Journal of Phylogenetics & Evolutionary Biology

Speciation Genomics of Protein-Coding Genes Common to Mycoplasmatales

Abstract

Dipaloke Mukherjee and Walter J Diehl

Identifying regions of a genome that evolve by natural selection, particularly as species diverge, has been a matter of considerable interest. The genomes of 12 species in the eubacterial order Mycoplasmatales were compared to test the hypothesis that natural selection targets genes by function and/or at given moments in the phylogenetic history of the species. These species possess some of the smallest genomes known, and analyses on the set of protein-coding genes common to all species in the study will shed light on the evolution of some of the most critical genes to living organisms. Genes that control cellular processes showed greater evidence of natural selection than genes of unknown function or genes associated with information processing and storage or metabolism. Moreover evidence of natural selection was only detected in the deepest branches of the Mycoplasmatales phylogeny, including one node where a host shift from land plants to insects likely occurred and another node where a host shift from land plants/insects to land vertebrates likely occurred. Many of the genes that showed the strongest evidence of natural selection (e.g. secA, secY, ftsH, ftsY, yidC, lepA, dnaK) encode proteins that are components of the Sec-dependent secretory pathway, which regulates the extracellular translocation of proteins. The Sec-dependent secretory pathway is proposed to play a role in speciation of Mycoplasmatales by altering the type and amount of secreted proteins, thereby affecting virulence of Mycoplasma sp. in response to infection of novel hosts.