The Genome Sequence of AlpineMegacarpaea delavayiIdentifies Species-Specific Whole-Genome Duplication

Megacarpaea delavayi(Brassicaceae), a plant found the high mountains of southwest China at high altitudes (3000-4800 m), is used as a vegetable or medicine. Here, we report a draft genome for this species. The assembly genome ofM. delavayiis 883 Mb, and 61.59% of the genome is composed of repeat sequences. Annotation of the genome identified a total of 41,114 protein-coding genes. We found thatM. delavayiexperienced an independent whole-genome duplication (WGD), paralleling those independent WGDs inIberis,Biscutella, andAnastaticain the early Miocene. Phylogenetic analyses based on the single-copy genes confirmed the position of the genusMegacarpaeawithin the expanded lineage II of the family and resolved its basal divergence to a subclade consisting ofAnastatica, Iberis, andBiscutella.Species-specific and fast-evolving genes inM. delavayiare mainly involved in "DNA repair" and "response to UV-B radiation." These genetic changes may together help this species survive in high-altitude environments. The reference genome reported here provides a valuable resource for studying adaptation of this and other alpine plants to the high-altitude habitats.