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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 of  M. delavayi  is 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 that  M. delavayi  experienced an independent whole-genome duplication (WGD), paralleling those independent WGDs in  Iberis ,  Biscutella , and  Anastatica  in the early Miocene. Phylogenetic analyses based on the single-copy genes confirmed the position of the genus  Megacarpaea  within the expanded lineage II of the family and resolved its basal divergence to a subclade consisting of  Anastatica, Iberis , and  Biscutella.  Species-specific and fast-evolving genes in  M. delavayi  are 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.

The Genome Sequence of Alpine Megacarpaea delavayi Identifies Species-Specific Whole-Genome Duplication