ArticleNature plants2022
The Cycas genome and the early evolution of seed plants.
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Article in Nature plants, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 104 papers.
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104citing papers in PubMed
88.2field-weighted citation impact, top 1% of its field
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104 citing papers in PubMed, 228 citations in OpenAlex.
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- A chromosome-level genome assembly of Platycladus orientalis and comparative genomics reveal pivotal roles of transposable elements in gene duplication and pseudogenization across gymnosperm giga-genomes.Plant communications · 2026Article
- Evolution ofPlants (Basel, Switzerland) · 2026Article
- A genomic perspective on adaptation to heterogeneous environments for Cycas segmentifida (Cycadaceae), an endemic cycad in southwest China.Annals of botany · 2026Article
- Cunninghamia lanceolata genome illuminates the evolutionary dynamics of gymnosperms.Cell reports · 2026Article
- The post-fertilization archegonium gene network of seedless plants contributed to the origin of seeds.Nature communications · 2026Article
- Natural selection and recombination interact to structure genome-wide variation in pines.The Plant journal : for cell and molecular biology · 2026Article
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- Intermediate evolutionary state of motile sperm and pollen tubes in the extant gymnospermProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Low genetic differentiation among morphologically distinct Cycas species informs the delineation of conservation management units.Annals of botany · 2026Article
- Phylogenomic profile of exon-intron organization across angiosperms, their relationships with protein domains, and functional implications.Nature communications · 2026Article
- A comprehensive phylogenomic framework for cycads (Cycadales).PhytoKeys · 2026Article
- Evolutionary analysis of the Dof family in plants and identification of its members in tobacco.Frontiers in plant science · 2026Article
- The complete mitochondrial genome ofFrontiers in plant science · 2026Article
- Developmentally regulated genes drive phylogenomic splits in ovule evolution.Nature communications · 2025Article
- Unraveling the evolutionary complexity ofPlant diversity · 2025Article
- NGATHA carpel development genes evolved in the common ancestor of seed plants.The Plant journal : for cell and molecular biology · 2025Article
- Resolving the Stasis-Dynamism Paradox: Genome Evolution in Tree Ferns.Molecular biology and evolution · 2025Article
44 more citing papers are in PubMed but not listed here.
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Authors and funding
65 authors at 20 institutions in 6 countries.
Yang Liu *State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China. yang.liu0508@gmail.com.ORCID http://orcid.org/0000-0002-5942-839X
Sibo Wang *State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
Linzhou Li *State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.ORCID http://orcid.org/0000-0003-0799-0900
Ting Yang *State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
Shanshan Dong *Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China.
Tong Wei *State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
Shengdan Wu *State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China.ORCID http://orcid.org/0000-0003-1481-4825
Yongbo Liu *State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China.ORCID http://orcid.org/0000-0003-1618-8813
Yiqing GongKey Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China.
Xiuyan FengKey Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
Jianchao MaKey Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China.
Guanxiao ChangKey Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China.
Jinling HuangKey Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.ORCID http://orcid.org/0000-0003-4893-4171
Yong YangCollege of Biology and Environment, Nanjing Forestry University, Nanjing, China.
Hongli WangState Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
Min LiuState Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
Yan XuState Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
Hongping LiangState Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.ORCID http://orcid.org/0000-0002-6139-191X
Jin YuState Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.ORCID http://orcid.org/0000-0002-1662-2862
Yuqing CaiState Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
Zhaowu ZhangState Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
Yannan FanState Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.ORCID http://orcid.org/0000-0003-3308-6878
Weixue MuState Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
Sunil Kumar SahuState Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.ORCID http://orcid.org/0000-0002-4742-9870
Shuchun LiuKey Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China.
Xiaoan LangKey Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China.
Leilei YangKey Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China.
Na LiKey Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China.
Sadaf HabibKey Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China.
Yongqiong YangSichuan Cycas panzhihuaensis National Nature Reserve, Panzhihua, China.
Anders J LindstromGlobal Biodiversity Conservancy, Chonburi, Thailand.ORCID http://orcid.org/0000-0003-0419-9136
Pei LiangDepartment of Entomology, China Agricultural University, Beijing, China.
Bernard GoffinetDepartment of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA.ORCID http://orcid.org/0000-0002-2754-3895
Sumaira ZamanDepartment of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA.
Jill L WegrzynDepartment of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA.
Dexiang LiNanning Botanical Garden, Nanning, China.
Jian LiuKey Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
Jie CuiGuangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China.ORCID http://orcid.org/0000-0003-4363-8672
Eva C SonnenscheinDepartment of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.ORCID http://orcid.org/0000-0001-6959-5100
Xiaobo WangShenzhen Agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China.ORCID http://orcid.org/0000-0001-6754-7404
Jue RuanShenzhen Agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China.ORCID http://orcid.org/0000-0003-3713-3192
Jia-Yu XueCollege of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China.
Zhu-Qing ShaoState Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.ORCID http://orcid.org/0000-0002-0431-0669
Chi SongChengdu University of Traditional Chinese Medicine, Chengdu, China.ORCID http://orcid.org/0000-0003-3904-963X
Guangyi FanState Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
Zhen LiDepartment of Plant Biotechnology and Bioinformatics, Ghent University, VIB UGent Center for Plant Systems Biology, Gent, Belgium.
Liangsheng ZhangCollege of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
Jianquan LiuThe College of Life Sciences, Sichuan University, Chengdu, China.ORCID http://orcid.org/0000-0002-4237-7418
Zhong-Jian LiuKey Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.ORCID http://orcid.org/0000-0003-4390-3878
Yuannian JiaoState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.ORCID http://orcid.org/0000-0002-8987-2782
Xiao-Quan WangState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.ORCID http://orcid.org/0000-0003-3978-0828
Hong WuCollege of Life Sciences, South China Agricultural University, Guangzhou, China.
Ertao WangNational Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.ORCID http://orcid.org/0000-0002-5178-3530
Michael LisbyDepartment of Biology, University of Copenhagen, Copenhagen, Denmark.ORCID http://orcid.org/0000-0002-4830-5247
Huanming YangState Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
Jian WangState Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
Xin LiuState Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.ORCID http://orcid.org/0000-0003-3256-2940
Xun XuState Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.ORCID http://orcid.org/0000-0002-5338-5173
Nan LiKey Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China.
Pamela S SoltisFlorida Museum of Natural History, University of Florida, Gainesville, FL, USA.ORCID http://orcid.org/0000-0001-9310-8659
Yves Van de PeerCollege of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China. yvpee@psb.vib-ugent.be.ORCID http://orcid.org/0000-0003-4327-3730
Douglas E SoltisFlorida Museum of Natural History, University of Florida, Gainesville, FL, USA. dsoltis@ufl.edu.ORCID http://orcid.org/0000-0001-8638-4137
Xun GongKey Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China. gongxun@mail.kib.ac.cn.ORCID http://orcid.org/0000-0003-1705-6935
Huan LiuState Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China. liuhuan@genomics.cn.ORCID http://orcid.org/0000-0003-3909-0931
Shouzhou ZhangKey Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China. shouzhouz@szbg.ac.cn.ORCID http://orcid.org/0000-0001-9070-0593
BGI Group (China) · CNChinese Academy of Sciences · CNKunming Institute of Botany · CNUniversity of Connecticut · USFlorida Museum of Natural History · USHenan University · CNNanjing Agricultural University · CNNanjing Forestry University · CNAgricultural Genomics Institute at Shenzhen · CNChengdu University of Traditional Chinese Medicine · CNChina Agricultural University · CNChonburi Hospital · THFujian Agriculture and Forestry University · CNHangzhou Botanical Garden · CNLanzhou University · CNNanjing University · CNSanya University · CNShenzhen University · CNSouth China Agricultural University · CNSun Yat-sen University · CN
Funding
No grant is acknowledged in the PubMed record.
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.
Indexed as
CycasCycadopsidaGenes, PlantGinkgo bilobaPhylogenySeeds
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