We sequenced the first wild barley genome. Differences between this wild barley genome and that of the international reference genome based on the cultivated genotype Morex were described in this publication.

Wild barley (Hordeum spontaneum) provides a rich source of genetic variations for barley (H. vulgare) improvement. We constructed the first genome assembly for this taxon. The genome assembly has a total length of 4.28 Gb. N50 lengths of the assembled sequence contigs and scaffolds were 35.4 kb and 724.9 kb, respectively. Analysing against the Benchmarking Universal Single-Copy Orthologs showed that the completeness of the wild barley genome is even better than that of the international reference genome based on the cultivar Morex. The wild barley genome is highly syntenic with that of the cultivated form. In addition to a large number of tRNA, small nucleolar RNAs, small nuclear snRNA and miRNAs and transcription factors, 36,395 high-confidence protein coding genes were identified from the wild barley assembly. Of these genes, 514 were not found in Morex. Compared with Morex, the wild barley genome contains a larger proportion of genes conferring resistance and tolerance to biotic and abiotic stresses. The genome size of the wild barley taxon is smaller than that of the cultivated form and the difference is attributed mainly to the quantity of retrotransposons and other types of repeat sequences. Distributions of SNVs between the genomes of the wild barley genotype and Morex suggest that exploiting the wild barley taxon in breeding would be particularly effective in enhancing diversity for genes in the pericentric regions of chromosomes 3H and 5H.