The Cycas genome and the early evolution of seed plants
Liu, Yang; Wang, Sibu; 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; 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
Date:
2022-04-18
Abstract:
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.
Description:
DATA AVAILABILITY : The genome and transcriptome data, genome assemblies and annotations can be found at https://db.cngb.org/codeplot/datasets/public_dataset?id=PwRftGHfPs5q G3gE. The raw genomic, transcriptomic and Hi-C data generated in this study were deposited in the NCBI Sequence Read Archive (SRA, BioProject PRJNA734434) and the CNGB data center (https://db.cngb.org/) under project number CNP0001756. Source data are provided with this paper.
SUPPLEMENTARY INFORMATION : Supplementary notes and figures for additional information of the manuscript.
SUPPLEMENTARY VIDEO 1 : A swimming sperm of Cycas.
SUPPLEMENTARY TABLE 1 : Supplementary tables.
SUPPLEMENTARY DATA : Raw gels figure for Supplementary Fig. 39.