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Dynamic genome evolution in a model fern.
Marchant, D Blaine; Chen, Guang; Cai, Shengguan; Chen, Fei; Schafran, Peter; Jenkins, Jerry; Shu, Shengqiang; Plott, Chris; Webber, Jenell; Lovell, John T; He, Guifen; Sandor, Laura; Williams, Melissa; Rajasekar, Shanmugam; Healey, Adam; Barry, Kerrie; Zhang, Yinwen; Sessa, Emily; Dhakal, Rijan R; Wolf, Paul G; Harkess, Alex; Li, Fay-Wei; Rössner, Clemens; Becker, Annette; Gramzow, Lydia; Xue, Dawei; Wu, Yuhuan; Tong, Tao; Wang, Yuanyuan; Dai, Fei; Hua, Shuijin; Wang, Hua; Xu, Shengchun; Xu, Fei; Duan, Honglang; Theißen, Günter; McKain, Michael R; Li, Zheng; McKibben, Michael T W; Barker, Michael S; Schmitz, Robert J; Stevenson, Dennis W; Zumajo-Cardona, Cecilia; Ambrose, Barbara A; Leebens-Mack, James H; Grimwood, Jane; Schmutz, Jeremy; Soltis, Pamela S; Soltis, Douglas E; Chen, Zhong-Hua.
Afiliação
  • Marchant DB; Department of Biology, Stanford University, Stanford, CA, USA. danielm1@stanford.edu.
  • Chen G; 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.
  • Cai S; College of Agriculture, Yangtze University, Jingzhou, China.
  • Chen F; College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
  • Schafran P; School of Science, Western Sydney University, Penrith, New South Wales, Australia.
  • Jenkins J; College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China.
  • Shu S; Boyce Thompson Institute, Ithaca, NY, USA.
  • Plott C; Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
  • Webber J; United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Lovell JT; Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
  • He G; Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
  • Sandor L; Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
  • Williams M; United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Rajasekar S; United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Healey A; United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Barry K; Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
  • Zhang Y; Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
  • Sessa E; Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
  • Dhakal RR; United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Wolf PG; Institute of Bioinformatics, University of Georgia, Athens, GA, USA.
  • Harkess A; Department of Biology, University of Florida, Gainesville, FL, USA.
  • Li FW; Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA.
  • Rössner C; Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA.
  • Becker A; Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
  • Gramzow L; Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, USA.
  • Xue D; Boyce Thompson Institute, Ithaca, NY, USA.
  • Wu Y; Plant Biology Section, Cornell University, Ithaca, NY, USA.
  • Tong T; Justus-Liebig-University, Department of Biology and Chemistry, Institute of Botany, Gießen, Germany.
  • Wang Y; Justus-Liebig-University, Department of Biology and Chemistry, Institute of Botany, Gießen, Germany.
  • Dai F; Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, Jena, Germany.
  • Hua S; College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China.
  • Wang H; College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China.
  • Xu S; College of Agriculture, Yangtze University, Jingzhou, China.
  • Xu F; Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
  • Duan H; College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
  • Theißen G; Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
  • McKain MR; 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.
  • Li Z; College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
  • McKibben MTW; College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
  • Barker MS; 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.
  • Schmitz RJ; Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, Jena, Germany.
  • Stevenson DW; Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA.
  • Zumajo-Cardona C; Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
  • Ambrose BA; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.
  • Leebens-Mack JH; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.
  • Grimwood J; Department of Genetics, University of Georgia, Athens, GA, USA.
  • Schmutz J; New York Botanical Garden, Bronx, NY, USA.
  • Soltis PS; New York Botanical Garden, Bronx, NY, USA.
  • Soltis DE; New York Botanical Garden, Bronx, NY, USA.
  • Chen ZH; Department of Plant Biology, University of Georgia, Athens, GA, USA. jleebensmack@uga.edu.
Nat Plants ; 8(9): 1038-1051, 2022 09.
Article em En | MEDLINE | ID: mdl-36050461
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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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Gleiquênias Tipo de estudo: Prognostic_studies Idioma: En Revista: Nat Plants Ano de publicação: 2022 Tipo de documento: Article País de afiliação: Estados Unidos
Texto completo
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PubMed Links
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Gleiquênias Tipo de estudo: Prognostic_studies Idioma: En Revista: Nat Plants Ano de publicação: 2022 Tipo de documento: Article País de afiliação: Estados Unidos