A phylogenetic analysis of the family Pseudonocardiaceae and the genera Actinokineospora and Saccharothrix with 16S rRNA sequences and a proposal to combine the genera Amycolata and Pseudonocardia in an emended genus Pseudonocardia

Abstract

The 16S rRNAs of 15 species of actinomycetes belonging to the genera Actinokineospora and Saccharothrix and the family Pseudonocardiaceae, including Amycolatopsis, Amycolata, Pseudonocardia, Saccharomonospora, and Saccharopolyspora species, were sequenced by using reverse transcriptase. The sequences were analyzed along with the sequences of reference actinomycetes by using distance matrix and parsimony methods. The wall chemotype IV genus Actinokineospora was found to be closely related to species of the genus Saccharothrix which have chemotype III walls. Together, these two genera formed a clade which was closely related to members of the family Pseudonocardiaceae which have chemotype IV walls. However, the phylogenetic branching pattern did not unambiguously resolve whether the members of all three taxa should be placed in a single family. We suggest, therefore, that the genera Actinokineospora and Saccharothrix should remain outside the family Pseudonocardiaceae until additional sequence or phenotypic data are available to decide the issue. The sequences of species belonging to the genera Amycolata and Pseudonocardia were always recovered as a mixed group in phylogenetic trees, and we propose that these organisms should be classified in an emended genus Pseudonocardia. This proposal is strongly supported by previously published lipid, ribosomal protein, and ultrastructure data.