Ravin Nikolai V, Smolyakov Dmitry D, Markov Nikita D, Beletsky Alexey V, Mardanov Andrey V, Rudenko Tatyana S, Grabovich Margarita Yu
Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia.
Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia.
Microorganisms. 2023 Oct 9;11(10):2521. doi: 10.3390/microorganisms11102521.
Currently, the phylogeny of the genus 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 . We found that the levels of similarity of the nucleotide sequences of the tRNA(Ile)-lysidine synthase () and the β subunit of RNA polymerase () genes are in good agreement with the average nucleotide identity (ANI) values between the genomes of various representatives of the genus . The genomes of strains MK1, WS, DNT52, DNT53, and H33 were sequenced. Taxonomic analysis using both whole genomes and the gene consistently showed that MK1 and WS belong to , while DNT52, DNT53, and H33 belong to . The gene fragments were subjected to high-throughput sequencing to profile the mat of a sulfidic spring, which revealed the presence of known species of and new species-level phylotypes. Thus, the use of and 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 .
目前，由于该属内16S核糖体RNA基因序列具有高度同源性，该属的系统发育基于比较全基因组分析。我们分析了使用各种保守基因作为该属系统发育标记的可能性。我们发现，异亮氨酰-tRNA赖氨酸合成酶（）和RNA聚合酶β亚基（）基因的核苷酸序列相似性水平与该属不同代表菌株基因组之间的平均核苷酸一致性（ANI）值高度吻合。对菌株MK1、WS、DNT52、DNT53和H33的基因组进行了测序。使用全基因组和基因进行的分类分析一致表明，MK1和WS属于，而DNT52、DNT53和H33属于。对基因片段进行高通量测序以描绘硫化泉的垫，这揭示了已知的物种和新的物种水平系统发育型的存在。因此，使用和作为系统发育标记将能够快速分析纯培养物和自然群落，以便对该属的代表进行系统发育鉴定。
