Liu Yang, Wang Sibo, Li Linzhou, Yang Ting, Dong Shanshan, Wei Tong, Wu Shengdan, Liu Yongbo, Gong Yiqing, Feng Xiuyan, Ma Jianchao, Chang Guanxiao, Huang Jinling, Yang Yong, Wang Hongli, Liu Min, Xu Yan, Liang Hongping, Yu Jin, Cai Yuqing, Zhang Zhaowu, Fan Yannan, Mu Weixue, Sahu Sunil Kumar, Liu Shuchun, Lang Xiaoan, Yang Leilei, Li Na, Habib Sadaf, Yang Yongqiong, Lindstrom Anders J, Liang Pei, Goffinet Bernard, Zaman Sumaira, Wegrzyn Jill L, Li Dexiang, Liu Jian, Cui Jie, Sonnenschein Eva C, Wang Xiaobo, Ruan Jue, Xue Jia-Yu, Shao Zhu-Qing, Song Chi, Fan Guangyi, Li Zhen, Zhang Liangsheng, Liu Jianquan, Liu Zhong-Jian, Jiao Yuannian, Wang Xiao-Quan, Wu Hong, Wang Ertao, Lisby Michael, Yang Huanming, Wang Jian, Liu Xin, Xu Xun, Li Nan, Soltis Pamela S, Van de Peer Yves, Soltis Douglas E, Gong Xun, Liu Huan, Zhang Shouzhou
State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China.
Nat Plants. 2022 Apr;8(4):389-401. doi: 10.1038/s41477-022-01129-7. Epub 2022 Apr 18.
Cycads represent one of the most ancient lineages of living seed plants. Identifying genomic features uniquely shared by cycads and other extant seed plants, but not non-seed-producing plants, may shed light on the origin of key innovations, as well as the early diversification of seed plants. Here, we report the 10.5-Gb reference genome of Cycas panzhihuaensis, complemented by the transcriptomes of 339 cycad species. Nuclear and plastid phylogenomic analyses strongly suggest that cycads and Ginkgo form a clade sister to all other living gymnosperms, in contrast to mitochondrial data, which place cycads alone in this position. We found evidence for an ancient whole-genome duplication in the common ancestor of extant gymnosperms. The Cycas genome contains four homologues of the fitD gene family that were likely acquired via horizontal gene transfer from fungi, and these genes confer herbivore resistance in cycads. The male-specific region of the Y chromosome of C. panzhihuaensis contains a MADS-box transcription factor expressed exclusively in male cones that is similar to a system reported in Ginkgo, suggesting that a sex determination mechanism controlled by MADS-box genes may have originated in the common ancestor of cycads and Ginkgo. The C. panzhihuaensis genome provides an important new resource of broad utility for biologists.
苏铁是现存种子植物中最古老的谱系之一。识别苏铁与其他现存种子植物所独有的基因组特征，而非非种子植物所共有的特征，可能有助于揭示关键创新的起源以及种子植物的早期多样化。在此，我们报告了攀枝花苏铁105亿碱基对的参考基因组，并辅以339种苏铁物种的转录组数据。核基因组和质体基因组分析有力地表明，苏铁和银杏形成了一个进化枝，是所有其他现存裸子植物的姐妹群，这与线粒体数据相反，线粒体数据显示苏铁单独处于这一位置。我们发现了现存裸子植物共同祖先中发生古老全基因组复制的证据。攀枝花苏铁基因组包含四个fitD基因家族的同源物，这些同源物可能是通过水平基因转移从真菌中获得的，并且这些基因赋予了苏铁抗食草动物的能力。攀枝花苏铁Y染色体的雄性特异性区域包含一个仅在雄球果中表达的MADS盒转录因子，该转录因子与银杏中报道的一个系统相似，这表明由MADS盒基因控制的性别决定机制可能起源于苏铁和银杏的共同祖先。攀枝花苏铁基因组为生物学家提供了一个具有广泛用途的重要新资源。
