1887

Abstract

Streptomycetes are a complex group of actinomycetes that produce diverse bioactive metabolites of commercial significance. Systematics can provide a useful framework for identifying species that may produce novel metabolites. However, previously proposed approaches to the systematics of have suffered from either poor interlaboratory comparability or insufficient resolution. In particular, the 16S rRNA gene clade is the most challenging and least defined group within the genus in terms of phylogeny. Here we report the results of a multilocus sequence analysis scheme developed to address the phylogeny of this clade. Sequence fragments of six housekeeping genes, , , , , and 16S rRNA, were obtained for 53 reference strains that represent 45 valid species and subspecies. Analysis of each individual locus confirmed the suitability of loci and the congruence of single-gene trees for concatenation. Concatenated trees of three, four, five and all six genes were constructed, and the stability of the topology and discriminatory power of each tree were analysed. It can be concluded from the results that phylogenetic analysis based on multilocus sequences is more accurate and robust for species delineation within . A multilocus phylogeny of six genes proved to be optimal for elucidating the interspecies relationships within the 16S rRNA gene clade. Our multilocus sequence analysis scheme provides a valuable tool that can be applied to other clades for refining the systematic framework of this genus.

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2008-01-01
2019-10-23
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Chromosomal locations of the genes used. The positions of the six genes are shown on a map of the genome sequence of A3(2). The 8,667,507 bp genome is divided into 10 segments, with each segment representing 866,751 bp.

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All the following trees were constructed using the neighbour-joing method. H37Rv was used as the outgroup. Numbers at nodes represent levels (%) of bootstrap support from 1000 resampled datasets. L and P indicate branches that were also recovered using maximum-likelihood and maximum-parsimony methods, respectively. The bar indicates 2 % estimated sequence divergence. Strains of clusters I, II, III and IV are highlighted with blue, yellow, green and red backgrounds, respectively. Figs S2-S9 are available in a single PDF file.

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vol. , part 1, pp. 149-159

In this paper, the following names have been incorrectly placed in quote marks. Although these names have been later transferred, they are all validly published names and should not therefore appear in quote marks throughout this paper.

An amended version of Table 1, with corrected type strains, is available hereas a PDF file.



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