Comparative Genomics within the Tribe Triticeae

Phylogenetic analyses in the tribe triticeae will help us understanding how the hybridization events in the pasta and in the bread wheat have affected the original progenitor genomes.

Homologues are typically classified in orthologues and paralogues. Orthologues are defined as two genes that diverged from a speciation event while paralogues are related by a duplication event.

Classical approaches involve building a phylogenetic tree for each gene family, annotate duplication and speciation events and derive orthologues and paralogues from the annotated tree. However, these methods do not take into account the hybridisation events that have occurred in the triticeae lineage, which are interpreted as additional duplication events. As a result, many orthologues would be misinterpreted as paralogues.

We take advantage of the availability of several closely related diploid genomes to re-annotate the homologies for the pasta wheat (allotetraploid) and bread wheat (allohexaploid) genomes.

Our whole-genome approach includes approximately 50,000 gene trees for the tribe triticeae. Orthologues are sub-classified as 1:1, 1:many, many:1 and many:many according to the number of genes in each species. For instance, the majority of orthologues between 2 diploid genomes are 1:1 (i.e. we find one single copy of that gene in each species), while most of the orthologies between the bread wheat genome and the closely related diploid genomes are many:1 (i.e. there are more than 1 copy in the bread wheat genome for each diploid one).