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
Corresponding AuthorVan Montagu, Marc(marc.vanmontagu@vib-ugent.be) ; Huang, Jinling(huangj@ecu.edu) ; Van de Peer, Yves(yves.vandepeer@psb.vib-ugent.be) ; Qiong, La(lhagchong@163.com)
2019-04-02
Source PublicationPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
ISSN0027-8424
Volume116Issue:14Pages:7137-7146
AbstractCrucihimalaya 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.
Keywordadaptive evolution natural selection extreme environment Qinghai-Tibet Plateau S-locus
DOI10.1073/pnas.1817580116
Indexed BySCI
Language英语
WOS Research AreaScience & Technology - Other Topics
WOS SubjectMultidisciplinary Sciences
WOS IDWOS:000463069900097
Citation statistics
Document Type期刊论文
Identifierhttp://ir.kib.ac.cn/handle/151853/66169
Collection中国科学院东亚植物多样性与生物地理学重点实验室
Corresponding AuthorVan Montagu, Marc; Huang, Jinling; Van de Peer, Yves; Qiong, La
Affiliation1.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
Recommended Citation
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]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA,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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