Gene Arrangements and Phylogeny in the Class Proteobacteria

• Published in: Journal of theoretical biology Vol. 213; no. 1; pp. 9 - 19
• Main Author: KUNISAWA, TAKASHI
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 07-11-2001
• Subjects: Aniline Compounds; Animals; Bacterial Proteins - genetics; Calcium Channels - genetics; Carbon-Nitrogen Ligases - genetics; DNA Transposable Elements - genetics; DNA, Bacterial - genetics; DNA-Binding Proteins - genetics; Escherichia coli Proteins; Eukaryotic Initiation Factor-1 - genetics; Genes, Bacterial - genetics; Genome, Bacterial; Phylogeny; Prokaryotic Initiation Factor-1; Proteobacteria; Proteobacteria - classification; Proteobacteria - genetics; Repressor Proteins; Ribosomal Proteins - genetics; RNA, Transfer - genetics; Transcription Factors; TRPC Cation Channels
• ISSN: 0022-5193; 1095-8541
• DOI: 10.1006/jtbi.2001.2396

A simple method is presented for reconstructing phylogenetic trees on the basis of gene transposition. It is shown that differences in gene arrangements among genomes could allow us to determine whether a gene transposition event has occurred before or after species divergence from parsimonious considerations. The method is applied to evolutionary relationships among the bacterial class Proteobacteria, for which complete genomic sequences most densely accumulate and comprehensive gene order comparisons are possible. We were able to infer the emergence order of proteobacterial subclasses asε ⇒β⇒γ. This order is consistent with sequence-based inferences, which conversely confirms the usefulness of the approach presented here.