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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 |
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Springer Science and Business Media LLC
2022
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<?xml version="1.0"?><rfc1807><datestamp>2022-11-04T17:57:48.8330034</datestamp><bib-version>v2</bib-version><id>61714</id><entry>2022-10-31</entry><title>The Cycas genome and the early evolution of seed plants</title><swanseaauthors><author><sid>f6a4027578a15ea3e6453a54b849c686</sid><ORCID>0000-0001-6959-5100</ORCID><firstname>Eva C.</firstname><surname>Sonnenschein</surname><name>Eva C. Sonnenschein</name><active>true</active><ethesisStudent>false</ethesisStudent></author></swanseaauthors><date>2022-10-31</date><deptcode>SBI</deptcode><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.</abstract><type>Journal Article</type><journal>Nature Plants</journal><volume>8</volume><journalNumber>4</journalNumber><paginationStart>389</paginationStart><paginationEnd>401</paginationEnd><publisher>Springer Science and Business Media LLC</publisher><placeOfPublication/><isbnPrint/><isbnElectronic/><issnPrint/><issnElectronic>2055-0278</issnElectronic><keywords/><publishedDay>18</publishedDay><publishedMonth>4</publishedMonth><publishedYear>2022</publishedYear><publishedDate>2022-04-18</publishedDate><doi>10.1038/s41477-022-01129-7</doi><url/><notes/><college>COLLEGE NANME</college><department>Biosciences</department><CollegeCode>COLLEGE CODE</CollegeCode><DepartmentCode>SBI</DepartmentCode><institution>Swansea University</institution><apcterm/><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/).</funders><projectreference/><lastEdited>2022-11-04T17:57:48.8330034</lastEdited><Created>2022-10-31T12:54:00.3839033</Created><path><level id="1">Faculty of Science and Engineering</level><level id="2">School of Biosciences, Geography and Physics - Biosciences</level></path><authors><author><firstname>Yang</firstname><surname>Liu</surname><orcid>0000-0002-5942-839x</orcid><order>1</order></author><author><firstname>Sibo</firstname><surname>Wang</surname><order>2</order></author><author><firstname>Linzhou</firstname><surname>Li</surname><orcid>0000-0003-0799-0900</orcid><order>3</order></author><author><firstname>Ting</firstname><surname>Yang</surname><order>4</order></author><author><firstname>Shanshan</firstname><surname>Dong</surname><order>5</order></author><author><firstname>Tong</firstname><surname>Wei</surname><order>6</order></author><author><firstname>Shengdan</firstname><surname>Wu</surname><orcid>0000-0003-1481-4825</orcid><order>7</order></author><author><firstname>Yongbo</firstname><surname>Liu</surname><orcid>0000-0003-1618-8813</orcid><order>8</order></author><author><firstname>Yiqing</firstname><surname>Gong</surname><order>9</order></author><author><firstname>Xiuyan</firstname><surname>Feng</surname><order>10</order></author><author><firstname>Jianchao</firstname><surname>Ma</surname><order>11</order></author><author><firstname>Guanxiao</firstname><surname>Chang</surname><order>12</order></author><author><firstname>Jinling</firstname><surname>Huang</surname><orcid>0000-0003-4893-4171</orcid><order>13</order></author><author><firstname>Yong</firstname><surname>Yang</surname><order>14</order></author><author><firstname>Hongli</firstname><surname>Wang</surname><order>15</order></author><author><firstname>Min</firstname><surname>Liu</surname><order>16</order></author><author><firstname>Yan</firstname><surname>Xu</surname><order>17</order></author><author><firstname>Hongping</firstname><surname>Liang</surname><orcid>0000-0002-6139-191x</orcid><order>18</order></author><author><firstname>Jin</firstname><surname>Yu</surname><orcid>0000-0002-1662-2862</orcid><order>19</order></author><author><firstname>Yuqing</firstname><surname>Cai</surname><order>20</order></author><author><firstname>Zhaowu</firstname><surname>Zhang</surname><order>21</order></author><author><firstname>Yannan</firstname><surname>Fan</surname><orcid>0000-0003-3308-6878</orcid><order>22</order></author><author><firstname>Weixue</firstname><surname>Mu</surname><order>23</order></author><author><firstname>Sunil 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2022-11-04T17:57:48.8330034 v2 61714 2022-10-31 The Cycas genome and the early evolution of seed plants f6a4027578a15ea3e6453a54b849c686 0000-0001-6959-5100 Eva C. Sonnenschein Eva C. Sonnenschein true false 2022-10-31 SBI 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. Journal Article Nature Plants 8 4 389 401 Springer Science and Business Media LLC 2055-0278 18 4 2022 2022-04-18 10.1038/s41477-022-01129-7 COLLEGE NANME Biosciences COLLEGE CODE SBI Swansea University 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/). 2022-11-04T17:57:48.8330034 2022-10-31T12:54:00.3839033 Faculty of Science and Engineering School of Biosciences, Geography and Physics - Biosciences Yang Liu 0000-0002-5942-839x 1 Sibo Wang 2 Linzhou Li 0000-0003-0799-0900 3 Ting Yang 4 Shanshan Dong 5 Tong Wei 6 Shengdan Wu 0000-0003-1481-4825 7 Yongbo Liu 0000-0003-1618-8813 8 Yiqing Gong 9 Xiuyan Feng 10 Jianchao Ma 11 Guanxiao Chang 12 Jinling Huang 0000-0003-4893-4171 13 Yong Yang 14 Hongli Wang 15 Min Liu 16 Yan Xu 17 Hongping Liang 0000-0002-6139-191x 18 Jin Yu 0000-0002-1662-2862 19 Yuqing Cai 20 Zhaowu Zhang 21 Yannan Fan 0000-0003-3308-6878 22 Weixue Mu 23 Sunil Kumar Sahu 0000-0002-4742-9870 24 Shuchun Liu 25 Xiaoan Lang 26 Leilei Yang 27 Na Li 28 Sadaf Habib 29 Yongqiong Yang 30 Anders J. Lindstrom 0000-0003-0419-9136 31 Pei Liang 32 Bernard Goffinet 0000-0002-2754-3895 33 Sumaira Zaman 34 Jill L. Wegrzyn 35 Dexiang Li 36 Jian Liu 37 Jie Cui 0000-0003-4363-8672 38 Eva C. Sonnenschein 0000-0001-6959-5100 39 Xiaobo Wang 0000-0001-6754-7404 40 Jue Ruan 0000-0003-3713-3192 41 Jia-Yu Xue 42 Zhu-Qing Shao 0000-0002-0431-0669 43 Chi Song 0000-0003-3904-963x 44 Guangyi Fan 45 Zhen Li 46 Liangsheng Zhang 47 Jianquan Liu 0000-0002-4237-7418 48 Zhong-Jian Liu 0000-0003-4390-3878 49 Yuannian Jiao 0000-0002-8987-2782 50 Xiao-Quan Wang 0000-0003-3978-0828 51 Hong Wu 52 Ertao Wang 0000-0002-5178-3530 53 Michael Lisby 0000-0002-4830-5247 54 Huanming Yang 55 Jian Wang 56 Xin Liu 0000-0003-3256-2940 57 Xun Xu 0000-0002-5338-5173 58 Nan Li 59 Pamela S. Soltis 0000-0001-9310-8659 60 Yves Van de Peer 0000-0003-4327-3730 61 Douglas E. Soltis 0000-0001-8638-4137 62 Xun Gong 0000-0003-1705-6935 63 Huan Liu 0000-0003-3909-0931 64 Shouzhou Zhang 0000-0001-9070-0593 65 61714__25660__8b9bd5b37ad34609b8d79c176aa6a6c5.pdf 61714.pdf 2022-11-04T17:56:31.2761070 Output 10806839 application/pdf Version of Record true © The Author(s) 2022. This article is licensed under a Creative Commons Attribution 4.0 International License true eng http://creativecommons.org/licenses/by/4.0/ |
| title |
The Cycas genome and the early evolution of seed plants |
| spellingShingle |
The Cycas genome and the early evolution of seed plants Eva C. Sonnenschein |
| title_short |
The Cycas genome and the early evolution of seed plants |
| title_full |
The Cycas genome and the early evolution of seed plants |
| title_fullStr |
The Cycas genome and the early evolution of seed plants |
| title_full_unstemmed |
The Cycas genome and the early evolution of seed plants |
| title_sort |
The Cycas genome and the early evolution of seed plants |
| author_id_str_mv |
f6a4027578a15ea3e6453a54b849c686 |
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f6a4027578a15ea3e6453a54b849c686_***_Eva C. Sonnenschein |
| author |
Eva C. Sonnenschein |
| author2 |
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 |
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Nature Plants |
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8 |
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389 |
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2022 |
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Swansea University |
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2055-0278 |
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10.1038/s41477-022-01129-7 |
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Springer Science and Business Media LLC |
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Faculty of Science and Engineering |
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School of Biosciences, Geography and Physics - Biosciences{{{_:::_}}}Faculty of Science and Engineering{{{_:::_}}}School of Biosciences, Geography and Physics - Biosciences |
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| description |
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. |
| published_date |
2022-04-18T04:20:44Z |
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1763754371712024576 |
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11.035634 |