Comparative Genomics Analysis Of Wheat Genome Structure And Reconstruction Of Chromosome Repatterning After Polyploidizations

Wheat and other grasses have experienced a common polyploidization during evolution.Moreover,common wheat is composed by ancestral genome A,B,and D,as a result of a hexaploidization.These events made the wheat genome extremely complex.At present,no study can clearly show the genomic structure of common wheat associated with the polyploidizations.Accurate analysis of this complex genomic structure will help better understand its ancient subgenomic structure and functional evolution.Here,I performed a hierarchical alignment of four wheat crops genomes and three out-groups genomes of rice,brachypodium,and pineapple.Then I constructed a list of the homologous genes clearly showing orthology and paralogy among them.In common wheat,the number of collinear genes produced by the grass-common whole-genome duplication event was 142.Compared with the other grasses,far fewer paralogous regions or genes were found between the common wheat A,B,and D subgenomes or within each of them.I found respectively 48,78,and 30 paralogous blocks that contained 217,225,and 89 collinear genes.This finding of many fewer collinear genes suggests that homoeologous recombination should have occurred between subgenomes,characterizing its genomic instability and gene loss.The study further explored the common ancestor of rice and pineapple experienced the whole-genome duplication event about 181 million years ago.Here,re-dating evolutionary events using coliner genes push them to be much older.Based on the collinearity results,I deduced the ancestral gene numbers of common ancestor of grasses and pineapple were at least 9079.In addition,I counted the distribution of starch synthesis genes in each species genome,and showed that the whole-genome duplication played an important role in the amplification of gene family.Based on the phylogenetic analysis,the evolutionary speed of starch synthesis genes in common wheat genome was faster than that in other grasses.In sum,this work contributes to the establishment of an important and timely comparative genomics platform for researchers in the wheat crops community and possibly beyond.