High-quality genome of allotetraploid Avena barbata provides insights into the origin and evolution of B subgenome in Avena.

Avena barbata, a wild oat species within the genus Avena, is a widely used model for studying plant ecological adaptation due to its strong environmental adaptability and disease resistance, serving as a valuable genetic resource for oat improvement. Here, we phased the high-quality chromosome-level genome assembly of A. barbata (6.88 Gb, contig N50 = 53.74 Mb) into A (3.57 Gb with 47,687 genes) and B (3.31 Gb with 46,029 genes) subgenomes. Comparative genomics and phylogenomic analyses clarified the evolutionary relationships and trajectories of A, B, C and D subgenomes in Avena. We inferred that the A subgenome donor of A. barbata was Avena hirtula, while the B subgenome donor was probably an extinct diploid species closely related to Avena wiestii. Genome evolution analysis revealed the dynamic transposable element (TE) content and subgenome divergence, as well as extensive structure variations across A, B, C, and D subgenomes in Avena. Population genetic analysis of 211 A. barbata accessions from distinct ecotypes identified several candidate genes related to environmental adaptability and drought resistance. Our study provides a comprehensive genetic resource for exploring the genetic basis underlying the strong environmental adaptability of A. barbata and the molecular identification of important agronomic traits for oat breeding.