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Eutrema is a genus in the Brassicaceae, which includes species of scientific and economic importance. Many Eutrema species are montane and/or alpine species that arose very recently, making them ideal candidates for comparative studies to understand both ecological speciation and high-altitude adaptation in plants. Here we provide de novo whole-genome assemblies for a pair of recently diverged perennials with contrasting altitude preferences, the high-altitude E. heterophyllum from the eastern Qinghai-Tibet Plateau and its lowland congener E. yunnanense. The two assembled genomes are 350 Mb and 412 Mb, respectively, with 29,606 and 28,881 predicted genes. Comparative analysis of the two species revealed contrasting demographic trajectories and evolution of gene families. Gene family expansions shared between E. heterophyllum and other alpine species were identified, including the disease resistance R genes (NBS-LRRs or NLRs). Genes that are duplicated specifically in the high-altitude E. heterophyllum are involved mainly in reproduction, DNA damage repair and cold tolerance. The two Eutrema genomes reported here constitute important genetic resources for diverse studies, including the evolution of the genus Eutrema, of the Brassicaceae as a whole and of alpine plants across the world.

The genomes of two Eutrema species provide insight into plant adaptation to high altitudes