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DOI10.1073/pnas.1817580116
Genome of Crucihimalaya himalaica, a close relative of Arabidopsis, shows ecological adaptation to high altitude
Zhang, Ticao1,2; Qiao, Qin3; Novikova, Polina Yu.4,5; Wang, Qia1; Yue, Jipei1; Guan, Yanlong1; Ming, Shengping6; Liu, Tianmeng6; De, Ji6; Liu, Yixuan6; Al-Shehbaz, Ihsan A.7; Sun, Hang2; Van Montagu, Marc4,5; Huang, Jinling1,8,9; Van de Peer, Yves4,5,10; Qiong, La6
发表日期2019
ISSN0027-8424
卷号116期号:14页码:7137-7146
英文摘要

Crucihimalaya himalaica, a close relative of Arabidopsis and Capsella, grows on the Qinghai-Tibet Plateau (QTP) about 4,000 m above sea level and represents an attractive model system for studying speciation and ecological adaptation in extreme environments. We assembled a draft genome sequence of 234.72 Mb encoding 27,019 genes and investigated its origin and adaptive evolutionary mechanisms. Phylogenomic analyses based on 4,586 single-copy genes revealed that C. himalaica is most closely related to Capsella (estimated divergence 8.8 to 12.2 Mya), whereas both species form a sister Glade to Arabidopsis thaliana and Arabidopsis lyrata, from which they diverged between 12.7 and 17.2 Mya. LTR retrotransposons in C. himalaica proliferated shortly after the dramatic uplift and climatic change of the Himalayas from the Late Pliocene to Pleistocene. Compared with closely related species, C himalaica showed significant contraction and pseudogenization in gene families associated with disease resistance and also significant expansion in gene families associated with ubiquitin-mediated proteolysis and DNA repair. We identified hundreds of genes involved in DNA repair, ubiquitin-mediated proteolysis, and reproductive processes with signs of positive selection. Gene families showing dramatic changes in size and genes showing signs of positive selection are likely candidates for C himalaica's adaptation to intense radiation, low temperature, and pathogen-depauperate environments in the QTP. Loss of function at the 5-locus, the reason for the transition to self-fertilization of C himalaica, might have enabled its QTP occupation. Overall, the genome sequence of C. himalaica provides insights into the mechanisms of plant adaptation to extreme environments.


WOS研究方向Science & Technology - Other Topics
来源期刊PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
文献类型期刊论文
条目标识符http://gcip.llas.ac.cn/handle/2XKMVOVA/96289
作者单位1.Chinese Acad Sci, Kunming Inst Bot, Key Lab Plant Divers & Biogeog East Asia, Kunming 650201, Yunnan, Peoples R China;
2.Yunnan Univ Chinese Med, Coll Chinese Mat Med, Kunming 650500, Yunnan, Peoples R China;
3.Yunnan Univ, Sch Agr, Kunming 650091, Yunnan, Peoples R China;
4.Univ Ghent, Dept Plant Biotechnol & Bioinformat, B-9052 Ghent, Belgium;
5.VIB, Ctr Plant Syst Biol, B-9052 Ghent, Belgium;
6.Tibet Univ, Coll Sci, Inst Biodivers Sci & Geobiol, Lhasa 850012, Peoples R China;
7.Missouri Bot Garden, Pob 299, St Louis, MO 63166 USA;
8.East Carolina Univ, Dept Biol, Greenville, NC 27858 USA;
9.Henan Univ, Sch Life Sci, State Key Lab Cotton Biol, Inst Plant Stress Biol, Kaifeng 475001, Peoples R China;
10.Univ Pretoria, Dept Biochem Genet & Microbiol, ZA-0028 Pretoria, South Africa
推荐引用方式
GB/T 7714
Zhang, Ticao,Qiao, Qin,Novikova, Polina Yu.,et al. Genome of Crucihimalaya himalaica, a close relative of Arabidopsis, shows ecological adaptation to high altitude[J],2019,116(14):7137-7146.
APA Zhang, Ticao.,Qiao, Qin.,Novikova, Polina Yu..,Wang, Qia.,Yue, Jipei.,...&Qiong, La.(2019).Genome of Crucihimalaya himalaica, a close relative of Arabidopsis, shows ecological adaptation to high altitude.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA,116(14),7137-7146.
MLA Zhang, Ticao,et al."Genome of Crucihimalaya himalaica, a close relative of Arabidopsis, shows ecological adaptation to high altitude".PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 116.14(2019):7137-7146.
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