Crucihimalaya himalaica, a close relative ofArabidopsisandCapsella, 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 thatC. himalaicais most closely related toCapsella(estimated divergence 8.8 to 12.2 Mya), whereas both species form a sister clade toArabidopsis thalianaandArabidopsis lyrata, from which they diverged between 12.7 and 17.2 Mya. LTR retrotransposons inC. himalaicaproliferated shortly after the dramatic uplift and climatic change of the Himalayas from the Late Pliocene to Pleistocene. Compared with closely related species,C. himalaicashowed 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 forC. 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 ofC. himalaica, might have enabled its QTP occupation. Overall, the genome sequence ofC. himalaicaprovides insights into the mechanisms of plant adaptation to extreme environments.

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Multiple closely related species with genomic sequences provide an ideal system for studies on comparative and evolutionary genomics, as well as the mechanism of speciation. The whole genome sequences of six strawberry species (Fragaria spp.) have been released, which provide one of the richest genomic resources of any plant genus. In this study, we first generated seven transcriptome sequences of Fragaria species de novo, with a total of 48,557–82,537 unigenes per species. Combined with 13 other species genomes in Rosales, we reconstructed a phylogenetic tree at the genomic level. The phylogenic tree shows that Fragaria closed grouped with Rubus and the Fragaria clade is divided into three subclades. East Asian species appeared in every subclade, suggesting that the genus originated in this area at ∼7.99 Mya. Four species found in mountains of Southwest China originated at ∼3.98 Mya, suggesting that rapid speciation occurred to adapt to changing environments following the uplift of the Qinghai–Tibet Plateau. Moreover, we identified 510 very significantly positively selected genes in the cultivated species F. × ananassa genome. This set of genes was enriched in functions related to specific agronomic traits, such as carbon metabolism and plant hormone signal transduction processes, which are directly related to fruit quality and flavor. These findings illustrate comprehensive evolutionary patterns in Fragaria and the genetic basis of fruit domestication of cultivated strawberry at the genomic/transcriptomic level.