Genome-Based Characterization of Biological Processes That Differentiate Closely Related Bacteria

Frontiers in Microbiology
Marike PalmerStephanus N Venter

Abstract

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 wit...Continue Reading

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Citations

May 16, 2018·Materials·Ilaria ArmentanoLuigi Torre

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Datasets Mentioned

BETA
MLFE00000000.1
CP001894.1
CP001893.1
CP002433.1
CP002434.1
CP002435.1
CP002436.1
CP002437.1
CP002438.1

Methods Mentioned

BETA
phosphotransferase

Software Mentioned

MEGA
InterproScan
blastp
HyPhy
CLC Genomics Workbench
Geneious
BLAST score R
EDGAR
GhostKOALA
MAFFT

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