Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 116, Issue 14, Pages 7137-7146Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1817580116
Keywords
adaptive evolution; natural selection; extreme environment; Qinghai-Tibet Plateau; S-locus
Categories
Funding
- National Natural Science Foundation of China [31770408, 31590823, 31760082, 31760127, U1802232, 91131901]
- National Key R&D Program of China [2017YF0505200]
- Strategic Priority Research Program of Chinese Academy of Sciences [XDA 20050203]
- National High Technology Research and Development Program of China [2014AA020528]
- Chinese Academy of Sciences Light of West China Program
- European Union Seventh Framework Programme Grant FP7/2007-2013 under European Research Council Advanced Grant [322739 - DOUBLEUP]
- Research Foundation-Flanders [12S9618N]
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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.
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