High-quality reference genome and population analysis of allotetraploid Elymus sibiricus provide insight into genome origin and environmental adaptations to the Qinghai-Tibetan Plateau.

Elymus sibiricus L., a member of the Triticeae tribe, is a grass widely used for forage and restoring degraded grasslands in the Qinghai-Tibetan Plateau (QTP) region. Here, we present a high-quality reference genome assembly of allotetraploid E. sibiricus, consisting of 14 pseudochromosomes. Our findings suggest that large-scale bursts of retrotransposon activity, especially by Gypsy elements and unclassified retrotransposon elements, have played a critical role in the genome expansion of E. sibiricus as compared with other Triticeae. We identified a translocation between chromosomes Es4H and Es6H with a low recombination rate. Population genomic analysis of 90 E. sibiricus accessions and 25 diploid accessions of proposed ancestors from different habitats revealed four distinct groups, although they are of monophyletic origin. Our population analysis supports the idea that the QTP is likely the center of origin and genetic diversity of E. sibiricus. Selective sweep analysis identified significant pathways related to photosynthesis and metabolism, which are likely associated with the multiple environmental adaptations of this species to the climatic conditions of the QTP. Collectively, our study not only provides genomic resources for genetic improvement of the Elymus genus, but also provides important insights on the evolutionary history of E. sibiricus from population genomic analysis and the evolution of the tribe Triticeae.