title: Gene arrangements and branching orders of gram-positive bacteria.
abstract: The availability of complete genomic sequence data allows one to develop new methods of reconstructing phylogenetic trees. A simple method of reconstructing branching orders based on gene transposition (or lateral transfer) is presented. It is argued that specific gene arrangements on four different genomes could determine a branching order. A computer search for such gene arrangements was carried out against gene order data of completely sequenced Gram-positive bacteria. Gene arrangements around ribosomal protein S4 gene, murC (UDP-N-acetylmuramate:alanine ligase) gene and dnaE (DNA polymerase III alpha chain) gene each suggest a branching order in which actinobacteria with a high genomic G+C content first branched off from other Gram-positives with a low G+C content and then a split occurred between Mycoplasma species and a group closely related to Bacillus subtilis. A recently sequenced thermophilic bacterium Thermoanaerobacter tengcongensis is suggested to have branched off from the lineage leading to the low G+C Gram-positives prior to the split between the Mycoplasma and Bacillus groups. By contrast to the indel analysis in which a single evolutionary event of insertion or deletion of a signature sequence is assumed, the present method does not necessarily require such a parsimonious assumption of gene transposition.
authors.affiliation: Department of Applied Biological Sciences, Science University of Tokyo, Noda 278-8510, Japan. kunisawa@rs.noda.tus.ac.jp
authors.forename: Takashi
authors.initials: T
authors.lastname: Kunisawa
mesh_terms: D004258:DNA Polymerase III / Q000235:genetics; D023061:Gene Order; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D006094:Gram-Positive Bacteria / Q000235:genetics*; D010453:Peptide Synthases / Q000235:genetics; D010802:Phylogeny; D012269:Ribosomal Proteins / Q000235:genetics
chemical_list: D012269:Ribosomal Proteins; C031798:ribosomal protein S4; C074904:DNA polymerase III, alpha subunit; D004258:DNA Polymerase III; D010453:Peptide Synthases; C023229:UDP-N-acetylmuramoyl-alanine synthetase