Defining the Gene-Rich Portion of the Barley Genome

Barley (Hordeum vulgare L.), one of the major world cereal crops, possesses a large and highly repetitive genome of 5.1 Gb which challenges complete sequencing. Although great advances, including the release of an extensive genome sequence resource, have been achieved primarily by the International Barley Sequencing Consortium, there is still a lack of fine resolution. To gain access to the gene-rich portion of the barley genome at higher resolution, we identified and sequenced gene-rich BACs from a library of cv. Morex. The library was screened with genic probes to identify 83,831 ‘gene-bearing’ (GB) BACs. These were fingerprinted for physical map construction. A total of 15,622 MTP clones were sequenced using Illumina HiSeq2000 and assembled using Velvet v.1.2.09. The assembly generated about 1.7 Gb of gene-rich genomic sequence, which would account for ~33 % of the barley genome. Using flow-sorted chromosomes that were shotgun sequenced and assembled, a k-mer-based tool was used to assign 97.4% of the GB-BACs  to chromosome 1H and arms of chromosomes 2H-7H. Previously predicted barley genes were used to annotate BAC assemblies, which contained 17,386 high-confidence and 21,175 low-confidence gene models. GB-BAC distribution along barley chromosomes showed that gene density is consistently high near the ends of chromosomes with additional notable hotspots. These new BAC sequences, together with all previously published sequenced BACs, can be accessed via an online interface (http://harvest-web.org/hweb/utilmenu.wc). This work was supported by grants from NSF and USDA-NIFA.