Intraspecific sequence comparisons reveal similar rates of non-collinear gene insertion in the B and D genomes of bread wheat

We used new-generation sequencing (NGS) to generate sequence of a Mb-sized region from wheat chromosome arm 3DS. Sequence assembly of 24 BAC clones resulted in two scaffolds of 1,264,820 and 333,768 bases. The sequence was annotated and compared to the homoeologous region on wheat chromosome 3B and orthologous loci of Brachypodium distachyon and rice. Among 39 coding sequences in the 3DS scaffolds, 32 have a homoeolog on chromosome 3B. In contrast, only fifteen and fourteen orthologs were identified in the corresponding regions in rice and Brachypodium, respectively. Interestingly, five pseudogenes were identified among the non-collinear coding sequences at the 3B locus, while none was found at the 3DS locus.Direct comparison of two Mb-sized regions of the B and D genomes of bread wheat revealed similar rates of non-collinear gene insertion in both genomes with a majority of gene duplications occurring before their divergence. Relatively low proportion of pseudogenes was identified among non-collinear coding sequences. Our data suggest that the pseudogenes did not originate from insertion of non-functional copies, but were formed later during the evolution of hexaploid wheat. Some evidence was found for gene erosion along the B genome locus.Polyploidy is considered one of the main driving forces of plant evolution and speciation. Whole genome duplication (WGD) provides a substrate for plant genome evolution, diversification and adaptation. The presence of two or more copies of the same gene reduces selection pressure and enables sub-functionalization and neo-functionalization. The analysis of whole-genome sequences revealed a frequent and often repeated occurrence of genome doubling during the evolution of higher plants. Even plants with relatively small genomes such as Arabidopsis thalianaBrachypodium distachyon and Malus domestica have experienced polyploidization events during their evolution [1-3].Some whole-genome duplication events occurred tens or even hundre