The draft genome of a wild barley genotype reveals its enrichment in genes related to biotic and abiotic stresses compared to cultivated barley

Abstract

Wild barley (Hordeum spontaneum) is the progenitor of cultivated barley (Hordeum vulgare) and provides a rich source of genetic variations for barley improvement. Currently, the genome sequences of wild barley and its differences with cultivated barley remain unclear. In this study, we report a high-quality draft assembly of wild barley accession (AWCS276; henceforth named as WB1), which consists of 4.28 Gb genome and 36 395 high-confidence protein-coding genes. BUSCO analysis revealed that the assembly included full lengths of 95.3% of the 956 single-copy plant genes, illustrating that the gene-containing regions have been well assembled. By comparing with the genome of the cultivated genotype Morex, it is inferred that the WB1 genome contains more genes involved in resistance and tolerance to biotic and abiotic stresses. The presence of the numerous WB1-specific genes indicates that, in addition to enhance allele diversity for genes already existing in the cultigen, exploiting the wild barley taxon in breeding should also allow the incorporation of novel genes. Furthermore, high levels of genetic variation in the pericentromeric regions were detected in chromosomes 3H and 5H between the wild and cultivated genotypes, which may be the results of domestication. This H. spontaneum draft genome assembly will help to accelerate wild barley research and be an invaluable resource for barley improvement and comparative genomics research.

Keywords: Hordeum spontaneum; Morex; genetic variation; genome; specific gene.

Figure 1

Gene families, phylogenetic, Ks distributions and divergence time between wild barley and other grasses. (a) Venn diagram of shared orthologous gene families among five grass genomes. The first number below the species name denotes the number of gene families clustered by OrthoMCL analysis. The second number indicates the number of genes within families for each taxon. (b) Phylogenetic relationship between the wild barley taxon and other grasses. The numbers in red and blue on each branch indicate the quantity of expanded (+) or contracted (−) orthologous clusters after the corresponding speciation, respectively. The tree is based on 100 bootstraps shown by black numbers. The dN/dS ratio of each branch is noted in parentheses. Arabidopsis thaliana is used as an outgroup. (c) Ks distributions of orthologous genes between wild barley genotype WB1 and other four grass species. (d) Divergence time between wild barley and other grasses. HSP: H. spontaneum; TUR: T. urartu; BDI: B. distachyon; OSA: O. sativa; SIT: S. italica; SBI: S. bicolor; ZMA: Z. mays.

Figure 2

Gene synteny between wild barley and cultivated barley (Morex). The Morex chromosomes are represented by blue blocks (e.g., HVU01). The wild barley scaffolds (length >500 kb) are represented by orange blocks. Aligned genes are connected by green lines. The lengths of the chromosomes and scaffolds are shown relative to a 50‐Mb scale bar.

Figure 3

Genes specific to the wild barley genotype WB1. (a) Comparison with Morex genome and genes. (b) The enriched KEGG pathways and matched immunity‐related genes (in bold and with grey background) for wild barley‐specific genes.

Figure 4

Expression patterns of NBS‐LRR genes in different WB1 tissues.

Figure 5

Distribution of SNV density (counts per 10 Mb interval) across the seven chromosomes of Morex. Interval length is 10 Mb for x‐axis. The vertical black dotted lines indicate the approximate locations of centromeres.