Two new species of Dulcicalothrix, D. adhikaryi sp. nov. and D. iyengarii sp. nov., were discovered in India and are characterized and described in accordance with the rules of the International Code of Nomenclature for algae, fungi, and plants (ICN). As a result of phylogenetic analysis, Calothrix elsteri is reassigned to Brunnivagina gen. nov. During comparison with all Dulcicalothrix for which sequence data were available, we observed that the genus has six ribosomal operons in three orthologous types. Each of the three orthologs could be identified based upon indels occurring in the D1-D1' helix sequence in the ITS rRNA region between the 16S and 23S rRNA genes, and in these three types, there were operons containing ITS rRNA regions with and without tRNA genes. Examination of complete genomes in Dulcicalothrix revealed that, at least in the three strains for which complete genomes are available, there are five ribosomal operons, two with tRNA genes and three with no tRNA genes in the ITS rRNA region. Internal transcribed spacer rRNA regions have been consistently used to differentiate species, both on the basis of secondary structure and percent dissimilarity. Our findings call into question the use of ITS rRNA regions to differentiate species in the absence of efforts to obtain multiple operons of the ITS rRNA region through cloning or targeted PCR amplicons. The ITS rRNA region data for Dulcicalothrix is woefully incomplete, but we provide herein a means for dealing with incomplete data using the polyphasic approach to analyze diverse molecular character sets. Caution is urged in using ITS rRNA data, but a way forward through the complexity is also proposed.
- Klíčová slova
- Dulcicalothrix, 16S‐23S ITS rRNA region, Brunnivagina gen. nov., Calotrichaceae, Cyanobacteria, ITS rRNA region percent dissimilarity, multiple ribosomal operons,
- MeSH
- fylogeneze * MeSH
- mezerníky ribozomální DNA analýza genetika MeSH
- operon MeSH
- RNA ribozomální 16S analýza genetika MeSH
- RNA ribozomální 23S genetika MeSH
- rRNA operon genetika MeSH
- sinice * genetika klasifikace MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Indie MeSH
- Názvy látek
- mezerníky ribozomální DNA MeSH
- RNA ribozomální 16S MeSH
- RNA ribozomální 23S MeSH
This study examined the sequences of the two rRNA (rrn) operons of pathogenic non-cultivable treponemes, comprising 11 strains of T. pallidum ssp. pallidum (TPA), five strains of T. pallidum ssp. pertenue (TPE), two strains of T. pallidum ssp. endemicum (TEN), a simian Fribourg-Blanc strain and a rabbit T. paraluiscuniculi (TPc) strain. PCR was used to determine the type of 16S-23S ribosomal intergenic spacers in the rrn operons from 30 clinical samples belonging to five different genotypes. When compared with the TPA strains, TPc Cuniculi A strain had a 17 bp deletion, and the TPE, TEN and Fribourg-Blanc isolates had a deletion of 33 bp. Other than these deletions, only 17 heterogeneous sites were found within the entire region (excluding the 16S-23S intergenic spacer region encoding tRNA-Ile or tRNA-Ala). The pattern of nucleotide changes in the rrn operons corresponded to the classification of treponemal strains, whilst two different rrn spacer patterns (Ile/Ala and Ala/Ile) appeared to be distributed randomly across species/subspecies classification, time and geographical source of the treponemal strains. It is suggested that the random distribution of tRNA genes is caused by reciprocal translocation between repetitive sequences mediated by a recBCD-like system.
- MeSH
- DNA bakterií chemie genetika MeSH
- fylogeneze MeSH
- genetická variace MeSH
- genom bakteriální MeSH
- genotyp MeSH
- mezerníky ribozomální DNA genetika MeSH
- molekulární sekvence - údaje MeSH
- RNA ribozomální 16S genetika MeSH
- RNA ribozomální 23S genetika MeSH
- rRNA operon * MeSH
- sekvence nukleotidů MeSH
- sekvenční analýza DNA MeSH
- sekvenční delece MeSH
- Treponema pallidum klasifikace genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- DNA bakterií MeSH
- mezerníky ribozomální DNA MeSH
- RNA ribozomální 16S MeSH
- RNA ribozomální 23S MeSH
