<br>模型蕨类植物的动态基因组进化,Nature Plants

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模型蕨类植物的动态基因组进化
Nature Plants ( IF 15.8 ) Pub Date : 2022-09-01 , DOI: 10.1038/s41477-022-01226-7
D Blaine Marchant ₁ , Guang Chen _{2,

3} , Shengguan Cai _{4,

5} , Fei Chen ₆ , Peter Schafran ₇ , Jerry Jenkins ₈ , Shengqiang Shu ₉ , Chris Plott ₈ , Jenell Webber ₈ , John T Lovell _{8,

9} , Guifen He ₉ , Laura Sandor ₉ , Melissa Williams ₈ , Shanmugam Rajasekar ₁₀ , Adam Healey ₈ , Kerrie Barry ₉ , Yinwen Zhang ₁₁ , Emily Sessa ₁₂ , Rijan R Dhakal ₁₃ , Paul G Wolf ₁₃ , Alex Harkess _{8,

14} , Fay-Wei Li _{7,

15} , Clemens Rössner ₁₆ , Annette Becker ₁₆ , Lydia Gramzow ₁₇ , Dawei Xue ₆ , Yuhuan Wu ₆ , Tao Tong ₃ , Yuanyuan Wang ₁₈ , Fei Dai ₄ , Shuijin Hua ₁₉ , Hua Wang ₂₀ , Shengchun Xu ₄ , Fei Xu ₄ , Honglang Duan ₂₁ , Günter Theißen ₁₇ , Michael R McKain ₂₂ , Zheng Li ₂₃ , Michael T W McKibben ₂₄ , Michael S Barker ₂₄ , Robert J Schmitz ₂₅ , Dennis W Stevenson ₂₆ , Cecilia Zumajo-Cardona ₂₆ , Barbara A Ambrose ₂₆ , James H Leebens-Mack ₂₇ , Jane Grimwood ₈ , Jeremy Schmutz _{8,

9} , Pamela S Soltis ₂₈ , Douglas E Soltis _{12,

28} , Zhong-Hua Chen _{5,

29}

Affiliation

Department of Biology, Stanford University, Stanford, CA, USA.
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.
College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
School of Science, Western Sydney University, Penrith, New South Wales, Australia.
College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China.
Boyce Thompson Institute, Ithaca, NY, USA.
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.
Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
Institute of Bioinformatics, University of Georgia, Athens, GA, USA.
Department of Biology, University of Florida, Gainesville, FL, USA.
Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA.
Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, USA.
Plant Biology Section, Cornell University, Ithaca, NY, USA.
Justus-Liebig-University, Department of Biology and Chemistry, Institute of Botany, Gießen, Germany.
Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, Jena, Germany.
Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
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.
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.
Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA.
Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.
Department of Genetics, University of Georgia, Athens, GA, USA.
New York Botanical Garden, Bronx, NY, USA.
Department of Plant Biology, University of Georgia, Athens, GA, USA.
Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia.

大多数蕨类植物基因组的庞大和复杂性阻碍了通过基因组研究来阐明蕨类生物学和陆地植物进化的基本方面的努力。在这里，我们提出了模型蕨类植物Ceratopteris richardii 的染色体基因组组装以及相关的甲基化组、转录组和代谢组分析。该组装揭示了一段非常动态的基因组进化历史，包括大约 6000 万年前最近一次全基因组复制后基因组内容和结构的快速变化。这些变化包括大量基因丢失、猖獗的串联复制和细菌的多重水平基因转移，导致防御相关基因家族的多样化。将转座元件插入内含子导致了角蕨基因组的巨大尺寸以及相对于其他植物而言异常长的基因。基因家族分析表明，指导种子发育的基因是从控制蕨类孢子囊发育的基因中选出的，为种子植物的进化提供了见解。我们的发现和带注释的基因组组装扩展了角蕨作为植物生物学研究和教学模型的实用性。

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更新日期：2022-09-02

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