Dynamic genome evolution in a model fern.
Dynamic genome evolution in a model fern.
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DOI：
10.1038/s41477-022-01226-7
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发表时间：
2022-09
期刊：
影响因子：
18
通讯作者：
Chen, Zhong-Hua
中科院分区：
文献类型：
--
作者：
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;Roessner, 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, Guenter;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
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阐明蕨类植物生物学和陆地植物进化的基本方面。在这里，我们提出了一个染色体基因组组装和相关的甲基化组，转录组和代谢组分析的模式蕨类植物物种水蕨richardii。该组装揭示了一个显着动态的基因组进化的历史，包括基因组内容和结构的快速变化，最近的全基因组复制大约6000万年前。这些变化包括大量的基因丢失，猖獗的串联重复和细菌的多个水平基因转移，有助于防御相关基因家族的多样化。转座因子插入内含子导致水蕨属基因组的大尺寸和相对于其他植物的异常长的基因。基因家族分析表明，指导种子发育的基因是从那些控制蕨类孢子囊发育的基因中挑选出来的，这为种子植物的进化提供了新的见解。我们的研究结果和注释的基因组组装扩展了水蕨属作为植物生物学研究和教学模型的实用性。模式蕨类物种Ceratopteris richardii的基因组揭示了一个显着的动态基因组进化的历史，包括基因组内容和结构的快速变化后，最近的全基因组复制约6000万年前。
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. The genome of the model fern species Ceratopteris richardii 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.
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影响因子：
14.9
作者：
NCBI Resource Coordinators
通讯作者：
NCBI Resource Coordinators
影响因子：
16.6
作者：
Cao C;Li MY;Cirauqui N;Wang YQ;Dal Peraro M;Tian H;Long YT
通讯作者：
Long YT
影响因子：
5.6
作者：
Akhter S;Kretzschmar WW;Nordal V;Delhomme N;Street NR;Nilsson O;Emanuelsson O;Sundström JF
通讯作者：
Sundström JF
影响因子：
12.3
作者：
Bewick AJ;Niederhuth CE;Ji L;Rohr NA;Griffin PT;Leebens-Mack J;Schmitz RJ
通讯作者：
Schmitz RJ
植物铬甲基转移酶的DNA甲基化特征。
影响因子：
4.5
作者：
Gouil Q;Baulcombe DC
通讯作者：
Baulcombe DC