title: Gene arrangements and phylogeny in the class Proteobacteria.
abstract: 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 as epsilon-->beta-->gamma. This order is consistent with sequence-based inferences, which conversely confirms the usefulness of the approach presented here.
authors.affiliation: Department of Applied Biological Sciences, Science University of Tokyo, Noda, 278-8510, Japan. kunisawa@rs.noda.sut.ac.jp
authors.forename: T
authors.initials: T
authors.lastname: Kunisawa
mesh_terms: D000814:Aniline Compounds; D000818:Animals; D001426:Bacterial Proteins / Q000235:genetics; D015220:Calcium Channels / Q000235:genetics; D019731:Carbon-Nitrogen Ligases / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D029968:Escherichia coli Proteins; D015977:Eukaryotic Initiation Factor-1 / Q000235:genetics; D005798:Genes, Bacterial / Q000235:genetics*; D016680:Genome, Bacterial; D010802:Phylogeny; D039861:Prokaryotic Initiation Factor-1; D020560:Proteobacteria / Q000145:classification / Q000235:genetics*; D012343:RNA, Transfer / Q000235:genetics; D012097:Repressor Proteins; D012269:Ribosomal Proteins / Q000235:genetics; D050052:TRPC Cation Channels; D014157:Transcription Factors
chemical_list: D000814:Aniline Compounds; D001426:Bacterial Proteins; D015220:Calcium Channels; D004251:DNA Transposable Elements; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D015977:Eukaryotic Initiation Factor-1; C489050:L33 ribosomal protein, bacteria; C095564:Map protein, Staphylococcus aureus; D039861:Prokaryotic Initiation Factor-1; D012097:Repressor Proteins; D012269:Ribosomal Proteins; D050052:TRPC Cation Channels; D014157:Transcription Factors; C489052:rpmG protein, E coli; C487557:4-trifluoromethylaniline; D012343:RNA, Transfer; D019731:Carbon-Nitrogen Ligases; C058125:birA protein, E coli