Phylo- and comparative genomics of the Pantoea core genome

Abstract

The delineation of bacterial species and genera has always been problematic as a clear definition of these concepts are lacking. In an attempt to classify bacteria into workable groups, operational criteria have been applied to delimitate boundaries for these taxonomic ranks. This approach has unfortunately led to artificial groupings that are often not comparable in terms of diversity in different groups of bacteria. A classification system needs to reflect natural groupings to depict the evolution of bacteria and predict the phenotypic and genetic diversity for these groups. In order to understand the forces that play a role in the evolution of a bacterial genus a review of the current literature was presented in Chapter 1. The major focus was on vertical inheritance and how this process can be used to depict the evolutionary path of members belonging to the same genus. The largest amount of genetic material in any one cell is thought to have been transferred from parent to progeny, supporting the idea that the vertical signal is recoverable and can in fact be the dominant signal present in the genome when looking at conserved genes. The effect of horizontal gene transfer (HGT) on the evolutionary picture obtained by vertical descent was also discussed. The core genome of a genus is defined as the genes conserved between all species of a genus and are thought to mostly include genes that are essential for the survival of members of that particular genus. In Chapter 2, the hypothesis was tested that the boundaries used to delineate genera could be based on an analysis of the shared core genome. For this purpose coherence within the core genome of the genus Pantoea was investigated. The core was characterised in terms of its functional diversity through Clusters of Orthologous Genes (COGs) and compared to the core genomes of other bacterial genera. It was seen that the core genome does give an indication of the coherence of a genus and that shared genome content can be used as a tool to delimitate genera. Previous taxonomic studies have shown that species in the genus Pantoea are well defined but that the phylogenetic relationships between these species are not well elucidated. Generally accepted approaches for phylogenetic inference, like 16S rRNA gene trees and multi-locus sequence analysis (MLSA), does not give sufficient resolution to determine the deeper evolutionary relationships between these species. In Chapter 3, phylogenomic analyses were performed to determine if a robust phylogeny, reflecting the evolutionary history of the genus, can be obtained using the core genome of the genus. The core genome as well as subsets thereof (based on COGs), was used for phylogenetic inference, to obtain a robust phylogeny for the genus.