The use of gyrB sequence analysis in the phylogeny of the genus Amycolatopsis
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Partial gyrB sequences (>1 kb) were obtained from 34 type strains of the genus Amycolatopsis. Phylogenetic trees were constructed to determine the effectiveness of using this gene to predict taxonomic relationships within the genus. The use of gyrB sequence analysis as an alternative to DNA–DNA hybridization was also assessed for distinguishing closely related species. The gyrB based phylogeny mostly confirmed the conventional 16S rRNA gene-based phylogeny and thus provides additional support for certain of these 16S rRNA gene-based phylogenetic groupings. Although pairwise gyrB sequence similarity cannot be used to predict the DNA relatedness between type strains, the gyrB genetic distance can be used as a means to assess quickly whether an isolate is likely to represent a new species in the genus Amycolatopsis. In particular a genetic distance of >0.02 between two Amycolatopsis strains (based on a 315 bp variable region of the gyrB gene) is proposed to provide a good indication that they belong to different species (and that polyphasic taxonomic characterization of the unknown strain is worth undertaking).
KeywordsAmycolatopsis DNA–DNA hybridization Genetic distance gyrB Phylogeny
The authors would like to thank Di James for DNA sequencing. G.J.E. holds a grantholder-linked bursary from the National Research Foundation of South Africa (NRF), a Harry Crossley Foundation Postgraduate Scholarship from the University of Cape Town (UCT), a Twamley Postgraduate Bursary (UCT), a KW Johnstone Research Scholarship (UCT) and a Postgraduate Research Associateship (UCT). This work was supported by research grants to P.R.M. from the Medical Research Council of South Africa, the NRF (grant number: 2073133) and the University Research Committee (UCT).
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