title: The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau.
abstract: The Tibetan hulless barley (Hordeum vulgare L. var. nudum), also called "Qingke" in Chinese and "Ne" in Tibetan, is the staple food for Tibetans and an important livestock feed in the Tibetan Plateau. The diploid nature and adaptation to diverse environments of the highland give it unique resources for genetic research and crop improvement. Here we produced a 3.89-Gb draft assembly of Tibetan hulless barley with 36,151 predicted protein-coding genes. Comparative analyses revealed the divergence times and synteny between barley and other representative Poaceae genomes. The expansion of the gene family related to stress responses was found in Tibetan hulless barley. Resequencing of 10 barley accessions uncovered high levels of genetic variation in Tibetan wild barley and genetic divergence between Tibetan and non-Tibetan barley genomes. Selective sweep analyses demonstrate adaptive correlations of genes under selection with extensive environmental variables. Our results not only construct a genomic framework for crop improvement but also provide evolutionary insights of highland adaptation of Tibetan hulless barley.
authors.affiliation: Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa 850002, China;
authors.forename: Xingquan
authors.initials: X
authors.lastname: Zeng
authors.affiliation: Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China;
authors.forename: Hai
authors.initials: H
authors.lastname: Long
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China;
authors.forename: Zhuo
authors.initials: Z
authors.lastname: Wang
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China;
authors.forename: Shancen
authors.initials: S
authors.lastname: Zhao
authors.affiliation: Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa 850002, China;
authors.forename: Yawei
authors.initials: Y
authors.lastname: Tang
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China;
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Huang
authors.affiliation: Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa 850002, China;
authors.forename: Yulin
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa 850002, China;
authors.forename: Qijun
authors.initials: Q
authors.lastname: Xu
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China;
authors.forename: Likai
authors.initials: L
authors.lastname: Mao
authors.affiliation: Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China;
authors.forename: Guangbing
authors.initials: G
authors.lastname: Deng
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China;
authors.forename: Xiaoming
authors.initials: X
authors.lastname: Yao
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China; College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China;
authors.forename: Xiangfeng
authors.initials: X
authors.lastname: Li
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China;
authors.forename: Lijun
authors.initials: L
authors.lastname: Bai
authors.affiliation: Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa 850002, China;
authors.forename: Hongjun
authors.initials: H
authors.lastname: Yuan
authors.affiliation: Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China;
authors.forename: Zhifen
authors.initials: Z
authors.lastname: Pan
authors.affiliation: Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa 850002, China;
authors.forename: Renjian
authors.initials: R
authors.lastname: Liu
authors.affiliation: Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China;
authors.forename: Xin
authors.initials: X
authors.lastname: Chen
authors.affiliation: Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa 850002, China;
authors.forename: QiMei
authors.initials: Q
authors.lastname: WangMu
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China;
authors.forename: Ming
authors.initials: M
authors.lastname: Chen
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China;
authors.forename: Lili
authors.initials: L
authors.lastname: Yu
authors.affiliation: Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China;
authors.forename: Junjun
authors.initials: J
authors.lastname: Liang
authors.affiliation: Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa 850002, China;
authors.forename: DaWa
authors.initials: D
authors.lastname: DunZhu
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China;
authors.forename: Yuan
authors.initials: Y
authors.lastname: Zheng
authors.affiliation: Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China;
authors.forename: Shuiyang
authors.initials: S
authors.lastname: Yu
authors.affiliation: Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa 850002, China;
authors.forename: ZhaXi
authors.initials: Z
authors.lastname: LuoBu
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China;
authors.forename: Xuanmin
authors.initials: X
authors.lastname: Guang
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China;
authors.forename: Jiang
authors.initials: J
authors.lastname: Li
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China;
authors.forename: Cao
authors.initials: C
authors.lastname: Deng
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China;
authors.forename: Wushu
authors.initials: W
authors.lastname: Hu
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China;
authors.forename: Chunhai
authors.initials: C
authors.lastname: Chen
authors.affiliation: Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa 850002, China;
authors.forename: XiongNu
authors.initials: X
authors.lastname: TaBa
authors.affiliation: Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa 850002, China;
authors.forename: Liyun
authors.initials: L
authors.lastname: Gao
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China;
authors.forename: Xiaodan
authors.initials: X
authors.lastname: Lv
authors.affiliation: Projects and Physics Section, Sapir Academic College, D.N. Hof Ashkelon 79165, Israel;
authors.forename: Yuval Ben
authors.initials: YB
authors.lastname: Abu
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China;
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Fang
authors.affiliation: Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel; nima_zhaxi@sina.com nevo@research.haifa.ac.il yumaoqun@cib.ac.cn wangj@genomics.org.cn.
authors.forename: Eviatar
authors.initials: E
authors.lastname: Nevo
authors.affiliation: Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China; nima_zhaxi@sina.com nevo@research.haifa.ac.il yumaoqun@cib.ac.cn wangj@genomics.org.cn.
authors.forename: Maoqun
authors.initials: M
authors.lastname: Yu
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China; Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark; and Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21441, Saudi Arabia nima_zhaxi@sina.com nevo@research.haifa.ac.il yumaoqun@cib.ac.cn wangj@genomics.org.cn.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa 850002, China; nima_zhaxi@sina.com nevo@research.haifa.ac.il yumaoqun@cib.ac.cn wangj@genomics.org.cn.
authors.forename: Nyima
authors.initials: N
authors.lastname: Tashi
mesh_terms: D000064:Acclimatization / Q000502:physiology*; D001483:Base Sequence; D014644:Genetic Variation / Q000502:physiology*; D018745:Genome, Plant / Q000502:physiology*; D001467:Hordeum / Q000235:genetics*; D008969:Molecular Sequence Data; D018609:Tibet
keywords: Tibetan hulless barley; Triticeae evolution; adaptation; genetic diversity; selective sweep