Genome of <i>Crucihimalaya himalaica</i> , a close relative of <i>Arabidopsis</i> , shows ecological adaptation to high altitude

<i>Crucihimalaya himalaica</i>, a close relative of <i>Arabidopsis</i> and <i>Capsella</i>, 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 <i>C. himalaica</i> is most closely related to <i>Capsella</i> (estimated divergence 8.8 to 12.2 Mya), whereas both species form a sister clade to <i>Arabidopsis thaliana</i> and <i>Arabidopsis lyrata</i>, from which they diverged between 12.7 and 17.2 Mya. LTR retrotransposons in <i>C. himalaica</i> proliferated shortly after the dramatic uplift and climatic change of the Himalayas from the Late Pliocene to Pleistocene. Compared with closely related species, <i>C. himalaica</i> 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 <i>C. himalaica</i>'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 <i>C. himalaica</i>, might have enabled its QTP occupation. Overall, the genome sequence of <i>C. himalaica</i> provides insights into the mechanisms of plant adaptation to extreme environments.