Towards a core genome: pairwise similarity searches on interspecific genomic data

TL;DR

This study identifies a core set of conserved genes across bacterial genomes, supporting the hypothesis of a shared ancestral core genome, with potential applications to eukaryotic species comparisons.

Contribution

The paper introduces a pairwise similarity search method to identify conserved core genomes across species using whole-genome data.

Findings

Identified 68 conserved genes across three bacterial strains.

Conserved genes are mainly housekeeping genes.

Method applicable to eukaryotic genome comparisons.

Abstract

The phenomenon of gene conservation is an interesting evolutionary problem related to speciation and adaptation. Conserved genes are acted upon in evolution in a way that preserves their function despite other structural and functional changes going on around them. The recent availability of whole-genomic data from closely related species allows us to test the hypothesis that a core genome present in a hypothetical common ancestor is inherited by all sister taxa. Furthermore, this core genome should serve essential functions such as genetic regulation and cellular repair. Whole-genome sequences from three strains of bacteria (Shewanella sp.) were used in this analysis. The open reading frames (ORFs) for each identified and putative gene were used for each genome. Reciprocal Blast searches were conducted on all three genomes, which distilled a list of thousands of genes to 68 genes that were identical across taxa. Based on functional annotation, these genes were identified as housekeeping genes, which confirmed the original hypothesis. This method could be used in eukaryotes as well, in particular the relationship between humans, chimps, and macaques.