Deep Transcriptome Sequencing Provides New Insights into the Bread Wheat Genome Structural and Functional Organization

Because of its size (17Gb), allohexaploid nature and high repeat content (>80%), the wheat genome has always been perceived as too complex for efficient molecular studies. As a consequence, our knowledge of the wheat genome structure is still very limited. In particular, the impact of the genome structure on the organisation, function and regulation of genes at a chromosome scale is poorly understood. Following a chromosome-specific approach, we generated a first reference sequence of a wheat chromosome (3B, 995 Mb).This novel resource was used in combination with RNA-Seq data from 15 different conditions to (1) identify transcriptionnally active regions, including novel transcribed regions, (2) draw the expression profiles of each gene over the course of the plant development, (3) identify alternative splicing events, and (4) study the subfunctionalization of homoeologous copies. Based on transcriptome data together with recombination pattern as well as gene and TE density, chromosome 3B was shown to be compartmentalized in three contrasting blocks. We used the same RNA-Seq approach on the draft assemblies of the 20 other chromosomes that have been generated recently by the IWGSC. This analysis showed a similar pattern for all wheat chromosomes but 4A whose segmentation reflected the recent evolutionary history. The detailed results of our analysis will be presented and their implications in terms ofrelationships between structure of the genome, function and regulation of the genes along wheat chromosomes will be discussed.