Comparative Analysis of Syntenic Genes in Grass Genomes Reveals Accelerated Rates of Gene Structure and Coding Sequence Evolution in Polyploid Wheat    

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 model grass genomes. In orthologous gene sets, significantly more acquired and lost exonic sequences were detected in wheat than in model grasses. In wheat, 35% of these gene structure rearrangements resulted in frame-shift mutations and premature termination codons. An increased codon mutation rate in the wheat lineage compared with Brachypodium distachyon was found for 17% of orthologs. The discovery of premature termination codons in 38% of expressed genes was consistent with ongoing pseudogenization of the wheat genome. The rates of AS within the individual wheat subgenomes (21%-25%) were similar to diploid plants. However, we uncovered a high level of AS pattern divergence between the duplicated homeologous copies of genes. Our results are consistent with the accelerated accumulation of AS isoforms, nonsynonymous mutations, and gene structure rearrangements in the wheat lineage, likely due to genetic redundancy created by WGDs. Whereas these processes mostly contribute to the degeneration of a duplicated genome and its diploidization, they have the potential to facilitate the origin of new functional variations, which, upon selection in the evolutionary lineage, may play an important role in the origin of novel traits.

Parallel natural selection in the cold-adapted crop-wild relative Tripsacum dactyloides and artificial selection in temperate adapted maize

“…Trans AS divergence more common than cis Consistent with observations from other plant systems (Akhunov et al, 2013;Barbazuk et al, 2008;Marquez et al, 2012), the most common single AS variants in tripsacum were -in descending order of frequency -intron retention (IntronR), exon skipping (ExonS), alternative donor (AltD), alternative acceptor (AltA), and mutually exclusive exons (MXEs). The remaining isoforms incorporated two or more types of changes and were classified as Complex AS (CompAS) ( Figure S4A).…”

Introgression of chromosome segments from multiple alien species in wheat breeding lines with wheat streak mosaic virus resistance

“…The order and location of these markers along the 1BS was largely as reported, although a few, for example, Xgwm1130 and Xgwm0911 (Ganal and Röder, 2007) were inverted. This discrepancy is not a rare phenomenon when wheat cultivars from different pedigrees are compared (Akhunov et al, 2013). The recombination BPs were all distal to the NOR on 1BS (Figure 4) suggesting the presence of recombination hot-spots in this region (Reddy et al, 2008).…”

Phenotypic and genotypic characterization of wheat landraces of Pakistan

“…Further it is fortuitous that another 700 landraces have been reported from the NARC genebank that will add further value to their exploitation after their stringent phenotyping together with genotyping assays based on GoldenGate (Chao et al, 2011), BeadExpress (Trebbi et al, 2011), Infinium platforms (Cavanagh et al, 2013) and 90K iSelect (Akhunov et al, 2013), or direct sequencing of populations through genotype-by-sequencing (GBS) approach (Davey et al, 2011;Poland et al, 2012).…”