气候变化领域集成服务门户(CCPortal): Genome of Crucihimalaya himalaica; a close relative of Arabidopsis; shows ecological adaptation to high altitude

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DOI	10.1073/pnas.1817580116
	Genome of Crucihimalaya himalaica; a close relative of Arabidopsis; shows ecological adaptation to high altitude
	Zhang T.; Qiao Q.; Novikova P.Yu.; Wang Q.; Yue J.; Guan Y.; Ming S.; Liu T.; De J.; Liu Y.; Al-Shehbaz I.A.; Sun H.; Van Montagu M.; Huang J.; Van de Peer Y.; Qiong L.
发表日期	2019
ISSN	0027-8424
起始页码	7137
结束页码	7146
卷号	116 期号:14
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 clade 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 S-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. © 2019 National Academy of Sciences. All Rights Reserved.
英文关键词	Adaptive evolution; Extreme environment; Natural selection; Qinghai–Tibet Plateau; S-locus
语种	英语
scopus关键词	contig; nuclear protein; plant protein; altitude acclimatization; Arabidopsis; Arabidopsis lyrata; Arabidopsis thaliana; Article; Capsella; copy number variation; Crucihimalaya himalaica; DNA repair; evolutionary adaptation; gene function; gene identification; gene locus; gene sequence; gene structure; genetic code; genetic variability; molecular genetics; nonhuman; phylogenomics; priority journal; protein degradation; retroposon; sequence analysis; species difference; acclimatization; adaptation; altitude; Arabidopsis; Brassicaceae; Capsella; climate change; disease resistance; extreme environment; gene dosage; genetic selection; genetics; phylogeny; physiology; plant gene; self fertilization; sequence alignment; Tibet; whole genome sequencing; Acclimatization; Adaptation, Physiological; Altitude; Arabidopsis; Brassicaceae; Capsella; Climate Change; Disease Resistance; DNA Repair; Extreme Environments; Gene Dosage; Genes, Plant; Nuclear Proteins; Phylogeny; Plant Proteins; Selection, Genetic; Self-Fertilization; Sequence Alignment; Tibet; Whole Genome Sequencing
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/159037
作者单位	Zhang, T., Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China, College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China; Qiao, Q., School of Agriculture, Yunnan University, Kunming, 650091, China; Novikova, P.Yu., Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium, Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium; Wang, Q., Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China; Yue, J., Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China; Guan, Y., Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China; Ming, S., Institute of Biodiversity Scien...
推荐引用方式 GB/T 7714	Zhang T.,Qiao Q.,Novikova P.Yu.,et al. Genome of Crucihimalaya himalaica; a close relative of Arabidopsis; shows ecological adaptation to high altitude[J],2019,116(14).
APA	Zhang T..,Qiao Q..,Novikova P.Yu..,Wang Q..,Yue J..,...&Qiong L..(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).
MLA	Zhang T.,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).