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The Cycas genome and the early evolution of seed plants
Yang Liu 
,
Sibo Wang,
Linzhou Li ,
Ting Yang,
Shanshan Dong,
Tong Wei,
Shengdan Wu ,
Yongbo Liu ,
Yiqing Gong,
Xiuyan Feng,
Jianchao Ma,
Guanxiao Chang,
Jinling Huang ,
Yong Yang,
Hongli Wang,
Min Liu,
Yan Xu,
Hongping Liang ,
Jin Yu ,
Yuqing Cai,
Zhaowu Zhang,
Yannan Fan ,
Weixue Mu,
Sunil Kumar Sahu ,
Shuchun Liu,
Xiaoan Lang,
Leilei Yang,
Na Li,
Sadaf Habib,
Yongqiong Yang,
Anders J. Lindstrom ,
Pei Liang,
Bernard Goffinet ,
Sumaira Zaman,
Jill L. Wegrzyn,
Dexiang Li,
Jian Liu,
Jie Cui ,
Eva C. Sonnenschein ,
Xiaobo Wang ,
Jue Ruan ,
Jia-Yu Xue,
Zhu-Qing Shao ,
Chi Song ,
Guangyi Fan,
Zhen Li,
Liangsheng Zhang,
Jianquan Liu ,
Zhong-Jian Liu ,
Yuannian Jiao ,
Xiao-Quan Wang ,
Hong Wu,
Ertao Wang ,
Michael Lisby ,
Huanming Yang,
Jian Wang,
Xin Liu ,
Xun Xu ,
Nan Li,
Pamela S. Soltis ,
Yves Van de Peer ,
Douglas E. Soltis ,
Xun Gong ,
Huan Liu ,
Shouzhou Zhang
,
Sibo Wang,
Linzhou Li ,
Ting Yang,
Shanshan Dong,
Tong Wei,
Shengdan Wu ,
Yongbo Liu ,
Yiqing Gong,
Xiuyan Feng,
Jianchao Ma,
Guanxiao Chang,
Jinling Huang ,
Yong Yang,
Hongli Wang,
Min Liu,
Yan Xu,
Hongping Liang ,
Jin Yu ,
Yuqing Cai,
Zhaowu Zhang,
Yannan Fan ,
Weixue Mu,
Sunil Kumar Sahu ,
Shuchun Liu,
Xiaoan Lang,
Leilei Yang,
Na Li,
Sadaf Habib,
Yongqiong Yang,
Anders J. Lindstrom ,
Pei Liang,
Bernard Goffinet ,
Sumaira Zaman,
Jill L. Wegrzyn,
Dexiang Li,
Jian Liu,
Jie Cui ,
Eva C. Sonnenschein ,
Xiaobo Wang ,
Jue Ruan ,
Jia-Yu Xue,
Zhu-Qing Shao ,
Chi Song ,
Guangyi Fan,
Zhen Li,
Liangsheng Zhang,
Jianquan Liu ,
Zhong-Jian Liu ,
Yuannian Jiao ,
Xiao-Quan Wang ,
Hong Wu,
Ertao Wang ,
Michael Lisby ,
Huanming Yang,
Jian Wang,
Xin Liu ,
Xun Xu ,
Nan Li,
Pamela S. Soltis ,
Yves Van de Peer ,
Douglas E. Soltis ,
Xun Gong ,
Huan Liu ,
Shouzhou Zhang
Nature Plants, Volume: 8, Issue: 4, Pages: 389 - 401
Swansea University Author:
Eva C. Sonnenschein
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DOI (Published version): 10.1038/s41477-022-01129-7
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,...
| Published in: | Nature Plants |
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| ISSN: | 2055-0278 |
| Published: |
Springer Science and Business Media LLC
2022
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| Online Access: |
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| URI: | https://cronfa.swan.ac.uk/Record/cronfa61714 |
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| 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. |
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| College: |
Faculty of Science and Engineering |
| Funders: |
This study was supported by the Scientific Foundation of Urban Management Bureau of Shenzhen (No. 201916 to Yang Liu, No. 202019 to Shouzhou Zhang and No. 202105 to Y.G.), the National Key R&D Program of China (No. 2019YFC1711000 to Huan Liu), the Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment, China (No. 2019HJ2096001006 to Shouzhou Zhang and Yongbo Liu), the Major Science and Technology Projects of Yunnan Province (Digitalization, development and application of biotic resource, No. 860 202002AA100007 to Huan Liu) and Shenzhen Municipal Government of China (No. JCYJ20151015162041454 to Huan Liu). Y.V.d.P. acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (No. 833522) and from Ghent University (Methusalem funding, BOF.MET.2021.0005.01). Plant illustrations were drawn by S. Li, Z. Li, D. Cui and X. Zeng. We are grateful to the Orchid Conservation and Research Centre of Shenzhen for allowing us to access their computing resources. We also acknowledge T. Wan (Fairy Lake Botanical Garden) and D. Stevenson (New York Botanical Garden), who kindly commented on an earlier draft of the manuscript, and T. Takaso (University of the Ryukyus), who provided the video for swimming sperm of Cycas. The study was supported by the National Cycad Conservation Center at Fairy Lake Botanical Garden. This work is part of the 10KP project (https://db.cngb.org/10kp/) and was also supported by China National GeneBank (CNGB; https://www.cngb.org/). |
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4 |
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