SRA

Chromosome 1H (ca 622 Mb) of barley (Hordeum vulgare L..) was isolated by flow sorting and shotgun sequenced by GSFLX pyrosequencing to 1.3-fold coverage. Fluorescence in situ hybridization (FISH) and stringent sequence comparison against genetically mapped barley genes revealed 95% purity of the sorted chromosome 1H fraction. Sequence comparison against the reference genomes of rice and sorghum and against wheat and barley EST datasets led to the estimation of 4,600 to 5,800 genes on chromosome 1H, and 38,000 to 48,000 genes in the whole barley genome. Syntenic relationships of chromosome 1H to rice chromosomes 5 and 10, and to sorghum chromosomes 1 and 9 were detected on a per gene resolution. Informed by the syntenic relationships to the two reference genomes, genic barley sequence reads were integrated and ordered to deduce a virtual gene map of barley chromosome 1H. We demonstrate that synteny-based analysis of low-pass shotgun sequenced flow-sorted Triticeae chromosomes can deliver linearly ordered high-resolution gene inventories of individual chromosomes, which complement extensive Triticeae EST datasets. Thus, integration of genomic, transcriptomic and synteny-derived information represents a major step towards developing reference sequences of chromosomes and complete genomes of the most important plant tribe for mankind.