Journal articles: 'RRNA gene analysis'

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Liu, Junjie, Peng Li, Liuyang Lu, Lanfen Xie, Xiling Chen, and Baizhong Zhang. "Selection and evaluation of potential reference genes for gene expression analysis in Avena fatua Linn." Plant Protection Science 55, No. 1 (November 20, 2018): 61–71. http://dx.doi.org/10.17221/20/2018-pps.

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Eight commonly used candidate reference genes, 18S ribosomal RNA (rRNA) (18S), 28S rRNA (28S), actin (ACT), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), elongation factor 1 alpha (EF1α), ribosomal protein L7 (RPL7), Alpha-tubulin (α-TUB), and TATA box binding protein-associated factor (TBP), were evaluated under various experimental conditions to assess their suitability in different developmental stages, tissues and herbicide treatments in Avena fatua. The results indicated the most suitable reference genes for the different experimental conditions. For developmental stages, 28S and EF1α were the optimal reference genes, both EF1α and 28S were suitable for experiments of different tissues, whereas for herbicide treatments, GAPDH and ACT were suitable for normalizations of expression data. In addition, GAPDH and EF1α were the suitable reference genes.

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Gonzalez-y-Merchand, J. A., M. J. Colston, and R. A. Cox. "Effects of Growth Conditions on Expression of Mycobacterial murA and tyrS Genes and Contributions of Their Transcripts to Precursor rRNA Synthesis." Journal of Bacteriology 181, no. 15 (August 1, 1999): 4617–27. http://dx.doi.org/10.1128/jb.181.15.4617-4627.1999.

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ABSTRACT All mycobacteria studied to date have an rRNA operon, designatedrrnA, located downstream from a single copy of themurA gene, which encodes an enzyme (EC 2.5.1.7 ) important for peptidoglycan synthesis. The rrnA operon has a promoter, P1(A), located within the coding region of murA, near the 3′ end. Samples of RNA were isolated from Mycobacterium tuberculosis at different stages of the growth cycle and fromMycobacterium smegmatis grown under different conditions. RNase protection assays were used to investigate transcripts of bothmurA and rrnA. Transcription ofmurA was found to continue into the 16S rRNA gene, as ifmurA and rrnA form a hybrid (protein coding-rRNA coding) operon. During the growth of M. tuberculosis, the hybrid operon contributed approximately 2% to total pre-rRNA. Analysis of M. smegmatis RNA revealed that the level of murA RNA depended on the growth rate and that the patterns of expression during the growth cycle were different formurA and rrnA. M. smegmatis has a second rRNA operon, rrnB, located downstream from a single copy of the tyrS gene, encoding tyrosyl-tRNA synthetase. Transcription of tyrS was found to continue into the 16S rRNA gene rrnB. The hybrid tyrS-rrnB operon contributed 0.2 to 0.6% to rrnB transcripts. The pattern of tyrS expression during the growth cycle matched the pattern of rrnB expression, reflecting the essential role of TyrS and rRNA in protein biosynthesis.

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Yap, Wai Ho, Zhenshui Zhang, and Yue Wang. "Distinct Types of rRNA Operons Exist in the Genome of the Actinomycete Thermomonospora chromogena and Evidence for Horizontal Transfer of an Entire rRNA Operon." Journal of Bacteriology 181, no. 17 (September 1, 1999): 5201–9. http://dx.doi.org/10.1128/jb.181.17.5201-5209.1999.

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ABSTRACT We describe here the presence of two distinct types of rRNA operons in the genome of a thermophilic actinomycete Thermomonospora chromogena. The genome of T. chromogena contains six rRNA operons (rrn), of which four complete and two incomplete ones were cloned and sequenced. Comparative analysis revealed that the operon rrnB exhibits high levels of sequence variations to the other five nearly identical ones throughout the entire length of the operon. The coding sequences for the 16S and 23S rRNA genes differ by approximately 6 and 10%, respectively, between the two types of operons. Normal functionality ofrrnB is concluded on the basis of the nonrandom distribution of nucleotide substitutions, the presence of compensating nucleotide covariations, the preservation of secondary and tertiary rRNA structures, and the detection of correctly processed rRNAs in the cell. Comparative sequence analysis also revealed a close evolutionary relationship between rrnB operon of T. chromogena and rrnA operon of another thermophilic actinomycete Thermobispora bispora. We propose thatT. chromogena acquired rrnB operon fromT. bispora or a related organism via horizontal gene transfer.

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Menendez, M. C., M. J. Garcia, M. C. Navarro, J. A. Gonzalez-y-Merchand, S. Rivera-Gutierrez, L. Garcia-Sanchez, and R. A. Cox. "Characterization of an rRNA Operon (rrnB) of Mycobacterium fortuitum and Other Mycobacterial Species: Implications for the Classification of Mycobacteria." Journal of Bacteriology 184, no. 4 (February 15, 2002): 1078–88. http://dx.doi.org/10.1128/jb.184.4.1078-1088.2002.

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ABSTRACT Mycobacteria are thought to have either one or two rRNA operons per genome. All mycobacteria investigated to date have an operon, designated rrnA, located downstream from the murA gene. We report that Mycobacteriun fortuitum has a second rrn operon, designated rrnB, which is located downstream from the tyrS gene; tyrS is very close to the 3" end of a gene (3-mag) coding for 3-methylpurine-DNA-glycosylase. The second rrn operon of Mycobacterium smegmatis was shown to have a similar organization, namely, 5" 3-mag-tyrS-rrnB 3". The rrnB operon of M. fortuitum was found to have a single dedicated promoter. During exponential growth in a rich medium, the rrnB and rrnA operons were the major and minor contributors, respectively, to pre-rRNA synthesis. Genomic DNA was isolated from eight other fast-growing mycobacterial species. Samples were investigated by Southern blot analysis using probes for murA, tyrS, and 16S rRNA sequences. The results revealed that both rrnA and rrnB operons were present in each species. The results form the basis for a proposed new scheme for the classification of mycobacteria. The approach, which is phylogenetic in concept, is based on particular properties of the rrn operons of a cell, namely, the number per genome and a feature of 16S rRNA gene sequences.

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Prammananan, Therdsak, Peter Sander, Burkhard Springer, and Erik C. Böttger. "RecA-Mediated Gene Conversion and Aminoglycoside Resistance in Strains Heterozygous for rRNA." Antimicrobial Agents and Chemotherapy 43, no. 3 (March 1, 1999): 447–53. http://dx.doi.org/10.1128/aac.43.3.447.

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ABSTRACT Clinical resistance to aminoglycosides in general is due to enzymatic drug modification. Mutational alterations of the small ribosomal subunit rRNA have recently been found to mediate acquired resistance in bacterial pathogens in vivo. In this study we investigated the effect of 16S rRNA heterozygosity (wild-type [wt] and mutant [mut] operons at position 1408 [1408wt/1408mut]) on aminoglycoside resistance. Using an integrative vector, we introduced a single copy of a mutated rRNA operon (1408 A→G) into Mycobacterium smegmatis, which carries two chromosomal wild-type rRNA operons; the resultant transformants exhibited an aminoglycoside-sensitive phenotype. In contrast, introduction of the mutated rRNA operon into anM. smegmatis rrnB knockout strain carrying a single functional chromosomal wild-type rRNA operon resulted in aminoglycoside-resistant transformants. Subsequent analysis by DNA sequencing and RNase protection assays unexpectedly demonstrated a homozygous mutant genotype, rRNAmut/rRNAmut, in the resistant transformants. To investigate whether RecA-mediated gene conversion was responsible for the aminoglycoside-resistant phenotype in the rRNAwt/rRNAmut strains, recAmutant strains were generated by allelic exchange techniques. Transformation of the recA rrnB M. smegmatis mutant strains with an integrative vector expressing a mutated rRNA operon (Escherichia coli position 1408 A→G) resulted in transformants with an aminoglycoside-sensitive phenotype. Subsequent analysis showed stable heterozygosity at 16S rRNA position 1408 with a single wild-type allele and a single resistant allele. These results demonstrate that rRNA-mediated mutational resistance to aminoglycosides is recessive.

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Springer, Burkhard, Yishak G. Kidan, Therdsak Prammananan, Kerstin Ellrott, Erik C. Böttger, and Peter Sander. "Mechanisms of Streptomycin Resistance: Selection of Mutations in the 16S rRNA Gene Conferring Resistance." Antimicrobial Agents and Chemotherapy 45, no. 10 (October 1, 2001): 2877–84. http://dx.doi.org/10.1128/aac.45.10.2877-2884.2001.

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ABSTRACT Chromosomally acquired streptomycin resistance is frequently due to mutations in the gene encoding the ribosomal protein S12,rpsL. The presence of several rRNA operons (rrn) and a single rpsL gene in most bacterial genomes prohibits the isolation of streptomycin-resistant mutants in which resistance is mediated by mutations in the 16S rRNA gene (rrs). Three strains were constructed in this investigation: Mycobacterium smegmatis rrnB,M. smegmatis rpsL 3+, and M. smegmatis rrnB rpsL 3+. M. smegmatis rrnB carries a single functional rrnoperon, i.e., rrnA (comprised of 16S, 23S, and 5S rRNA genes) and a single rpsL +gene; M. smegmatis rpsL 3+ is characterized by the presence of two rrn operons (rrnA and rrnB) and threerpsL + genes; and M. smegmatis rrnB rpsL 3+ carries a single functionalrrn operon (rrnA) and threerpsL + genes. By genetically altering the number of rpsL and rrs alleles in the bacterial genome, mutations in rrs conferring streptomycin resistance could be selected, as revealed by analysis of streptomycin-resistant derivatives of M. smegmatis rrnB rpsL 3+. Besides mutations well known to confer streptomycin resistance, novel streptomycin resistance conferring mutations were isolated. Most of the mutations were found to map to a functional pseudoknot structure within the 530 loop region of the 16S rRNA. One of the mutations observed, i.e., 524G→C, severely distorts the interaction between nucleotides 524G and 507C, a Watson-Crick interaction which has been thought to be essential for ribosome function. The use of the single rRNA allelic M. smegmatis strain should help to elucidate the principles of ribosome-drug interactions.

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KÃ¶hler, Gerwald, Wolfgang Ludwig, and Karl Heinz Schleifer. "Differentiation of lactococci by rRNA gene restriction analysis." FEMS Microbiology Letters 84, no. 3 (December 1991): 307–12. http://dx.doi.org/10.1111/j.1574-6968.1991.tb04615.x.

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Miyashita, Mika, Takeshi Sakane, Ken-ichiro Suzuki, and Yasuyoshi Nakagawa. "16S rRNA gene and 16S-23S rRNA gene internal transcribed spacer sequences analysis of the genus Myxococcus." FEMS Microbiology Letters 282, no. 2 (April 4, 2008): 241–45. http://dx.doi.org/10.1111/j.1574-6968.2008.01127.x.

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9

Paul, Bobby. "Concatenated 16S rRNA sequence analysis improves bacterial taxonomy." F1000Research 11 (December 19, 2022): 1530. http://dx.doi.org/10.12688/f1000research.128320.1.

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Background: Microscopic, biochemical, molecular, and computer-based approaches are extensively used to identify and classify bacterial populations. Advances in DNA sequencing and bioinformatics workflows have facilitated sophisticated genome-based methods for microbial taxonomy although sequencing of the 16S rRNA gene is widely employed to identify and classify the bacterial community as a cost-effective and single-gene approach. However, the 16S rRNA sequence-based species identification accuracy is limited by multiple copies of the gene and their higher sequence identity between closely related species. The availability of a large volume of bacterial whole-genome data provided an opportunity to develop comprehensive species-specific 16S rRNA reference libraries. Methods: The 16S rRNA copies were retrieved from the whole genomes in the complete stage at the Genome database. With defined rules, four 16S rRNA gene copy variants were concatenated to develop a species-specific reference library. The sequence similarity search was performed with a web-based BLAST program, and MEGA software was used to construct the phylogenetic tree. Results: Using this approach, species-specific 16S rRNA gene libraries were developed for four closely related Streptococcus species (S. gordonii, S. mitis, S. oralis, and S. pneumoniae). Sequence similarity and phylogenetic analysis using concatenated 16S rRNA copies yielded better resolution than single gene copy approaches. Conclusions: The approach is very effective in classifying genetically related species and may reduce misclassification of bacterial species and genome assemblies.

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Baylis, H. A., and M. J. Bibb. "Transcriptional analysis of the 16S rRNA gene of the rrnD gene set of Streptomyces coelicolor A3(2)." Molecular Microbiology 2, no. 5 (September 1988): 569–79. http://dx.doi.org/10.1111/j.1365-2958.1988.tb00065.x.

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Lee, I. M., K. D. Bottner-Parker, Y. Zhao, R. E. Davis, and N. A. Harrison. "Phylogenetic analysis and delineation of phytoplasmas based on secY gene sequences." International Journal of Systematic and Evolutionary Microbiology 60, no. 12 (December 1, 2010): 2887–97. http://dx.doi.org/10.1099/ijs.0.019695-0.

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The secY gene sequence is more variable than that of the 16S rRNA gene. Comparative phylogenetic analyses with 16S rRNA and secY gene sequences from 80 and 83 phytoplasma strains, respectively, were performed to assess the efficacy of these sequences for delineating phytoplasma strains within each 16Sr group. The phylogenetic interrelatedness among phytoplasma taxa inferred by secY gene-based phylogeny was nearly congruent with that inferred by 16S rRNA gene-based phylogeny. Phylogenetic analysis based on the secY gene permitted finer differentiation of phytoplasma strains, however. The secY gene-based phylogeny not only readily resolved 16Sr subgroups within a given 16Sr group, but also delineated distinct lineages irresolvable by 16S rRNA gene-based phylogeny. Such high resolving power makes the secY gene a more useful genetic marker than the 16S rRNA gene for finer differentiation of closely related phytoplasma strains based on RFLP analysis with selected restriction enzymes. Such strains were readily identified by collective secY RFLP patterns. The genetic interrelationships among these strains were determined by pattern similarity coefficients, which coincided with delineations by phylogenetic analysis. This study also revealed two heterogeneous spc operons present in the phytoplasma clade. This latter finding may have significant implications for phytoplasma evolution.

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Musters, W., J. Venema, G. van der Linden, H. van Heerikhuizen, J. Klootwijk, and R. J. Planta. "A system for the analysis of yeast ribosomal DNA mutations." Molecular and Cellular Biology 9, no. 2 (February 1989): 551–59. http://dx.doi.org/10.1128/mcb.9.2.551-559.1989.

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To develop a system for the analysis of eucaryotic ribosomal DNA (rDNA) mutations, we cloned a complete, transcriptionally active rDNA unit from the yeast Saccharomyces cerevisiae on a centromere-containing yeast plasmid. To distinguish the plasmid-derived ribosomal transcripts from those encoded by the rDNA locus, we inserted a tag of 18 base pairs within the first expansion segment of domain I of the 26S rRNA gene. We demonstrate that this insertion behaves as a neutral mutation since tagged 26S rRNA is normally processed and assembled into functional ribosomal subunits. This system allows us to study the effect of subsequent mutations within the tagged rDNA unit on the biosynthesis and function of the rRNA. As a first application, we wanted to ascertain whether the assembly of a 60S subunit is dependent on the presence in cis of an intact 17S rRNA gene. We found that a deletion of two-thirds of the 17S rRNA gene has no effect on the accumulation of active 60S subunits derived from the same operon. On the other hand, deletions within the second domain of the 26S rRNA gene completely abolished the accumulation of mature 26S rRNA.

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Musters, W., J. Venema, G. van der Linden, H. van Heerikhuizen, J. Klootwijk, and R. J. Planta. "A system for the analysis of yeast ribosomal DNA mutations." Molecular and Cellular Biology 9, no. 2 (February 1989): 551–59. http://dx.doi.org/10.1128/mcb.9.2.551.

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To develop a system for the analysis of eucaryotic ribosomal DNA (rDNA) mutations, we cloned a complete, transcriptionally active rDNA unit from the yeast Saccharomyces cerevisiae on a centromere-containing yeast plasmid. To distinguish the plasmid-derived ribosomal transcripts from those encoded by the rDNA locus, we inserted a tag of 18 base pairs within the first expansion segment of domain I of the 26S rRNA gene. We demonstrate that this insertion behaves as a neutral mutation since tagged 26S rRNA is normally processed and assembled into functional ribosomal subunits. This system allows us to study the effect of subsequent mutations within the tagged rDNA unit on the biosynthesis and function of the rRNA. As a first application, we wanted to ascertain whether the assembly of a 60S subunit is dependent on the presence in cis of an intact 17S rRNA gene. We found that a deletion of two-thirds of the 17S rRNA gene has no effect on the accumulation of active 60S subunits derived from the same operon. On the other hand, deletions within the second domain of the 26S rRNA gene completely abolished the accumulation of mature 26S rRNA.

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Bhandari, Yashodhar, Pankaj Dabir, Krithika Nandhakumar, Kannayakanahalli Maheshwarappa Dayananda, Yogesh Shripad Shouche, and Maryada Venkata Rami Reddy. "Analysis of Polymorphism of 18S rRNA Gene inWuchereria bancroftiMicrofilariae." Microbiology and Immunology 49, no. 10 (October 2005): 909–14. http://dx.doi.org/10.1111/j.1348-0421.2005.tb03682.x.

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Takeuchi, Mariko, and Akira Yokota. "Phylogenetic analysis ofKineococcus aurantiacusbased on 16S rRNA gene sequences." FEMS Microbiology Letters 116, no. 1 (February 1994): 7–11. http://dx.doi.org/10.1111/j.1574-6968.1994.tb06667.x.

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Laughery, Jacob M., Audrey O. T. Lau, Stephen N. White, Jeanne M. Howell, and Carlos E. Suarez. "Babesia bovis: Transcriptional analysis of rRNA gene unit expression." Experimental Parasitology 123, no. 1 (September 2009): 45–50. http://dx.doi.org/10.1016/j.exppara.2009.05.016.

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Virtanen, Seppo, Ilkka Kalliala, Pekka Nieminen, and Anne Salonen. "Comparative analysis of vaginal microbiota sampling using 16S rRNA gene analysis." PLOS ONE 12, no. 7 (July 19, 2017): e0181477. http://dx.doi.org/10.1371/journal.pone.0181477.

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Fisher, Ross, Adrianna Henson, Paola Quarello, Anna Aspesi, Jason E. Farrar, Robert J. Arceci, David M. Bodine, et al. "Insights Into Diagnosis and Etiology of Diamond Blackfan Anemia by Analysis of Pre-rRNA Processing." Blood 120, no. 21 (November 16, 2012): 3476. http://dx.doi.org/10.1182/blood.v120.21.3476.3476.

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Abstract Abstract 3476 Most cases of Diamond Blackfan anemia are caused by haploinsufficiency for genes encoding proteins of the large or small ribosomal subunit. All of the ribosomal proteins affected in DBA are essential components of the ribosome required for the assembly of their respective subunits, including processing of the primary pre-rRNA transcript to mature 18S, 5.8S, and 28S rRNAs. Pre-rRNA processing signatures associated with ribosomal protein haploinsufficiency demonstrate a role for individual proteins in subunit assembly and can differ depending on which protein is affected. A facile pre-rRNA processing assay that can discriminate between loss of function alleles for different ribosomal protein genes would be an invaluable aide to DBA diagnosis and gene discovery efforts. Such an assay could also provide insight into different aspects of DBA pathophysiology. We have developed a robust procedure to assess pre-rRNA processing patterns in activated lymphocytes from the peripheral blood of patients with known or suspected Diamond Blackfan anemia. This assay typically involves the electrophoretic separation of total RNA from activated lymphocytes followed by Northern blotting with various hybridization probes to different rRNA precursors. Using this assay, we have found a common 32S pre-rRNA processing intermediate present in RNA from DBA patients with mutations in virtually all known large ribosomal subunit genes. This 32S pre-rRNA can be visualized in situ in gels stained with ethidium bromide (see accompanying figure) greatly simplifying the identification of large subunit ribosomal protein genes harboring loss of function mutations. As more and more ribosomal protein genes are identified within the DBA population, it has become increasingly important to distinguish between variants that affect ribosomal protein function and benign polymorphisms. Therefore, an analysis of pre-rRNA processing can be used to identify causative genes in patients with complex genotypes where sequence variants are found in more than one ribosomal protein gene. We analyzed a patient with variants in genes encoding RPS19 and RPL11, two known DBA genes, plus a deletion containing the RPL31 gene that has not been previously linked to DBA. Data analyses overwhelmingly support the deletion of RPL31 as the causative lesion in this patient and identify RPL31 as a new DBA gene. Analysis of pre-rRNA processing can also guide additional gene discovery efforts. We performed pre-rRNA processing studies on two patients lacking mutations in known DBA genes. In one case, we observed a clear defect in the18S rRNA pathway, implicating a gene involved in the biogenesis of the small ribosomal subunit, whereas in a second patient there is no evidence of a ribosome biogenesis defect suggesting that the underlying mutation may not affect ribosome synthesis. These results will help guide further efforts to identify causative genes in this patient cohort. Finally, we have used pre-rRNA processing patterns to begin to examine the mechanisms underlying remission in DBA patients. To date, we have examined two samples from DBA patients in remission and showed the ribosome synthesis defect is retained even while in remission for one of these patients, whereas the pre-rRNA processing defect has resolved in the other patient. Disclosures: No relevant conflicts of interest to declare.

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Dewhirst, Floyd E., Zeli Shen, Michael S. Scimeca, Lauren N. Stokes, Tahani Boumenna, Tsute Chen, Bruce J. Paster, and James G. Fox. "Discordant 16S and 23S rRNA Gene Phylogenies for the Genus Helicobacter: Implications for Phylogenetic Inference and Systematics." Journal of Bacteriology 187, no. 17 (September 1, 2005): 6106–18. http://dx.doi.org/10.1128/jb.187.17.6106-6118.2005.

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ABSTRACT Analysis of 16S rRNA gene sequences has become the primary method for determining prokaryotic phylogeny. Phylogeny is currently the basis for prokaryotic systematics. Therefore, the validity of 16S rRNA gene-based phylogenetic analyses is of fundamental importance for prokaryotic systematics. Discrepancies between 16S rRNA gene analyses and DNA-DNA hybridization and phenotypic analyses have been noted in the genus Helicobacter. To clarify these discrepancies, we sequenced the 23S rRNA genes for 55 helicobacter strains representing 41 taxa (>2,700 bases per sequence). Phylogenetic-tree construction using neighbor-joining, parsimony, and maximum likelihood methods for 23S rRNA gene sequence data yielded stable trees which were consistent with other phenotypic and genotypic methods. The 16S rRNA gene sequence-derived trees were discordant with the 23S rRNA gene trees and other data. Discrepant 16S rRNA gene sequence data for the helicobacters are consistent with the horizontal transfer of 16S rRNA gene fragments and the creation of mosaic molecules with loss of phylogenetic information. These results suggest that taxonomic decisions must be supported by other phylogenetically informative macromolecules, such as the 23S rRNA gene, when 16S rRNA gene-derived phylogeny is discordant with other credible phenotypic and genotypic methods. This study found Wolinella succinogenes to branch with the unsheathed-flagellum cluster of helicobacters by 23S rRNA gene analyses and whole-genome comparisons. This study also found intervening sequences (IVSs) in the 23S rRNA genes of strains of 12 Helicobacter species. IVSs were found in helices 10, 25, and 45, as well as between helices 31′ and 27′. Simultaneous insertion of IVSs at three sites was found in H. mesocricetorum.

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Muscarella, D. E., V. M. Vogt, and S. E. Bloom. "The ribosomal RNA gene cluster in aneuploid chickens: evidence for increased gene dosage and regulation of gene expression." Journal of Cell Biology 101, no. 5 (November 1, 1985): 1749–56. http://dx.doi.org/10.1083/jcb.101.5.1749.

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In the chicken, the nucleolus organizer regions, or sites of the genes encoding 18S, 5.8S, and 28S ribosomal RNA (rRNA), map to one pair of microchromosomes that can be identified by silver nitrate cytochemistry. This nucleolar organizer chromosome also contains the major histocompatibility complex. Chickens aneuploid for this chromosome have been identified and reproduced for over seven generations. Crossing two trisomic parents results in the production of viable disomic, trisomic, and tetrasomic progeny, showing two, three, and four nucleoli and nucleolar organizers per cell, respectively. A molecular analysis of rRNA genes was undertaken to establish the gene copy numbers in the aneuploid genotypes, and to determine if elevated numbers of rRNA genes are stably maintained and inherited over multiple generations. Gene copy numbers were determined using hybridization analysis of erythrocyte DNA obtained from individuals comprising a family which segregated disomic, trisomic, and tetrasomic genotypes. The values obtained were 290, 420, and 570 rDNA repeats per cell for disomic, trisomic, and tetrasomic animals, respectively. These results provide molecular confirmation of the two aneuploid states and show that elevated gene copy numbers have been maintained over multiple generations. Fibroblasts derived from disomic and tetrasomic embryos were found to grow at similar rates in culture, and mature rRNA levels in chicken embryo fibroblasts from disomic, trisomic and tetrasomic embryos were also found to have similar levels of mature rRNA. Therefore, despite the increase in rDNA content, the level of rRNA is regulated to diploid amounts in aneuploid fibroblasts.

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Fujimoto, Naoshi, Keigo Mizuno, Tomoki Yokoyama, Akihiro Ohnishi, Masaharu Suzuki, Satoru Watanabe, Kenji Komatsu, et al. "Community analysis of picocyanobacteria in an oligotrophic lake by cloning 16S rRNA gene and 16S rRNA gene amplicon sequencing." Journal of General and Applied Microbiology 61, no. 5 (2015): 171–76. http://dx.doi.org/10.2323/jgam.61.171.

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Hrytseva, N. "DEVELOPMENT OF SPECIFIC PRIMERS FOR 16S rRNA GENE ANALYSIS IN THE DETECTION OF Ralstonia solanacearum SPECIES COMPLEX." Biotechnologia Acta 15, no. 3 (June 30, 2022): 5–12. http://dx.doi.org/10.15407/biotech15.03.005.

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Members of Ralstonia solanacearum species complex (RSSC) are causal agents of vascular wilt disease in more than 450 crop species, including solanaceous plants such as potatoes, tomatoes, bell pepper, eggplant, etc. These phytopathogens cause serious yield loss mostly in solanaceous crops which are grown in tropical, subtropical, and temperate regions of the world. Yield losses comprise 80%–100% in potato, up to 91% for tomato, 10%–30% in tobacco, 33%–90% in banana, and reduce crop productivity and yield. PCR-methods are specific, sensitive and cost-effective approaches for the detection and identification of RSSC members. The objective of this study was to compare specificity of routinely used primer mix for PCR RSSC detection with the newly developed pairs of species-specific primers for ease of use diagnostics in a laboratory. Materials and Methods. The conserved genomic regions of the 16S rRNA sequences of R. solanacearum, R. pseudosolanacearum, and R. syzygii were selected for the design of primers for this study. Newly created primer species specificity was tested in PCR using the DNA of the two targets and 13 non-target strains of bacteria. Results. Three pairs of newly created primers Rs-28(F)/Rs-193(R), Rs-28(F)/OLI-160(R), Rs28(F)/OLI248(R) produced single specific fragments for bacterial strains of Ralstonia solanacearum: 166 bp, 132 bp, and 220 bp. products respectively. No PCR products were obtained during amplification with the negative control or non-target DNA templates from other bacterial species. Conclusion. Designed primers can be used for the development of PCR system for the qualitative and quantitative detection of RSSC members.

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Khot, Prasanna D., Daisy L. Ko, and David N. Fredricks. "Sequencing and Analysis of Fungal rRNA Operons for Development of Broad-Range Fungal PCR Assays." Applied and Environmental Microbiology 75, no. 6 (January 9, 2009): 1559–65. http://dx.doi.org/10.1128/aem.02383-08.

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ABSTRACT rRNA genes are attractive targets for developing PCR assays targeting human fungal pathogens. Most studies have focused on the 18S rRNA gene, internal transcribed spacers, and the 5′ end of the 28S rRNA gene. An approximately 2,900-bp region of the 28S rRNA gene remains largely unexplored because sequences of many medically relevant fungi are either unavailable or undefined in genomic databases. The internal transcribed spacers and 28S rRNA gene of nine medically and phylogenetically important fungi were sequenced. In addition, 42 sequences from this region were acquired from public databases, resulting in an alignment of 51 fungal sequences spanning 30 fungal genera. For the nearly 3,950-bp region from the 3′ end of 18S rRNA gene to the 3′ end of the 28S rRNA gene, 27 broad-range PCR primers were designed such that their sequence homology with the human rRNA gene was minimal. All 62 possible amplicons in the size range from 75 to 400 bp from 27 primers were screened using fungal genomic DNA from 26 species spanning 14 genera. Eleven of the 62 amplicons did not cross-react with 1 μg/PCR human DNA but simultaneously amplified 10 fg of fungal DNA. Phylogenetic distance matrices were calculated for regions covered by these 11 amplicons based on 51 fungi. Two of these 11 amplicons successfully amplified 30 fg of fungal DNA from 25 of 26 fungi and provided the most phylogenetic information for species identification based on the distance matrices. These PCR assays hold promise for detection and identification of fungal pathogens in human tissues.

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Guo, Jiarong, James R. Cole, Qingpeng Zhang, C. Titus Brown, and James M. Tiedje. "Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes." Applied and Environmental Microbiology 82, no. 1 (October 16, 2015): 157–66. http://dx.doi.org/10.1128/aem.02772-15.

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ABSTRACTShotgun metagenomic sequencing does not depend on gene-targeted primers or PCR amplification; thus, it is not affected by primer bias or chimeras. However, searching rRNA genes from large shotgun Illumina data sets is computationally expensive, and no approach exists for unsupervised community analysis of small-subunit (SSU) rRNA gene fragments retrieved from shotgun data. We present a pipeline, SSUsearch, to achieve the faster identification of short-subunit rRNA gene fragments and enabled unsupervised community analysis with shotgun data. It also includes classification and copy number correction, and the output can be used by traditional amplicon analysis platforms. Shotgun metagenome data using this pipeline yielded higher diversity estimates than amplicon data but retained the grouping of samples in ordination analyses. We applied this pipeline to soil samples with paired shotgun and amplicon data and confirmed bias againstVerrucomicrobiain a commonly used V6-V8 primer set, as well as discovering likely bias againstActinobacteriaand forVerrucomicrobiain a commonly used V4 primer set. This pipeline can utilize all variable regions in SSU rRNA and also can be applied to large-subunit (LSU) rRNA genes for confirmation of community structure. The pipeline can scale to handle large amounts of soil metagenomic data (5 Gb memory and 5 central processing unit hours to process 38 Gb [1 lane] of trimmed Illumina HiSeq2500 data) and is freely available athttps://github.com/dib-lab/SSUsearchunder a BSD license.

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UNER, Mahmut Celalettin, Gülşen HASÇELİK, and Hamit Kaan MÜŞTAK. "Antimicrobial Susceptibilities of Clinical Nocardia Isolates Identified by 16S rRNA Gene Sequence Analysis." Mikrobiyoloji Bulteni 50, no. 1 (January 7, 2016): 11–20. http://dx.doi.org/10.5578/mb.10639.

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Zamoroka, A. "Іs clytini monophyletic? The evidence from five-gene phylogenetic analysis." Proceedings of the State Natural History Museum, no. 37 (January 1, 2022): 191–214. http://dx.doi.org/10.36885/nzdpm.2021.37.191-214.

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Tribe Clytini (Coleoptera: Cerambycidae) is one of the largest within the long horn beetles, having over 1500 species. Until now, the tribe was considered monophyletic, despite the fact that it combines several different morphological groups. Morphological data alone could not shed enough light on the taxonomy and phylogeny of Clytini. The data for the last decade on molecular phylogenetics have challenged the Clytini monophyletic hypothesis. In this study, I conducted a comprehensive phylogenetic analysis of Clytini based on the three mitochondrial genes 12S rRNA 16S rRNA COI and two nuclear genes 18S rRNA 28S rRNA. The results of the analysis with high reliability confirmed the hypothesis of polyphyly of Clytini. The tribe includes two phylogenetically different and morphologically distinct evolutionary branches, which gave me reason to conduct a taxonomic revision of Clytini. I proposed new nomenclature acts including 1 new supertribe, 1 new tribe, 4 new subtribes, 3 new genera, 4 new subgenera, 3 new statuses, 22 new combinations, 2 new synonyms. In addition, I redescribed 1 tribe and 3 genera.

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de la Haba, Rafael R., M. Carmen Márquez, R. Thane Papke, and Antonio Ventosa. "Multilocus sequence analysis of the family Halomonadaceae." International Journal of Systematic and Evolutionary Microbiology 62, Pt_3 (March 1, 2012): 520–38. http://dx.doi.org/10.1099/ijs.0.032938-0.

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Multilocus sequence analysis (MLSA) protocols have been developed for species circumscription for many taxa. However, at present, no studies based on MLSA have been performed within any moderately halophilic bacterial group. To test the usefulness of MLSA with these kinds of micro-organisms, the family Halomonadaceae, which includes mainly halophilic bacteria, was chosen as a model. This family comprises ten genera with validly published names and 85 species of environmental, biotechnological and clinical interest. In some cases, the phylogenetic relationships between members of this family, based on 16S rRNA gene sequence comparisons, are not clear and a deep phylogenetic analysis using several housekeeping genes seemed appropriate. Here, MLSA was applied using the 16S rRNA, 23S rRNA, atpA, gyrB, rpoD and secA genes for species of the family Halomonadaceae. Phylogenetic trees based on the individual and concatenated gene sequences revealed that the family Halomonadaceae formed a monophyletic group of micro-organisms within the order Oceanospirillales. With the exception of the genera Halomonas and Modicisalibacter, all other genera within this family were phylogenetically coherent. Five of the six studied genes (16S rRNA, 23S rRNA, gyrB, rpoD and secA) showed a consistent evolutionary history. However, the results obtained with the atpA gene were different; thus, this gene may not be considered useful as an individual gene phylogenetic marker within this family. The phylogenetic methods produced variable results, with those generated from the maximum-likelihood and neighbour-joining algorithms being more similar than those obtained by maximum-parsimony methods. Horizontal gene transfer (HGT) plays an important evolutionary role in the family Halomonadaceae; however, the impact of recombination events in the phylogenetic analysis was minimized by concatenating the six loci, which agreed with the current taxonomic scheme for this family. Finally, the findings of this study also indicated that the 16S rRNA, gyrB and rpoD genes were the most suitable genes for future taxonomic studies using MLSA within the family Halomonadaceae.

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Nechayeva, Anastasia, Konstantin Boyarshin, Olga Bespalova, Violetta Klyueva, Olesya Makanina, and Irina Batlutskaya. "Analysis of 16S rRNA gene variability in soil nitrifying bacteria of the genus Nitrosomonas." BIO Web of Conferences 30 (2021): 05007. http://dx.doi.org/10.1051/bioconf/20213005007.

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The main goal of the work was to assess variability of 16S rRNA gene sequence within the nitrifying bacterial genus Nitrosomonas to find specific sequences for its detection. To achieve it, we had to find and to assess sequences that are highly conservative on the level of the genus and to find and to assess sequences variable on the level of genus but conserved on the level of species. In the SILVA database of ribosomal RNA sequences, 231 sequences of 16S rRNAs of bacteria of the genus Nitrosomonas were collected, of which were sorted 132 sequences by length from 1400 to 1541 (full-sized gene) nucleotides. We conducted an analysis of the taxon-specificity of sequences conserved at the genus level. More than a hundred full matches were found by the BLAST program in the nr database with other genera of the same and other families. So, in Nitrosomonas 16S rRNA gene are present some highly conservative regions, but they are not genus-specific due to high coincidence with other genera. Wherein, a variable region 994-1041 is highly species-specific for the species N. eutropha. Generally, the sequence of 994-1041 region of Nitrosomonas 16S rRNA genes tends to be clustered, being very close between some species.

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Clarridge, Jill E. "Impact of 16S rRNA Gene Sequence Analysis for Identification of Bacteria on Clinical Microbiology and Infectious Diseases." Clinical Microbiology Reviews 17, no. 4 (October 2004): 840–62. http://dx.doi.org/10.1128/cmr.17.4.840-862.2004.

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SUMMARY The traditional identification of bacteria on the basis of phenotypic characteristics is generally not as accurate as identification based on genotypic methods. Comparison of the bacterial 16S rRNA gene sequence has emerged as a preferred genetic technique. 16S rRNA gene sequence analysis can better identify poorly described, rarely isolated, or phenotypically aberrant strains, can be routinely used for identification of mycobacteria, and can lead to the recognition of novel pathogens and noncultured bacteria. Problems remain in that the sequences in some databases are not accurate, there is no consensus quantitative definition of genus or species based on 16S rRNA gene sequence data, the proliferation of species names based on minimal genetic and phenotypic differences raises communication difficulties, and microheterogeneity in 16S rRNA gene sequence within a species is common. Despite its accuracy, 16S rRNA gene sequence analysis lacks widespread use beyond the large and reference laboratories because of technical and cost considerations. Thus, a future challenge is to translate information from 16S rRNA gene sequencing into convenient biochemical testing schemes, making the accuracy of the genotypic identification available to the smaller and routine clinical microbiology laboratories.

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Chang, Miwha, Haeyong Lee, Joo-Young Kim, Won-Hae Lee, Chong Min Choung, and Seohyun Moon. "부검체 유래의 Escherichia coli와 Shigella spp. 동정을 위한 16S rRNA 유전자 염기서열, API 20E 및 RT-PCR 분석법의 비교." Korean Academy of Scientific Criminal Investigation 16, no. 3 (September 30, 2022): 163–77. http://dx.doi.org/10.20297/jsci.2022.16.3.163.

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Practical techniques to differentiate Escherichia coli from Shigella spp. remains underexplored in the field of forensic microbiology. We aimed to compare the performance of 16S rRNA gene sequencing, and two commercially available API 20E and RT-PCR systems to distinguish between E. coli and Shigella spp. on the basis of analysis of 24 isolates collected from 12 forensic autopsies to evaluate the level of species identification. The accuracy of 16S rRNA gene sequencing at the species level was ranged from 16.7% to 33.3%. However, 79.2% (19/24) were unidentified, even though analyzed using three distinct databases (MicroSEQ 500 library, BLAST, EzTaxon). Phylogenetic analysis confirmed that 16S rRNA gene sequencing could not differentiate Shigella spp. and E. coli. Of the 19 isolates, the API 20E showed complete identification of 78.9% (15/19) at the species level, whereas RT-PCR analysis showed complete identification of 19 isolates (100%) at the species level. Our comparison analyses revealed that only 16S rRNA gene sequencing is not enough to differentiate E. coli and Shigella spp., and the accuracy and rapidity order was as follows: RT-PCR >API 20E>standard analysis. These results suggest that the polyphasic strategy with the standard analysis and RT-PCR or API 20E techniques are ideal for differentiation of these microbes.

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Xiang, Fu, Liqing Li, Wenwen Jin, and Longjiang Yu. "Effect of DNA Methylation on 18S rRNA Gene Sequences during Culture of Taxus chinensis Cells." Zeitschrift für Naturforschung C 64, no. 5-6 (June 1, 2009): 418–20. http://dx.doi.org/10.1515/znc-2009-5-620.

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Cell suspension culture has rapidly become an alternative source of taxol, an anticancer compound. To investigate the role of DNA methylation in the cultural course of Taxus chinensis cells, analyses of 18S rRNA gene sequences of cultured T. chinensis cells and related species were conducted. The phylogenetic analysis of 18S rRNA gene sequences indicated that HG-1 (the cultured T. chinensis cells), like T. mairei (the natural variety of T. chinensis), should be a new variety of T. chinensis, and cell culture can change the 18S rRNA gene sequence at the level of species despite 18S rRNA is the most conserved gene. The analyses of the CpG and TpG+CpA relative abundance and GC content of the 18S rRNA gene sequences made clear that DNA methylation contributed to changes of the 18S rRNA gene sequence of HG-1 at the level of species, which can make HG-1 to become a new variety of T. chinensis.

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Chalker, Victoria J., and Joe Brownlie. "Taxonomy of the canine Mollicutes by 16S rRNA gene and 16S/23S rRNA intergenic spacer region sequence comparison." International Journal of Systematic and Evolutionary Microbiology 54, no. 2 (March 1, 2004): 537–42. http://dx.doi.org/10.1099/ijs.0.02869-0.

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The taxonomy of canine Mollicutes is described, based on phylogenetic analysis of 16S rRNA gene and 16S/23S rRNA intergenic spacer (IGS) region sequences. The nucleotide sequences of the 16S rRNA gene of two untyped mycoplasmas and the IGS region of 11 Mycoplasma species were determined and used for phylogenetic analysis. The two untyped Mycoplasma strains, HRC 689 and VJC 358, were found to be distinct from all known canine mycoplasmas and all published mycoplasma 16S rRNA gene sequences.

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Singh, Mahipal, Pushpa Yadav, and Anand K. Yadav. "Cloning and Sequence Analysis of 5S Ribosomal RNA Gene(s) and Associated Intergenic Spacer Regions in Carica Species." International Journal of Biology 13, no. 1 (March 30, 2021): 1. http://dx.doi.org/10.5539/ijb.v13n1p1.

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The 5S ribosomal RNA gene(s) and their associated intergenic spacer regions were amplified from Carica papaya and Carica quercifolia by polymerase chain reaction. Both Carica species exhibited differently sized amplification products. Sequence analysis of these PCR products revealed that the 5S rRNA genes are arranged as tandem repeats in these regions. Sequence data revealed that the 5S rRNA gene from Carica quercifolia was 119 bp in length. Sequence variation was observed in various 5S rRNA gene copies cloned from Carica quercifolia. Only truncated 5S rRNA gene but with its full spacer region was recovered from Carica papaya. Interestingly, intergenic spacer sequence cloned from Carica papaya contained two specific domains, a 30bp “CT” rich domain exhibiting 95-100% homology to several human chromosomes and a domain matching with mitrocomin precursor, a photo-protein from Mitrocoma cellularia. The role of 5S rRNA gene and their spacer regions in discerning the germplasm and in adaptation of the species is discussed.

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Oliveira, Cássia, Lauren Gunderman, Cathryn Coles, Jason Lochmann, Megan Parks, Ethan Ballard, Galina Glazko, Yasir Rahmatallah, Alan Tackett, and David Thomas. "16S rRNA Gene-Based Metagenomic Analysis of Ozark Cave Bacteria." Diversity 9, no. 3 (August 15, 2017): 31. http://dx.doi.org/10.3390/d9030031.

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Sharma, Anju, Satish K. Sharma, Kiran Rana, and Anil Kumar Verma. "Phylogenetic Analysis of 28S rRNA Gene of Indigenous Xiphinema pachydermum." International Journal of Current Microbiology and Applied Sciences 8, no. 07 (July 10, 2019): 1960–68. http://dx.doi.org/10.20546/ijcmas.2019.807.233.

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Ding, Linxian, and Akira Yokota. "Phylogenetic analysis of the genusAquaspirillumbased on 16S rRNA gene sequences." FEMS Microbiology Letters 212, no. 2 (July 2002): 165–69. http://dx.doi.org/10.1111/j.1574-6968.2002.tb11261.x.

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Peng, Zhihua, and Erik Bateman. "Analysis of the 5S rRNA gene promoter from Acanthamoeba castellanii." Molecular Microbiology 52, no. 4 (April 2, 2004): 1123–32. http://dx.doi.org/10.1111/j.1365-2958.2004.04034.x.

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Takeuchi, Mariko, and Akira Yokota. "Phylogenetic analysis of the genusMicrobacteriumbased on 16S rRNA gene sequences." FEMS Microbiology Letters 124, no. 1 (November 1994): 11–16. http://dx.doi.org/10.1111/j.1574-6968.1994.tb07254.x.

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Bimi, L., A. R. Freeman, M. L. Eberhard, E. Ruiz-Tiben, and N. J. Pieniazek. "DifferentiatingDracunculusmedinensisfromD.insignis, by the sequence analysis of the 18S rRNA gene." Annals of Tropical Medicine & Parasitology 99, no. 5 (July 2005): 511–17. http://dx.doi.org/10.1179/136485905x51355.

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Forsum, U., H.-J. Monstein, and A. Tiveljung. "The genus Mobiluncus: 16S rRNA gene analysis versus phenotypic characteristics." International Journal of STD & AIDS 8, no. 1_suppl (December 1997): 7–8. http://dx.doi.org/10.1258/0956462971919480.

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Andriiash, G. S. "GENE 16S RRNA SEQUENCE PHYLOGENETIC ANALYSIS OF LYSINE PRODUCERS STRAINS." Biotechnologia acta 7, no. 6 (2014): 40–45. http://dx.doi.org/10.15407/biotech7.06.040.

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Pang, H., and H. H. Winkler. "Transcriptional analysis of the 16s rRNA gene in Rickettsia prowazekii." Journal of bacteriology 178, no. 6 (1996): 1750–55. http://dx.doi.org/10.1128/jb.178.6.1750-1755.1996.

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Go, Yuk-Seak, Suk-Kyun Han, Il-Gyu Lee, and Tae-Young Ahn. "Diversity of the domain Archaea as determined by 16S rRNA gene analysis in the sediments of Lake Soyang." Fundamental and Applied Limnology 149, no. 3 (November 14, 2000): 459–66. http://dx.doi.org/10.1127/archiv-hydrobiol/149/2000/459.

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Valiunas, Deividas, Rasa Jomantiene, and Robert Edward Davis. "Evaluation of the DNA-dependent RNA polymerase β-subunit gene (rpoB) for phytoplasma classification and phylogeny." International Journal of Systematic and Evolutionary Microbiology 63, Pt_10 (October 1, 2013): 3904–14. http://dx.doi.org/10.1099/ijs.0.051912-0.

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Phytoplasmas are classified into 16Sr groups and subgroups and ‘Candidatus Phytoplasma ’ species, largely or entirely based on analysis of 16S rRNA gene sequences. Yet, distinctions among closely related ‘Ca. Phytoplasma ’ species and strains based on 16S rRNA genes alone have limitations imposed by the high degree of rRNA nucleotide sequence conservation across diverse phytoplasma lineages and by the presence in a phytoplasma genome of two, sometimes sequence-heterogeneous, copies of the 16S rRNA gene. Since the DNA-dependent RNA polymerase (DpRp) β-subunit gene (rpoB) exists as a single copy in the phytoplasma genome, we explored the use of rpoB for phytoplasma classification and phylogenetic analysis. We sequenced a clover phyllody (CPh) phytoplasma genetic locus containing ribosomal protein genes, a complete rpoB gene and a partial rpoC gene encoding the β′-subunit of DpRp. Primers and reaction conditions were designed for PCR-mediated amplification of rpoB gene fragments from diverse phytoplasmas. The rpoB gene sequences from phytoplasmas classified in groups 16SrI, 16SrII, 16SrIII, 16SrX and 16SrXII were subjected to sequence similarity and phylogenetic analyses. The rpoB gene sequences were more variable than 16S rRNA gene sequences, more clearly distinguishing among phytoplasma lineages. Phylogenetic trees based on 16S rRNA and rpoB gene sequences had similar topologies, and branch lengths in the rpoB tree facilitated distinctions among closely related phytoplasmas. Virtual RFLP analysis of rpoB gene sequences also improved distinctions among closely related lineages. The results indicate that the rpoB gene provides a useful additional marker for phytoplasma classification that should facilitate studies of disease aetiology and epidemiology.

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Dixit, Kunal. "Benchmarking of 16S rRNA gene databases using known strain sequences." Bioinformation 17, no. 3 (March 31, 2021): 377–91. http://dx.doi.org/10.6026//97320630017377.

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16S rRNA gene analysis is the most convenient and robust method for microbiome studies. Inaccurate taxonomic assignment of bacterial strains could have deleterious effects as all downstream analyses rely heavily on the accurate assessment of microbial taxonomy. The use of mock communities to check the reliability of the results has been suggested. However, often the mock communities used in most of the studies represent only a small fraction of taxa and are used mostly as validation of sequencing run to estimate sequencing artifacts. Moreover, a large number of databases and tools available for classification and taxonomic assignment of the 16S rRNA gene make it challenging to select the best-suited method for a particular dataset. In the present study, we used authentic and validly published 16S rRNA gene type strain sequences (full length, V3-V4 region) and analyzed them using a widely used QIIME pipeline along with different parameters of OTU clustering and QIIME compatible databases. Data Analysis Measures (DAM) revealed a high discrepancy in ratifying the taxonomy at different taxonomic hierarchies. Beta diversity analysis showed clear segregation of different DAMs. Limited differences were observed in reference data set analysis using partial (V3-V4) and full-length 16S rRNA gene sequences, which signify the reliability of partial 16S rRNA gene sequences in microbiome studies. Our analysis also highlights common discrepancies observed at varioustaxonomic levels using various methods and databases.

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Dixit, Kunal. "Benchmarking of 16S rRNA gene databases using known strain sequences." Bioinformation 17, no. 3 (March 31, 2021): 377–91. http://dx.doi.org/10.6026/97320630017377.

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16S rRNA gene analysis is the most convenient and robust method for microbiome studies. Inaccurate taxonomic assignment of bacterial strains could have deleterious effects as all downstream analyses rely heavily on the accurate assessment of microbial taxonomy. The use of mock communities to check the reliability of the results has been suggested. However, often the mock communities used in most of the studies represent only a small fraction of taxa and are used mostly as validation of sequencing run to estimate sequencing artifacts. Moreover, a large number of databases and tools available for classification and taxonomic assignment of the 16S rRNA gene make it challenging to select the best-suited method for a particular dataset. In the present study, we used authentic and validly published 16S rRNA gene type strain sequences (full length, V3-V4 region) and analyzed them using a widely used QIIME pipeline along with different parameters of OTU clustering and QIIME compatible databases. Data Analysis Measures (DAM) revealed a high discrepancy in ratifying the taxonomy at different taxonomic hierarchies. Beta diversity analysis showed clear segregation of different DAMs. Limited differences were observed in reference data set analysis using partial (V3-V4) and full-length 16S rRNA gene sequences, which signify the reliability of partial 16S rRNA gene sequences in microbiome studies. Our analysis also highlights common discrepancies observed at varioustaxonomic levels using various methods and databases.

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Thompson, Cristiane C., Fabiano L. Thompson, Ana Carolina P. Vicente, and Jean Swings. "Phylogenetic analysis of vibrios and related species by means of atpA gene sequences." International Journal of Systematic and Evolutionary Microbiology 57, no. 11 (November 1, 2007): 2480–84. http://dx.doi.org/10.1099/ijs.0.65223-0.

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We investigated the use of atpA gene sequences as alternative phylogenetic and identification markers for vibrios. A fragment of 1322 bp (corresponding to approximately 88 % of the coding region) was analysed in 151 strains of vibrios. The relationships observed were in agreement with the phylogeny inferred from 16S rRNA gene sequence analysis. For instance, the Vibrio cholerae, Vibrio halioticoli, Vibrio harveyi and Vibrio splendidus species groups appeared in the atpA gene phylogenetic analyses, suggesting that these groups may be considered as separate genera within the current Vibrio genus. Overall, atpA gene sequences appeared to be more discriminatory for species differentiation than 16S rRNA gene sequences. 16S rRNA gene sequence similarities above 97 % corresponded to atpA gene sequences similarities above 80 %. The intraspecies variation in the atpA gene sequence was about 99 % sequence similarity. The results showed clearly that atpA gene sequences are a suitable alternative for the identification and phylogenetic study of vibrios.

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Beumer, Amy, and Jayne B. Robinson. "A Broad-Host-Range, Generalized Transducing Phage (SN-T) Acquires 16S rRNA Genes from Different Genera of Bacteria." Applied and Environmental Microbiology 71, no. 12 (December 2005): 8301–4. http://dx.doi.org/10.1128/aem.71.12.8301-8304.2005.

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ABSTRACT Genomic analysis has revealed heterogeneity among bacterial 16S rRNA gene sequences within a single species; yet the cause(s) remains uncertain. Generalized transducing bacteriophages have recently gained recognition for their abundance as well as their ability to affect lateral gene transfer and to harbor bacterial 16S rRNA gene sequences. Here, we demonstrate the ability of broad-host-range, generalized transducing phages to acquire 16S rRNA genes and gene sequences. Using PCR and primers specific to conserved regions of the 16S rRNA gene, we have found that generalized transducing phages (D3112, UT1, and SN-T), but not specialized transducing phages (D3), acquired entire bacterial 16S rRNA genes. Furthermore, we show that the broad-host-range, generalized transducing phage SN-T is capable of acquiring the 16S rRNA gene from two different genera: Sphaerotilus natans, the host from which SN-T was originally isolated, and Pseudomonas aeruginosa. In sequential infections, SN-T harbored only 16S rRNA gene sequences of the final host as determined by restriction fragment length polymorphism analysis. The frequency of 16S rRNA gene sequences in SN-T populations was determined to be 1 × 10−9 transductants/PFU. Our findings further implicate transduction in the horizontal transfer of 16S rRNA genes between different species or genera of bacteria.

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Pegova, Anna N., Elena D. Krasnova, and Vladimir V. Aleshin. "Evidence from the small and large ribosomal RNA structure suggests that Anoplostoma rectospiculum Gal'tsova, 1976 (Nematoda: Anoplostomatidae) is a member of the superfamily Enoploidea, not Oncholaimoidea." Nematology 6, no. 3 (2004): 413–21. http://dx.doi.org/10.1163/1568541042360474.

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Abstract Analyses of the primary structure of the 18S rRNA gene and D3 segment of the 28S rRNA, as well as evidence from the secondary structure of the SSU rRNA V7 region, suggest that Anoplostoma rectospiculum (Anoplostomatidae) has closer relationships to the family Enoplidae than to the Oncholaimidae. In phylogenetic trees derived from full length SSU rRNA gene and partial LSU rRNA gene (D3 expansion segment) sequence analyses, A. rectospiculum exhibits long branches. The associated artefacts of long branch attraction (LBA) are circumvented because of the presence of an undoubted molecular synapomorphy – a low homoplastic 1. b. p. insertion in helix 43 of the SSU rRNA which is shared jointly by Anoplostomatidae and Enoplidae. Analysis of low homoplastic apomorphic characters is considered to be a tool for testing phylogenies against LBA artefacts.

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Wang, Li-Ting, Fwu-Ling Lee, Chun-Ju Tai, and Hiroaki Kasai. "Comparison of gyrB gene sequences, 16S rRNA gene sequences and DNA–DNA hybridization in the Bacillus subtilis group." International Journal of Systematic and Evolutionary Microbiology 57, no. 8 (August 1, 2007): 1846–50. http://dx.doi.org/10.1099/ijs.0.64685-0.

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The Bacillus subtilis group comprises eight closely related species that are indistinguishable from one another by 16S rRNA gene sequence analysis. Therefore, the gyrB gene, which encodes the subunit B protein of DNA gyrase, was selected as an alternative phylogenetic marker. To determine whether gyrB gene sequence analysis could be used for phylogenetic analysis and species identification of members of the B. subtilis group, the congruence of gyrB grouping with both 16S rRNA gene sequencing and DNA–DNA hybridization data was evaluated. Ranges of gyrB nucleotide and translated amino acid sequence similarities among the eight type strains were 75.4–95.0 % and 88.5–99.2 %, respectively, whereas 16S rRNA gene sequence similarities were 98.1–99.8 %. Results showed that gyrB gene sequences provide higher resolution than 16S rRNA gene sequences. The classification achieved by gyrB sequence analysis was in agreement with results obtained with DNA–DNA hybridization. It is concluded that the gyrB gene may be an efficient alternative target for identification and taxonomic analysis of members of the B. subtilis group.

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Journal articles on the topic 'RRNA gene analysis'

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