Location: Cereal Crops ResearchTitle: Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat) Author
Submitted to: Plant Physiology
Publication Type: Peer reviewed journal
Publication Acceptance Date: 12/1/2012
Publication Date: 1/12/2013
Publication URL: http://handle.nal.usda.gov/10113/57875
Citation: Akhunov, E.D., Sehgal, S., Liang, H., Wang, S., Akhunova, A.R., Kaur, G., Li, W., Forrest, K.L., See, D., Simkova, H., Ma, Y., Hayden, M.J., Luo, M., Faris, J.D., Dolezel, J., Gill, B.S. 2013. Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat. Plant Physiology. 161:252-265. Interpretive Summary: Through the evolutionary formation of common wheat, hybridization of three related ancestral grasses led to the combination of three closely related genomes in the same nucleus. Here, we studied how these whole genome duplications affected and shaped the structure of duplicated genes. By comparing specific genes in wheat with the same genes in model grasses such as rice and Brachypodium, we determined that structural alterations were more common among the genes in wheat than the model grasses. These results indicate that the structures of genes are more dynamic in the wheat lineage, which is likely due to genetic redundancy created by the whole genome duplications. Whereas these processes mostly contribute to degeneration of a duplicated genome, they have the potential to facilitate the origin of new genetic variation, which, upon selection in the evolutionary lineage, may play an important role in the origin of novel traits.
Technical Abstract: Cycles of whole genome duplication (WGD) and diploidization are hallmarks of eukaryotic genome evolution and speciation. Polyploid wheat (Triticum aestivum) has had a massive increase in genome size largely due to recent WGDs. How these processes may impact the dynamics of gene evolution was studied by comparing the patterns of gene structure changes, alternative splicing (AS), and codon substitution rates among wheat and the model grass genomes. In orthologous gene sets, significantly more acquired and lost exonic sequences were detected in wheat than in model grasses. In wheat, thirty five percent of these gene structure rearrangements resulted in frameshift mutations and premature termination codons (PTCs). An increased codon mutation rate in the wheat lineage compared to Brachypodium was found for 17% of orthologs. Discovery of PTCs in 38% of expressed genes was consistent with ongoing pseudogenization of the wheat genome. The rates of AS within the individual wheat subgenomes (25%) were similar to diploid plants. However, we uncovered a high level of AS pattern divergence (42%) between the duplicated homoeologous copies of genes. Our results are consistent with the accelerated accumulation of AS isoforms, non-synonymous mutations and gene structure rearrangements in the wheat lineage, likely due to genetic redundancy created by WGDs. Whereas these processes mostly contribute to degeneration of a duplicated genome and its diploidization, they have the potential to facilitate the origin of new functional variation, which, upon selection in the evolutionary lineage, may play an important role in the origin of novel traits.