Dynamic genome evolution in a model fern

作者：D. Blaine Marchant, Guang Jing Chen, Shengguan Cai, Fei Chen, Peter Schafran, Jerry W. Jenkins, Shengqiang Shu, Christopher B. Plott, Jenell Webber, John T. Lovell, Guifen He, Laura Sandor, Melissa E. Williams, Shanmugam Rajasekar, Adam L. Healey, Kerrie Barry, Yinwen Zhang, Emily B. Sessa, Rijan R. Dhakal, Paul G. Wolf, Alex Harkess, Fay‐Wei Li, Clemens Rössner, Annette Becker, Lydia Gramzow, Dawei Xue, Yuhuan Wu, Tao Tong, Yuanyuan Wang, Fei Dai, Shuijin Hua, Hua Wang, Shengchun Xu, Fei Xu, Honglang Duan, Günter Theißen, Michael R. McKain, Zheng Li, Michael T. W. McKibben, Michael S. Barker, Robert J. Schmitz, Dennis William Stevenson, Cecilia Zumajo‐Cardona, Barbara A. Ambrose, Jim Leebens‐Mack, Jane Grimwood, Jeremy Schmutz, Pamela S. Soltis, Douglas E. Soltis, Zhong‐Hua Chen · 发表于：Nature Plants · 年份：2022 · DOI：10.1038/s41477-022-01226-7 · 被引用次数：204 · 研究领域：Fern and Epiphyte Biology、Plant Taxonomy and Phylogenetics、Plant Diversity and Evolution

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.