AUTHOR=Yang Qiao , Bi Hao , Yang Wenjie , Li Ting , Jiang Jiebei , Zhang Lei , Liu Jianquan , Hu Quanjun 

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

JOURNAL=Frontiers in Genetics

VOLUME=11

YEAR=2020

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2020.00812

DOI=10.3389/fgene.2020.00812

ISSN=1664-8021

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