Phylogenetic placement of whole genome duplications in yeasts through quantitative analysis of hierarchical orthologous groups

Abstract

Background: Whole genome duplications (WGD) are genomic events leading to formation of polyploid organisms. Resulting duplicated genes play important roles in driving species evolution and diversification. After such events, the initial ploidy is usually restored, complicating their detection across evolution. With the advance of bioinformatics and the rising number of new well-assembled genomes, new detection methods are ongoingly being developed to overcome the weaknesses of different approaches. Results: Here we propose a novel method for detecting WGD in yeast lineages based on the quantitative and comparative analysis of hierarchical orthologous groups (HOGs) of duplicated genes for a given set of organisms. We reconstruct ancestral genomes to obtain evolutionary information for each phylogenetic branch. This reconstruction relies on the inference of HOGs from the selected species’ proteomes. To estimate WGD events, the number of HOGs of duplicated genes across all taxonomic ranges are adjusted according to the molecular clock hypothesis and by the average genome size. Branches with a significant increase in the adjusted number of duplicated gene families are kept as candidates for WGD placement. The developed method was tested on two real datasets and showed promising results in phylogenetic WGD placements on the yeast lineage.