Contrasted Microcolinearity and Gene Evolution Within a Homoeologous Region of Wheat and Barley Species

Abstract

We study here the evolution of genes located in the same physical locus using the recently sequenced Ha locus in seven wheat genomes in diploid, tetraploid, and hexaploid species and compared them with barley and rice orthologous regions. We investigated both the conservation of microcolinearity and the molecular evolution of genes, including coding and noncoding sequences. Microcolinearity is restricted to two groups of genes (Unknown gene-2, VAMP, BGGP, Gsp-1, and Unknown gene-8 surrounded by several copies of ATPase), almost conserved in rice and barley, but in a different relative position. Highly conserved genes between wheat and rice run along with genes harboring different copy numbers and highly variable sequences between close wheat genomes. The coding sequence evolution appeared to be submitted to heterogeneous selective pressure and intronic sequences analysis revealed that the molecular clock hypothesis is violated in most cases.

Fine Mapping and Marker Development for the Crossability Gene SKr on Chromosome 5BS of Hexaploid Wheat (Triticum aestivum L.)

“…Only one out of 30 markers originating from the BAC 1793L02 showed polymorphism between CS and Ct and no single sequence difference was found over 1464 bp of sequence including an intronic region for the ATPase1-5B gene. This is very similar to the observations of Chantret et al (2005Chantret et al ( , 2008 who found only 58 SNPs and a few short indels between the T. aestivum and the T. turgidum orthologous sequences at the GSP locus on chromosome 5BS. A possible explanation is that deletions in some of the genes present in this region are highly deleterious and have been counter-selected through the domestication and selection processes.…”

Genome evolution in diploid and tetraploid Coffea species as revealed by comparative analysis of orthologous genome segments

“…On the other hand, comparative analysis can also be performed at a smaller scale on long stretches of genomic sequences to infer the evolutionary history of the genomes . Fine comparative analysis of orthologous regions enables insight into the evolution of specific loci and provides details about the phenomena and mechanisms that drive evolution at sequence level (Fu and Dooner 2002;Chantret et al 2005Chantret et al , 2008Ammiraju et al 2008;Cho et al 2010;Lin et al 2010).…”

Grass Genomic Synteny Illuminates Plant Genome Function and Evolution

“…In grasses, polyploidy has been a recurrent theme, with many lineages exhibiting full genome duplications over the last few million years. Local sequence comparisons in these species, such as maize [40,53,64], wheat [27,46,90,34,16,15] and sugarcane [42], have revealed interesting features of gene and genome evolution in recent polyploids. LTR retrotransposon amplification and altered regulation (e.g., silencing) or loss of duplicated genes are repeated themes.…”