BASE: a novel workflow to integrate non-ubiquitous genes in comparative genomics analyses for selection

Abstract

Inferring the selective forces that different ortholog genes underwent across different lineages can make us understand the evolutionary processes which shaped their extant diversity. The more widespread metric to estimate coding sequences selection regimes across across their sites and species phylogeny is the ratio of nonsynonymous to synonymous substitutions (dN/dS, also known as ω). Nowadays, modern sequencing technologies and the large amount of already available sequence data allow the retrieval of thousands of genes orthology groups across large numbers of species. Nonetheless, the tools available to explore selection regimes are not designed to automatically process all orthogroups and practical usage is often restricted to those consisting of single-copy genes which are ubiquitous across the species considered (i.e. the subset of genes which is shared by all the species considered). This approach limits the scale of the analysis to a fraction of single-copy genes, which can be as lower as an order of magnitude in respect to non-ubiquitous ones (i.e. those which are not present across all the species considered). Here we present a workflow named BASE that - leveraging the CodeML framework - ease the inference and interpretation of selection regimes in the context of comparative genomics. Although a number of bioinformatics tools have already been developed to facilitate this kind of analyses, BASE is the first to be specifically designed to ease the integration of non-ubiquitous genes orthogroups. The workflow - along with all the relevant documentation - is available at github.com/for-giobbe/BASE.