HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Full Text Full Text (PDF) Supplementary Material Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via CrossRef Google Scholar Articles by Mignard, S. Articles by Flandrois, J.-P. PubMed PubMed Citation Articles by Mignard, S. Articles by Flandrois, J.-P. Agricola Articles by Mignard, S. Articles by Flandrois, J.-P.

A seven-gene, multilocus, genus-wide approach to the phylogeny of mycobacteria using supertrees

¹ Université de Lyon, Université de Lyon 1, CNRS UMR 5558, Biometrie et biologie evolutive, Villeurbanne F-69622, France
² Laboratoire de bacteriologie, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre-Benite F-69495, France

Correspondence
Sophie Mignard
sophie.mignard{at}chu-lyon.fr

This is the first study that estimates mycobacterial phylogeny using the maximum-likelihood method (PhyML-aLRT) on a seven-gene concatenate (hsp65, rpoB, 16S rRNA, smpB, sodA, tmRNA and tuf) and the super distance matrix (SDM) supertree method. Two sets of sequences were studied: a complete seven gene sequence set (set R, type strains of 87 species) and an incomplete set (set W, 132 species) with some missing data. Congruencies were computed by using the CONSENSE program (PHYLIP package). The evolution rate of each gene was determined, as was the evolution rate of each strain for a given gene. Maximum-likelihood trees resulting from concatenation of the R and W sets resulted in a similar phylogeny, usually showing an early separation between slow-growing (SG) and rapidly growing (RG) mycobacteria. The SDM tree for the W set resulted in a different phylogeny. The separation of SG and RG was still evident, but it was located later in the nodes. The SG were therefore positioned as a subgroup of RG. Maximum-likelihood phylogenetic reconstruction was less affected by increasing the number of strains (with incomplete data), but did seem to cushion the variability of the evolution rate (ER), whereas the SDM method seemed to be more accurate and took into account both the differing ER values and the incomplete data. With regard to ER, it was observed that the 16S rRNA gene was the gene that displayed the slowest evolution, whereas smpB was the most rapidly evolving gene. Surprisingly, these two genes alone accurately separated the SG from the RG on the basis of their ER values. This study focused on the differences in ER between genes and in some cases linked the ER to the phenotypic classification of the mycobacteria.

The strain numbers and GenBank sequence accession numbers of the type strains of the 125 species of the genus Mycobacterium used in this study and the details of the primers used for the amplification of the smpB gene are available in supplementary tables with the online version of this paper. A neighbour-joining phylogenetic tree and two additional figures constructed by multi-tree graphical analysis using TREEDYN are also available as supplementary figures.