Alternative splicing and coding sequence evolution in polyploid wheat

The wheat chromosome 3A was sequenced at 7-8 fold coverage using the 454 sequencing technology. The N50 of assembled contigs and scaffolds was 1.6 and 6 kb, respectively. Comparison with small grass genomes revealed the increased rate of coding sequence, gene intron-exon structure and alternative splicing evolution in the wheat genome. Among 226 orthologous genes showing accelerated codon mutations rates in the Brachypodium and wheat genomes 85% evolve faster in wheat than in Brachypodium lineages. We described the patterns of alternative splicing (AS) on the wheat chromosome 3A and compared it to that of other grass genomes. The level of AS (25-31%) observed in polyploid wheat was similar to that reported for other plant species. However, when compared to small genomes wheat contained more retained introns and less conserved exons than model genomes when they are compared to each other. Taken together our results suggest that coding sequences in the wheat genome evolve faster than in smaller grass genomes providing high level of genome plasticity with the ability to generate new molecular and structural variation.