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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 60, Issue 3

Taxonomic evaluation of the clade using multilocus sequence analysis and DNA–DNA hybridization, with proposal to combine 29 species and three subspecies as 11 genomic species Free

Abstract

and related species form the biggest but least well-defined clade in the whole 16S rRNA gene tree. Multilocus sequence analysis (MLSA) has shown promising potential for refining systematics. In this investigation, strains of 18 additional clade species were analysed and data from a previous pilot study were integrated in a larger MLSA phylogeny. The results demonstrated that MLSA of five housekeeping genes (, , , and ) is better than the previous six-gene scheme, as it provides equally good resolution and stability and is more cost-effective; MLSA using three or four of the genes also shows good resolution and robustness for differentiating most of the strains and is therefore of value for everyday use. MLSA is more suitable for discriminating strains that show >99 % 16S rRNA gene sequence similarity. DNA–DNA hybridization (DDH) between strains with representative MLSA distances revealed a strong correlation between the data of MLSA and DDH. The 70 % DDH value for current species definition corresponds to a five-gene MLSA distance of 0.007, which could be considered as the species cut-off for the clade. It is concluded that the MLSA procedure can be a practical, reliable and robust alternative to DDH for the identification and classification of streptomycetes at the species and intraspecies levels. Based on the data from MLSA and DDH, as well as cultural and morphological characteristics, 18 species and three subspecies of the clade are considered to be later heterotypic synonyms of 11 genomic species: and as synonyms of ; as a synonym of ; as a synonym of ; as a synonym of ; subsp. as a synonym of ; , , and as synonyms of ; as a synonym of ; , ‘’ and as synonyms of ; as a synonym of ; , subsp. , subsp. and as synonyms of ; and and as synonyms of

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Keyword(s): DDH, DNA–DNA hybridization , ML, maximum-likelihood , MLSA, multilocus sequence analysis , MP, maximum-parsimony and NJ, neighbour-joining
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2010-03-01
2024-04-20
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Taxonomic evaluation of the Streptomyces griseus clade using multilocus sequence analysis and DNA–DNA hybridization, with proposal to combine 29 species and three subspecies as 11 genomic species
Int J Syst Evol Microbiol 60, 696 (2010); https://doi.org/10.1099/ijs.0.012419-0
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