Barley WCA Chr1H
Gene content and virtual gene order of barley chromosome 1H
In this study, we demonstrate the potential of high-throughput next generation sequencing of flow-sorted chromosomes for genome analysis, sequencing and the development of a high resolution gene map. As few as 10,000 copies of chromosome 1H were flow-sorted from cultivar 'Morex' and used as a template to assess gene content and genomic composition of this chromosome. Information about sequence and synteny conservation to the rice and sorghum genomes was obtained at unprecedented density and resolution and allowed synteny and homology information to be integrated into a virtual high-density gene map of barley chromosome 1H
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.