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Partial sequence comparison of the rpoB, sodA, groEL and gyrB genes within the genus Streptococcus

Laboratoire de Bactériologie – Virologie, Hôpital de la Timone, CNRS UMR 6236, IFR48, 264 rue Saint-Pierre, 13385 Marseille, Cedex 05, France

Correspondence
Véronique Roux
vroux91{at}hotmail.com

Phylogenetic analysis and species identification of members of the genus Streptococcus were carried out using partial sequence comparison of the 16S rRNA gene (1468–1478 bp), rpoB, encoding the β subunit of RNA polymerase (659–680 bp), sodA, encoding the manganese-dependent superoxide dismutase (435–462 bp), groEL, encoding the 60 kDa heat-shock protein (757 bp), and gyrB, encoding the B subunit of DNA gyrase (458–461 bp). For the first time, most species within the genus Streptococcus were represented in the study (65 strains, representing 58 species and nine subspecies). Phylogenies inferred from rpoB, sodA, gyrB and groEL sequence comparisons were more discriminative than those inferred from 16S rRNA gene sequence comparison, and showed common clusters. The minimal interspecies divergence was 0.3, 2.7, 0, 2.5 and 3.4 % for the 16S rRNA gene, rpoB, sodA, gyrB and groEL, respectively. In general, groEL partial gene sequence comparison represented the best tool for identifying species and subspecies and for phylogenetic analysis.

Details of primers, strains and sequence accession numbers, neighbour-joining trees derived from 16S rRNA gene, sodA, rpoB and gyrB sequences and a representation of the distribution of pairwise similarity for each gene are available as supplementary material with the online version of this paper.