Gene content, loss, conservation and genetic variation among Triticum aestivum group 7 chromosomes

Complex Triticeae genomes pose a challenge to genome sequencing efforts due to their size and repetitive nature.  Recently, second generation sequencing technologies have been applied to genomic portions of both barley and wheat, allowing further investigation of the biology of their genomes. Genome sequencing can reveal details of gene conservation, loss and chromosome rearrangements between related genomes. We have applied Illumina second generation sequencing technology to sequence all the genes and low copy regions of the wheat group 7 chromosome arms. The majority of genes in the group 7 chromosome arms are conserved between homoeologs, though some gene movement is observed. Comparison of wheat homoeologs allows the delimitation of translocation events with a resolution of one or a few genes. The availability of these chromosome assemblies enables the discovery of high density SNPs, the differentiation between homeologous and intervarietal SNPs, and are a foundation for genotyping by sequencing in this important crop species. Assemblies based on the syntenic relationships between plants is a useful method for deconvoluting the gene-rich regions of wheat, and could be applied more generally to other complex polyploid genomes.