Genome-based characterization of biological processes that differentiate closely related bacteria

Bacteriologists have strived toward attaining a natural classification system based on evolutionary relationships for nearly 100 years. In the early twentieth century it was accepted that a phylogeny-based system would be the most appropriate, but in the absence of molecular data, this approach proved exceedingly difficult. Subsequent technical advances and the increasing availability of genome sequencing have allowed for the generation of robust phylogenies at all taxonomic levels. In this study, we explored the possibility of linking biological characters to higher-level taxonomic groups in bacteria by making use of whole genome sequence information. For this purpose, we specifically targeted the genus Pantoea and its four main lineages. The shared gene sets were determined for Pantoea, the four lineages within the genus, as well as its sister-genus Tatumella. This was followed by functional characterization of the gene sets using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. In comparison to Tatumella, various traits involved in nutrient cycling were identified within Pantoea, providing evidence for increased efficacy in recycling of metabolites within the genus. Additionally, a number of traits associated with pathogenicity were identified within species often associated with opportunistic infections, with some support for adaptation toward overcoming host defenses. Some traits were also only conserved within specific lineages, potentially acquired in an ancestor to the lineage and subsequently maintained. It was also observed that the species isolated from the most diverse sources were generally the most versatile in their carbon metabolism. By investigating evolution, based on the more variable genomic regions, it may be possible to detect biologically relevant differences associated with the course of evolution and speciation.Supplementary Table S1 | Environmental information processing traits with differences among the lineages.Supplementary File S1 | Output from GhostKOALA for the Pantoea and Tatumella shared gene sets. This file contains the differences observed for the overview maps and the specific pathways for Pantoea and Tatumella. The overlay figures of the overview and pathway maps are also indicated.Supplementary File S2 | Output from GhostKOALA for the lineages within Pantoea. This file contains the differences observed for the overview maps as well as the overlay figures of the overview maps for the different lineages.Supplementary File S3 | The summary of differences in pathways requiring 2 or more genes, as well as a summary of the BLAST confirmations of these genes.Supplementary File S4 | The results from the selection analyses and the figures for the gene clusters not indicated in text.Supplementary File S5 | The differences for pathways involved in “Environmental Information Processing”. A summary of the BLAST confirmation is also included as well as the maps for each lineage for the ABC transporters, two-component systems and the PTSs.Supplementary File S6 | Summary of the Blast2GO analyses as well as the BLAST hits for genes not annotated with Blast2GO. A pie chart indicating the distribution of BLAST hits is also indicated.The National Research Foundation for student funding through the Centre of Excellence in Tree Health Biotechnology (CTHB) and the University of Pretoria.http://www.frontiersin.org/Microbiologyam2018Forestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog