The Cycas genome and the early evolution of seed plants

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,...

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Published inNature plants Vol. 8; no. 4; pp. 389 - 401
Main Authors 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
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 01.04.2022
Nature Publishing Group
Subjects
631/181
631/449
Biomedical and Life Sciences
Chromosomes
Cones
Cycadophyta
Cycadopsida - genetics
Cycas
Cycas - genetics
Cycas panzhihuaensis
Evolution
Ferns
Gene transfer
Genes
Genes, Plant
Genomes
Ginkgo
Ginkgo biloba - genetics
Gymnosperms
Homology
Horizontal transfer
Life Sciences
Males
Mitochondria
Phylogeny
Plant Sciences
Seeds
Seeds - genetics
Sex determination
Transcriptomes
Online AccessGet full text

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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.
AbstractList 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.
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.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.
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.
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.
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.
Author Li, Zhen
Wang, Ertao
Wei, Tong
Song, Chi
Soltis, Pamela S.
Lindstrom, Anders J.
Xue, Jia-Yu
Li, Nan
Habib, Sadaf
Zhang, Liangsheng
Wang, Xiao-Quan
Xu, Yan
Yu, Jin
Gong, Xun
Goffinet, Bernard
Yang, Leilei
Wang, Xiaobo
Liu, Yongbo
Yang, Huanming
Mu, Weixue
Feng, Xiuyan
Chang, Guanxiao
Wu, Shengdan
Liu, Yang
Fan, Guangyi
Wu, Hong
Liu, Min
Li, Linzhou
Dong, Shanshan
Liu, Shuchun
Huang, Jinling
Soltis, Douglas E.
Xu, Xun
Van de Peer, Yves
Ma, Jianchao
Liu, Jianquan
Ruan, Jue
Fan, Yannan
Yang, Yongqiong
Liu, Jian
Jiao, Yuannian
Wang, Sibo
Liang, Pei
Yang, Yong
Liu, Zhong-Jian
Zaman, Sumaira
Wang, Jian
Liu, Huan
Liang, Hongping
Li, Na
Zhang, Shouzhou
Gong, Yiqing
Zhang, Zhaowu
Sahu, Sunil Kumar
Cui, Jie
Cai, Yuqing
Shao, Zhu-Qing
Li, Dexiang
Wang, Hongli
Wegrzyn, Jill L.
Lisby, Michael
Lang, Xiaoan
Yang, Ting
Liu, Xin
Sonnenschein, Eva C.
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  organization: Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences
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– reference: 35437000 - Nat Plants. 2022 Apr;8(4):326-327
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Snippet Cycads represent one of the most ancient lineages of living seed plants. Identifying genomic features uniquely shared by cycads and other extant seed plants,...
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SubjectTerms 631/181
631/449
Biomedical and Life Sciences
Chromosomes
Cones
Cycadophyta
Cycadopsida - genetics
Cycas
Cycas - genetics
Cycas panzhihuaensis
Evolution
Ferns
Gene transfer
Genes
Genes, Plant
Genomes
Ginkgo
Ginkgo biloba - genetics
Gymnosperms
Homology
Horizontal transfer
Life Sciences
Males
Mitochondria
Phylogeny
Plant Sciences
Seeds
Seeds - genetics
Sex determination
Transcriptomes
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Title The Cycas genome and the early evolution of seed plants
URI https://link.springer.com/article/10.1038/s41477-022-01129-7
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Volume 8
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