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.. The first draft genome sequence for wild barley (Hordeum spontaneum)

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.

野生二棱大麦（Hordeum spontaneum）为普通栽培大麦（H. vulgare）的遗传改良提供了丰富的遗传变异资源。本研究构建了该类群的首个基因组组装序列，其总长度为4.28 Gb。组装得到的序列重叠群（contig）与支架（scaffold）的N50长度分别为35.4 kb与724.9 kb。通过通用单拷贝同源基因基准集（Benchmarking Universal Single-Copy Orthologs）分析显示，本研究组装的野生大麦基因组完整性优于以栽培品种Morex为材料构建的国际参考基因组。野生大麦基因组与栽培大麦基因组间存在高度共线性。除鉴定到大量转运RNA（tRNA）、核仁小RNA（snoRNA）、核小RNA（snRNA）、微小RNA（miRNA）及转录因子外，本研究从该野生大麦基因组组装中共注释得到36395个高可信度蛋白质编码基因，其中514个基因为Morex参考基因组中未收录的新基因。与Morex参考基因组相比，野生大麦基因组中赋予生物与非生物胁迫抗性及耐受性的基因占比更高。该野生大麦类群的基因组尺寸小于栽培大麦，二者差异主要由反转录转座子（retrotransposon）与其他类型重复序列的数量差异所致。野生大麦基因型与Morex基因组间的单核苷酸变异（SNV）分布特征表明，在育种实践中利用该野生大麦类群，可有效提升3H号与5H号染色体着丝粒周边区域的基因多样性。