<i>tilS</i> and <i>rpoB</i>: New Molecular Markers for Phylogenetic and Biodiversity Studies of the Genus <i>Thiothrix</i>
2023
Nikolai V. Ravin | Dmitry D. Smolyakov | Nikita D. Markov | Alexey V. Beletsky | Andrey V. Mardanov | Tatyana S. Rudenko | Margarita Yu. Grabovich
Currently, the phylogeny of the genus <i>Thiothrix</i> is based on comparative whole genome analysis because of the high homology of the 16S ribosomal RNA gene sequences within the genus. We analyzed the possibility of using various conservative genes as phylogenetic markers for the genus <i>Thiothrix</i>. We found that the levels of similarity of the nucleotide sequences of the tRNA(Ile)-lysidine synthase (<i>tilS</i>) and the β subunit of RNA polymerase (<i>rpoB</i>) genes are in good agreement with the average nucleotide identity (ANI) values between the genomes of various representatives of the genus <i>Thiothrix</i>. The genomes of <i>Thiothrix</i> strains MK1, WS, DNT52, DNT53, and H33 were sequenced. Taxonomic analysis using both whole genomes and the <i>tilS</i> gene consistently showed that MK1 and WS belong to <i>Thiothrix lacustris</i>, while DNT52, DNT53, and H33 belong to <i>Thiothrix subterranea</i>. The <i>tilS</i> gene fragments were subjected to high-throughput sequencing to profile the <i>Thiothrix</i> mat of a sulfidic spring, which revealed the presence of known species of <i>Thiothrix</i> and new species-level phylotypes. Thus, the use of <i>tilS</i> and <i>rpoB</i> as phylogenetic markers will allow for rapid analyses of pure cultures and natural communities for the purpose of phylogenetic identification of representatives of the genus <i>Thiothrix</i>.
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