<i>tilS</i> and <i>rpoB</i>: New Molecular Markers for Phylogenetic and Biodiversity Studies of the Genus <i>Thiothrix</i>
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 genu...
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| Format: | Article |
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MDPI AG
2023-10-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/11/10/2521 |
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| author | Nikolai V. Ravin Dmitry D. Smolyakov Nikita D. Markov Alexey V. Beletsky Andrey V. Mardanov Tatyana S. Rudenko Margarita Yu. Grabovich |
| author_facet | Nikolai V. Ravin Dmitry D. Smolyakov Nikita D. Markov Alexey V. Beletsky Andrey V. Mardanov Tatyana S. Rudenko Margarita Yu. Grabovich |
| author_sort | Nikolai V. Ravin |
| collection | DOAJ |
| description | 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>. |
| first_indexed | 2024-03-10T21:01:19Z |
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| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T21:01:19Z |
| publishDate | 2023-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-1ee5764a72254561aba13f2b34848f4c2023-11-19T17:28:01ZengMDPI AGMicroorganisms2076-26072023-10-011110252110.3390/microorganisms11102521<i>tilS</i> and <i>rpoB</i>: New Molecular Markers for Phylogenetic and Biodiversity Studies of the Genus <i>Thiothrix</i>Nikolai V. Ravin0Dmitry D. Smolyakov1Nikita D. Markov2Alexey V. Beletsky3Andrey V. Mardanov4Tatyana S. Rudenko5Margarita Yu. Grabovich6Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, RussiaDepartment of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, RussiaDepartment of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, RussiaInstitute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, RussiaInstitute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, RussiaDepartment of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, RussiaDepartment of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, RussiaCurrently, 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>.https://www.mdpi.com/2076-2607/11/10/2521<i>Thiothrix</i>genomeMAG<i>tilS</i><i>rpoB</i>set of bacterial core genes |
| spellingShingle | Nikolai V. Ravin Dmitry D. Smolyakov Nikita D. Markov Alexey V. Beletsky Andrey V. Mardanov Tatyana S. Rudenko Margarita Yu. Grabovich <i>tilS</i> and <i>rpoB</i>: New Molecular Markers for Phylogenetic and Biodiversity Studies of the Genus <i>Thiothrix</i> Microorganisms <i>Thiothrix</i> genome MAG <i>tilS</i> <i>rpoB</i> set of bacterial core genes |
| title | <i>tilS</i> and <i>rpoB</i>: New Molecular Markers for Phylogenetic and Biodiversity Studies of the Genus <i>Thiothrix</i> |
| title_full | <i>tilS</i> and <i>rpoB</i>: New Molecular Markers for Phylogenetic and Biodiversity Studies of the Genus <i>Thiothrix</i> |
| title_fullStr | <i>tilS</i> and <i>rpoB</i>: New Molecular Markers for Phylogenetic and Biodiversity Studies of the Genus <i>Thiothrix</i> |
| title_full_unstemmed | <i>tilS</i> and <i>rpoB</i>: New Molecular Markers for Phylogenetic and Biodiversity Studies of the Genus <i>Thiothrix</i> |
| title_short | <i>tilS</i> and <i>rpoB</i>: New Molecular Markers for Phylogenetic and Biodiversity Studies of the Genus <i>Thiothrix</i> |
| title_sort | i tils i and i rpob i new molecular markers for phylogenetic and biodiversity studies of the genus i thiothrix i |
| topic | <i>Thiothrix</i> genome MAG <i>tilS</i> <i>rpoB</i> set of bacterial core genes |
| url | https://www.mdpi.com/2076-2607/11/10/2521 |
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