Format: ORAL

Yang Liu1,2,34?, Sibo Wang1,34, Linzhou Li1,34, Ting Yang1,34, Shanshan Dong2,34, Tong Wei1,34, Shengdan Wu3,34, Yongbo Liu4,34, Yiqing Gong2, Xiuyan Feng5, Jianchao Ma6, Guanxiao Chang6, Jinling Huang5,6,7, Yong Yang8, Hongli Wang1,9, Min Liu1, Yan Xu1,9, Hongping Liang1,9, Jin Yu1,9, Yuqing Cai1,9, Zhaowu Zhang1,9, Yannan Fan1, Weixue Mu1, Sunil Kumar Sahu1, Shuchun Liu2, Xiaoan Lang2,10, Leilei Yang2, Na Li2, Sadaf Habib2,11, Yongqiong Yang12, Anders J. Lindstrom13, Pei Liang14, Bernard Goffinet15, Sumaira Zaman15, Jill L. Wegrzyn15, Dexiang Li10, Jian Liu5, Jie Cui16, Eva C. Sonnenschein17, Xiaobo Wang18, Jue Ruan18, Jia-Yu Xue19, Zhu-Qing Shao20, Chi Song21, Guangyi Fan1, Zhen Li22, Liangsheng Zhang23,24, Jianquan Liu25, Zhong-Jian Liu26, Yuannian Jiao27, Xiao-Quan Wang27, Hong Wu28, Ertao Wang29, Michael Lisby30, Huanming Yang1, Jian Wang1, Xin Liu1, Xun Xu1, Nan Li2, Pamela S. Soltis31,Yves Van de Peer19,22,32?, Douglas E. Soltis31,33?, Xun Gong5?, Huan Liu1?and Shouzhou Zhang2?

1State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China. 2Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China. 3State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China. 4State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China. 5Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China. 6Key Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China. 7Department of Biology, East Carolina University, Greenville, NC, USA. 8College of Biology and Environment, Nanjing Forestry University, Nanjing, China. 9College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China. 10Nanning Botanical Garden, Nanning, China. 11School of Life Sciences, Sun Yat-sen University, Guangzhou, China. 12Sichuan Cycas panzhihuaensis National Nature Reserve, Panzhihua, China. 13Global Biodiversity Conservancy, Chonburi, Thailand. 14Department of Entomology, China Agricultural University, Beijing, China. 15Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA. 16Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China. 17Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark. 18Shenzhen Agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China. 19College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China. 20State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China. 21Chengdu University of Traditional Chinese Medicine, Chengdu, China. 22Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB UGent Center for Plant Systems Biology, Gent, Belgium. 23College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China. 24Hainan Institute of Zhejiang University, Sanya, China. 25The College of Life Sciences, Sichuan University, Chengdu, China. 26Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China. 27State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China. 28College of Life Sciences, South China Agricultural University, Guangzhou, China. 29National 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. 30Department of Biology, University of Copenhagen, Copenhagen, Denmark. 31Florida Museum of Natural History, University of Florida, Gainesville, FL, USA. 32Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa. 33Department of Biology, University of Florida, Gainesville, FL, USA. 34These authors contributed equally: Yang Liu, Sibo Wang, Linzhou Li, Ting Yang, Shanshan Dong, Tong Wei, Shengdan Wu, Yongbo Liu. ?e-mail: yang.liu0508@gmail.com; yvpee@psb.vib-ugent.be; dsoltis@ufl.edu; gongxun@mail.kib.ac.cn; liuhuan@genomics.cn; shouzhouz@szbg.ac.cn

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.