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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, et al.
(2022) NATURE PLANTS. 8(4). p.389-401
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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. The study assembled a chromosome-level genome of Cycas panzhihuaensis, the last major lineage of seed plants for which a high-quality genome assembly was lacking. The study closes an important gap in our understanding of genome structure and evolution in seed plants.
Keywords
Plant Science, PHYLOGENETIC ANALYSIS, SEX-CHROMOSOMES, SEQUENCE, RECONSTRUCTION, PROGRAM, GENE, TOOL, IDENTIFICATION, POLYPLOIDY, METABOLISM

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MLA
Liu, Yang, et al. “The Cycas Genome and the Early Evolution of Seed Plants.” NATURE PLANTS, vol. 8, no. 4, 2022, pp. 389–401, doi:10.1038/s41477-022-01129-7.
APA
Liu, Y., Wang, S., Li, L., Yang, T., Dong, S., Wei, T., … Zhang, S. (2022). The Cycas genome and the early evolution of seed plants. NATURE PLANTS, 8(4), 389–401. https://doi.org/10.1038/s41477-022-01129-7
Chicago author-date
Liu, Yang, Sibo Wang, Linzhou Li, Ting Yang, Shanshan Dong, Tong Wei, Shengdan Wu, et al. 2022. “The Cycas Genome and the Early Evolution of Seed Plants.” NATURE PLANTS 8 (4): 389–401. https://doi.org/10.1038/s41477-022-01129-7.
Chicago author-date (all authors)
Liu, Yang, 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, and Shouzhou Zhang. 2022. “The Cycas Genome and the Early Evolution of Seed Plants.” NATURE PLANTS 8 (4): 389–401. doi:10.1038/s41477-022-01129-7.
Vancouver
1.
Liu Y, Wang S, Li L, Yang T, Dong S, Wei T, et al. The Cycas genome and the early evolution of seed plants. NATURE PLANTS. 2022;8(4):389–401.
IEEE
[1]
Y. Liu et al., “The Cycas genome and the early evolution of seed plants,” NATURE PLANTS, vol. 8, no. 4, pp. 389–401, 2022.
@article{8751561,
  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.

The study assembled a chromosome-level genome of Cycas panzhihuaensis, the last major lineage of seed plants for which a high-quality genome assembly was lacking. The study closes an important gap in our understanding of genome structure and evolution in seed plants.}},
  author       = {{Liu, Yang and Wang, Sibo and Li, Linzhou and Yang, Ting and Dong, Shanshan and Wei, Tong and Wu, Shengdan and Liu, Yongbo and Gong, Yiqing and Feng, Xiuyan and Ma, Jianchao and Chang, Guanxiao and Huang, Jinling and Yang, Yong and Wang, Hongli and Liu, Min and Xu, Yan and Liang, Hongping and Yu, Jin and Cai, Yuqing and Zhang, Zhaowu and Fan, Yannan and Mu, Weixue and Sahu, Sunil Kumar and Liu, Shuchun and Lang, Xiaoan and Yang, Leilei and Li, Na and Habib, Sadaf and Yang, Yongqiong and Lindstrom, Anders J. and Liang, Pei and Goffinet, Bernard and Zaman, Sumaira and Wegrzyn, Jill L. and Li, Dexiang and Liu, Jian and Cui, Jie and Sonnenschein, Eva C. and Wang, Xiaobo and Ruan, Jue and Xue, Jia-Yu and Shao, Zhu-Qing and Song, Chi and Fan, Guangyi and Li, Zhen and Zhang, Liangsheng and Liu, Jianquan and Liu, Zhong-Jian and Jiao, Yuannian and Wang, Xiao-Quan and Wu, Hong and Wang, Ertao and Lisby, Michael and Yang, Huanming and Wang, Jian and Liu, Xin and Xu, Xun and Li, Nan and Soltis, Pamela S. and Van de Peer, Yves and Soltis, Douglas E. and Gong, Xun and Liu, Huan and Zhang, Shouzhou}},
  issn         = {{2055-026X}},
  journal      = {{NATURE PLANTS}},
  keywords     = {{Plant Science,PHYLOGENETIC ANALYSIS,SEX-CHROMOSOMES,SEQUENCE,RECONSTRUCTION,PROGRAM,GENE,TOOL,IDENTIFICATION,POLYPLOIDY,METABOLISM}},
  language     = {{eng}},
  number       = {{4}},
  pages        = {{389--401}},
  title        = {{The Cycas genome and the early evolution of seed plants}},
  url          = {{http://doi.org/10.1038/s41477-022-01129-7}},
  volume       = {{8}},
  year         = {{2022}},
}
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