Contrasted patterns of organization and evolution of the wheat gene and transposable element spaces revealed by megabase level genome sequencing

To improve our understanding of the composition and evolution of the large (17 Gb) and complex hexaploid wheat genome and prepare for its future sequencing, we sequenced and annotated 13 Mb-sized contigs (18.2 Mb in total) originating from different regions of the largest wheat chromosome, 3B (1 Gb), and produced a 2x chromosome survey by shotgun Solexa sequencing. Analysis of this unique data set provided novel insights into the gene and Transposable Element (TE) distribution and illustrated the potential of a high quality annotated genome for unlimited marker development to support molecular breeding. All BAC contigs carried genes irrespective of their chromosomal location. However, gene distribution was not random with 75% of the genes clustered into small islands containing 3 genes on average and a maximum of 800 kb of gene-less region. Analyses indicated a 2-fold increase of gene density towards the telomeres likely due to high tandem and interchromosomal duplication activities. Most of the TEs were found complete but highly nested and spread over distances as large as 200 kb. Furthermore, a succession of amplification waves involving different TE families led to contrasted sequence compositions between the proximal and distal regions of the chromosome. With an estimate of 50,000 genes per diploid genome, wheat may carry a higher gene number than other cereals. Comparisons with rice and Brachypodium distachyon revealed that these additional non collinear genes are interspersed within a very conserved ancestral grass gene backbone supporting the idea of an accelerated evolution in the Triticeae lineages.