dmitry A., Giaretta, Augusto, Gibernau, Marc, Gillespie, Lynn J., González, Cynthia C., Goyder, David J., Graham, Sean W., Grall, Aurélie, Green, Laura, Gunn, Bee F., Gutiérrez, Diego G., Hackel, Jan, Haevermans, Thomas, Haigh, Anna, Hall, Jocelyn C., Hall, Tony, Harrison, Melissa J., Hatt, Sebastian A., Hidalgo, Oriane, Hodkinson, Trevor R., Holmes, Gareth D., Hopkins, Helen C. F., Jackson, Christopher J., James, Shelley A., Jobson, Richard W., Kadereit, Gudrun, Kahandawala, Imalka M., Kainulainen, Kent, Kato, Masahiro, Kellogg, Elizabeth A., King, Graham J., Klejevskaja, Beata, Klitgaard, Bente B., Klopper, Ronell R., Knapp, Sandra, Koch, Marcus A., Leebens-Mack, James H., Lens, Frederic, Leon, Christine J., Léveillé-Bourret, Étienne, Lewis, Gwilym P., Li, De-Zhu, Li, Lan, Liede-Schumann, Sigrid, Livshultz, Tatyana, Lorence, David, Lu, Meng, Lu-Irving, Patricia, Luber, Jaquelini, Lucas, Eve J., Luján, Manuel, Lum, Mabel, Macfarlane, Terry D., Magdalena, Carlos, Mansano, Vidal F., Masters, Lizo E., Mayo, Simon J., McColl, Kristina, McDonnell, Angela J., McDougall, Andrew E., McLay, Todd G. B., McPherson, Hannah, Meneses, Rosa I., Merckx, Vincent S. F. T., Michelangeli, Fabián A., Mitchell, John D., Monro, Alexandre K., Moore, Michael J., Mueller, Taryn L., Mummenhoff, Klaus, Munzinger, Jérôme, Muriel, Priscilla, Murphy, Daniel J., Nargar, Katharina, Nauheimer, Lars, Nge, Francis J., Nyffeler, Reto, Orejuela, Andrés, Ortiz, Edgardo M., Palazzesi, Luis, Peixoto, Ariane Luna, Pell, Susan K., Pellicer, Jaume, Penneys, Darin S., Perez-Escobar, Oscar A., Persson, Claes, Pignal, Marc, Pillon, Yohan, Pirani, José R., Plunkett, Gregory M., Powell, Robyn F., Prance, Ghillean T., Puglisi, Carmen, Qin, Ming, Rabeler, Richard K., Rees, Paul E. J., Renner, Matthew, Roalson, Eric H., Rodda, Michele, Rogers, Zachary S., Rokni, Saba, Rutishauser, Rolf, de Salas, Miguel F., Schaefer, Hanno, Schley, Rowan J., Schmidt-Lebuhn, Alexander, Shapcott, Alison, Al-Shehbaz, Ihsan, Shepherd, Kelly A., Simmons, Mark P., Simões, André O., Simões, Ana Rita G., Siros, Michelle, Smidt, Eric C., Smith, James F., Snow, Neil, Soltis, Douglas E., Soltis, Pamela S., Soreng, Robert J., Sothers, Cynthia A., Starr, Julian R., Stevens, Peter F., Straub, Shannon C. K., Struwe, Lena, Taylor, Jennifer M., Telford, Ian R. H., Thornhill, Andrew H., Tooth, Ifeanna, Trias-Blasi, Anna, Udovicic, Frank, Utteridge, Timothy M. A., Del Valle, Jose C., Verboom, G. Anthony, Vonow, Helen P., Vorontsova, Maria S., de Vos, Jurriaan M., Al-Wattar, Noor, Waycott, Michelle, Welker, Cassiano A. D., White, Adam J., Wieringa, Jan J., Williamson, Luis T., Wilson, Trevor C., Wong, Sin Yeng, Woods, Lisa A., Woods, Roseina, Worboys, Stuart, Xanthos, Martin, Yang, Ya, Zhang, Yu-Xiao, Zhou, Meng-Yuan, Zmarzty, Sue, Zuloaga, Fernando O., Antonelli, Alexandre, Bellot, Sidonie, Crayn, Darren M., Grace, Olwen M., Kersey, Paul J., Leitch, Ilia J., Sauquet, Hervé, Smith, Stephen A., Eiserhardt, Wolf L., Forest, Félix, and Baker, William J.

Published
2024
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3. Dynamic genome evolution in a model fern

Author

Marchant, D Blaine, Chen, Guang, Cai, Shengguan, Chen, Fei, Schafran, Peter, Jenkins, Jerry, Shu, Shengqiang, Plott, Chris, Webber, Jenell, Lovell, John T, He, Guifen, Sandor, Laura, Williams, Melissa, Rajasekar, Shanmugam, Healey, Adam, Barry, Kerrie, Zhang, Yinwen, Sessa, Emily, Dhakal, Rijan R, Wolf, Paul G, Harkess, Alex, Li, Fay-Wei, Rössner, Clemens, Becker, Annette, Gramzow, Lydia, Xue, Dawei, Wu, Yuhuan, Tong, Tao, Wang, Yuanyuan, Dai, Fei, Hua, Shuijin, Wang, Hua, Xu, Shengchun, Xu, Fei, Duan, Honglang, Theißen, Günter, McKain, Michael R, Li, Zheng, McKibben, Michael TW, Barker, Michael S, Schmitz, Robert J, Stevenson, Dennis W, Zumajo-Cardona, Cecilia, Ambrose, Barbara A, Leebens-Mack, James H, Grimwood, Jane, Schmutz, Jeremy, Soltis, Pamela S, Soltis, Douglas E, and Chen, Zhong-Hua

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, DNA Transposable Elements, Evolution, Molecular, Ferns, Genome, Plant, Plants, Plant Biology, Crop and Pasture Production, Ecology, Plant biology
Abstract

The large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects of fern biology and land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly and associated methylome, transcriptome and metabolome analyses for the model fern species Ceratopteris richardii. The assembly reveals a history of remarkably dynamic genome evolution including rapid changes in genome content and structure following the most recent whole-genome duplication approximately 60 million years ago. These changes include massive gene loss, rampant tandem duplications and multiple horizontal gene transfers from bacteria, contributing to the diversification of defence-related gene families. The insertion of transposable elements into introns has led to the large size of the Ceratopteris genome and to exceptionally long genes relative to other plants. Gene family analyses indicate that genes directing seed development were co-opted from those controlling the development of fern sporangia, providing insights into seed plant evolution. Our findings and annotated genome assembly extend the utility of Ceratopteris as a model for investigating and teaching plant biology.

Published
2022

4. The genomic basis of the plant island syndrome in Darwin’s giant daisies

Author

Cerca, José, Petersen, Bent, Lazaro-Guevara, José Miguel, Rivera-Colón, Angel, Birkeland, Siri, Vizueta, Joel, Li, Siyu, Li, Qionghou, Loureiro, João, Kosawang, Chatchai, Díaz, Patricia Jaramillo, Rivas-Torres, Gonzalo, Fernández-Mazuecos, Mario, Vargas, Pablo, McCauley, Ross A, Petersen, Gitte, Santos-Bay, Luisa, Wales, Nathan, Catchen, Julian M, Machado, Daniel, Nowak, Michael D, Suh, Alexander, Sinha, Neelima R, Nielsen, Lene R, Seberg, Ole, Gilbert, M Thomas P, Leebens-Mack, James H, Rieseberg, Loren H, and Martin, Michael D

Subjects
Biological Sciences, Ecology, Evolutionary Biology, Genetics, Human Genome, Biotechnology, Biological Evolution, DNA Transposable Elements, Genomics, Synteny
Abstract

The repeated, rapid and often pronounced patterns of evolutionary divergence observed in insular plants, or the 'plant island syndrome', include changes in leaf phenotypes, growth, as well as the acquisition of a perennial lifestyle. Here, we sequence and describe the genome of the critically endangered, Galápagos-endemic species Scalesia atractyloides Arnot., obtaining a chromosome-resolved, 3.2-Gbp assembly containing 43,093 candidate gene models. Using a combination of fossil transposable elements, k-mer spectra analyses and orthologue assignment, we identify the two ancestral genomes, and date their divergence and the polyploidization event, concluding that the ancestor of all extant Scalesia species was an allotetraploid. There are a comparable number of genes and transposable elements across the two subgenomes, and while their synteny has been mostly conserved, we find multiple inversions that may have facilitated adaptation. We identify clear signatures of selection across genes associated with vascular development, growth, adaptation to salinity and flowering time, thus finding compelling evidence for a genomic basis of the island syndrome in one of Darwin's giant daisies.

Published
2022

5. One thousand plant transcriptomes and the phylogenomics of green plants

Author

Leebens-Mack, James H, Barker, Michael S, Carpenter, Eric J, Deyholos, Michael K, Gitzendanner, Matthew A, Graham, Sean W, Grosse, Ivo, Li, Zheng, Melkonian, Michael, Mirarab, Siavash, Porsch, Martin, Quint, Marcel, Rensing, Stefan A, Soltis, Douglas E, Soltis, Pamela S, Stevenson, Dennis W, Ullrich, Kristian K, Wickett, Norman J, DeGironimo, Lisa, Edger, Patrick P, Jordon-Thaden, Ingrid E, Joya, Steve, Liu, Tao, Melkonian, Barbara, Miles, Nicholas W, Pokorny, Lisa, Quigley, Charlotte, Thomas, Philip, Villarreal, Juan Carlos, Augustin, Megan M, Barrett, Matthew D, Baucom, Regina S, Beerling, David J, Benstein, Ruben Maximilian, Biffin, Ed, Brockington, Samuel F, Burge, Dylan O, Burris, Jason N, Burris, Kellie P, Burtet-Sarramegna, Valerie, Caicedo, Ana L, Cannon, Steven B, Cebi, Zehra, Chang, Ying, Chater, Caspar, Cheeseman, John M, Chen, Tao, Clarke, Neil D, Clayton, Harmony, Covshoff, Sarah, Crandall-Stotler, Barbara J, Cross, Hugh, dePamphilis, Claude W, Der, Joshua P, Determann, Ron, Dickson, Rowan C, Di Stilio, Veronica S, Ellis, Shona, Fast, Eva, Feja, Nicole, Field, Katie J, Filatov, Dmitry A, Finnegan, Patrick M, Floyd, Sandra K, Fogliani, Bruno, Garcia, Nicolas, Gateble, Gildas, Godden, Grant T, Goh, Falicia Qi Yun, Greiner, Stephan, Harkess, Alex, Heaney, James Mike, Helliwell, Katherine E, Heyduk, Karolina, Hibberd, Julian M, Hodel, Richard GJ, Hollingsworth, Peter M, Johnson, Marc TJ, Jost, Ricarda, Joyce, Blake, Kapralov, Maxim V, Kazamia, Elena, Kellogg, Elizabeth A, Koch, Marcus A, Von Konrat, Matt, Konyves, Kalman, Kutchan, Toni M, Lam, Vivienne, Larsson, Anders, Leitch, Andrew R, Lentz, Roswitha, Li, Fay-Wei, Lowe, Andrew J, Ludwig, Martha, Manos, Paul S, Mavrodiev, Evgeny, McCormick, Melissa K, McKain, Michael, McLellan, Tracy, and McNeal, Joel R

Subjects
Biotechnology, Genetics, Human Genome, Biological Evolution, Databases, Genetic, Evolution, Molecular, Genome, Plant, Phylogeny, Transcriptome, Viridiplantae, One Thousand Plant Transcriptomes Initiative, General Science & Technology
Abstract

Green plants (Viridiplantae) include around 450,000-500,000 species1,2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.

Published
2019

6. RACCROCHE: Ancestral Flowering Plant Chromosomes and Gene Orders Based on Generalized Adjacencies and Chromosomal Gene Co-occurrences

Author

Xu, Qiaoji, Jin, Lingling, Zheng, Chunfang, Leebens Mack, James H., Sankoff, David, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Jha, Sumit Kumar, editor, Măndoiu, Ion, editor, Rajasekaran, Sanguthevar, editor, Skums, Pavel, editor, and Zelikovsky, Alex, editor

Published
2021
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7. The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism.

Author

Yang, Xiaohan, Hu, Rongbin, Yin, Hengfu, Jenkins, Jerry, Shu, Shengqiang, Tang, Haibao, Liu, Degao, Weighill, Deborah A, Cheol Yim, Won, Ha, Jungmin, Heyduk, Karolina, Goodstein, David M, Guo, Hao-Bo, Moseley, Robert C, Fitzek, Elisabeth, Jawdy, Sara, Zhang, Zhihao, Xie, Meng, Hartwell, James, Grimwood, Jane, Abraham, Paul E, Mewalal, Ritesh, Beltrán, Juan D, Boxall, Susanna F, Dever, Louisa V, Palla, Kaitlin J, Albion, Rebecca, Garcia, Travis, Mayer, Jesse A, Don Lim, Sung, Man Wai, Ching, Peluso, Paul, Van Buren, Robert, De Paoli, Henrique Cestari, Borland, Anne M, Guo, Hong, Chen, Jin-Gui, Muchero, Wellington, Yin, Yanbin, Jacobson, Daniel A, Tschaplinski, Timothy J, Hettich, Robert L, Ming, Ray, Winter, Klaus, Leebens-Mack, James H, Smith, J Andrew C, Cushman, John C, Schmutz, Jeremy, and Tuskan, Gerald A

Subjects
Plants, Kalanchoe, Acids, Carbon Dioxide, Water, Evolution, Molecular, Phylogeny, Photosynthesis, Gene Duplication, Genome, Plant, Evolution, Molecular, Genome, Plant, Genetics, Human Genome, Biotechnology
Abstract

Crassulacean acid metabolism (CAM) is a water-use efficient adaptation of photosynthesis that has evolved independently many times in diverse lineages of flowering plants. We hypothesize that convergent evolution of protein sequence and temporal gene expression underpins the independent emergences of CAM from C3 photosynthesis. To test this hypothesis, we generate a de novo genome assembly and genome-wide transcript expression data for Kalanchoë fedtschenkoi, an obligate CAM species within the core eudicots with a relatively small genome (~260 Mb). Our comparative analyses identify signatures of convergence in protein sequence and re-scheduling of diel transcript expression of genes involved in nocturnal CO2 fixation, stomatal movement, heat tolerance, circadian clock, and carbohydrate metabolism in K. fedtschenkoi and other CAM species in comparison with non-CAM species. These findings provide new insights into molecular convergence and building blocks of CAM and will facilitate CAM-into-C3 photosynthesis engineering to enhance water-use efficiency in crops.

Published
2017

9. Diversity of ABC transporter genes across the plant kingdom and their potential utility in biotechnology

Author

Lane, Thomas S, Rempe, Caroline S, Davitt, Jack, Staton, Margaret E, Peng, Yanhui, Soltis, Douglas Edward, Melkonian, Michael, Deyholos, Michael, Leebens-Mack, James H, Chase, Mark, Rothfels, Carl J, Stevenson, Dennis, Graham, Sean W, Yu, Jun, Liu, Tao, Pires, J Chris, Edger, Patrick P, Zhang, Yong, Xie, Yinlong, Zhu, Ying, Carpenter, Eric, Wong, Gane Ka-Shu, and Stewart, C Neal

Subjects
Genetics, Biotechnology, ATP-Binding Cassette Transporters, Chromosome Mapping, Data Mining, Databases, Protein, Genes, Plant, Genetic Variation, Genome, Plant, Plant Proteins, Plants, Species Specificity, ABC transporter, Transcriptomics, Computational biology, Taxonomic diversity, Biological Sciences, Technology
Abstract

BackgroundThe ATP-binding cassette (ABC) transporter gene superfamily is ubiquitous among extant organisms and prominently represented in plants. ABC transporters act to transport compounds across cellular membranes and are involved in a diverse range of biological processes. Thus, the applicability to biotechnology is vast, including cancer resistance in humans, drug resistance among vertebrates, and herbicide and other xenobiotic resistance in plants. In addition, plants appear to harbor the highest diversity of ABC transporter genes compared with any other group of organisms. This study applied transcriptome analysis to survey the kingdom-wide ABC transporter diversity in plants and suggest biotechnology applications of this diversity.ResultsWe utilized sequence similarity-based informatics techniques to infer the identity of ABC transporter gene candidates from 1295 phylogenetically-diverse plant transcriptomes. A total of 97,149 putative (approximately 25 % were full-length) ABC transporter gene members were identified; each RNA-Seq library (plant sample) had 88 ± 30 gene members. As expected, simpler organisms, such as algae, had fewer unique members than vascular land plants. Differences were also noted in the richness of certain ABC transporter subfamilies. Land plants had more unique ABCB, ABCC, and ABCG transporter gene members on average (p

Published
2016

10. Comparative transcriptomics of Venus flytrap (Dionaea muscipula) across stages of prey capture and digestion.

Author

Rentsch, Jeremy D., Blanco, Summer Rose, and Leebens-Mack, James H.

Subjects
BIOLOGICAL evolution, GENOMICS, TRANSCRIPTOMES, NUTRIENT uptake, CARNIVOROUS plants
Abstract

The Venus flytrap, Dionaea muscipula, is perhaps the world's best-known botanical carnivore. The act of prey capture and digestion along with its rapidly closing, charismatic traps make this species a compelling model for studying the evolution and fundamental biology of carnivorous plants. There is a growing body of research on the genome, transcriptome, and digestome of Dionaea muscipula, but surprisingly limited information on changes in trap transcript abundance over time since feeding. Here we present the results of a comparative transcriptomics project exploring the transcriptomic changes across seven timepoints in a 72-hour time series of prey digestion and three timepoints directly comparing triggered traps with and without prey items. We document a dynamic response to prey capture including changes in abundance of transcripts with Gene Ontology (GO) annotations related to digestion and nutrient uptake. Comparisons of traps with and without prey documented 174 significantly differentially expressed genes at 1 hour after triggering and 151 genes with significantly different abundances at 24 hours. Approximately 50% of annotated protein-coding genes in Venus flytrap genome exhibit change (10041 of 21135) in transcript abundance following prey capture. Whereas peak abundance for most of these genes was observed within 3 hours, an expression cluster of 3009 genes exhibited continuously increasing abundance over the 72-hour sampling period, and transcript for these genes with GO annotation terms including both catabolism and nutrient transport may continue to accumulate beyond 72 hours. [ABSTRACT FROM AUTHOR]

Published
2024
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12. Evolution of chloroplast retrograde signaling facilitates green plant adaptation to land

Author

Zhao, Chenchen, Wang, Yuanyuan, Chan, Kai Xun, Marchant, D. Blaine, Franks, Peter J., Randall, David, Tee, Estee E., Chen, Guang, Ramesh, Sunita, Phua, Su Yin, Zhang, Ben, Hills, Adrian, Dai, Fei, Xue, Dawei, Gilliham, Matthew, Tyerman, Steve, Nevo, Eviatar, Wu, Feibo, Zhang, Guoping, Wong, Gane K.-S., Leebens-Mack, James H., Melkonian, Michael, Blatt, Michael R., Soltis, Pamela S., Soltis, Douglas E., Pogson, Barry J., and Chen, Zhong-Hua

Published
2019

19. 150 Years of Coevolution Research: Evolution and Ecology of Yucca Moths (Prodoxidae) and Their Hosts.

Author

Smith, Christopher Irwin and Leebens-Mack, James H.

Abstract

Yucca moths (Tegeticula and Parategeticula) are specialized pollinators of yucca plants, possessing unique, tentacle-like mouthparts used to actively collect pollen and deposit it onto the flowers of their hosts. The moths' larvae feed on the developing seeds and fruit tissue. First described in 1873, the yucca–yucca moth pollination system is now considered the archetypical example of a coevolved intimate mutualism. Research conducted over the past three decades has transformed our understanding of yucca moth diversity and host plant interactions. We summarize the current understanding of the diversity, ecology, and evolution of this group, review evidence for coevolution of the insects and their hosts, and describe how the nature of the interaction varies across evolutionary time and ecological contexts. Finally, we identify unresolved questions and areas for future research. [ABSTRACT FROM AUTHOR]

Published
2024
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24. Comprehending Cornales: phylogenetic reconstruction of the order using the Angiosperms353 probe set

Author

University of Georgia Research Foundation, Thomas, Shawn K [0000-0002-6198-8847], Du, Zhi-Yuan [0000-0003-4016-3878], Pokorny, Lisa [0000-0002-2478-8555], Qiu-Yun(Jenny) Xiang [0000-0002-9016-0678], Leebens-Mack, James H [0000-0003-4811-2231], Thomas, Shawn K, Liu, Xiang, Du, Zhi-Yuan, Dong, Yibo, Cummings, Amanda, Pokorny, Lisa, Xiang, Qui-Yun Jenny, Leebens-Mack, James H, University of Georgia Research Foundation, Thomas, Shawn K [0000-0002-6198-8847], Du, Zhi-Yuan [0000-0003-4016-3878], Pokorny, Lisa [0000-0002-2478-8555], Qiu-Yun(Jenny) Xiang [0000-0002-9016-0678], Leebens-Mack, James H [0000-0003-4811-2231], Thomas, Shawn K, Liu, Xiang, Du, Zhi-Yuan, Dong, Yibo, Cummings, Amanda, Pokorny, Lisa, Xiang, Qui-Yun Jenny, and Leebens-Mack, James H

Abstract

Cornales is an order of flowering plants containing ecologically and horticulturally important families, including Cornaceae (dogwoods) and Hydrangeaceae (hydrangeas), among others. While many relationships in Cornales are strongly supported by previous studies, some uncertainty remains with regards to the placement of Hydrostachyaceae and to relationships among families in Cornales and within Cornaceae. Here we analyzed hundreds of nuclear loci to test published phylogenetic hypotheses and estimated a robust species tree for Cornales.

Published
2021

26. The Earth BioGenome Project 2020: Starting the clock

Author

Lewin, Harris A., Richards, Stephen, Aiden, Erez, Allende, Miguel L., Archibald, John M., Bálint, Miklós M., Barker, Katharine M., Baumgartnerk, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark, Cai, Jing, Caperello, Nicolette, Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu-Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., Di Palma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott, Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Marshall Graves, Jennifer A., Greely, Henry, Grigoriev, Igor, Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J.M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin-Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K.N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sofhie, Mazet, Jonna, Mazzoni, Camila J., Myers, Eugene W., O'Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene, Roquet, Cristina, Ryder, Oliver, Sabir, Jamal S.M., Shaffer, Howard Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela, Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne, Zhang, Guojie, Lewin, Harris A., Richards, Stephen, Aiden, Erez, Allende, Miguel L., Archibald, John M., Bálint, Miklós M., Barker, Katharine M., Baumgartnerk, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark, Cai, Jing, Caperello, Nicolette, Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu-Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., Di Palma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott, Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Marshall Graves, Jennifer A., Greely, Henry, Grigoriev, Igor, Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J.M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin-Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K.N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sofhie, Mazet, Jonna, Mazzoni, Camila J., Myers, Eugene W., O'Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene, Roquet, Cristina, Ryder, Oliver, Sabir, Jamal S.M., Shaffer, Howard Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela, Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne, and Zhang, Guojie

Published
2022

27. The Earth BioGenome Project 2020:Starting the clock

Author

Lewin, Harris A., Richards, Stephen, Aiden, Erez Lieberman, Allende, Miguel L., Archibald, John M., Bálint, Miklós, Barker, Katharine B., Baumgartner, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark L., Cai, Jing, Caperello, Nicolette D., Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., DiPalma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott V., Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Graves, Jennifer Marshall, Greely, Henry T., Grigoriev, Igor V., Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J. M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K. N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sophie, Mazet, Jonna A. K., Mazzoni, Camila J., Myers, Eugene W., O’Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene E., Roquet, Cristina, Ryder, Oliver A., Sabir, Jamal S. M., Shaffer, H. Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela S., Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne D., Zhang, Guojie, Lewin, Harris A., Richards, Stephen, Aiden, Erez Lieberman, Allende, Miguel L., Archibald, John M., Bálint, Miklós, Barker, Katharine B., Baumgartner, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark L., Cai, Jing, Caperello, Nicolette D., Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., DiPalma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott V., Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Graves, Jennifer Marshall, Greely, Henry T., Grigoriev, Igor V., Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J. M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K. N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sophie, Mazet, Jonna A. K., Mazzoni, Camila J., Myers, Eugene W., O’Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene E., Roquet, Cristina, Ryder, Oliver A., Sabir, Jamal S. M., Shaffer, H. Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela S., Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne D., and Zhang, Guojie

Published
2022

28. ASSEMBLING THE TREE OF THE MONOCOTYLEDONS: PLASTOME SEQUENCE PHYLOGENY AND EVOLUTION OF POALES

Author

Givnish, Thomas J., Armes, Mercedes, McNeal, Joel R., McKain, Michael R., Steele, P. Roxanne, dePamphilis, Claude W., Graham, Sean W., Pires, J. Chris, Stevenson, Dennis W., Zomlefer, Wendy B., Briggs, Barbara G., Duvall, Melvin R., Moore, Michael J., Heaney, J. Michael, Soltis, Douglas E., Soltis, Pamela S., Thiele, Kevin, and Leebens-Mack, James H.

Published
2010
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29. The genomic basis of the plant island syndrome in Darwin’s giant daisies

Author

Cerca, José, primary, Petersen, Bent, additional, Lazaro Guevara, José Miguel, additional, Rivera-Colón, Angel, additional, Birkeland, Siri, additional, Vizueta, Joel, additional, Li, Siyu, additional, Loureiro, João, additional, Kosawang, Chatchai, additional, Díaz, Patricia Jaramillo, additional, Rivas-Torres, Gonzalo, additional, Fernández-Mazuecos, Mario, additional, Vargas, Pablo, additional, McCauley, Ross, additional, Petersen, Gitte, additional, Santos-Bay, Luisa, additional, Wales, Nathan, additional, Catchen, Julian, additional, Machado, Daniel, additional, Nowak, Michael D., additional, Suh, Alexander, additional, Sinha, Neelima, additional, Nielsen, Lene R., additional, Seberg, Ole, additional, Gilbert, M. Thomas P., additional, Leebens-Mack, James H., additional, Rieseberg, Loren, additional, and Martin, Michael D., additional

Published
2022
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31. The Earth BioGenome Project 2020: Starting the clock

Author

Lewin, Harris A., primary, Richards, Stephen, additional, Lieberman Aiden, Erez, additional, Allende, Miguel L., additional, Archibald, John M., additional, Bálint, Miklós, additional, Barker, Katharine B., additional, Baumgartner, Bridget, additional, Belov, Katherine, additional, Bertorelle, Giorgio, additional, Blaxter, Mark L., additional, Cai, Jing, additional, Caperello, Nicolette D., additional, Carlson, Keith, additional, Castilla-Rubio, Juan Carlos, additional, Chaw, Shu-Miaw, additional, Chen, Lei, additional, Childers, Anna K., additional, Coddington, Jonathan A., additional, Conde, Dalia A., additional, Corominas, Montserrat, additional, Crandall, Keith A., additional, Crawford, Andrew J., additional, DiPalma, Federica, additional, Durbin, Richard, additional, Ebenezer, ThankGod E., additional, Edwards, Scott V., additional, Fedrigo, Olivier, additional, Flicek, Paul, additional, Formenti, Giulio, additional, Gibbs, Richard A., additional, Gilbert, M. Thomas P., additional, Goldstein, Melissa M., additional, Graves, Jennifer Marshall, additional, Greely, Henry T., additional, Grigoriev, Igor V., additional, Hackett, Kevin J., additional, Hall, Neil, additional, Haussler, David, additional, Helgen, Kristofer M., additional, Hogg, Carolyn J., additional, Isobe, Sachiko, additional, Jakobsen, Kjetill Sigurd, additional, Janke, Axel, additional, Jarvis, Erich D., additional, Johnson, Warren E., additional, Jones, Steven J. M., additional, Karlsson, Elinor K., additional, Kersey, Paul J., additional, Kim, Jin-Hyoung, additional, Kress, W. John, additional, Kuraku, Shigehiro, additional, Lawniczak, Mara K. N., additional, Leebens-Mack, James H., additional, Li, Xueyan, additional, Lindblad-Toh, Kerstin, additional, Liu, Xin, additional, Lopez, Jose V., additional, Marques-Bonet, Tomas, additional, Mazard, Sophie, additional, Mazet, Jonna A. K., additional, Mazzoni, Camila J., additional, Myers, Eugene W., additional, O’Neill, Rachel J., additional, Paez, Sadye, additional, Park, Hyun, additional, Robinson, Gene E., additional, Roquet, Cristina, additional, Ryder, Oliver A., additional, Sabir, Jamal S. M., additional, Shaffer, H. Bradley, additional, Shank, Timothy M., additional, Sherkow, Jacob S., additional, Soltis, Pamela S., additional, Tang, Boping, additional, Tedersoo, Leho, additional, Uliano-Silva, Marcela, additional, Wang, Kun, additional, Wei, Xiaofeng, additional, Wetzer, Regina, additional, Wilson, Julia L., additional, Xu, Xun, additional, Yang, Huanming, additional, Yoder, Anne D., additional, and Zhang, Guojie, additional

Published
2022
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41. Focus on the biology of plant genomes

Author

Eckardt, Nancy A, primary, Birchler, James A, additional, Brady, Siobhán M, additional, Buell, C Robin, additional, Leebens-Mack, James H, additional, and Meyers, Blake C, additional

Published
2021
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42. Evolution of rapid blue‐light response linked to explosive diversification of ferns in angiosperm forests

Author

Cai, Shengguan, primary, Huang, Yuqing, additional, Chen, Fei, additional, Zhang, Xin, additional, Sessa, Emily, additional, Zhao, Chenchen, additional, Marchant, D. Blaine, additional, Xue, Dawei, additional, Chen, Guang, additional, Dai, Fei, additional, Leebens‐Mack, James H., additional, Zhang, Guoping, additional, Shabala, Sergey, additional, Christie, John M., additional, Blatt, Michael R., additional, Nevo, Eviatar, additional, Soltis, Pamela S., additional, Soltis, Douglas E., additional, Franks, Peter J., additional, Wu, Feibo, additional, and Chen, Zhong‐Hua, additional

Published
2021
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43. The evolution of the SEPALLATA subfamily of MADS-box genes: a preangiosperm origin with multiple duplications throughout angiosperm history

Author

Zahn, Laura M., Kong, Hongzhi, Leebens-Mack, James H., Kim, Sangtae, Soltis, Pamela S., Landherr, Lena L., Soltis, Douglas E., dePamphilis, Claude W., and Ma, Hong

Subjects
Plant genetics -- Research, Angiosperms -- Research, Angiosperms -- Genetic aspects, Biological sciences
Abstract

Members of the SEPALLATA (SEP) MADS-box subfamily are required for specifying the 'floral state' by contributing to floral organ and meristem identity. SEP genes have not been detected in gymnosperms and seem to have originated since the lineage leading to extant angiosperms diverged from extant gymnosperms. Therefore, both functional and evolutionary studies suggest that SEP genes may have been critical for the origin of the flower. To gain insights into the evolution of SEP genes, we isolated nine genes from plants that occupy phylogenetically important positions. Phylogenetic analyses of SEP sequences show that several gene duplications occurred during the evolution of this subfamily, providing potential opportunities for functional divergence. The first duplication occurred prior to the origin of the extant angiosperms, resulting in the AGL2/3/4 and AGL9 clades. Subsequent duplications occurred within these clades in the eudicots and monocots. The timing of the first SEP duplication approximately coincides with duplications in the DEFICIENS/GLOBOSA and AGAMOUS MADS-box subfamilies, which may have resulted from either a proposed genome-wide duplication in the ancestor of extant angiosperms or multiple independent duplication events. Regardless of the mechanism of gene duplication, these pairs of duplicate transcription factors provided new possibilities of genetic interactions that may have been important in the origin of the flower.

Published
2005

47. One thousand plant transcriptomes and the phylogenomics of green plants

Author

Leebens-Mack, James H., Barker, Michael S., Carpenter, Eric J., Deyholos, Michael K., Gitzendanner, Matthew A., Graham, Sean W., Grosse, Ivo, Li, Zheng, Melkonian, Michael, Mirarab, Siavash, Porsch, Martin, Quint, Marcel, Rensing, Stefan A., Soltis, Douglas E., Soltis, Pamela S., Stevenson, Dennis W., Ullrich, Kristian K., Wickett, Norman J., DeGironimo, Lisa, Edger, Patrick P., Jordon-Thaden, Ingrid E., Joya, Steve, Liu, Tao, Melkonian, Barbara, Miles, Nicholas W., Pokorny, Lisa, Quigley, Charlotte, Thomas, Philip, Villarreal, Juan Carlos, Augustin, Megan M., Barrett, Matthew D., Baucom, Regina S., Beerling, David J., Benstein, Ruben Maximilian, Biffin, Ed, Brockington, Samuel F., Burge, Dylan O., Burris, Jason N., Burris, Kellie P., Burtet-Sarramegna, Valerie, Caicedo, Ana L., Cannon, Steven B., Cebi, Zehra, Chang, Ying, Chater, Caspar, Cheeseman, John M., Chen, Tao, Clarke, Neil D., Clayton, Harmony, Covshoff, Sarah, Crandall-Stotler, Barbara J., Cross, Hugh, dePamphilis, Claude W., Der, Joshua P., Determann, Ron, Dickson, Rowan C., Di Stilio, Veronica S., Ellis, Shona, Fast, Eva, Feja, Nicole, Field, Katie J., Filatov, Dmitry A., Finnegan, Patrick M., Floyd, Sandra K., Fogliani, Bruno, Garcia, Nicolas, Gateble, Gildas, Godden, Grant T., Goh, Falicia (Qi Yun), Greiner, Stephan, Harkess, Alex, Heaney, James Mike, Helliwell, Katherine E., Heyduk, Karolina, Hibberd, Julian M., Hodel, Richard G. J., Hollingsworth, Peter M., Johnson, Marc T. J., Jost, Ricarda, Joyce, Blake, Kapralov, Maxim V., Kazamia, Elena, Kellogg, Elizabeth A., Koch, Marcus A., Von Konrat, Matt, Konyves, Kalman, Kutchan, Toni M., Lam, Vivienne, Larsson, Anders, Leitch, Andrew R., Lentz, Roswitha, Li, Fay-Wei, Lowe, Andrew J., Ludwig, Martha, Manos, Paul S., Mavrodiev, Evgeny, McCormick, Melissa K., McKain, Michael, McLellan, Tracy, McNeal, Joel R., Miller, Richard E., Nelson, Matthew N., Peng, Yanhui, Ralph, Paula, Real, Daniel, Riggins, Chance W., Ruhsam, Markus, Sage, Rowan F., Sakai, Ann K., Scascitella, Moira, Schilling, Edward E., Schlosser, Eva-Marie, Sederoff, Heike, Servick, Stein, Sessa, Emily B., Shaw, A. Jonathan, Shaw, Shane W., Sigel, Erin M., Skema, Cynthia, Smith, Alison G., Smithson, Ann, Stewart, C. Neal, Jr., Stinchcombe, John R., Szovenyi, Peter, Tate, Jennifer A., Tiebel, Helga, Trapnell, Dorset, Villegente, Matthieu, Wang, Chun-Neng, Weller, Stephen G., Wenzel, Michael, Weststrand, Stina, Westwood, James H., Whigham, Dennis F., Wu, Shuangxiu, Wulff, Adrien S., Yang, Yu, Zhu, Dan, Zhuang, Cuili, Zuidof, Jennifer, Chase, Mark W., Pires, J. Chris, Rothfels, Carl J., Yu, Jun, Chen, Cui, Chen, Li, Cheng, Shifeng, Li, Juanjuan, Li, Ran, Li, Xia, Lu, Haorong, Ou, Yanxiang, Sun, Xiao, Tan, Xuemei, Tang, Jingbo, Tian, Zhijian, Wang, Feng, Wang, Jun, Wei, Xiaofeng, Xu, Xun, Yan, Zhixiang, Yang, Fan, Zhong, Xiaoni, Zhou, Feiyu, Zhu, Ying, Zhang, Yong, Ayyampalayam, Saravanaraj, Barkman, Todd J., Nguyen, Nam-Phuong, Matasci, Naim, Nelson, David R., Sayyari, Erfan, Wafula, Eric K., Walls, Ramona L., Warnow, Tandy, An, Hong, Arrigo, Nils, Baniaga, Anthony E., Galuska, Sally, Jorgensen, Stacy A., Kidder, Thomas I., Kong, Hanghui, Lu-Irving, Patricia, Marx, Hannah E., Qi, Xinshuai, Reardon, Chris R., Sutherland, Brittany L., Tiley, George P., Welles, Shana R., Yu, Rongpei, Zhan, Shing, Gramzow, Lydia, Theissen, Gunter, Wong, Gane Ka-Shu, Leebens-Mack, James H., Barker, Michael S., Carpenter, Eric J., Deyholos, Michael K., Gitzendanner, Matthew A., Graham, Sean W., Grosse, Ivo, Li, Zheng, Melkonian, Michael, Mirarab, Siavash, Porsch, Martin, Quint, Marcel, Rensing, Stefan A., Soltis, Douglas E., Soltis, Pamela S., Stevenson, Dennis W., Ullrich, Kristian K., Wickett, Norman J., DeGironimo, Lisa, Edger, Patrick P., Jordon-Thaden, Ingrid E., Joya, Steve, Liu, Tao, Melkonian, Barbara, Miles, Nicholas W., Pokorny, Lisa, Quigley, Charlotte, Thomas, Philip, Villarreal, Juan Carlos, Augustin, Megan M., Barrett, Matthew D., Baucom, Regina S., Beerling, David J., Benstein, Ruben Maximilian, Biffin, Ed, Brockington, Samuel F., Burge, Dylan O., Burris, Jason N., Burris, Kellie P., Burtet-Sarramegna, Valerie, Caicedo, Ana L., Cannon, Steven B., Cebi, Zehra, Chang, Ying, Chater, Caspar, Cheeseman, John M., Chen, Tao, Clarke, Neil D., Clayton, Harmony, Covshoff, Sarah, Crandall-Stotler, Barbara J., Cross, Hugh, dePamphilis, Claude W., Der, Joshua P., Determann, Ron, Dickson, Rowan C., Di Stilio, Veronica S., Ellis, Shona, Fast, Eva, Feja, Nicole, Field, Katie J., Filatov, Dmitry A., Finnegan, Patrick M., Floyd, Sandra K., Fogliani, Bruno, Garcia, Nicolas, Gateble, Gildas, Godden, Grant T., Goh, Falicia (Qi Yun), Greiner, Stephan, Harkess, Alex, Heaney, James Mike, Helliwell, Katherine E., Heyduk, Karolina, Hibberd, Julian M., Hodel, Richard G. J., Hollingsworth, Peter M., Johnson, Marc T. J., Jost, Ricarda, Joyce, Blake, Kapralov, Maxim V., Kazamia, Elena, Kellogg, Elizabeth A., Koch, Marcus A., Von Konrat, Matt, Konyves, Kalman, Kutchan, Toni M., Lam, Vivienne, Larsson, Anders, Leitch, Andrew R., Lentz, Roswitha, Li, Fay-Wei, Lowe, Andrew J., Ludwig, Martha, Manos, Paul S., Mavrodiev, Evgeny, McCormick, Melissa K., McKain, Michael, McLellan, Tracy, McNeal, Joel R., Miller, Richard E., Nelson, Matthew N., Peng, Yanhui, Ralph, Paula, Real, Daniel, Riggins, Chance W., Ruhsam, Markus, Sage, Rowan F., Sakai, Ann K., Scascitella, Moira, Schilling, Edward E., Schlosser, Eva-Marie, Sederoff, Heike, Servick, Stein, Sessa, Emily B., Shaw, A. Jonathan, Shaw, Shane W., Sigel, Erin M., Skema, Cynthia, Smith, Alison G., Smithson, Ann, Stewart, C. Neal, Jr., Stinchcombe, John R., Szovenyi, Peter, Tate, Jennifer A., Tiebel, Helga, Trapnell, Dorset, Villegente, Matthieu, Wang, Chun-Neng, Weller, Stephen G., Wenzel, Michael, Weststrand, Stina, Westwood, James H., Whigham, Dennis F., Wu, Shuangxiu, Wulff, Adrien S., Yang, Yu, Zhu, Dan, Zhuang, Cuili, Zuidof, Jennifer, Chase, Mark W., Pires, J. Chris, Rothfels, Carl J., Yu, Jun, Chen, Cui, Chen, Li, Cheng, Shifeng, Li, Juanjuan, Li, Ran, Li, Xia, Lu, Haorong, Ou, Yanxiang, Sun, Xiao, Tan, Xuemei, Tang, Jingbo, Tian, Zhijian, Wang, Feng, Wang, Jun, Wei, Xiaofeng, Xu, Xun, Yan, Zhixiang, Yang, Fan, Zhong, Xiaoni, Zhou, Feiyu, Zhu, Ying, Zhang, Yong, Ayyampalayam, Saravanaraj, Barkman, Todd J., Nguyen, Nam-Phuong, Matasci, Naim, Nelson, David R., Sayyari, Erfan, Wafula, Eric K., Walls, Ramona L., Warnow, Tandy, An, Hong, Arrigo, Nils, Baniaga, Anthony E., Galuska, Sally, Jorgensen, Stacy A., Kidder, Thomas I., Kong, Hanghui, Lu-Irving, Patricia, Marx, Hannah E., Qi, Xinshuai, Reardon, Chris R., Sutherland, Brittany L., Tiley, George P., Welles, Shana R., Yu, Rongpei, Zhan, Shing, Gramzow, Lydia, Theissen, Gunter, and Wong, Gane Ka-Shu

Abstract

Green plants (Viridiplantae) include around 450,000-500,000 species(1,2) of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.

Published
2019
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48. One thousand plant transcriptomes and the phylogenomics of green plants

Author

School of Plant and Environmental Sciences, Leebens-Mack, James H., Barker, Michael S., Carpenter, Eric J., Deyholos, Michael K., Gitzendanner, Matthew A., Graham, Sean W., Grosse, Ivo, Li, Zheng, Melkonian, Michael, Mirarab, Siavash, Porsch, Martin, Quint, Marcel, Rensing, Stefan A., Soltis, Douglas E., Soltis, Pamela S., Stevenson, Dennis W., Ullrich, Kristian K., Wickett, Norman J., DeGironimo, Lisa, Edger, Patrick P., Jordon-Thaden, Ingrid E., Joya, Steve, Liu, Tao, Melkonian, Barbara, Miles, Nicholas W., Pokorny, Lisa, Quigley, Charlotte, Thomas, Philip, Villarreal, Juan Carlos, Augustin, Megan M., Barrett, Matthew D., Baucom, Regina S., Beerling, David J., Benstein, Ruben Maximilian, Biffin, Ed, Brockington, Samuel F., Burge, Dylan O., Burris, Jason N., Burris, Kellie P., Burtet-Sarramegna, Valerie, Caicedo, Ana L., Cannon, Steven B., Cebi, Zehra, Chang, Ying, Chater, Caspar, Cheeseman, John M., Chen, Tao, Clarke, Neil D., Clayton, Harmony, Covshoff, Sarah, Crandall-Stotler, Barbara J., Cross, Hugh, dePamphilis, Claude W., Der, Joshua P., Determann, Ron, Dickson, Rowan C., Di Stilio, Veronica S., Ellis, Shona, Fast, Eva, Feja, Nicole, Field, Katie J., Filatov, Dmitry A., Finnegan, Patrick M., Floyd, Sandra K., Fogliani, Bruno, Garcia, Nicolas, Gateble, Gildas, Godden, Grant T., Goh, Falicia (Qi Yun), Greiner, Stephan, Harkess, Alex, Heaney, James Mike, Helliwell, Katherine E., Heyduk, Karolina, Hibberd, Julian M., Hodel, Richard G. J., Hollingsworth, Peter M., Johnson, Marc T. J., Jost, Ricarda, Joyce, Blake, Kapralov, Maxim V., Kazamia, Elena, Kellogg, Elizabeth A., Koch, Marcus A., Von Konrat, Matt, Konyves, Kalman, Kutchan, Toni M., Lam, Vivienne, Larsson, Anders, Leitch, Andrew R., Lentz, Roswitha, Li, Fay-Wei, Lowe, Andrew J., Ludwig, Martha, Manos, Paul S., Mavrodiev, Evgeny, McCormick, Melissa K., McKain, Michael, McLellan, Tracy, McNeal, Joel R., Miller, Richard E., Nelson, Matthew N., Peng, Yanhui, Ralph, Paula E., Real, Daniel, Riggins, Chance W., Ruhsam, Markus, Sage, Rowan F., Sakai, Ann K., Scascitella, Moira, Schilling, Edward E., Schlosser, Eva-Marie, Sederoff, Heike, Servick, Stein, Sessa, Emily B., Shaw, A. Jonathan, Shaw, Shane W., Sigel, Erin M., Skema, Cynthia, Smith, Alison G., Smithson, Ann, Stewart, C. Neal, Jr., Stinchcombe, John R., Szovenyi, Peter, Tate, Jennifer A., Tiebel, Helga, Trapnell, Dorset, Villegente, Matthieu, Wang, Chun-Neng, Weller, Stephen G., Wenzel, Michael, Weststrand, Stina, Westwood, James H., Whigham, Dennis F., Wu, Shuangxiu, Wulff, Adrien S., Yang, Yu, Zhu, Dan, Zhuang, Cuili, Zuidof, Jennifer, Chase, Mark W., Pires, J. Chris, Rothfels, Carl J., Yu, Jun, Chen, Cui, Chen, Li, Cheng, Shifeng, Li, Juanjuan, Li, Ran, Li, Xia, Lu, Haorong, Ou, Yanxiang, Sun, Xiao, Tan, Xuemei, Tang, Jingbo, Tian, Zhijian, Wang, Feng, Wang, Jun, Wei, Xiaofeng, Xu, Xun, Yan, Zhixiang, Yang, Fan, Zhong, Xiaoni, Zhou, Feiyu, Zhu, Ying, Zhang, Yong, Ayyampalayam, Saravanaraj, Barkman, Todd J., Nam-Phuong Nguyen, Matasci, Naim, Nelson, David R., Sayyari, Erfan, Wafula, Eric K., Walls, Ramona L., Warnow, Tandy, An, Hong, Arrigo, Nils, Baniaga, Anthony E., Galuska, Sally, Jorgensen, Stacy A., Kidder, Thomas I., Kong, Hanghui, Lu-Irving, Patricia, Marx, Hannah E., Qi, Xinshuai, Reardon, Chris R., Sutherland, Brittany L., Tiley, George P., Welles, Shana R., Yu, Rongpei, Zhan, Shing, Gramzow, Lydia, Theissen, Gunter, Wong, Gane Ka-Shu, School of Plant and Environmental Sciences, Leebens-Mack, James H., Barker, Michael S., Carpenter, Eric J., Deyholos, Michael K., Gitzendanner, Matthew A., Graham, Sean W., Grosse, Ivo, Li, Zheng, Melkonian, Michael, Mirarab, Siavash, Porsch, Martin, Quint, Marcel, Rensing, Stefan A., Soltis, Douglas E., Soltis, Pamela S., Stevenson, Dennis W., Ullrich, Kristian K., Wickett, Norman J., DeGironimo, Lisa, Edger, Patrick P., Jordon-Thaden, Ingrid E., Joya, Steve, Liu, Tao, Melkonian, Barbara, Miles, Nicholas W., Pokorny, Lisa, Quigley, Charlotte, Thomas, Philip, Villarreal, Juan Carlos, Augustin, Megan M., Barrett, Matthew D., Baucom, Regina S., Beerling, David J., Benstein, Ruben Maximilian, Biffin, Ed, Brockington, Samuel F., Burge, Dylan O., Burris, Jason N., Burris, Kellie P., Burtet-Sarramegna, Valerie, Caicedo, Ana L., Cannon, Steven B., Cebi, Zehra, Chang, Ying, Chater, Caspar, Cheeseman, John M., Chen, Tao, Clarke, Neil D., Clayton, Harmony, Covshoff, Sarah, Crandall-Stotler, Barbara J., Cross, Hugh, dePamphilis, Claude W., Der, Joshua P., Determann, Ron, Dickson, Rowan C., Di Stilio, Veronica S., Ellis, Shona, Fast, Eva, Feja, Nicole, Field, Katie J., Filatov, Dmitry A., Finnegan, Patrick M., Floyd, Sandra K., Fogliani, Bruno, Garcia, Nicolas, Gateble, Gildas, Godden, Grant T., Goh, Falicia (Qi Yun), Greiner, Stephan, Harkess, Alex, Heaney, James Mike, Helliwell, Katherine E., Heyduk, Karolina, Hibberd, Julian M., Hodel, Richard G. J., Hollingsworth, Peter M., Johnson, Marc T. J., Jost, Ricarda, Joyce, Blake, Kapralov, Maxim V., Kazamia, Elena, Kellogg, Elizabeth A., Koch, Marcus A., Von Konrat, Matt, Konyves, Kalman, Kutchan, Toni M., Lam, Vivienne, Larsson, Anders, Leitch, Andrew R., Lentz, Roswitha, Li, Fay-Wei, Lowe, Andrew J., Ludwig, Martha, Manos, Paul S., Mavrodiev, Evgeny, McCormick, Melissa K., McKain, Michael, McLellan, Tracy, McNeal, Joel R., Miller, Richard E., Nelson, Matthew N., Peng, Yanhui, Ralph, Paula E., Real, Daniel, Riggins, Chance W., Ruhsam, Markus, Sage, Rowan F., Sakai, Ann K., Scascitella, Moira, Schilling, Edward E., Schlosser, Eva-Marie, Sederoff, Heike, Servick, Stein, Sessa, Emily B., Shaw, A. Jonathan, Shaw, Shane W., Sigel, Erin M., Skema, Cynthia, Smith, Alison G., Smithson, Ann, Stewart, C. Neal, Jr., Stinchcombe, John R., Szovenyi, Peter, Tate, Jennifer A., Tiebel, Helga, Trapnell, Dorset, Villegente, Matthieu, Wang, Chun-Neng, Weller, Stephen G., Wenzel, Michael, Weststrand, Stina, Westwood, James H., Whigham, Dennis F., Wu, Shuangxiu, Wulff, Adrien S., Yang, Yu, Zhu, Dan, Zhuang, Cuili, Zuidof, Jennifer, Chase, Mark W., Pires, J. Chris, Rothfels, Carl J., Yu, Jun, Chen, Cui, Chen, Li, Cheng, Shifeng, Li, Juanjuan, Li, Ran, Li, Xia, Lu, Haorong, Ou, Yanxiang, Sun, Xiao, Tan, Xuemei, Tang, Jingbo, Tian, Zhijian, Wang, Feng, Wang, Jun, Wei, Xiaofeng, Xu, Xun, Yan, Zhixiang, Yang, Fan, Zhong, Xiaoni, Zhou, Feiyu, Zhu, Ying, Zhang, Yong, Ayyampalayam, Saravanaraj, Barkman, Todd J., Nam-Phuong Nguyen, Matasci, Naim, Nelson, David R., Sayyari, Erfan, Wafula, Eric K., Walls, Ramona L., Warnow, Tandy, An, Hong, Arrigo, Nils, Baniaga, Anthony E., Galuska, Sally, Jorgensen, Stacy A., Kidder, Thomas I., Kong, Hanghui, Lu-Irving, Patricia, Marx, Hannah E., Qi, Xinshuai, Reardon, Chris R., Sutherland, Brittany L., Tiley, George P., Welles, Shana R., Yu, Rongpei, Zhan, Shing, Gramzow, Lydia, Theissen, Gunter, and Wong, Gane Ka-Shu

Abstract

Green plants (Viridiplantae) include around 450,000-500,000 species(1,2) of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.

Published
2019

49. A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering

Author

Texas Tech University, National Science Foundation (US), Royal Botanical Gardens, Kew, Johnson, Matthew, Pokorny, Lisa, Dodsworth, Steven, Botigué, Laura R., Cowan, Robyn, Devault, Alison, Eiserhardt, Wolf, Epitawalage, Niroshini, Forest, Félix, Kim, Jan, Leebens-Mack, James H., Leitch, Ilia J., Maurin, Olivier, Soltis, Douglas E., Soltis, Pamela S., Wong, Gane Ka-shu, Baker, William J., Wickett, Norman, Texas Tech University, National Science Foundation (US), Royal Botanical Gardens, Kew, Johnson, Matthew, Pokorny, Lisa, Dodsworth, Steven, Botigué, Laura R., Cowan, Robyn, Devault, Alison, Eiserhardt, Wolf, Epitawalage, Niroshini, Forest, Félix, Kim, Jan, Leebens-Mack, James H., Leitch, Ilia J., Maurin, Olivier, Soltis, Douglas E., Soltis, Pamela S., Wong, Gane Ka-shu, Baker, William J., and Wickett, Norman

Abstract

Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the cost of developing targeted sequencing approaches is associated with the generation of preliminary data needed for the identification of orthologous loci for probe design. In plants, identifying orthologous loci has proven difficult due to a large number of whole-genome duplication events, especially in the angiosperms (flowering plants). We used multiple sequence alignments from over 600 angiosperms for 353 putatively single-copy protein-coding genes identified by the One Thousand Plant Transcriptomes Initiative to design a set of targeted sequencing probes for phylogenetic studies of any angiosperm group. To maximize the phylogenetic potential of the probes, while minimizing the cost of production, we introduce a k-medoids clustering approach to identify the minimum number of sequences necessary to represent each coding sequence in the final probe set. Using this method, 5–15 representative sequences were selected per orthologous locus, representing the sequence diversity of angiosperms more efficiently than if probes were designed using available sequenced genomes alone. To test our approximately 80,000 probes, we hybridized libraries from 42 species spanning all higher-order groups of angiosperms, with a focus on taxa not present in the sequence alignments used to design the probes. Out of a possible 353 coding sequences, we recovered an average of 283 per species and at least 100 in all species. Differences among taxa in sequence recovery could not be explained by relatedness to the representative taxa selected for probe design, suggesting that there is no phylogenetic bias in the probe set. Our probe set, which targeted 260 kbp of coding sequence, achieved a median recovery of 137 kbp per taxon in coding regions, a maximum recovery of 250 kbp, and an additional median of 212 kb

Published
2019

50. One thousand plant transcriptomes and the phylogenomics of green plants

Author

National Key Research and Development Program (China), Ministry of Science and Technology of the People's Republic of China, Leebens-Mack, James H., Barker, M. S., Carpenter, Eric J., Deyholos, Michael K., Gitzendanner, Matthew A., Graham, Sean W., Grosse,Ivo, Li, Zheng, Melkonian, Michael, Mirarab, Siavash, Porsch, Martin, Nelson, Matthew N., Peng, Yanhui, Ralph, Paula, Real, Daniel, Riggins, Chance W., Ruhsam, Markus, Sage, Rowan F., Sakai, Ann K., Scascitella, Moira, Schilling, Edward E., Quint, Marcel, Schlösser, Eva-Marie, Sederoff, Heike, Servick, Stein, Sessa, Emily B., Shaw, Jonathan, Shane W., Sigel, Erin M., Skema, Cynthia, Smith, Alison G., Smithson, Ann, Rensing, Stefan A., Stewart Jr, Neal, Stinchcombe, John R., Szövényi, Peter, Tate, Jennifer A., Tiebel, Helga, Trapnell, Dorset, Villegente, Matthieu, Wang, Chun-Neng, Weller, Stephen G., Wenzel, Michael, Soltis, Douglas E., Weststrand, Stina, Westwood, James H., Whigham, Dennis F., Wu, Shuangxiu, Wulff , Adrien S., Yang, Yu, Zhu, Dan, Zhuang, Cuili, Zuidof, Jennifer, Pires, J. Chris, Soltis, Pamela S., Chase, Mark W., Rothfels, Carl J., Yu, Jun, Chen, Cui, Chen, Li, Cheng, Shifeng, Li, Juanjuan, Li, Ran, Li, Xia, Lu, Haorong, Stevenson, Dennis W., Ou, Yanxiang, Sun, Xiao, Tan, Xuemei, Tang, Jingbo, Tian, Zhijian, Wang, Feng, Wang, Jun, Wei, Xiaofeng, Xu, Xun, Yan, Zhixiang, Ullrich, Kristian K., Yang, Fan, Zhong, Xiaoni, Zhou, Feiyu, Zhu, Ying, Zhang, Yong, Ayyampalayam, Saravanaraj, Barkman, Todd J., Nguyen, Nam-phuong, Matasci, Naim, Nelson, David R., Wickett, Norman J., Sayyari, Erfan, Wafula, Eric K., Walls, Ramona L., Warnow, Tandy, An, Hong, Arrigo, Nils, Baniaga, Anthony E., Galuska, Sally, Jorgensen, Stacy A., Kidder, Thomas I., DeGironimo, Lisa, Kong, Hanghui, Lu-Irving, Patricia, Marx, Hannah E., Qi, Xinshuai, Reardon, Chris R., Sutherland, Brittany L., Tiley, George P., Welles, Shana R., Yu, Rongpei, Zhan, Shing, Edger, Patrick P., Gramzow, Lydia, Theißen, Günter, Wong, Gane Ka-Shu, Jordon-Thaden, Ingrid E., Joya. Steve, Melkonian, Barbara, Miles, Nicholas W., Pokorny, Lisa, Quigley, Charlotte, Thomas, Philip, Villarreal, Juan Carlos, Augustin, Megan M., Barrett, Matthew D., Baucom, Regina S., Beerling, David J., Benstein, Ruben Maximilian, Biffin, Ed, Brockington, Samuel F., Burge, Dylan O., Burris, Jason N., Burris, Kellie P., Burtet-Sarramegna, Valérie, Caicedo, Ana L., Cannon, Steven B., Çebi, Zehra, Chang, Ying, Chater, Caspar, Cheeseman, John M., Chen, Tao, Clarke, Neil D., Clayton, Harmony, Covshoff, Sarah, Crandall-Stotler, Barbara J., Cross, Hugh, dePamphilis,Claude W., Der, Joshua P., Determann, Ron, Dickson, Rowan C., Di Stilio, Verónica S., Ellis, Shona, Fast, Eva, Feja, Nicole, Field, Katie J., Filatov, Dmitry A., Finnegan, Patrick M., Floyd, Sandra K., Fogliani, Bruno, García, Nicolás, Gâteblé, Gildas, Godden, Grant T., Goh, Falicia (Qi Yun), Greiner, Stephan, Harkess, Alex, Heaney, James Mike, Helliwell, Katherine E., Heyduk, Karolina, Hibberd, Julian M., Hodel, Richard G. J., Hollingsworth, Peter M., Johnson, Marc T. J., Jost, Ricarda, Joyce, Blake, Kapralov, Maxim V., Kazamia, Elena, Kellogg, Elizabeth A., Koch, Marcus A., Konrat, Matt von, Könyves, Kálmán, Kutchan, Toni M., Lam, Vivienne, Larsson, Anders, Leitch, Andrew R., Lentz, Roswitha, Li, Fay-Wei, Lowe, Andrew J., Ludwig, Martha, Manos, Paul S., Mavrodiev, Evgeny, McCormick, Melissa K., McKain, Michael, McLellan, Tracy, McNeal, Joel R., Miller, Richard E., National Key Research and Development Program (China), Ministry of Science and Technology of the People's Republic of China, Leebens-Mack, James H., Barker, M. S., Carpenter, Eric J., Deyholos, Michael K., Gitzendanner, Matthew A., Graham, Sean W., Grosse,Ivo, Li, Zheng, Melkonian, Michael, Mirarab, Siavash, Porsch, Martin, Nelson, Matthew N., Peng, Yanhui, Ralph, Paula, Real, Daniel, Riggins, Chance W., Ruhsam, Markus, Sage, Rowan F., Sakai, Ann K., Scascitella, Moira, Schilling, Edward E., Quint, Marcel, Schlösser, Eva-Marie, Sederoff, Heike, Servick, Stein, Sessa, Emily B., Shaw, Jonathan, Shane W., Sigel, Erin M., Skema, Cynthia, Smith, Alison G., Smithson, Ann, Rensing, Stefan A., Stewart Jr, Neal, Stinchcombe, John R., Szövényi, Peter, Tate, Jennifer A., Tiebel, Helga, Trapnell, Dorset, Villegente, Matthieu, Wang, Chun-Neng, Weller, Stephen G., Wenzel, Michael, Soltis, Douglas E., Weststrand, Stina, Westwood, James H., Whigham, Dennis F., Wu, Shuangxiu, Wulff , Adrien S., Yang, Yu, Zhu, Dan, Zhuang, Cuili, Zuidof, Jennifer, Pires, J. Chris, Soltis, Pamela S., Chase, Mark W., Rothfels, Carl J., Yu, Jun, Chen, Cui, Chen, Li, Cheng, Shifeng, Li, Juanjuan, Li, Ran, Li, Xia, Lu, Haorong, Stevenson, Dennis W., Ou, Yanxiang, Sun, Xiao, Tan, Xuemei, Tang, Jingbo, Tian, Zhijian, Wang, Feng, Wang, Jun, Wei, Xiaofeng, Xu, Xun, Yan, Zhixiang, Ullrich, Kristian K., Yang, Fan, Zhong, Xiaoni, Zhou, Feiyu, Zhu, Ying, Zhang, Yong, Ayyampalayam, Saravanaraj, Barkman, Todd J., Nguyen, Nam-phuong, Matasci, Naim, Nelson, David R., Wickett, Norman J., Sayyari, Erfan, Wafula, Eric K., Walls, Ramona L., Warnow, Tandy, An, Hong, Arrigo, Nils, Baniaga, Anthony E., Galuska, Sally, Jorgensen, Stacy A., Kidder, Thomas I., DeGironimo, Lisa, Kong, Hanghui, Lu-Irving, Patricia, Marx, Hannah E., Qi, Xinshuai, Reardon, Chris R., Sutherland, Brittany L., Tiley, George P., Welles, Shana R., Yu, Rongpei, Zhan, Shing, Edger, Patrick P., Gramzow, Lydia, Theißen, Günter, Wong, Gane Ka-Shu, Jordon-Thaden, Ingrid E., Joya. Steve, Melkonian, Barbara, Miles, Nicholas W., Pokorny, Lisa, Quigley, Charlotte, Thomas, Philip, Villarreal, Juan Carlos, Augustin, Megan M., Barrett, Matthew D., Baucom, Regina S., Beerling, David J., Benstein, Ruben Maximilian, Biffin, Ed, Brockington, Samuel F., Burge, Dylan O., Burris, Jason N., Burris, Kellie P., Burtet-Sarramegna, Valérie, Caicedo, Ana L., Cannon, Steven B., Çebi, Zehra, Chang, Ying, Chater, Caspar, Cheeseman, John M., Chen, Tao, Clarke, Neil D., Clayton, Harmony, Covshoff, Sarah, Crandall-Stotler, Barbara J., Cross, Hugh, dePamphilis,Claude W., Der, Joshua P., Determann, Ron, Dickson, Rowan C., Di Stilio, Verónica S., Ellis, Shona, Fast, Eva, Feja, Nicole, Field, Katie J., Filatov, Dmitry A., Finnegan, Patrick M., Floyd, Sandra K., Fogliani, Bruno, García, Nicolás, Gâteblé, Gildas, Godden, Grant T., Goh, Falicia (Qi Yun), Greiner, Stephan, Harkess, Alex, Heaney, James Mike, Helliwell, Katherine E., Heyduk, Karolina, Hibberd, Julian M., Hodel, Richard G. J., Hollingsworth, Peter M., Johnson, Marc T. J., Jost, Ricarda, Joyce, Blake, Kapralov, Maxim V., Kazamia, Elena, Kellogg, Elizabeth A., Koch, Marcus A., Konrat, Matt von, Könyves, Kálmán, Kutchan, Toni M., Lam, Vivienne, Larsson, Anders, Leitch, Andrew R., Lentz, Roswitha, Li, Fay-Wei, Lowe, Andrew J., Ludwig, Martha, Manos, Paul S., Mavrodiev, Evgeny, McCormick, Melissa K., McKain, Michael, McLellan, Tracy, McNeal, Joel R., and Miller, Richard E.

Abstract

Green plants (Viridiplantae) include around 450,000–500,000 species of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.

Published
2019

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