1
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Mabry ME, Abrahams RS, Al-Shehbaz IA, Baker WJ, Barak S, Barker MS, Barrett RL, Beric A, Bhattacharya S, Carey SB, Conant GC, Conran JG, Dassanayake M, Edger PP, Hall JC, Hao Y, Hendriks KP, Hibberd JM, King GJ, Kliebenstein DJ, Koch MA, Leitch IJ, Lens F, Lysak MA, McAlvay AC, McKibben MTW, Mercati F, Moore RC, Mummenhoff K, Murphy DJ, Nikolov LA, Pisias M, Roalson EH, Schranz ME, Thomas SK, Yu Q, Yocca A, Pires JC, Harkess AE. Complementing model species with model clades. Plant Cell 2024; 36:1205-1226. [PMID: 37824826 PMCID: PMC11062466 DOI: 10.1093/plcell/koad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/07/2023] [Accepted: 09/22/2023] [Indexed: 10/14/2023]
Abstract
Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant tree of life continues to improve. The intersection of these 2 research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the utility of the Arabidopsis thaliana model species, especially the ability to connect its genetic and functional resources, to species across the entire Brassicales order. We focus on the utility of using genomics and phylogenomics to bridge the evolution and diversification of several traits across the Brassicales to the resources in Arabidopsis, thereby extending scope from a model species by establishing a "model clade." These Brassicales-wide traits are discussed in the context of both the model species Arabidopsis and the family Brassicaceae. We promote the utility of such a "model clade" and make suggestions for building global networks to support future studies in the model order Brassicales.
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Affiliation(s)
- Makenzie E Mabry
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - R Shawn Abrahams
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN 47906, USA
| | | | | | - Simon Barak
- Ben-Gurion University of the Negev, French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Midreshet Ben-Gurion, 8499000, Israel
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Russell L Barrett
- National Herbarium of New South Wales, Australian Botanic Garden, Locked Bag 6002, Mount Annan, NSW 2567, Australia
| | - Aleksandra Beric
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, St. Louis, MO 63108, USA
| | - Samik Bhattacharya
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Sarah B Carey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Gavin C Conant
- Department of Biological Sciences, Bioinformatics Research Center, Program in Genetics, North Carolina State University, Raleigh, NC 27695, USA
| | - John G Conran
- ACEBB and SGC, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI 48864, USA
| | - Jocelyn C Hall
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Yue Hao
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Kasper P Hendriks
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
- Functional Traits, Naturalis Biodiversity Center, PO Box 9517, Leiden 2300 RA, the Netherlands
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | | | - Marcus A Koch
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Frederic Lens
- Functional Traits, Naturalis Biodiversity Center, PO Box 9517, Leiden 2300 RA, the Netherlands
- Institute of Biology Leiden, Plant Sciences, Leiden University, 2333 BE Leiden, the Netherlands
| | - Martin A Lysak
- CEITEC, and NCBR, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Alex C McAlvay
- Institute of Economic Botany, New York Botanical Garden, The Bronx, NY 10458, USA
| | - Michael T W McKibben
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Francesco Mercati
- National Research Council (CNR), Institute of Biosciences and Bioresource (IBBR), Palermo 90129, Italy
| | | | - Klaus Mummenhoff
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Daniel J Murphy
- Royal Botanic Gardens Victoria, Melbourne, VIC 3004, Australia
| | | | - Michael Pisias
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Eric H Roalson
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, 6708 PB Wageningen, the Netherlands
| | - Shawn K Thomas
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
- Bioinformatics and Analytics Core, University of Missouri, Columbia, MO 65211, USA
| | - Qingyi Yu
- Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Hilo, HI 96720, USA
| | - Alan Yocca
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - J Chris Pires
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523-1170, USA
| | - Alex E Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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2
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Goldberg JK, Olcerst A, McKibben M, Hare JD, Barker MS, Bronstein JL. A de novo long-read genome assembly of the sacred datura plant (Datura wrightii) reveals a role of tandem gene duplications in the evolution of herbivore-defense response. BMC Genomics 2024; 25:15. [PMID: 38166627 PMCID: PMC10759348 DOI: 10.1186/s12864-023-09894-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
The sacred datura plant (Solanales: Solanaceae: Datura wrightii) has been used to study plant-herbivore interactions for decades. The wealth of information that has resulted leads it to have potential as a model system for studying the ecological and evolutionary genomics of these interactions. We present a de novo Datura wrightii genome assembled using PacBio HiFi long-reads. Our assembly is highly complete and contiguous (N50 = 179Mb, BUSCO Complete = 97.6%). We successfully detected a previously documented ancient whole genome duplication using our assembly and have classified the gene duplication history that generated its coding sequence content. We use it as the basis for a genome-guided differential expression analysis to identify the induced responses of this plant to one of its specialized herbivores (Coleoptera: Chrysomelidae: Lema daturaphila). We find over 3000 differentially expressed genes associated with herbivory and that elevated expression levels of over 200 genes last for several days. We also combined our analyses to determine the role that different gene duplication categories have played in the evolution of Datura-herbivore interactions. We find that tandem duplications have expanded multiple functional groups of herbivore responsive genes with defensive functions, including UGT-glycosyltranserases, oxidoreductase enzymes, and peptidase inhibitors. Overall, our results expand our knowledge of herbivore-induced plant transcriptional responses and the evolutionary history of the underlying herbivore-response genes.
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Affiliation(s)
- Jay K Goldberg
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.
| | - Aaron Olcerst
- Department of Entomology, University of California Riverside, Riverside, CA, USA
| | - Michael McKibben
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - J Daniel Hare
- Department of Entomology, University of California Riverside, Riverside, CA, USA
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Judith L Bronstein
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
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3
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Blischak PD, Sajan M, Barker MS, Gutenkunst RN. Demographic history inference and the polyploid continuum. Genetics 2023; 224:iyad107. [PMID: 37279657 PMCID: PMC10411560 DOI: 10.1093/genetics/iyad107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 04/17/2023] [Accepted: 05/18/2023] [Indexed: 06/08/2023] Open
Abstract
Polyploidy is an important generator of evolutionary novelty across diverse groups in the Tree of Life, including many crops. However, the impact of whole-genome duplication depends on the mode of formation: doubling within a single lineage (autopolyploidy) versus doubling after hybridization between two different lineages (allopolyploidy). Researchers have historically treated these two scenarios as completely separate cases based on patterns of chromosome pairing, but these cases represent ideals on a continuum of chromosomal interactions among duplicated genomes. Understanding the history of polyploid species thus demands quantitative inferences of demographic history and rates of exchange between subgenomes. To meet this need, we developed diffusion models for genetic variation in polyploids with subgenomes that cannot be bioinformatically separated and with potentially variable inheritance patterns, implementing them in the dadi software. We validated our models using forward SLiM simulations and found that our inference approach is able to accurately infer evolutionary parameters (timing, bottleneck size) involved with the formation of auto- and allotetraploids, as well as exchange rates in segmental allotetraploids. We then applied our models to empirical data for allotetraploid shepherd's purse (Capsella bursa-pastoris), finding evidence for allelic exchange between the subgenomes. Taken together, our model provides a foundation for demographic modeling in polyploids using diffusion equations, which will help increase our understanding of the impact of demography and selection in polyploid lineages.
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Affiliation(s)
- Paul D Blischak
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
- Bayer Crop Science, Chesterfield, MO 63017, USA
| | - Mathews Sajan
- Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Ryan N Gutenkunst
- Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
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4
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Sessa EB, Masalia RR, Arrigo N, Barker MS, Pelosi JA. GOgetter: A pipeline for summarizing and visualizing GO slim annotations for plant genetic data. Appl Plant Sci 2023; 11:e11536. [PMID: 37601315 PMCID: PMC10439822 DOI: 10.1002/aps3.11536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 06/09/2023] [Accepted: 06/15/2023] [Indexed: 08/22/2023]
Abstract
Premise The functional annotation of genes is a crucial component of genomic analyses. A common way to summarize functional annotations is with hierarchical gene ontologies, such as the Gene Ontology (GO) Resource. GO includes information about the cellular location, molecular function(s), and products/processes that genes produce or are involved in. For a set of genes, summarizing GO annotations using pre-defined, higher-order terms (GO slims) is often desirable in order to characterize the overall function of the data set, and it is impractical to do this manually. Methods and Results The GOgetter pipeline consists of bash and Python scripts. From an input FASTA file of nucleotide gene sequences, it outputs text and image files that list (1) the best hit for each input gene in a set of reference gene models, (2) all GO terms and annotations associated with those hits, and (3) a summary and visualization of GO slim categories for the data set. These output files can be queried further and analyzed statistically, depending on the downstream need(s). Conclusions GO annotations are a widely used "universal language" for describing gene functions and products. GOgetter is a fast and easy-to-implement pipeline for obtaining, summarizing, and visualizing GO slim categories associated with a set of genes.
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Affiliation(s)
| | - Rishi R. Masalia
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizonaUSA
| | | | - Michael S. Barker
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizonaUSA
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5
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Marchant DB, Chen G, Cai S, Chen F, Schafran P, Jenkins J, Shu S, Plott C, Webber J, Lovell JT, He G, Sandor L, Williams M, Rajasekar S, Healey A, Barry K, Zhang Y, Sessa E, Dhakal RR, Wolf PG, Harkess A, Li FW, Rössner C, Becker A, Gramzow L, Xue D, Wu Y, Tong T, Wang Y, Dai F, Hua S, Wang H, Xu S, Xu F, Duan H, Theißen G, McKain MR, Li Z, McKibben MTW, Barker MS, Schmitz RJ, Stevenson DW, Zumajo-Cardona C, Ambrose BA, Leebens-Mack JH, Grimwood J, Schmutz J, Soltis PS, Soltis DE, Chen ZH. Dynamic genome evolution in a model fern. Nat Plants 2022; 8:1038-1051. [PMID: 36050461 PMCID: PMC9477723 DOI: 10.1038/s41477-022-01226-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 07/15/2022] [Indexed: 05/31/2023]
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.
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Affiliation(s)
| | - Guang Chen
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Shengguan Cai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
| | - Fei Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | | | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Shengqiang Shu
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jenell Webber
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - John T Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Guifen He
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Laura Sandor
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Melissa Williams
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Shanmugam Rajasekar
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Adam Healey
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Kerrie Barry
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yinwen Zhang
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Emily Sessa
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Rijan R Dhakal
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA
| | - Paul G Wolf
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA
| | - Alex Harkess
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, USA
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
| | - Clemens Rössner
- Justus-Liebig-University, Department of Biology and Chemistry, Institute of Botany, Gießen, Germany
| | - Annette Becker
- Justus-Liebig-University, Department of Biology and Chemistry, Institute of Botany, Gießen, Germany
| | - Lydia Gramzow
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, Jena, Germany
| | - Dawei Xue
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yuhuan Wu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Tao Tong
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Yuanyuan Wang
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fei Dai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Shuijin Hua
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hua Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Shengchun Xu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Fei Xu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Honglang Duan
- Institute for Forest Resources & Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, China
| | - Günter Theißen
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, Jena, Germany
| | - Michael R McKain
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA
| | - Zheng Li
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Michael T W McKibben
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | | | | | | | | | | | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, USA.
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, New South Wales, Australia.
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia.
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6
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Heckenhauer J, Frandsen PB, Sproul JS, Li Z, Paule J, Larracuente AM, Maughan PJ, Barker MS, Schneider JV, Stewart RJ, Pauls SU. Genome size evolution in the diverse insect order Trichoptera. Gigascience 2022; 11:6537159. [PMID: 35217860 PMCID: PMC8881205 DOI: 10.1093/gigascience/giac011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 11/25/2021] [Accepted: 01/21/2022] [Indexed: 12/30/2022] Open
Abstract
Background Genome size is implicated in the form, function, and ecological success of a species. Two principally different mechanisms are proposed as major drivers of eukaryotic genome evolution and diversity: polyploidy (i.e., whole-genome duplication) or smaller duplication events and bursts in the activity of repetitive elements. Here, we generated de novo genome assemblies of 17 caddisflies covering all major lineages of Trichoptera. Using these and previously sequenced genomes, we use caddisflies as a model for understanding genome size evolution in diverse insect lineages. Results We detect a ∼14-fold variation in genome size across the order Trichoptera. We find strong evidence that repetitive element expansions, particularly those of transposable elements (TEs), are important drivers of large caddisfly genome sizes. Using an innovative method to examine TEs associated with universal single-copy orthologs (i.e., BUSCO genes), we find that TE expansions have a major impact on protein-coding gene regions, with TE-gene associations showing a linear relationship with increasing genome size. Intriguingly, we find that expanded genomes preferentially evolved in caddisfly clades with a higher ecological diversity (i.e., various feeding modes, diversification in variable, less stable environments). Conclusion Our findings provide a platform to test hypotheses about the potential evolutionary roles of TE activity and TE-gene associations, particularly in groups with high species, ecological, and functional diversities.
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Affiliation(s)
- Jacqueline Heckenhauer
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt 60325, Germany.,Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt 60325, Germany
| | - Paul B Frandsen
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt 60325, Germany.,Department of Plant & Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA.,Data Science Lab, Smithsonian Institution, Washington, DC 20560, USA
| | - John S Sproul
- Department of Biology, University of Rochester, Rochester, NY 14620, USA.,Department of Biology, University of Nebraska Omaha, Omaha, NE 68182, USA
| | - Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Juraj Paule
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt 60325, Germany
| | | | - Peter J Maughan
- Department of Plant & Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Julio V Schneider
- Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt 60325, Germany
| | - Russell J Stewart
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Steffen U Pauls
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt 60325, Germany.,Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt 60325, Germany.,Institute for Insect Biotechnology, Justus-Liebig-University, Gießen 35390, Germany
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7
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Abstract
Substantial morphological variation in land plants remains inaccessible to genetic analysis because current models lack variation in important ecological and agronomic traits. The genus Gilia was historically a model for biosystematics studies and includes variation in morphological traits that are poorly understood at the genetic level. We assembled a chromosome-scale reference genome of G. yorkii and used it to investigate genome evolution in the Polemoniaceae. We performed QTL (quantitative trait loci) mapping in a G. yorkii×G. capitata interspecific population for traits related to inflorescence architecture and flower color. The genome assembly spans 2.75 Gb of the estimated 2.80-Gb genome, with 96.7% of the sequence contained in the nine largest chromosome-scale scaffolds matching the haploid chromosome number. Gilia yorkii experienced at least one round of whole-genome duplication shared with other Polemoniaceae after the eudicot paleohexaploidization event. We identified QTL linked to variation in inflorescence architecture and petal color, including a candidate for the major flower color QTL—a tandem duplication of flavanol 3′,5′-hydroxylase. Our results demonstrate the utility of Gilia as a forward genetic model for dissecting the evolution of development in plants including the causal loci underlying inflorescence architecture transitions.
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Affiliation(s)
- David E Jarvis
- Plant and Wildlife Sciences Department, Brigham Young University, USA
| | - Peter J Maughan
- Plant and Wildlife Sciences Department, Brigham Young University, USA
| | | | | | - Zheng Li
- Department of Integrative Biology, University of Texas, Austin, USA
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, USA
| | | | - Clinton J Whipple
- Biology Department, Brigham Young University, USA
- Corresponding author: E-mail:
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8
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Bayer PE, Scheben A, Golicz AA, Yuan Y, Faure S, Lee H, Chawla HS, Anderson R, Bancroft I, Raman H, Lim YP, Robbens S, Jiang L, Liu S, Barker MS, Schranz ME, Wang X, King GJ, Pires JC, Chalhoub B, Snowdon RJ, Batley J, Edwards D. Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids. Plant Biotechnol J 2021; 19:2488-2500. [PMID: 34310022 PMCID: PMC8633514 DOI: 10.1111/pbi.13674] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/11/2021] [Accepted: 07/20/2021] [Indexed: 05/26/2023]
Abstract
Plant genomes demonstrate significant presence/absence variation (PAV) within a species; however, the factors that lead to this variation have not been studied systematically in Brassica across diploids and polyploids. Here, we developed pangenomes of polyploid Brassica napus and its two diploid progenitor genomes B. rapa and B. oleracea to infer how PAV may differ between diploids and polyploids. Modelling of gene loss suggests that loss propensity is primarily associated with transposable elements in the diploids while in B. napus, gene loss propensity is associated with homoeologous recombination. We use these results to gain insights into the different causes of gene loss, both in diploids and following polyploidization, and pave the way for the application of machine learning methods to understanding the underlying biological and physical causes of gene presence/absence.
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Affiliation(s)
- Philipp E. Bayer
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Armin Scheben
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Agnieszka A. Golicz
- Plant Molecular Biology and Biotechnology LaboratoryFaculty of Veterinary and Agricultural SciencesUniversity of MelbourneParkvilleVICAustralia
| | - Yuxuan Yuan
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | | | - HueyTyng Lee
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig University GiessenGiessenGermany
| | - Harmeet Singh Chawla
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig University GiessenGiessenGermany
| | - Robyn Anderson
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | | | - Harsh Raman
- NSW Department of Primary IndustriesWagga Wagga Agricultural Institute, PMBWagga WaggaNSWAustralia
| | - Yong Pyo Lim
- Department of HorticultureChungnam National UniversityDaejeonSouth Korea
| | | | - Lixi Jiang
- Institute of crop scienceDepartment of Agronomy and Plant BreedingZhejiang UniversityHangzhouChina
| | - Shengyi Liu
- Chinese Academy of Agricultural SciencesOil Crops Research InstituteWuhanChina
| | - Michael S. Barker
- Department of Ecology & Evolutionary BiologyUniversity of ArizonaTucsonAZUSA
| | - M. Eric Schranz
- Biosystematics GroupWageningen University and Research CenterWageningenThe Netherlands
| | - Xiaowu Wang
- Institute of Vegetables and FlowersChinese Academy of Agricultural Sciences (IVF, CAAS)BeijingChina
| | - Graham J. King
- Southern Cross Plant ScienceSouthern Cross UniversityLismoreNSWAustralia
| | - J. Chris Pires
- Division of Biological SciencesBond Life Sciences CenterUniversity of MissouriColumbiaMissouriUSA
| | - Boulos Chalhoub
- Institute of crop scienceDepartment of Agronomy and Plant BreedingZhejiang UniversityHangzhouChina
| | - Rod J. Snowdon
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig University GiessenGiessenGermany
| | - Jacqueline Batley
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - David Edwards
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
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9
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Blischak PD, Barker MS, Gutenkunst RN. Chromosome-scale inference of hybrid speciation and admixture with convolutional neural networks. Mol Ecol Resour 2021; 21:2676-2688. [PMID: 33682305 PMCID: PMC8675098 DOI: 10.1111/1755-0998.13355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 01/26/2021] [Accepted: 02/05/2021] [Indexed: 11/30/2022]
Abstract
Inferring the frequency and mode of hybridization among closely related organisms is an important step for understanding the process of speciation and can help to uncover reticulated patterns of phylogeny more generally. Phylogenomic methods to test for the presence of hybridization come in many varieties and typically operate by leveraging expected patterns of genealogical discordance in the absence of hybridization. An important assumption made by these tests is that the data (genes or SNPs) are independent given the species tree. However, when the data are closely linked, it is especially important to consider their nonindependence. Recently, deep learning techniques such as convolutional neural networks (CNNs) have been used to perform population genetic inferences with linked SNPs coded as binary images. Here, we use CNNs for selecting among candidate hybridization scenarios using the tree topology (((P1 , P2 ), P3 ), Out) and a matrix of pairwise nucleotide divergence (dXY ) calculated in windows across the genome. Using coalescent simulations to train and independently test a neural network showed that our method, HyDe-CNN, was able to accurately perform model selection for hybridization scenarios across a wide breath of parameter space. We then used HyDe-CNN to test models of admixture in Heliconius butterflies, as well as comparing it to phylogeny-based introgression statistics. Given the flexibility of our approach, the dropping cost of long-read sequencing and the continued improvement of CNN architectures, we anticipate that inferences of hybridization using deep learning methods like ours will help researchers to better understand patterns of admixture in their study organisms.
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Affiliation(s)
- Paul D. Blischak
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
- Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Michael S. Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Ryan N. Gutenkunst
- Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA
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10
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Román-Palacios C, Medina CA, Zhan SH, Barker MS. Animal chromosome counts reveal a similar range of chromosome numbers but with less polyploidy in animals compared to flowering plants. J Evol Biol 2021; 34:1333-1339. [PMID: 34101952 DOI: 10.1111/jeb.13884] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 12/24/2022]
Abstract
Understanding the mechanisms that underlie chromosome evolution could provide insights into the processes underpinning the origin, persistence and evolutionary tempo of lineages. Here, we present the first database of chromosome counts for animals (the Animal Chromosome Count database, ACC) summarizing chromosome numbers for ~15,000 species. We found remarkable a similarity in the distribution of chromosome counts between animals and flowering plants. Nevertheless, the similarity in the distribution of chromosome numbers between animals and plants is likely to be explained by different drivers. For instance, we found that while animals and flowering plants exhibit similar frequencies of speciation-related changes in chromosome number, plant speciation is more often related to changes in ploidy. By leveraging the largest data set of chromosome counts for animals, we describe a previously undocumented pattern across the Tree of Life-animals and flowering plants show remarkably similar distributions of haploid chromosome numbers.
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Affiliation(s)
| | - Cesar A Medina
- Department of Neuroscience, University of Arizona, Tucson, AZ, USA
| | - Shing H Zhan
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.,Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
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11
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Abstract
Most land plants are now known to be ancient polyploids that have rediploidized. Diploidization involves many changes in genome organization that ultimately restore bivalent chromosome pairing and disomic inheritance, and resolve dosage and other issues caused by genome duplication. In this review, we discuss the nature of polyploidy and its impact on chromosome pairing behavior. We also provide an overview of two major and largely independent processes of diploidization: cytological diploidization and genic diploidization/fractionation. Finally, we compare variation in gene fractionation across land plants and highlight the differences in diploidization between plants and animals. Altogether, we demonstrate recent advancements in our understanding of variation in the patterns and processes of diploidization in land plants and provide a road map for future research to unlock the mysteries of diploidization and eukaryotic genome evolution.
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Affiliation(s)
- Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Michael T W McKibben
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Geoffrey S Finch
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Paul D Blischak
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Brittany L Sutherland
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
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12
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Liu Y, Wang B, Shu S, Li Z, Song C, Liu D, Niu Y, Liu J, Zhang J, Liu H, Hu Z, Huang B, Liu X, Liu W, Jiang L, Alami MM, Zhou Y, Ma Y, He X, Yang Y, Zhang T, Hu H, Barker MS, Chen S, Wang X, Nie J. Analysis of the Coptis chinensis genome reveals the diversification of protoberberine-type alkaloids. Nat Commun 2021; 12:3276. [PMID: 34078898 PMCID: PMC8172641 DOI: 10.1038/s41467-021-23611-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 05/07/2021] [Indexed: 02/04/2023] Open
Abstract
Chinese goldthread (Coptis chinensis Franch.), a member of the Ranunculales, represents an important early-diverging eudicot lineage with diverse medicinal applications. Here, we present a high-quality chromosome-scale genome assembly and annotation of C. chinensis. Phylogenetic and comparative genomic analyses reveal the phylogenetic placement of this species and identify a single round of ancient whole-genome duplication (WGD) shared by the Ranunculaceae. We characterize genes involved in the biosynthesis of protoberberine-type alkaloids in C. chinensis. In particular, local genomic tandem duplications contribute to member amplification of a Ranunculales clade-specific gene family of the cytochrome P450 (CYP) 719. The functional versatility of a key CYP719 gene that encodes the (S)-canadine synthase enzyme involved in the berberine biosynthesis pathway may play critical roles in the diversification of other berberine-related alkaloids in C. chinensis. Our study provides insights into the genomic landscape of early-diverging eudicots and provides a valuable model genome for genetic and applied studies of Ranunculales.
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Affiliation(s)
- Yifei Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China.
| | - Bo Wang
- Hubei Institute for Drug Control, Wuhan, China
| | - Shaohua Shu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Chi Song
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, China
| | - Di Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Yan Niu
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, China
| | - Jinxin Liu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jingjing Zhang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Heping Liu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhigang Hu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Bisheng Huang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Xiuyu Liu
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wei Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Liping Jiang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | | | - Yuxin Zhou
- Hubei Institute for Drug Control, Wuhan, China
| | - Yutao Ma
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiangxiang He
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, China
| | - Yicheng Yang
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, China
| | - Tianyuan Zhang
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, China
| | - Hui Hu
- Jing Brand Chizhengtang Pharmaceutical Company Limited, Huangshi, China
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Xuekui Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
| | - Jing Nie
- Hubei Institute for Drug Control, Wuhan, China.
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13
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Hao Y, Mabry ME, Edger PP, Freeling M, Zheng C, Jin L, VanBuren R, Colle M, An H, Abrahams RS, Washburn JD, Qi X, Barry K, Daum C, Shu S, Schmutz J, Sankoff D, Barker MS, Lyons E, Pires JC, Conant GC. The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible. Genome Res 2021; 31:799-810. [PMID: 33863805 PMCID: PMC8092008 DOI: 10.1101/gr.270033.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 03/05/2021] [Indexed: 01/08/2023]
Abstract
The members of the tribe Brassiceae share a whole-genome triplication (WGT), and one proposed model for its formation is a two-step pair of hybridizations producing hexaploid descendants. However, evidence for this model is incomplete, and the evolutionary and functional constraints that drove evolution after the hexaploidy are even less understood. Here, we report a new genome sequence of Crambe hispanica, a species sister to most sequenced Brassiceae. Using this new genome and three others that share the hexaploidy, we traced the history of gene loss after the WGT using the Polyploidy Orthology Inference Tool (POInT). We confirm the two-step formation model and infer that there was a significant temporal gap between those two allopolyploidizations, with about a third of the gene losses from the first two subgenomes occurring before the arrival of the third. We also, for the 90,000 individual genes in our study, make parental subgenome assignments, inferring, with measured uncertainty, from which of the progenitor genomes of the allohexaploidy each gene derives. We further show that each subgenome has a statistically distinguishable rate of homoeolog losses. There is little indication of functional distinction between the three subgenomes: the individual subgenomes show no patterns of functional enrichment, no excess of shared protein-protein or metabolic interactions between their members, and no biases in their likelihood of having experienced a recent selective sweep. We propose a "mix and match" model of allopolyploidy, in which subgenome origin drives homoeolog loss propensities but where genes from different subgenomes function together without difficulty.
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Affiliation(s)
- Yue Hao
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Makenzie E Mabry
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
- Genetics and Genome Sciences, Michigan State University, East Lansing, Michigan 48824, USA
| | - Michael Freeling
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Chunfang Zheng
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Lingling Jin
- Department of Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9, Canada
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, Michigan 48824, USA
| | - Marivi Colle
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
| | - Hong An
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - R Shawn Abrahams
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - Jacob D Washburn
- Plant Genetics Research Unit, USDA-ARS, Columbia, Missouri 65211, USA
| | - Xinshuai Qi
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Christopher Daum
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Shengqiang Shu
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - David Sankoff
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Eric Lyons
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
- BIO5 Institute, University of Arizona, Tucson, Arizona 85721, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri 65211, USA
- Informatics Institute, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - Gavin C Conant
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27695, USA
- Program in Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
- Division of Animal Sciences, University of Missouri-Columbia, Columbia, Missouri 65211, USA
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14
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Blischak PD, Barker MS, Gutenkunst RN. Inferring the Demographic History of Inbred Species from Genome-Wide SNP Frequency Data. Mol Biol Evol 2021; 37:2124-2136. [PMID: 32068861 DOI: 10.1093/molbev/msaa042] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/04/2020] [Accepted: 02/13/2020] [Indexed: 01/04/2023] Open
Abstract
Demographic inference using the site frequency spectrum (SFS) is a common way to understand historical events affecting genetic variation. However, most methods for estimating demography from the SFS assume random mating within populations, precluding these types of analyses in inbred populations. To address this issue, we developed a model for the expected SFS that includes inbreeding by parameterizing individual genotypes using beta-binomial distributions. We then take the convolution of these genotype probabilities to calculate the expected frequency of biallelic variants in the population. Using simulations, we evaluated the model's ability to coestimate demography and inbreeding using one- and two-population models across a range of inbreeding levels. We also applied our method to two empirical examples, American pumas (Puma concolor) and domesticated cabbage (Brassica oleracea var. capitata), inferring models both with and without inbreeding to compare parameter estimates and model fit. Our simulations showed that we are able to accurately coestimate demographic parameters and inbreeding even for highly inbred populations (F = 0.9). In contrast, failing to include inbreeding generally resulted in inaccurate parameter estimates in simulated data and led to poor model fit in our empirical analyses. These results show that inbreeding can have a strong effect on demographic inference, a pattern that was especially noticeable for parameters involving changes in population size. Given the importance of these estimates for informing practices in conservation, agriculture, and elsewhere, our method provides an important advancement for accurately estimating the demographic histories of these species.
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Affiliation(s)
- Paul D Blischak
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ.,Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ
| | - Ryan N Gutenkunst
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ
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15
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Qi X, An H, Hall TE, Di C, Blischak PD, McKibben MTW, Hao Y, Conant GC, Pires JC, Barker MS. Genes derived from ancient polyploidy have higher genetic diversity and are associated with domestication in Brassica rapa. New Phytol 2021; 230:372-386. [PMID: 33452818 DOI: 10.1111/nph.17194] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
Many crops are polyploid or have a polyploid ancestry. Recent phylogenetic analyses have found that polyploidy often preceded the domestication of crop plants. One explanation for this observation is that increased genetic diversity following polyploidy may have been important during the strong artificial selection that occurs during domestication. In order to test the connection between domestication and polyploidy, we identified and examined candidate genes associated with the domestication of the diverse crop varieties of Brassica rapa. Like all 'diploid' flowering plants, B. rapa has a diploidized paleopolyploid genome and experienced many rounds of whole genome duplication (WGD). We analyzed transcriptome data of more than 100 cultivated B. rapa accessions. Using a combination of approaches, we identified > 3000 candidate genes associated with the domestication of four major B. rapa crop varieties. Consistent with our expectation, we found that the candidate genes were significantly enriched with genes derived from the Brassiceae mesohexaploidy. We also observed that paleologs were significantly more diverse than non-paleologs. Our analyses find evidence for that genetic diversity derived from ancient polyploidy played a key role in the domestication of B. rapa and provide support for its importance in the success of modern agriculture.
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Affiliation(s)
- Xinshuai Qi
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Hong An
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Tara E Hall
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Chenlu Di
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Paul D Blischak
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Michael T W McKibben
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Yue Hao
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Gavin C Conant
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
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16
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Marx HE, Jorgensen SA, Wisely E, Li Z, Dlugosch KM, Barker MS. Pilot RNA-seq data from 24 species of vascular plants at Harvard Forest. Appl Plant Sci 2021; 9:e11409. [PMID: 33680580 PMCID: PMC7910807 DOI: 10.1002/aps3.11409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Large-scale projects such as the National Ecological Observatory Network (NEON) collect ecological data on entire biomes to track climate change. NEON provides an opportunity to launch community transcriptomic projects that ask integrative questions in ecology and evolution. We conducted a pilot study to investigate the challenges of collecting RNA-seq data from diverse plant communities. METHODS We generated >650 Gbp of RNA-seq for 24 vascular plant species representing 12 genera and nine families at the Harvard Forest NEON site. Each species was sampled twice in 2016 (July and August). We assessed transcriptome quality and content with TransRate, BUSCO, and Gene Ontology annotations. RESULTS Only modest differences in assembly quality were observed across multiple k-mers. On average, transcriptomes contained hits to >70% of loci in the BUSCO database. We found no significant difference in the number of assembled and annotated transcripts between diploid and polyploid transcriptomes. DISCUSSION We provide new RNA-seq data sets for 24 species of vascular plants in Harvard Forest. Challenges associated with this type of study included recovery of high-quality RNA from diverse species and access to NEON sites for genomic sampling. Overcoming these challenges offers opportunities for large-scale studies at the intersection of ecology and genomics.
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Affiliation(s)
- Hannah E. Marx
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona85721USA
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMichigan48109‐1048USA
| | - Stacy A. Jorgensen
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona85721USA
| | - Eldridge Wisely
- Genetics Graduate Interdisciplinary ProgramUniversity of ArizonaTucsonArizona85721USA
| | - Zheng Li
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona85721USA
| | - Katrina M. Dlugosch
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona85721USA
| | - Michael S. Barker
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona85721USA
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17
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Marx HE, Scheidt S, Barker MS, Dlugosch KM. TagSeq for gene expression in non-model plants: A pilot study at the Santa Rita Experimental Range NEON core site. Appl Plant Sci 2020; 8:e11398. [PMID: 33304661 PMCID: PMC7705334 DOI: 10.1002/aps3.11398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 08/20/2020] [Indexed: 05/12/2023]
Abstract
PREMISE TagSeq is a cost-effective approach for gene expression studies requiring a large number of samples. To date, TagSeq studies in plants have been limited to those with a high-quality reference genome. We tested the suitability of reference transcriptomes for TagSeq in non-model plants, as part of a study of natural gene expression variation at the Santa Rita Experimental Range National Ecological Observatory Network (NEON) core site. METHODS Tissue for TagSeq was sampled from multiple individuals of four species (Bouteloua aristidoides and Eragrostis lehmanniana [Poaceae], Tidestromia lanuginosa [Amaranthaceae], and Parkinsonia florida [Fabaceae]) at two locations on three dates (56 samples total). One sample per species was used to create a reference transcriptome via standard RNA-seq. TagSeq performance was assessed by recovery of reference loci, specificity of tag alignments, and variation among samples. RESULTS A high fraction of tags aligned to each reference and mapped uniquely. Expression patterns were quantifiable for tens of thousands of loci, which revealed consistent spatial differentiation in expression for all species. DISCUSSION TagSeq using de novo reference transcriptomes was an effective approach to quantifying gene expression in this study. Tags were highly locus specific and generated biologically informative profiles for four non-model plant species.
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Affiliation(s)
- Hannah E. Marx
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona85721USA
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMichigan48109‐1048USA
| | - Stephen Scheidt
- Howard University2400 6th Street NWWashingtonD.C.20059USA
- Solar System Exploration DivisionNASA Goddard Space Flight CenterGreenbeltMaryland20771USA
- Center for Research and Exploration in Space Science and TechnologyNASA Goddard Space Flight CenterGreenbeltMaryland20771USA
| | - Michael S. Barker
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona85721USA
| | - Katrina M. Dlugosch
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona85721USA
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18
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Román-Palacios C, Molina-Henao YF, Barker MS. Polyploids increase overall diversity despite higher turnover than diploids in the Brassicaceae. Proc Biol Sci 2020; 287:20200962. [PMID: 32873209 PMCID: PMC7542780 DOI: 10.1098/rspb.2020.0962] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/10/2020] [Indexed: 12/21/2022] Open
Abstract
Although polyploidy is widespread across the plant Tree of Life, its long-term evolutionary significance is still poorly understood. Here, we examine the effects of polyploidy in explaining the large-scale evolutionary patterns within angiosperms by focusing on a single family exhibiting extensive interspecific variation in chromosome numbers. We inferred ploidy from haploid chromosome numbers for 80% of species in the most comprehensive species-level chronogram for the Brassicaceae. After evaluating a total of 94 phylogenetic models of diversification, we found that ploidy influences diversification rates across the Brassicaceae. We also found that despite diversifying at a similar rate to diploids, polyploids have played a significant role in driving present-day differences in species richness among clades. Overall, in addition to highlighting the complexity in the evolutionary consequences of polyploidy, our results suggest that rare successful polyploids persist while significantly contributing to the long-term evolution of clades. Our findings further indicate that polyploidy has played a major role in driving the long-term evolution of the Brassicaceae and highlight the potential of polyploidy in shaping present-day diversity patterns across the plant Tree of Life.
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Affiliation(s)
- Cristian Román-Palacios
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Y. Franchesco Molina-Henao
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- The Arnold Arboretum, Harvard University, Boston, MA 02131, USA
- Departamento de Biología, Universidad del Valle, Cali, Valle 760032, Colombia
| | - Michael S. Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
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Lv Q, Qiu J, Liu J, Li Z, Zhang W, Wang Q, Fang J, Pan J, Chen Z, Cheng W, Barker MS, Huang X, Wei X, Cheng K. The Chimonanthus salicifolius genome provides insight into magnoliid evolution and flavonoid biosynthesis. Plant J 2020; 103:1910-1923. [PMID: 32524692 DOI: 10.1111/tpj.14874] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 05/25/2020] [Accepted: 06/02/2020] [Indexed: 05/11/2023]
Abstract
Chimonanthus salicifolius, a member of the Calycanthaceae of magnoliids, is one of the most famous medicinal plants in Eastern China. Here, we report a chromosome-level genome assembly of C. salicifolius, comprising 820.1 Mb of genomic sequence with a contig N50 of 2.3 Mb and containing 36 651 annotated protein-coding genes. Phylogenetic analyses revealed that magnoliids were sister to the eudicots. Two rounds of ancient whole-genome duplication were inferred in the C. salicifolious genome. One is shared by Calycanthaceae after its divergence with Lauraceae, and the other is in the ancestry of Magnoliales and Laurales. Notably, long genes with > 20 kb in length were much more prevalent in the magnoliid genomes compared with other angiosperms, which could be caused by the length expansion of introns inserted by transposon elements. Homologous genes within the flavonoid pathway for C. salicifolius were identified, and correlation of the gene expression and the contents of flavonoid metabolites revealed potential critical genes involved in flavonoids biosynthesis. This study not only provides an additional whole-genome sequence from the magnoliids, but also opens the door to functional genomic research and molecular breeding of C. salicifolius.
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Affiliation(s)
- Qundan Lv
- Chemical Biology Center, Lishui Institute of Agriculture and Forestry Sciences, Lishui, China
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jie Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, USA
| | - Wenting Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Qin Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jie Fang
- Chemical Biology Center, Lishui Institute of Agriculture and Forestry Sciences, Lishui, China
| | - Junjie Pan
- Chemical Biology Center, Lishui Institute of Agriculture and Forestry Sciences, Lishui, China
| | - Zhengdao Chen
- Chemical Biology Center, Lishui Institute of Agriculture and Forestry Sciences, Lishui, China
| | - Wenliang Cheng
- Chemical Biology Center, Lishui Institute of Agriculture and Forestry Sciences, Lishui, China
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, USA
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xin Wei
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Kejun Cheng
- Chemical Biology Center, Lishui Institute of Agriculture and Forestry Sciences, Lishui, China
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Mabry ME, Brose JM, Blischak PD, Sutherland B, Dismukes WT, Bottoms CA, Edger PP, Washburn JD, An H, Hall JC, McKain MR, Al‐Shehbaz I, Barker MS, Schranz ME, Conant GC, Pires JC. Phylogeny and multiple independent whole-genome duplication events in the Brassicales. Am J Bot 2020; 107:1148-1164. [PMID: 32830865 PMCID: PMC7496422 DOI: 10.1002/ajb2.1514] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 05/05/2020] [Indexed: 05/04/2023]
Abstract
PREMISE Whole-genome duplications (WGDs) are prevalent throughout the evolutionary history of plants. For example, dozens of WGDs have been phylogenetically localized across the order Brassicales, specifically, within the family Brassicaceae. A WGD event has also been identified in the Cleomaceae, the sister family to Brassicaceae, yet its placement, as well as that of WGDs in other families in the order, remains unclear. METHODS Phylo-transcriptomic data were generated and used to infer a nuclear phylogeny for 74 Brassicales taxa. Genome survey sequencing was also performed on 66 of those taxa to infer a chloroplast phylogeny. These phylogenies were used to assess and confirm relationships among the major families of the Brassicales and within Brassicaceae. Multiple WGD inference methods were then used to assess the placement of WGDs on the nuclear phylogeny. RESULTS Well-supported chloroplast and nuclear phylogenies for the Brassicales and the putative placement of the Cleomaceae-specific WGD event Th-ɑ are presented. This work also provides evidence for previously hypothesized WGDs, including a well-supported event shared by at least two members of the Resedaceae family, and a possible event within the Capparaceae. CONCLUSIONS Phylogenetics and the placement of WGDs within highly polyploid lineages continues to be a major challenge. This study adds to the conversation on WGD inference difficulties by demonstrating that sampling is especially important for WGD identification and phylogenetic placement. Given its economic importance and genomic resources, the Brassicales continues to be an ideal group for assessing WGD inference methods.
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Affiliation(s)
- Makenzie E. Mabry
- Division of Biological Sciences and Christopher S. Bond Life Sciences CenterUniversity of MissouriColumbiaMissouri65211USA
| | - Julia M. Brose
- Division of Biological Sciences and Christopher S. Bond Life Sciences CenterUniversity of MissouriColumbiaMissouri65211USA
| | - Paul D. Blischak
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona85719USA
| | - Brittany Sutherland
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona85719USA
| | - Wade T. Dismukes
- Division of Biological Sciences and Christopher S. Bond Life Sciences CenterUniversity of MissouriColumbiaMissouri65211USA
| | - Christopher A. Bottoms
- Informatics Research Core Facility and Christopher S. Bond Life Sciences CenterUniversity of MissouriColumbiaMissouri65211USA
| | - Patrick P. Edger
- Department of HorticultureMichigan State UniversityEast LansingMichigan48824USA
| | | | - Hong An
- Division of Biological Sciences and Christopher S. Bond Life Sciences CenterUniversity of MissouriColumbiaMissouri65211USA
| | - Jocelyn C. Hall
- Department of Biological SciencesUniversity of AlbertaEdmontonT6G 2E9Canada
| | - Michael R. McKain
- Department of Biological SciencesThe University of AlabamaTuscaloosaAlabama35401USA
| | | | - Michael S. Barker
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona85719USA
| | | | - Gavin C. Conant
- Bioinformatics Research CenterProgram in Genetics and Department of Biological SciencesNorth Carolina State UniversityRaleighNorth Carolina27695USA
| | - J. Chris Pires
- Division of Biological Sciences and Christopher S. Bond Life Sciences CenterUniversity of MissouriColumbiaMissouri65211USA
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Wong GKS, Soltis DE, Leebens-Mack J, Wickett NJ, Barker MS, Van de Peer Y, Graham SW, Melkonian M. Sequencing and Analyzing the Transcriptomes of a Thousand Species Across the Tree of Life for Green Plants. Annu Rev Plant Biol 2020; 71:741-765. [PMID: 31851546 DOI: 10.1146/annurev-arplant-042916-041040] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The 1,000 Plants (1KP) initiative was the first large-scale effort to collect next-generation sequencing (NGS) data across a phylogenetically representative sampling of species for a major clade of life, in this case theViridiplantae, or green plants. As an international multidisciplinary consortium, we focused on plant evolution and its practical implications. Among the major outcomes were the inference of a reference species tree for green plants by phylotranscriptomic analysis of low-copy genes, a survey of paleopolyploidy (whole-genome duplications) across the Viridiplantae, the inferred evolutionary histories for many gene families and biological processes, the discovery of novel light-sensitive proteins for optogenetic studies in mammalian neuroscience, and elucidation of the genetic network for a complex trait (C4 photosynthesis). Altogether, 1KP demonstrated how value can be extracted from a phylodiverse sequencing data set, providing a template for future projects that aim to generate even more data, including complete de novo genomes, across the tree of life.
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Affiliation(s)
- Gane Ka-Shu Wong
- Department of Biological Sciences and Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2E9, Canada;
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Douglas E Soltis
- Florida Museum of Natural History, Gainesville, Florida 32611, USA
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Norman J Wickett
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, Illinois 60022, USA
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, VIB Center for Plant Systems Biology, Ghent University, 9052 Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Michael Melkonian
- Faculty of Biology, University of Duisburg-Essen, D-45141 Essen, Germany
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22
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Li FW, Nishiyama T, Waller M, Frangedakis E, Keller J, Li Z, Fernandez-Pozo N, Barker MS, Bennett T, Blázquez MA, Cheng S, Cuming AC, de Vries J, de Vries S, Delaux PM, Diop IS, Harrison CJ, Hauser D, Hernández-García J, Kirbis A, Meeks JC, Monte I, Mutte SK, Neubauer A, Quandt D, Robison T, Shimamura M, Rensing SA, Villarreal JC, Weijers D, Wicke S, Wong GKS, Sakakibara K, Szövényi P. Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts. Nat Plants 2020; 6:259-272. [PMID: 32170292 PMCID: PMC8075897 DOI: 10.1038/s41477-020-0618-2] [Citation(s) in RCA: 150] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/11/2020] [Indexed: 05/12/2023]
Abstract
Hornworts comprise a bryophyte lineage that diverged from other extant land plants >400 million years ago and bears unique biological features, including a distinct sporophyte architecture, cyanobacterial symbiosis and a pyrenoid-based carbon-concentrating mechanism (CCM). Here, we provide three high-quality genomes of Anthoceros hornworts. Phylogenomic analyses place hornworts as a sister clade to liverworts plus mosses with high support. The Anthoceros genomes lack repeat-dense centromeres as well as whole-genome duplication, and contain a limited transcription factor repertoire. Several genes involved in angiosperm meristem and stomatal function are conserved in Anthoceros and upregulated during sporophyte development, suggesting possible homologies at the genetic level. We identified candidate genes involved in cyanobacterial symbiosis and found that LCIB, a Chlamydomonas CCM gene, is present in hornworts but absent in other plant lineages, implying a possible conserved role in CCM function. We anticipate that these hornwort genomes will serve as essential references for future hornwort research and comparative studies across land plants.
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Affiliation(s)
- Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA.
- Plant Biology Section, Cornell University, Ithaca, NY, USA.
| | - Tomoaki Nishiyama
- Advanced Science Research Center, Kanazawa University, Ishikawa, Japan
| | - Manuel Waller
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | | | - Jean Keller
- LRSV, Université de Toulouse, CNRS, UPS Castanet-Tolosan, Toulouse, France
| | - Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | | | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Tom Bennett
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Miguel A Blázquez
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica de Valencia, Valencia, Spain
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Andrew C Cuming
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Jan de Vries
- Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Georg-August University Göttingen, Göttingen, Germany
| | - Sophie de Vries
- Institute of Population Genetics, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Pierre-Marc Delaux
- LRSV, Université de Toulouse, CNRS, UPS Castanet-Tolosan, Toulouse, France
| | - Issa S Diop
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - C Jill Harrison
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - Jorge Hernández-García
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica de Valencia, Valencia, Spain
| | - Alexander Kirbis
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - John C Meeks
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, USA
| | - Isabel Monte
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Sumanth K Mutte
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Anna Neubauer
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Dietmar Quandt
- Nees Institute for Biodiversity of Plants, University of Bonn, Bonn, Germany
| | - Tanner Robison
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
| | - Masaki Shimamura
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Stefan A Rensing
- Faculty of Biology, Philipps University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Marburg, Germany
| | - Juan Carlos Villarreal
- Department of Biology, Laval University, Quebec City, Quebec, Canada
- Smithsonian Tropical Research Institute, Balboa, Panamá
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Susann Wicke
- Institute for Evolution and Biodiversity, University of Muenster, Münster, Germany
| | - Gane K-S Wong
- Department of Biological Sciences, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
- BGI-Shenzhen, Shenzhen, China
| | | | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland.
- Zurich-Basel Plant Science Center, Zurich, Switzerland.
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23
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Li Z, Barker MS. Inferring putative ancient whole-genome duplications in the 1000 Plants (1KP) initiative: access to gene family phylogenies and age distributions. Gigascience 2020; 9:giaa004. [PMID: 32043527 PMCID: PMC7011446 DOI: 10.1093/gigascience/giaa004] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 12/10/2019] [Accepted: 01/10/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Polyploidy, or whole-genome duplications (WGDs), repeatedly occurred during green plant evolution. To examine the evolutionary history of green plants in a phylogenomic framework, the 1KP project sequenced >1,000 transcriptomes across the Viridiplantae. The 1KP project provided a unique opportunity to study the distribution and occurrence of WGDs across the green plants. As an accompaniment to the capstone publication, this article provides expanded methodological details, results validation, and descriptions of newly released datasets that will aid researchers who wish to use the extended data generated by the 1KP project. RESULTS In the 1KP capstone analyses, we used a total evidence approach that combined inferences of WGDs from Ks and phylogenomic methods to infer and place 244 putative ancient WGDs across the Viridiplantae. Here, we provide an expanded explanation of our approach by describing our methodology and walk-through examples. We also evaluated the consistency of our WGD inferences by comparing them to evidence from published syntenic analyses of plant genome assemblies. We find that our inferences are consistent with whole-genome synteny analyses and our total evidence approach may minimize the false-positive rate throughout the dataset. CONCLUSIONS We release 383,679 nuclear gene family phylogenies and 2,306 gene age distributions with Ks plots from the 1KP capstone paper. These resources will be useful for many future analyses on gene and genome evolution in green plants.
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Affiliation(s)
- Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E. Lowell St., Tucson, AZ 85721, USA
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E. Lowell St., Tucson, AZ 85721, USA
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24
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Baniaga AE, Marx HE, Arrigo N, Barker MS. Polyploid plants have faster rates of multivariate niche differentiation than their diploid relatives. Ecol Lett 2019; 23:68-78. [PMID: 31637845 DOI: 10.1111/ele.13402] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/01/2019] [Accepted: 09/16/2019] [Indexed: 01/02/2023]
Abstract
Polyploid speciation entails substantial and rapid postzygotic reproductive isolation of nascent species that are initially sympatric with one or both parents. Despite strong postzygotic isolation, ecological niche differentiation has long been thought to be important for polyploid success. Using biogeographic data from across vascular plants, we tested whether the climatic niches of polyploid species are more differentiated than their diploid relatives and if the climatic niches of polyploid species differentiated faster than those of related diploids. We found that polyploids are often more climatically differentiated from their diploid parents than the diploids are from each other. Consistent with this pattern, we estimated that polyploid species generally have higher rates of multivariate niche differentiation than their diploid relatives. In contrast to recent analyses, our results confirm that ecological niche differentiation is an important component of polyploid speciation and that niche differentiation is often significantly faster in polyploids.
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Affiliation(s)
- Anthony E Baniaga
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Hannah E Marx
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Nils Arrigo
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
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25
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Martin AK, Barker MS, Gibson EC, Robinson GA. Response initiation and inhibition and the relationship with fluid intelligence across the adult lifespan. Arch Clin Neuropsychol 2019; 36:231-242. [DOI: 10.1093/arclin/acz044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 01/03/2019] [Accepted: 08/14/2019] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Cognitive processes associated with frontal lobe functioning are often termed “executive functions.” Two such processes are initiation and inhibition or the starting and stopping of responses. It has recently been claimed dysfunction of executive abilities can be explained by a single measure of fluid intelligence. Here, we test this claim, specifically for the executive abilities of response initiation and inhibition, across the healthy lifespan.
Method
In a cohort of 336 healthy adults (18–89 years), initiation and inhibition were assessed with the Hayling test, Stroop test, and phonemic and semantic verbal fluency. All participants also completed a measure of fluid intelligence. The relationship between fluid intelligence and executive measures was explored across the lifespan using a continuous approach. Mediation models were computed to assess whether age-related decline across the four initiation/inhibition tasks could be fully explained by a single measure of fluid intelligence.
Results
Age was negatively correlated with response initiation/inhibition and fluid intelligence. The mediation analyses identified only partial mediation of fluid intelligence for age and Hayling performance. By contrast, fluid intelligence did not mediate performance on the Stroop test or phonemic and semantic verbal fluency.
Conclusions
Response initiation/inhibition are not able to be explained by fluid intelligence. The results support a multifactorial theory of executive functions and provide evidence for the inclusion of multiple specific executive measures in a thorough neuropsychological assessment of age-related cognitive decline.
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Affiliation(s)
- A K Martin
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
- Department of Psychology, Durham University, Durham, UK
| | - M S Barker
- Neuropsychology Research Unit, School of Psychology, The University of Queensland, Brisbane, Queensland, Australia
- Taub Institute, Department of Neurology, Columbia University Medical Centre, New York, USA
| | - E C Gibson
- Neuropsychology Research Unit, School of Psychology, The University of Queensland, Brisbane, Queensland, Australia
| | - G A Robinson
- Neuropsychology Research Unit, School of Psychology, The University of Queensland, Brisbane, Queensland, Australia
- Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
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26
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Carpenter EJ, Matasci N, Ayyampalayam S, Wu S, Sun J, Yu J, Jimenez Vieira FR, Bowler C, Dorrell RG, Gitzendanner MA, Li L, Du W, K. Ullrich K, Wickett NJ, Barkmann TJ, Barker MS, Leebens-Mack JH, Wong GKS. Access to RNA-sequencing data from 1,173 plant species: The 1000 Plant transcriptomes initiative (1KP). Gigascience 2019; 8:giz126. [PMID: 31644802 PMCID: PMC6808545 DOI: 10.1093/gigascience/giz126] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/08/2019] [Accepted: 09/28/2019] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The 1000 Plant transcriptomes initiative (1KP) explored genetic diversity by sequencing RNA from 1,342 samples representing 1,173 species of green plants (Viridiplantae). FINDINGS This data release accompanies the initiative's final/capstone publication on a set of 3 analyses inferring species trees, whole genome duplications, and gene family expansions. These and previous analyses are based on de novo transcriptome assemblies and related gene predictions. Here, we assess their data and assembly qualities and explain how we detected potential contaminations. CONCLUSIONS These data will be useful to plant and/or evolutionary scientists with interests in particular gene families, either across the green plant tree of life or in more focused lineages.
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Affiliation(s)
- Eric J Carpenter
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Naim Matasci
- CyVerse, University of Arizona, AZ,1657 East Helen St, Tucson AZ, USA 85721 USA
| | | | - Shuangxiu Wu
- CAS Key Laboratory of Genome Sciences and Information, Beijing, Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Sun
- CAS Key Laboratory of Genome Sciences and Information, Beijing, Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing, Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Fabio Rocha Jimenez Vieira
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Chris Bowler
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Richard G Dorrell
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | | | - Ling Li
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Wensi Du
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Kristian K. Ullrich
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Norman J Wickett
- Chicago Botanic Garden, Glencoe, IL 60022
- Program in Biological Sciences, Northwestern University, Evanston, IL 60208, USA
| | - Todd J Barkmann
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008-5410, USA
| | - Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | | | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada
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27
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An H, Qi X, Gaynor ML, Hao Y, Gebken SC, Mabry ME, McAlvay AC, Teakle GR, Conant GC, Barker MS, Fu T, Yi B, Pires JC. Transcriptome and organellar sequencing highlights the complex origin and diversification of allotetraploid Brassica napus. Nat Commun 2019; 10:2878. [PMID: 31253789 PMCID: PMC6599199 DOI: 10.1038/s41467-019-10757-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 05/31/2019] [Indexed: 12/19/2022] Open
Abstract
Brassica napus, an allotetraploid crop, is hypothesized to be a hybrid from unknown varieties of Brassica rapa and Brassica oleracea. Despite the economic importance of B. napus, much is unresolved regarding its phylogenomic relationships, genetic structure, and diversification. Here we conduct a comprehensive study among diverse accessions from 183 B. napus (including rapeseed, rutabaga, and Siberian kale), 112 B. rapa, and 62 B. oleracea and its wild relatives. Using RNA-seq of B. napus accessions, we define the genetic diversity and sub-genome variance of six genetic clusters. Nuclear and organellar phylogenies for B. napus and its progenitors reveal varying patterns of inheritance and post-formation introgression. We discern regions with signatures of selective sweeps and detect 8,187 differentially expressed genes with implications for B. napus diversification. This study highlights the complex origin and evolution of B. napus providing insights that can further facilitate B. napus breeding and germplasm preservation.
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Affiliation(s)
- Hong An
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, P. R. China
| | - Xinshuai Qi
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Michelle L Gaynor
- Department of Biology, University of Central Florida, Orlando, FL, 32816, USA
| | - Yue Hao
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Sarah C Gebken
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Makenzie E Mabry
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Alex C McAlvay
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14850, USA
| | - Graham R Teakle
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Gavin C Conant
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Tingdong Fu
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, P. R. China
| | - Bin Yi
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, P. R. China.
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA.
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28
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Tiley GP, Barker MS, Burleigh JG. Assessing the Performance of Ks Plots for Detecting Ancient Whole Genome Duplications. Genome Biol Evol 2018; 10:2882-2898. [PMID: 30239709 PMCID: PMC6225891 DOI: 10.1093/gbe/evy200] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2018] [Indexed: 02/06/2023] Open
Abstract
Genomic data have provided evidence of previously unknown ancient whole genome duplications (WGDs) and highlighted the role of WGDs in the evolution of many eukaryotic lineages. Ancient WGDs often are detected by examining distributions of synonymous substitutions per site (Ks) within a genome, or “Ks plots.” For example, WGDs can be detected from Ks plots by using univariate mixture models to identify peaks in Ks distributions. We performed gene family simulation experiments to evaluate the effects of different Ks estimation methods and mixture models on our ability to detect ancient WGDs from Ks plots. The simulation experiments, which accounted for variation in substitution rates and gene duplication and loss rates across gene families, tested the effects of WGD age and gene retention rates following WGD on inferring WGDs from Ks plots. Our simulations reveal limitations of Ks plot analyses. Strict interpretations of mixture model analyses often overestimate the number of WGD events, and Ks plot analyses typically fail to detect WGDs when ≤10% of the duplicated genes are retained following the WGD. However, WGDs can accurately be characterized over an intermediate range of Ks. The simulation results are supported by empirical analyses of transcriptomic data, which also suggest that biases in gene retention likely affect our ability to detect ancient WGDs. Although our results indicate mixture model results should be interpreted with great caution, using node-averaged Ks estimates and applying more appropriate mixture models can improve the accuracy of detecting WGDs.
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Affiliation(s)
- George P Tiley
- Department of Biology, University of Florida.,Department of Biology, Duke University
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona
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29
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Li FW, Brouwer P, Carretero-Paulet L, Cheng S, de Vries J, Delaux PM, Eily A, Koppers N, Kuo LY, Li Z, Simenc M, Small I, Wafula E, Angarita S, Barker MS, Bräutigam A, dePamphilis C, Gould S, Hosmani PS, Huang YM, Huettel B, Kato Y, Liu X, Maere S, McDowell R, Mueller LA, Nierop KGJ, Rensing SA, Robison T, Rothfels CJ, Sigel EM, Song Y, Timilsena PR, Van de Peer Y, Wang H, Wilhelmsson PKI, Wolf PG, Xu X, Der JP, Schluepmann H, Wong GKS, Pryer KM. Fern genomes elucidate land plant evolution and cyanobacterial symbioses. Nat Plants 2018; 4:460-472. [PMID: 29967517 PMCID: PMC6786969 DOI: 10.1038/s41477-018-0188-8] [Citation(s) in RCA: 246] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/24/2018] [Indexed: 05/18/2023]
Abstract
Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata (Salviniales) and present evidence for episodic whole-genome duplication in ferns-one at the base of 'core leptosporangiates' and one specific to Azolla. One fern-specific gene that we identified, recently shown to confer high insect resistance, seems to have been derived from bacteria through horizontal gene transfer. Azolla coexists in a unique symbiosis with N2-fixing cyanobacteria, and we demonstrate a clear pattern of cospeciation between the two partners. Furthermore, the Azolla genome lacks genes that are common to arbuscular mycorrhizal and root nodule symbioses, and we identify several putative transporter genes specific to Azolla-cyanobacterial symbiosis. These genomic resources will help in exploring the biotechnological potential of Azolla and address fundamental questions in the evolution of plant life.
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Affiliation(s)
- Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA.
- Plant Biology Section, Cornell University, Ithaca, NY, USA.
| | - Paul Brouwer
- Molecular Plant Physiology Department, Utrecht University, Utrecht, the Netherlands
| | - Lorenzo Carretero-Paulet
- Bioinformatics Institute Ghent and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Shifeng Cheng
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | - Jan de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Castanet Tolosan, France
| | - Ariana Eily
- Department of Biology, Duke University, Durham, NC, USA
| | - Nils Koppers
- Department of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Dusseldorf, Germany
| | | | - Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Mathew Simenc
- Department of Biological Science, California State University, Fullerton, CA, USA
| | - Ian Small
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Eric Wafula
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Stephany Angarita
- Department of Biological Science, California State University, Fullerton, CA, USA
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | | | - Claude dePamphilis
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Sven Gould
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Dusseldorf, Germany
| | | | | | - Bruno Huettel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding, Cologne, Germany
| | - Yoichiro Kato
- Institute for Sustainable Agro-ecosystem Services, University of Tokyo, Tokyo, Japan
| | - Xin Liu
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | - Steven Maere
- Bioinformatics Institute Ghent and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Rose McDowell
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | | | - Klaas G J Nierop
- Geolab, Faculty of Geosciences, Utrecht University, Utrecht, the Netherlands
| | | | - Tanner Robison
- Department of Biology, Utah State University, Logan, UT, USA
| | - Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Erin M Sigel
- Department of Biology, University of Louisiana, Lafayette, LA, USA
| | - Yue Song
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | - Prakash R Timilsena
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Yves Van de Peer
- Bioinformatics Institute Ghent and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Hongli Wang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | | | - Paul G Wolf
- Department of Biology, Utah State University, Logan, UT, USA
| | - Xun Xu
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | - Joshua P Der
- Department of Biological Science, California State University, Fullerton, CA, USA
| | | | - Gane K-S Wong
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- Department of Biological Sciences, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
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30
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Landis JB, Soltis DE, Li Z, Marx HE, Barker MS, Tank DC, Soltis PS. Impact of whole-genome duplication events on diversification rates in angiosperms. Am J Bot 2018; 105:348-363. [PMID: 29719043 DOI: 10.1002/ajb2.1060] [Citation(s) in RCA: 171] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/12/2017] [Indexed: 05/18/2023]
Abstract
PREMISE OF THE STUDY Polyploidy or whole-genome duplication (WGD) pervades the evolutionary history of angiosperms. Despite extensive progress in our understanding of WGD, the role of these events in promoting diversification is still not well understood. We seek to clarify the possible association between WGD and diversification rates in flowering plants. METHODS Using a previously published phylogeny spanning all land plants (31,749 tips) and WGD events inferred from analyses of the 1000 Plants (1KP) transcriptome data, we analyzed the association of WGDs and diversification rates following numerous WGD events across the angiosperms. We used a stepwise AIC approach (MEDUSA), a Bayesian mixture model approach (BAMM), and state-dependent diversification analyses (MuSSE) to investigate patterns of diversification. Sister-clade comparisons were used to investigate species richness after WGDs. KEY RESULTS Based on the density of 1KP taxon sampling, 106 WGDs were unambiguously placed on the angiosperm phylogeny. We identified 334-530 shifts in diversification rates. We found that 61 WGD events were tightly linked to changes in diversification rates, and state-dependent diversification analyses indicated higher speciation rates for subsequent rounds of WGD. Additionally, 70 of 99 WGD events showed an increase in species richness compared to the sister clade. CONCLUSIONS Forty-six of the 106 WGDs analyzed appear to be closely associated with upshifts in the rate of diversification in angiosperms. Shifts in diversification do not appear more likely than random within a four-node lag phase following a WGD; however, younger WGD events are more likely to be followed by an upshift in diversification than older WGD events.
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Affiliation(s)
- Jacob B Landis
- Department of Botany and Plant Sciences, University of California-Riverside, Riverside, California, 92521, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, Florida, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, 32611, USA
| | - Zheng Li
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona, 85721, USA
| | - Hannah E Marx
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona, 85721, USA
| | - Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona, 85721, USA
| | - David C Tank
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, 83844, USA
- Stillinger Herbarium, University of Idaho, Moscow, Idaho, 83844, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, 32611, USA
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31
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Barker MS. A Gneato nuclear genome. Nat Plants 2018; 4:63-64. [PMID: 29379154 DOI: 10.1038/s41477-018-0102-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Affiliation(s)
- Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.
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32
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Mandáková T, Li Z, Barker MS, Lysak MA. Diverse genome organization following 13 independent mesopolyploid events in Brassicaceae contrasts with convergent patterns of gene retention. Plant J 2017; 91:3-21. [PMID: 28370611 DOI: 10.1111/tpj.13553] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/17/2017] [Accepted: 03/23/2017] [Indexed: 05/10/2023]
Abstract
Hybridization and polyploidy followed by genome-wide diploidization had a significant impact on the diversification of land plants. The ancient At-α whole-genome duplication (WGD) preceded the diversification of crucifers (Brassicaceae). Some genera and tribes also experienced younger, mesopolyploid WGDs concealed by subsequent genome diploidization. Here we tested if multiple base chromosome numbers originated due to genome diploidization after independent mesopolyploid WGDs and how diploidization affected post-polyploid gene retention. Sixteen species representing 10 Brassicaceae tribes were analyzed by comparative chromosome painting and/or whole-transcriptome analysis of gene age distributions and phylogenetic analyses of gene duplications. Overall, we found evidence for at least 13 independent mesopolyploidies followed by different degrees of diploidization across the Brassicaceae. New mesotetraploid events were uncovered for the tribes Anastaticeae, Iberideae and Schizopetaleae, and mesohexaploid WGDs for Cochlearieae and Physarieae. In contrast, we found convergent patterns of gene retention and loss among these independent WGDs. Our combined analyses of genomic data for Brassicaceae indicate that extant chromosome number variation in many plant groups, and especially monophyletic taxa with multiple base chromosome numbers, can result from clade-specific genome duplications followed by diploidization. Our observation of parallel gene retention and loss across multiple independent WGDs provides one of the first multi-species tests of the predictability of patterns of post-polyploid genome evolution.
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Affiliation(s)
- Terezie Mandáková
- Plant Cytogenomics Research Group, CEITEC-Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
| | - Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Martin A Lysak
- Plant Cytogenomics Research Group, CEITEC-Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
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33
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Qi X, An H, Ragsdale AP, Hall TE, Gutenkunst RN, Chris Pires J, Barker MS. Genomic inferences of domestication events are corroborated by written records in Brassica rapa. Mol Ecol 2017; 26:3373-3388. [PMID: 28371014 DOI: 10.1111/mec.14131] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/15/2017] [Accepted: 03/17/2017] [Indexed: 12/26/2022]
Abstract
Demographic modelling is often used with population genomic data to infer the relationships and ages among populations. However, relatively few analyses are able to validate these inferences with independent data. Here, we leverage written records that describe distinct Brassica rapa crops to corroborate demographic models of domestication. Brassica rapa crops are renowned for their outstanding morphological diversity, but the relationships and order of domestication remain unclear. We generated genomewide SNPs from 126 accessions collected globally using high-throughput transcriptome data. Analyses of more than 31,000 SNPs across the B. rapa genome revealed evidence for five distinct genetic groups and supported a European-Central Asian origin of B. rapa crops. Our results supported the traditionally recognized South Asian and East Asian B. rapa groups with evidence that pak choi, Chinese cabbage and yellow sarson are likely monophyletic groups. In contrast, the oil-type B. rapa subsp. oleifera and brown sarson were polyphyletic. We also found no evidence to support the contention that rapini is the wild type or the earliest domesticated subspecies of B. rapa. Demographic analyses suggested that B. rapa was introduced to Asia 2,400-4,100 years ago, and that Chinese cabbage originated 1,200-2,100 years ago via admixture of pak choi and European-Central Asian B. rapa. We also inferred significantly different levels of founder effect among the B. rapa subspecies. Written records from antiquity that document these crops are consistent with these inferences. The concordance between our age estimates of domestication events with historical records provides unique support for our demographic inferences.
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Affiliation(s)
- Xinshuai Qi
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Hong An
- Division of Biological Sciences, University of Missouri, Columbia, MI, USA.,National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Aaron P Ragsdale
- Program in Applied Mathematics, University of Arizona, Tucson, AZ, USA
| | - Tara E Hall
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Ryan N Gutenkunst
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MI, USA
| | - Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, USA
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34
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Barker MS, Li Z, Kidder TI, Reardon CR, Lai Z, Oliveira LO, Scascitelli M, Rieseberg LH. Most Compositae (Asteraceae) are descendants of a paleohexaploid and all share a paleotetraploid ancestor with the Calyceraceae. Am J Bot 2016; 103:1203-11. [PMID: 27313199 DOI: 10.3732/ajb.1600113] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 05/06/2016] [Indexed: 05/20/2023]
Abstract
PREMISE OF THE STUDY Like many other flowering plants, members of the Compositae (Asteraceae) have a polyploid ancestry. Previous analyses found evidence for an ancient duplication or possibly triplication in the early evolutionary history of the family. We sought to better place this paleopolyploidy in the phylogeny and assess its nature. METHODS We sequenced new transcriptomes for Barnadesia, the lineage sister to all other Compositae, and four representatives of closely related families. Using a recently developed algorithm, MAPS, we analyzed nuclear gene family phylogenies for evidence of paleopolyploidy. KEY RESULTS We found that the previously recognized Compositae paleopolyploidy is also in the ancestry of the Calyceraceae. Our phylogenomic analyses uncovered evidence for a successive second round of genome duplication among all sampled Compositae except Barnadesia. CONCLUSIONS Our analyses of new samples with new tools provide a revised view of paleopolyploidy in the Compositae. Together with results from a high density Lactuca linkage map, our results suggest that the Compositae and Calyceraceae have a common paleotetraploid ancestor and that most Compositae are descendants of a paleohexaploid. Although paleohexaploids have been previously identified, this is the first example where the paleotetraploid and paleohexaploid lineages have survived over tens of millions of years. The complex polyploidy in the ancestry of the Compositae and Calyceraceae represents a unique opportunity to study the long-term evolutionary fates and consequences of different ploidal levels.
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Affiliation(s)
- Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, P. O. Box 210088, Tucson, Arizona 85721 USA
| | - Zheng Li
- Department of Ecology & Evolutionary Biology, University of Arizona, P. O. Box 210088, Tucson, Arizona 85721 USA
| | - Thomas I Kidder
- Department of Ecology & Evolutionary Biology, University of Arizona, P. O. Box 210088, Tucson, Arizona 85721 USA
| | - Chris R Reardon
- Department of Ecology & Evolutionary Biology, University of Arizona, P. O. Box 210088, Tucson, Arizona 85721 USA
| | - Zhao Lai
- Department of Biology and Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana 47405 USA
| | - Luiz O Oliveira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa 36570-900, Viçosa, Brazil
| | - Moira Scascitelli
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, V6T 1Z4 Canada
| | - Loren H Rieseberg
- Department of Biology and Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana 47405 USA Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, V6T 1Z4 Canada
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Barker MS, Husband BC, Pires JC. Spreading Winge and flying high: The evolutionary importance of polyploidy after a century of study. Am J Bot 2016; 103:1139-45. [PMID: 27480249 DOI: 10.3732/ajb.1600272] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 07/20/2016] [Indexed: 05/10/2023]
Affiliation(s)
- Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona 85721 USA
| | - Brian C Husband
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1 Canada
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 USA
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36
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Arrigo N, de La Harpe M, Litsios G, Zozomová-Lihová J, Španiel S, Marhold K, Barker MS, Alvarez N. Is hybridization driving the evolution of climatic niche in Alyssum montanum. Am J Bot 2016; 103:1348-57. [PMID: 27206461 DOI: 10.3732/ajb.1500368] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 02/12/2016] [Indexed: 05/20/2023]
Abstract
PREMISE OF THE STUDY After decades of interest, the contribution of hybridization to ecological diversification remains unclear. Hybridization is a potent source of novelty, but nascent hybrid lineages must overcome reproductive and ecological competition from their parental species. Here, we assess whether hybrid speciation is advantageous over alternative modes of speciation, by comparing the geographical and ecological ranges and climatic niche evolutionary rates of stabilized allopolyploid vs. autopolyploids in the Alyssum montanum species complex. METHODS We combined an extensive review of studies addressing the systematics and genetic diversity of A. montanum s.l., with flow cytometry and cloning of nuclear markers, to establish the ploidy level and putative hybrid nature of 205 populations. The respective geographic distribution and climatic niche evolution dynamics of the allo- and autopolyploids were investigated using multivariate analyses and comparative phylogenetic approaches. KEY RESULTS As expected by theory, allopolyploids occur mainly along contact zones and are generally spatially overlapping with their diploid counterparts. However, they demonstrate higher rates of niche evolution and expand into different climatic conditions than those of their diploid congeners. In contrast, autopolyploids show lower rates of niche evolution, occupy ecological niches similar to their ancestors and are restricted to less competitive and peripheral geographic areas. CONCLUSIONS Hybridization thus seems advantageous by promoting ecological niche evolution and more readily allowing escape from competitive exclusion.
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Affiliation(s)
- Nils Arrigo
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Marylaure de La Harpe
- Unit of Ecology & Evolution, Department of Biology, University of Fribourg, CH-1700 Fribourg, Switzerland
| | - Glenn Litsios
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Judita Zozomová-Lihová
- Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84523 Bratislava, Slovakia
| | - Stanislav Španiel
- Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84523 Bratislava, Slovakia Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-12801 Praha 2, Czech Republic
| | - Karol Marhold
- Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84523 Bratislava, Slovakia Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-12801 Praha 2, Czech Republic
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, P.O. Box 210088, Tucson, Arizona 85721 USA
| | - Nadir Alvarez
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
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Abstract
The haploid nuclear genome size (1C DNA) of vascular land plants varies over several orders of magnitude. Much of this observed diversity in genome size is due to the proliferation and deletion of transposable elements. To date, all vascular land plant lineages with extremely small nuclear genomes represent recently derived states, having ancestors with much larger genome sizes. The Selaginellaceae represent an ancient lineage with extremely small genomes. It is unclear how small nuclear genomes evolved in Selaginella We compared the rates of nuclear genome size evolution in Selaginella and major vascular plant clades in a comparative phylogenetic framework. For the analyses, we collected 29 new flow cytometry estimates of haploid genome size in Selaginella to augment publicly available data. Selaginella possess some of the smallest known haploid nuclear genome sizes, as well as the lowest rate of genome size evolution observed across all vascular land plants included in our analyses. Additionally, our analyses provide strong support for a history of haploid nuclear genome size stasis in Selaginella Our results indicate that Selaginella, similar to other early diverging lineages of vascular land plants, has relatively low rates of genome size evolution. Further, our analyses highlight that a rapid transition to a small genome size is only one route to an extremely small genome.
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Affiliation(s)
| | - Nils Arrigo
- Department of Ecology & Evolutionary Biology, University of Arizona Department of Ecology & Evolution, University of Lausanne, Switzerland
| | - Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona
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Marques I, Montgomery SA, Barker MS, Macfarlane TD, Conran JG, Catalán P, Rieseberg LH, Rudall PJ, Graham SW. Transcriptome-derived evidence supports recent polyploidization and a major phylogeographic division in Trithuria submersa (Hydatellaceae, Nymphaeales). New Phytol 2016; 210:310-323. [PMID: 26612464 DOI: 10.1111/nph.13755] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 10/12/2015] [Indexed: 06/05/2023]
Abstract
Relatively little is known about species-level genetic diversity in flowering plants outside the eudicots and monocots, and it is often unclear how to interpret genetic patterns in lineages with whole-genome duplications. We addressed these issues in a polyploid representative of Hydatellaceae, part of the water-lily order Nymphaeales. We examined a transcriptome of Trithuria submersa for evidence of recent whole-genome duplication, and applied transcriptome-derived microsatellite (expressed-sequence tag simple-sequence repeat (EST-SSR)) primers to survey genetic variation in populations across its range in mainland Australia. A transcriptome-based Ks plot revealed at least one recent polyploidization event, consistent with fixed heterozygous genotypes representing underlying sets of homeologous loci. A strong genetic division coincides with a trans-Nullarbor biogeographic boundary. Patterns of 'allelic' variation (no more than two variants per EST-SSR genotype) and recently published chromosomal evidence are consistent with the predicted polyploidization event and substantial homozygosity underlying fixed heterozygote SSR genotypes, which in turn reflect a selfing mating system. The Nullarbor Plain is a barrier to gene flow between two deep lineages of T. submersa that may represent cryptic species. The markers developed here should also be useful for further disentangling species relationships, and provide a first step towards future genomic studies in Trithuria.
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Affiliation(s)
- Isabel Marques
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, 6804 Marine Drive SW, Vancouver, BC, V6T 1Z4, Canada
- Department of Agricultural and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, C/Carretera de Cuarte Km 1, Huesca, E22071, Spain
| | - Sean A Montgomery
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, 6804 Marine Drive SW, Vancouver, BC, V6T 1Z4, Canada
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Terry D Macfarlane
- Western Australian Herbarium, Science and Conservation Division, Department of Parks and Wildlife, Locked Bag 104, Bentley Delivery Centre, Bentley, WA, 6983, Australia
| | - John G Conran
- School of Biological Sciences, Australian Centre for Evolutionary Biology and Biodiversity & Sprigg Geobiology Centre, The University of Adelaide, Benham Bldg DX 650 312, Adelaide, SA, 5005, Australia
| | - Pilar Catalán
- Department of Agricultural and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, C/Carretera de Cuarte Km 1, Huesca, E22071, Spain
- Department of Botany, Institute of Biology, Tomsk State University, Lenin Av. 36, Tomsk, 634050, Russia
| | - Loren H Rieseberg
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - Paula J Rudall
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Sean W Graham
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, 6804 Marine Drive SW, Vancouver, BC, V6T 1Z4, Canada
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Affiliation(s)
- Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Nils Arrigo
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
- Department of Ecology and Evolution, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Anthony E Baniaga
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Donald A Levin
- Section of Integrative Biology, University of Texas, Austin, TX, 78713, USA
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Li Z, Baniaga AE, Sessa EB, Scascitelli M, Graham SW, Rieseberg LH, Barker MS. Early genome duplications in conifers and other seed plants. Sci Adv 2015; 1:e1501084. [PMID: 26702445 PMCID: PMC4681332 DOI: 10.1126/sciadv.1501084] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/14/2015] [Indexed: 05/18/2023]
Abstract
Polyploidy is a common mode of speciation and evolution in angiosperms (flowering plants). In contrast, there is little evidence to date that whole genome duplication (WGD) has played a significant role in the evolution of their putative extant sister lineage, the gymnosperms. Recent analyses of the spruce genome, the first published conifer genome, failed to detect evidence of WGDs in gene age distributions and attributed many aspects of conifer biology to a lack of WGDs. We present evidence for three ancient genome duplications during the evolution of gymnosperms, based on phylogenomic analyses of transcriptomes from 24 gymnosperms and 3 outgroups. We use a new algorithm to place these WGD events in phylogenetic context: two in the ancestry of major conifer clades (Pinaceae and cupressophyte conifers) and one in Welwitschia (Gnetales). We also confirm that a WGD hypothesized to be restricted to seed plants is indeed not shared with ferns and relatives (monilophytes), a result that was unclear in earlier studies. Contrary to previous genomic research that reported an absence of polyploidy in the ancestry of contemporary gymnosperms, our analyses indicate that polyploidy has contributed to the evolution of conifers and other gymnosperms. As in the flowering plants, the evolution of the large genome sizes of gymnosperms involved both polyploidy and repetitive element activity.
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Affiliation(s)
- Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Anthony E. Baniaga
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Emily B. Sessa
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Moira Scascitelli
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Sean W. Graham
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Loren H. Rieseberg
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Michael S. Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Corresponding author. E-mail:
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Mayrose I, Zhan SH, Rothfels CJ, Arrigo N, Barker MS, Rieseberg LH, Otto SP. Methods for studying polyploid diversification and the dead end hypothesis: a reply to Soltis et al. (2014). New Phytol 2015; 206:27-35. [PMID: 25472785 DOI: 10.1111/nph.13192] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Affiliation(s)
- Itay Mayrose
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Shing H Zhan
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6J 3S7, Canada
| | - Carl J Rothfels
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6J 3S7, Canada
| | - Nils Arrigo
- Department of Ecology and Evolution, University of Lausanne, CH - 105, Lausanne, Switzerland
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Loren H Rieseberg
- Department of Botany & Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6J 3S7, Canada
| | - Sarah P Otto
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6J 3S7, Canada
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Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter E, Matasci N, Ayyampalayam S, Barker MS, Burleigh JG, Gitzendanner MA, Ruhfel BR, Wafula E, Der JP, Graham SW, Mathews S, Melkonian M, Soltis DE, Soltis PS, Miles NW, Rothfels CJ, Pokorny L, Shaw AJ, DeGironimo L, Stevenson DW, Surek B, Villarreal JC, Roure B, Philippe H, dePamphilis CW, Chen T, Deyholos MK, Baucom RS, Kutchan TM, Augustin MM, Wang J, Zhang Y, Tian Z, Yan Z, Wu X, Sun X, Wong GKS, Leebens-Mack J. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proc Natl Acad Sci U S A 2014; 111:E4859-68. [PMID: 25355905 PMCID: PMC4234587 DOI: 10.1073/pnas.1323926111] [Citation(s) in RCA: 748] [Impact Index Per Article: 74.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.
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Affiliation(s)
- Norman J Wickett
- Chicago Botanic Garden, Glencoe, IL 60022; Program in Biological Sciences, Northwestern University, Evanston, IL 60208;
| | - Siavash Mirarab
- Department of Computer Science, University of Texas, Austin, TX 78712
| | - Nam Nguyen
- Department of Computer Science, University of Texas, Austin, TX 78712
| | - Tandy Warnow
- Department of Computer Science, University of Texas, Austin, TX 78712
| | - Eric Carpenter
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
| | - Naim Matasci
- iPlant Collaborative, Tucson, AZ 85721; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721
| | | | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721
| | | | - Matthew A Gitzendanner
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611
| | - Brad R Ruhfel
- Department of Biology and Department of Biological Sciences, Eastern Kentucky University, Richmond, KY 40475; Florida Museum of Natural History, Gainesville, FL 32611
| | - Eric Wafula
- Department of Biology, Pennsylvania State University, University Park, PA 16803
| | - Joshua P Der
- Department of Biology, Pennsylvania State University, University Park, PA 16803
| | | | - Sarah Mathews
- Arnold Arboretum of Harvard University, Cambridge, MA 02138
| | | | - Douglas E Soltis
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611; Florida Museum of Natural History, Gainesville, FL 32611
| | - Pamela S Soltis
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611; Florida Museum of Natural History, Gainesville, FL 32611
| | | | - Carl J Rothfels
- Department of Biology, Duke University, Durham, NC 27708; Department of Zoology, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Lisa Pokorny
- Department of Biology, Duke University, Durham, NC 27708; Department of Biodiversity and Conservation, Real Jardín Botánico-Consejo Superior de Investigaciones Cientificas, 28014 Madrid, Spain
| | | | | | | | - Barbara Surek
- Botanical Institute, Universität zu Köln, Cologne D-50674, Germany
| | - Juan Carlos Villarreal
- Department fur Biologie, Systematische Botanik und Mykologie, Ludwig-Maximilians-Universitat, 80638 Munich, Germany
| | - Béatrice Roure
- Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale Centre-Ville, Montreal, QC, Canada H3C 3J7
| | - Hervé Philippe
- Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale Centre-Ville, Montreal, QC, Canada H3C 3J7; CNRS, Station d' Ecologie Expérimentale du CNRS, Moulis, 09200, France
| | | | - Tao Chen
- Shenzhen Fairy Lake Botanical Garden, The Chinese Academy of Sciences, Shenzhen, Guangdong 518004, China
| | - Michael K Deyholos
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
| | - Regina S Baucom
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109
| | - Toni M Kutchan
- Donald Danforth Plant Science Center, St. Louis, MO 63132
| | | | - Jun Wang
- BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and
| | - Yong Zhang
- CNRS, Station d' Ecologie Expérimentale du CNRS, Moulis, 09200, France
| | - Zhijian Tian
- BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and
| | - Zhixiang Yan
- BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and
| | - Xiaolei Wu
- BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and
| | - Xiao Sun
- BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9; BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and Department of Medicine, University of Alberta, Edmonton, AB, Canada T6G 2E1
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Sessa EB, Banks JA, Barker MS, Der JP, Duffy AM, Graham SW, Hasebe M, Langdale J, Li FW, Marchant DB, Pryer KM, Rothfels CJ, Roux SJ, Salmi ML, Sigel EM, Soltis DE, Soltis PS, Stevenson DW, Wolf PG. Between two fern genomes. Gigascience 2014; 3:15. [PMID: 25324969 PMCID: PMC4199785 DOI: 10.1186/2047-217x-3-15] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 09/18/2014] [Indexed: 11/10/2022] Open
Abstract
Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves.
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Affiliation(s)
- Emily B Sessa
- Department of Biology, Box 118525, University of Florida, Gainesville, FL 32611, USA ; Genetics Institute, University of Florida, Box 103610, Gainesville, FL 32611, USA
| | - Jo Ann Banks
- Department of Botany and Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN 47907, USA
| | - Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, 1041 East Lowell Street, Tucson, AZ 85721, USA
| | - Joshua P Der
- Department of Biology, Penn State University, 201 Life Science Building, University Park, PA 16801, USA ; Current address: Department of Biological Science, California State University, 800 N. State College Blvd., Fullerton, CA 92831, USA
| | - Aaron M Duffy
- Ecology Center and Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT 84322, USA
| | - Sean W Graham
- Department of Botany, University of British Columbia, 3529-6720 University Blvd., Vancouver, BC V6T 1Z4, Canada
| | - Mitsuyasu Hasebe
- National Institute for Basic Biology, 38 Nishigounaka, Myo-daiji-cho, Okazaki 444-8585, Japan
| | - Jane Langdale
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Fay-Wei Li
- Department of Biology, Duke University, Post Office Box 90338, Durham, NC 27708, USA
| | - D Blaine Marchant
- Department of Biology, Box 118525, University of Florida, Gainesville, FL 32611, USA ; Florida Museum of Natural History, Dickinson Hall, University of Florida, Gainesville, FL 32611, USA
| | - Kathleen M Pryer
- Department of Biology, Duke University, Post Office Box 90338, Durham, NC 27708, USA
| | - Carl J Rothfels
- Department of Zoology, University of British Columbia, 2329 W. Mall, WAITING Vancouver, BC V6T 1Z4, Canada ; Current address: University Herbarium and Department of Integrative Biology, University of California, 1001 Valley Life Sciences Building, Berkeley, Berkeley, CA 94720, USA
| | - Stanley J Roux
- Department of Molecular Biosciences, University of Texas, 205 W. 24th Street, Austin, TX 78712, USA
| | - Mari L Salmi
- Department of Molecular Biosciences, University of Texas, 205 W. 24th Street, Austin, TX 78712, USA
| | - Erin M Sigel
- Department of Biology, Duke University, Post Office Box 90338, Durham, NC 27708, USA
| | - Douglas E Soltis
- Department of Biology, Box 118525, University of Florida, Gainesville, FL 32611, USA ; Genetics Institute, University of Florida, Box 103610, Gainesville, FL 32611, USA ; Florida Museum of Natural History, Dickinson Hall, University of Florida, Gainesville, FL 32611, USA
| | - Pamela S Soltis
- Genetics Institute, University of Florida, Box 103610, Gainesville, FL 32611, USA ; Florida Museum of Natural History, Dickinson Hall, University of Florida, Gainesville, FL 32611, USA
| | - Dennis W Stevenson
- New York Botanical Garden, 2900 Southern Boulevard, Bronx, NY 10458, USA
| | - Paul G Wolf
- Ecology Center and Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT 84322, USA
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Hodgins KA, Lai Z, Oliveira LO, Still DW, Scascitelli M, Barker MS, Kane NC, Dempewolf H, Kozik A, Kesseli RV, Burke JM, Michelmore RW, Rieseberg LH. Genomics of Compositae crops: reference transcriptome assemblies and evidence of hybridization with wild relatives. Mol Ecol Resour 2013; 14:166-77. [DOI: 10.1111/1755-0998.12163] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 08/14/2013] [Accepted: 08/15/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Kathryn A. Hodgins
- Department of Botany and Biodiversity Research Centre; University of British Columbia; Vancouver BC V6T 1Z4 Canada
| | - Zhao Lai
- Department of Biology and Center for Genomics and Bioinformatics; Indiana University; Bloomington IN 47405 USA
| | - Luiz O. Oliveira
- Departamento de Bioquímica e Biologia Molecular; Universidade Federal de Viçosa; 36570-000 Viçosa Brazil
| | - David W. Still
- Department of Plant Sciences; Cal Poly Pomona; Pomona CA 91768 USA
| | - Moira Scascitelli
- Department of Botany and Biodiversity Research Centre; University of British Columbia; Vancouver BC V6T 1Z4 Canada
| | - Michael S. Barker
- Department of Ecology and Evolutionary Biology; University of Arizona; Tucson AZ 85721 USA
| | - Nolan C. Kane
- Department of Ecology and Evolutionary Biology; University of Colorado Boulder; Boulder CO 80309 USA
| | - Hannes Dempewolf
- Department of Botany and Biodiversity Research Centre; University of British Columbia; Vancouver BC V6T 1Z4 Canada
| | - Alex Kozik
- The Genome Center; University of California; Davis CA 95616 USA
| | | | - John M. Burke
- Department of Plant Biology; University of Georgia; Athens GA 30602 USA
| | - Richard W. Michelmore
- The Genome Center; University of California; Davis CA 95616 USA
- Departments of Plant Sciences, Molecular & Cellular Biology, and Medical Microbiology & Immunology; University of California; Davis CA 95616 USA
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research Centre; University of British Columbia; Vancouver BC V6T 1Z4 Canada
- Department of Biology and Center for Genomics and Bioinformatics; Indiana University; Bloomington IN 47405 USA
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Dempewolf H, Kane NC, Ostevik KL, Geleta M, Barker MS, Lai Z, Stewart ML, Bekele E, Engels JMM, Cronk QCB, Rieseberg LH. Establishing genomic tools and resources for Guizotia abyssinica (L.f.) Cass.-the development of a library of expressed sequence tags, microsatellite loci, and the sequencing of its chloroplast genome. Mol Ecol Resour 2013; 10:1048-58. [PMID: 21565115 DOI: 10.1111/j.1755-0998.2010.02859.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present an EST library, chloroplast genome sequence, and nuclear microsatellite markers that were developed for the semi-domesticated oilseed crop noug (Guizotia abyssinica) from Ethiopia. The EST library consists of 25 711 Sanger reads, assembled into 17 538 contigs and singletons, of which 4781 were functionally annotated using the Arabidopsis Information Resource (TAIR). The age distribution of duplicated genes in the EST library shows evidence of two paleopolyploidizations-a pattern that noug shares with several other species in the Heliantheae tribe (Compositae family). From the EST library, we selected 43 microsatellites and then designed and tested primers for their amplification. The number of microsatellite alleles varied between 2 and 10 (average 4.67), and the average observed and expected heterozygosities were 0.49 and 0.54, respectively. The chloroplast genome was sequenced de novo using Illumina's sequencing technology and completed with traditional Sanger sequencing. No large re-arrangements were found between the noug and sunflower chloroplast genomes, but 1.4% of sites have indels and 1.8% show sequence divergence between the two species. We identified 34 tRNAs, 4 rRNA sequences, and 80 coding sequences, including one region (trnH-psbA) with 15% sequence divergence between noug and sunflower that may be particularly useful for phylogeographic studies in noug and its wild relatives.
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Affiliation(s)
- Hannes Dempewolf
- The Biodiversity Research Centre and Department of Botany, 3529-6270 University Blvd, University of British Columbia, Vancouver, British Columbia, Canada
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Arrigo N, Therrien J, Anderson CL, Windham MD, Haufler CH, Barker MS. A total evidence approach to understanding phylogenetic relationships and ecological diversity in Selaginella subg. Tetragonostachys. Am J Bot 2013; 100:1672-82. [PMID: 23935110 DOI: 10.3732/ajb.1200426] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
PREMISE OF THE STUDY Several members of Selaginella are renowned for their ability to survive extreme drought and "resurrect" when conditions improve. Many of these belong to subgenus Tetragonostachys, a group of ∼45 species primarily found in North and Central America, with substantial diversity in the Sonoran and Chihuahuan Deserts. We evaluated the monophyly and the age of subgenus Tetragonostachys and assess how drought tolerance contributed to the evolution of this clade. METHODS Our study included most Tetragonostachys species, using plastid and nuclear sequences, fossil and herbarium records, and climate variables to describe the species diversity, phylogenetic relationships, divergence times, and climatic niche evolution in the subgenus. KEY RESULTS We found that subgenus Tetragonostachys forms a monophyletic group sister to Selaginella lepidophylla and may have diverged from other Selaginella because of a Gondwanan-Laurasian vicariance event ca. 240 mya. The North American radiation of Tetragonostachys appears to be much more recent and to have occurred during the Early Cretaceous-late Paleocene interval. We identified two significant and nested ecological niche shifts during the evolution of Tetragonostachys associated with extreme drought tolerance and a more recent shift to cold climates. Our analyses suggest that drought tolerance evolved in the warm deserts of southwest North America and may have been advantageous for colonization of cold and dry boreal climates. CONCLUSIONS Our investigation provides a foundation for future research addressing the genomics of ecological niche evolution and the potential role of reticulate evolution in Selaginella subgenus Tetragonostachys.
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Affiliation(s)
- Nils Arrigo
- Department of Ecology and Evolutionary Biology, University of Arizona, P.O. Box 210088, Tucson, Arizona 85721, USA
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Arrigo N, Albert LP, Mickelson PG, Barker MS. Quantitative visualization of biological data in Google Earth using R2G2, an R CRAN package. Mol Ecol Resour 2012; 12:1177-9. [PMID: 22994899 DOI: 10.1111/1755-0998.12012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 07/31/2012] [Accepted: 08/01/2012] [Indexed: 11/29/2022]
Abstract
We briefly introduce R2G2, an R CRAN package to visualize spatially explicit biological data within the Google Earth interface. Our package combines a collection of basic graph-editing features, including automated placement of dots, segments, polygons, images (including graphs produced with R), along with several complex three-dimensional (3D) representations such as phylogenies, histograms and pie charts. We briefly present some example data sets and show the immediate benefits in communication gained from using the Google Earth interface to visually explore biological results. The package is distributed with detailed help pages providing examples and annotated source scripts with the hope that users will have an easy time using and further developing this package. R2G2 is distributed on http://cran.r-project.org/web/packages.
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Affiliation(s)
- Nils Arrigo
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
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Arrigo N, Barker MS. Rarely successful polyploids and their legacy in plant genomes. Curr Opin Plant Biol 2012; 15:140-6. [PMID: 22480430 DOI: 10.1016/j.pbi.2012.03.010] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 03/13/2012] [Accepted: 03/14/2012] [Indexed: 05/20/2023]
Abstract
Polyploidy, or whole genome duplication, is recognized as an important feature of eukaryotic genome evolution. Among eukaryotes, polyploidy has probably had the largest evolutionary impact on vascular plants where many contemporary species are of recent polyploid origin. Genomic analyses have uncovered evidence of at least one round of polyploidy in the ancestry of most plants, fueling speculation that genome duplications lead to increases in net diversity. In spite of the frequency of ancient polyploidy, recent analyses have found that recently formed polyploid species have higher extinction rates than their diploid relatives. These results suggest that despite leaving a substantial legacy in plant genomes, only rare polyploids survive over the long term and most are evolutionary dead-ends.
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Affiliation(s)
- Nils Arrigo
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
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Lai Z, Kane NC, Kozik A, Hodgins KA, Dlugosch KM, Barker MS, Matvienko M, Yu Q, Turner KG, Pearl SA, Bell GDM, Zou Y, Grassa C, Guggisberg A, Adams KL, Anderson JV, Horvath DP, Kesseli RV, Burke JM, Michelmore RW, Rieseberg LH. Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression. Am J Bot 2012; 99:209-18. [PMID: 22058181 DOI: 10.3732/ajb.1100313] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
PREMISE OF STUDY Weeds cause considerable environmental and economic damage. However, genomic characterization of weeds has lagged behind that of model plants and crop species. Here we describe the development of genomic tools and resources for 11 weeds from the Compositae family that will serve as a basis for subsequent population and comparative genomic analyses. Because hybridization has been suggested as a stimulus for the evolution of invasiveness, we also analyze these genomic data for evidence of hybridization. METHODS We generated 22 expressed sequence tag (EST) libraries for the 11 targeted weeds using Sanger, 454, and Illumina sequencing, compared the coverage and quality of sequence assemblies, and developed NimbleGen microarrays for expression analyses in five taxa. When possible, we also compared the distributions of Ks values between orthologs of congeneric taxa to detect and quantify hybridization and introgression. RESULTS Gene discovery was enhanced by sequencing from multiple tissues, normalization of cDNA libraries, and especially greater sequencing depth. However, assemblies from short sequence reads sometimes failed to resolve close paralogs. Substantial introgression was detected in Centaurea and Helianthus, but not in Ambrosia and Lactuca. CONCLUSIONS Transcriptome sequencing using next-generation platforms has greatly reduced the cost of genomic studies of nonmodel organisms, and the ESTs and microarrays reported here will accelerate evolutionary and molecular investigations of Compositae weeds. Our study also shows how ortholog comparisons can be used to approximately estimate the genome-wide extent of introgression and to identify genes that have been exchanged between hybridizing taxa.
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Affiliation(s)
- Zhao Lai
- Department of Biology and Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana 47405, USA
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Abstract
Polyploidy, the doubling of genomic content, is a widespread feature, especially among plants, yet its macroevolutionary impacts are contentious. Traditionally, polyploidy has been considered an evolutionary dead end, whereas recent genomic studies suggest that polyploidy has been a key driver of macroevolutionary success. We examined the consequences of polyploidy on the time scale of genera across a diverse set of vascular plants, encompassing hundreds of inferred polyploidization events. Likelihood-based analyses indicate that polyploids generally exhibit lower speciation rates and higher extinction rates than diploids, providing the first quantitative corroboration of the dead-end hypothesis. The increased speciation rates of diploids can, in part, be ascribed to their capacity to speciate via polyploidy. Only particularly fit lineages of polyploids may persist to enjoy longer-term evolutionary success.
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Affiliation(s)
- Itay Mayrose
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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