scholarly journals BOPAL 2.0 and a study of tRNA and rRNA gene evolution in Clostridium

2021 ◽  
Author(s):  
Meghan Chua ◽  
Anthony Tan ◽  
Olivier Tremblay-Savard
Keyword(s):  
Gene Evolution ◽  
Rrna Genes ◽  
Genome Comparison ◽  
Rrna Gene ◽  
Context Aware ◽  
Bacterial Genomes ◽  
Orthologous Genes ◽  
Ancestral Gene ◽  
Wide Range ◽  
Alignment Step

We present BOPAL 2.0, an improved version of the BOPAL algorithm for the evolutionary history inference of tRNA and rRNA genes in bacterial genomes. Our approach can infer complete evolutionary scenarios and ancestral gene orders on a phylogeny and considers a wide range of events such as duplications, deletions, substitutions, inversions and transpositions. It is based on the fact that tRNA and rRNA genes are often organized in operons/clusters in bacteria, and this information is used to help identify orthologous genes for each genome comparison. BOPAL 2.0 introduces new features, such as a triple-wise alignment step, context-aware singleton matching and a second pass of the algorithm. Evaluation on simulated datasets shows that BOPAL 2.0 outperforms the original BOPAL in terms of the accuracy of inferred events and ancestral genomes. We also present a study of the tRNA/rRNA gene evolution in the Clostridium genus, in which the organization of these genes is very divergent. Our results indicate that tRNA and rRNA genes in Clostridium have evolved through numerous duplications, losses, transpositions and substitutions, but very few inversions were inferred.

scholarly journals Phylogenetic Relationship Among Brackishwater Vibrio Species

2020 ◽  
Vol 16 ◽  
pp. 117693432090328
Author(s):  
J Ashok Kumar ◽  
K Vinaya Kumar ◽  
S Avunje ◽  
V Akhil ◽  
S Ashok ◽  
...  
Keyword(s):  
16S Rrna ◽  
Vibrio Vulnificus ◽  
Single Copy ◽  
Vibrio Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Nucleotide Polymorphisms ◽  
Orthologous Genes ◽  
Phylogenetic Relations

Vibriosis is regarded as an important disease of penaeid shrimps affecting larvae in hatcheries. Among the Vibrio species, Vibrio parahaemolyticus, Vibrio vulnificus, Vibrio furnissii, Vibrio campbellii, Vibrio harveyi, Vibrio alginolyticus, and Vibrio anguillarum are often associated with diseases in finfish and shellfish of brackishwater ecosystem. Accurate species differentiating methods for the organisms present in an ecosystem are required for precise classification of the species and to take steps for their management. Conventional methods like 16s rRNA phylogeny and multilocus sequence typing (MLST) have often failed to correctly identify Vibrio species. This has necessitated a comprehensive investigation on methodologies available to distinguish Vibrio species associated with brackishwater aquaculture system. To achieve this, 35 whole genomes belonging to 7 Vibrio species were subjected to phylogenetic analysis based on 16s rRNA gene, MLST genes, single-copy orthologous genes, and single-nucleotide polymorphisms. In addition, genome-based similarity indices like average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) were computed as confirmatory tests to verify the phylogenetic relations. There were some misclassifications occurred regarding phylogenetic relations based on 16s rRNA genes and MLST genes, while phylogeny with single-copy orthologous genes produced accurate species-level clustering. Study reveals that the species identification based on whole genome-based estimates or genome-wide variants are more precise than the ones done with single or subset of genes.

Molecular identification ofSarcocystisspp. helped to define the origin of green pythons (Morelia viridis) confiscated in Germany

Parasitology ◽  
2013 ◽  
Vol 141 (5) ◽  
pp. 646-651 ◽  
Author(s):  
GASTÓN MORÉ ◽  
NIKOLA PANTCHEV ◽  
DALAND C. HERRMANN ◽  
MAJDA GLOBOKAR VRHOVEC ◽  
SABINE ÖFNER ◽  
...  
Keyword(s):  
18S Rrna ◽  
Sequence Data ◽  
18S Rrna Gene ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Intermediate Hosts ◽  
Apicomplexan Parasites ◽  
Large Numbers ◽  
Wide Range ◽  
18S Rrna Genes

SUMMARYSarcocystisspp. represent apicomplexan parasites. They usually have a heteroxenous life cycle. Around 200 species have been described, affecting a wide range of animals worldwide, including reptiles. In recent years, large numbers of reptiles have been imported into Europe as pets and, as a consequence, animal welfare and species protection issues emerged. A sample of pooled feces from four confiscated green pythons (Morelia viridis) containingSarcocystisspp. sporocysts was investigated. These snakes were imported for the pet trade and declared as being captive-bred. Full length 18S rRNA genes were amplified, cloned into plasmids and sequenced. Two differentSarcocystisspp. sequences were identified and registered asSarcocystissp. fromM. viridisin GenBank. Both showed a 95–97% sequence identity with the 18S rRNA gene ofSarcocystis singaporensis.Phylogenetic analysis positioned these sequences together with otherSarcocystisspp. from snakes and rodents as definitive and intermediate hosts (IH), respectively. Sequence data and also the results of clinical and parasitological examinations suggest that the snakes were definitive hosts forSarcocystisspp. that circulate in wild IH. Thus, it seems unlikely that the infected snakes had been legally bred. Our research shows that information on the infection of snakes withSarcocystisspp. may be used to assess compliance with regulations on the trade with wildlife species.

scholarly journals A Comparative Study: Taxonomic Grouping of Alkaline Protease Producing Bacilli

2017 ◽  
Vol 66 (1) ◽  
pp. 39-56
Author(s):  
Nilgun Tekin ◽  
Arzu Coleri Cihan ◽  
Basar Karaca ◽  
Cumhur Cokmus
Keyword(s):  
16S Rrna ◽  
Alkaline Protease ◽  
Phylogenetic Analyses ◽  
Molecular Techniques ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Protease Production ◽  
Rrna Gene ◽  
Wide Range ◽  
Its Pcr

Alkaline proteases have biotechnological importance due to their activity and stability at alkaline pH. 56 bacteria, capable of growing under alkaline conditions were isolated and their alkaline protease activities were carried out at different parameters to determine their optimum alkaline protease production conditions. Seven isolates were showed higher alkaline protease production capacity than the reference strains. The highest alkaline protease producing isolates (103125 U/g), E114 and C265, were identified as Bacillus licheniformis with 99.4% and Bacillus mojavensis 99.8% based on 16S rRNA gene sequence similarities, respectively. Interestingly, the isolates identified as Bacillus safensis were also found to be high alkaline protease producing strains. Genotypic characterizations of the isolates were also determined by using a wide range of molecular techniques (ARDRA, ITS-PCR, (GTG)5-PCR, BOX-PCR). These different techniques allowed us to differentiate the alkaliphilic isolates and the results were in concurrence with phylogenetic analyses of the 16S rRNA genes. While ITS-PCR provided the highest correlation with 16S rRNA groups, (GTG)5-PCR showed the highest differentiation at species and intra-species level. In this study, each of the biotechnologically valuable alkaline protease producing isolates was grouped into their taxonomic positions with multi-genotypic analyses.

Morphological and molecular characterisation of several Paratylenchus Micoletzky, 1922 (Tylenchida: Paratylenchidae) species from South Africa and USA, together with some taxonomic notes

Nematology ◽  
2014 ◽  
Vol 16 (3) ◽  
pp. 323-358 ◽  
Author(s):  
Esther Van den Berg ◽  
Esther Van den Berg ◽  
Louwrens R. Tiedt ◽  
Esther Van den Berg ◽  
Louwrens R. Tiedt ◽  
...  
Keyword(s):  
South Africa ◽  
Rrna Genes ◽  
Morphological Identification ◽  
Rrna Gene ◽  
28S Rrna ◽  
Molecular Characterisation ◽  
Electron Microscopic ◽  
Wide Range ◽  
Its Rrna Gene ◽  
Its Rrna

Pin nematodes of the genus Paratylenchus are widely distributed across the world and associated with many plant species. Morphological identification of Paratylenchus species is a difficult task because it relies on many characters with a wide range of intraspecific variation. In this study we provide morphological and molecular characterisation of several pin nematodes: Paratylenchus aquaticus, P. dianthus, P. hamatus, P. nanus and P. straeleni, collected in different states of the USA and South Africa. Paratylenchus aquaticus is reported from South Africa and Hawaii and P. nanus is found from South Africa for the first time. Morphological descriptions, morphometrics, light and scanning electron microscopic photos and drawings are given for these species. Molecular characterisation of nematodes using the D2-D3 of 28S rRNA and ITS rRNA gene sequence revealed that samples morphologically identified as P. aquaticus, P. hamatus and P. nanus indeed represent species complexes containing several species. Sequences of the rRNA genes are also provided for several unidentified Paratylenchus. Phylogenetic relationships within the genus Paratylenchus are given as inferred from the analyses of the D2-D3 of 28S rRNA and ITS rRNA gene sequences. We present here the most complete phylogenetic analysis of the genus.

scholarly journals Computer-simulated RFLP analysis of 16S rRNA genes: identification of ten new phytoplasma groups

2007 ◽  
Vol 57 (8) ◽  
pp. 1855-1867 ◽  
Author(s):  
Wei Wei ◽  
Robert E. Davis ◽  
Ing-Ming Lee ◽  
Yan Zhao
Keyword(s):  
16S Rrna ◽  
Classification Scheme ◽  
Rflp Analysis ◽  
Plant Diseases ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Similarity Coefficients ◽  
Wide Range

Phytoplasmas are cell wall-less bacteria that cause numerous plant diseases. As no phytoplasma has been cultured in cell-free medium, phytoplasmas cannot be differentiated and classified by the traditional methods which are applied to culturable prokaryotes. Over the past decade, the establishment of a phytoplasma classification scheme based on 16S rRNA restriction fragment length polymorphism (RFLP) patterns has enabled the accurate and reliable identification and classification of a wide range of phytoplasmas. In the present study, we expanded this classification scheme through the use of computer-simulated RFLP analysis, achieving rapid differentiation and classification of phytoplasmas. Over 800 publicly available phytoplasma 16S rRNA gene sequences were aligned using the clustal_x program and the aligned 1.25 kb fragments were exported to pDRAW32 software for in silico restriction digestion and virtual gel plotting. Based on distinctive virtual RFLP patterns and calculated similarity coefficients, phytoplasma strains were classified into 28 groups. The results included the classification of hundreds of previously unclassified phytoplasmas and the delineation of 10 new phytoplasma groups representing three recently described and seven novel putative ‘Candidatus Phytoplasma’ taxa.

scholarly journals Biochemical, molecular and antibiotic resistance profile of multi-potential toluene metabolizing bacteria isolated from tannery effluents

2018 ◽  
Author(s):  
Fatima Muccee ◽  
Samina Ejaz
Keyword(s):  
Phylogenetic Trees ◽  
Biochemical Characterization ◽  
Similarity Index ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Growth Curve Analysis ◽  
Biomass Hydrolysis ◽  
Biochemical Tests ◽  
Tannery Effluents ◽  
Wide Range

AbstractThe focus of present study was to isolate and characterize bacteria which can be effectively used for toluene, a highly recalcitrant pollutant, bioremediation. For isolation of bacteria from the tannery effluents selective enrichment and serial dilution methods were employed. The isolated bacteria were subjected to growth curve analysis, estimation of toluene removal efficiencies, biochemical tests, antibiotic sensitivity assays and molecular characterization based upon 16S rRNA gene. The rRNA genes sequences were analyzed through BLAST to determine similarity index of isolates with bacterial database sequences. To trace the evolutionary history, phylogenetic trees were constructed using MEGA version 7. Total twenty toluene metabolizing bacteria (IUBT1-2, 4-12, 16, 19, 21, 23-26, 28 and 30) were isolated and characterized. Their rRNA gene sequences have been submitted to Genbank. Fifteen of the twenty isolates showed homology toBrevibacillus agristrain NBRC 15538, four found similar toBacillus paralicheniformisstrain KJ-16 and one homologous toBurkholderia latastrain 383. All bacterial isolates were resistant to chloramphenicol but sensitive to teicoplanin and linezolid. However, few (i. e.; IUBT9 and 26) were sensitive to oxacillin. Biochemical characterization indicated all bacteria positive for alkaline phosphatases (100%). While many were found positive for p-nitrophenyl N-acetyl β, D-glucosaminidase (35%), hydroxyproline β-naphthylaminopeptidase (15%), esculinase (65%), mannitol (75%), sorbitol (95%) and inulin (90%) fermentation. Biochemical profile suggests the use of isolated bacteria for future exploitation in several fields like bioremediation of toluene, ethanol production, biomass hydrolysis, biosensors, biofertilizers, as a marker for milk pasteurization in dairy industries and evaluation of soil quality.ImportanceToluene is a highly toxic environmental pollutant. We have isolated bacteria which can be effectively used for the removal of toluene from environmental resources. Moreover, these bacteria are capable to produce many valuable enzymes which can be used in many industrial processes for the production of a wide range of products. Further study may help to exploit these bacterial for the benefit of humanity.

scholarly journals PCR effects of melting temperature adjustment of individual primers in degenerate primer pools

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6570 ◽  
Author(s):  
Ankur Naqib ◽  
Trisha Jeon ◽  
Kevin Kunstman ◽  
Weihua Wang ◽  
Yiding Shen ◽  
...  
Keyword(s):  
Microbial Community ◽  
Temperature Variation ◽  
Melting Temperature ◽  
Degenerate Primer ◽  
Microbial Community Analysis ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Melting Temperatures ◽  
Wide Range

Deep sequencing of small subunit ribosomal RNA (SSU rRNA) gene amplicons continues to be the most common approach for characterization of complex microbial communities. PCR amplifications of conserved regions of SSU rRNA genes often employ degenerate pools of primers to enable targeting of a broad spectrum of organisms. One little noticed feature of such degenerate primer sets is the potential for a wide range of melting temperatures between the primer variants. The melting temperature variation of primers in a degenerate pool could lead to variable amplification efficiencies and PCR bias. Thus, we sought to adjust the melting temperature of each primer variant individually. Individual primer modifications were used to reduce theoretical melting temperature variation between primers, as well as to introduce inter-cluster nucleotide diversity during Illumina sequencing of primer regions. We demonstrate here the suitability of such primers for microbial community analysis. However, no substantial differences in microbial community structure were revealed when using primers with adjusted melting temperatures, though the optimal annealing temperature decreased.

scholarly journals Amplicon sequence variants artificially split bacterial genomes into separate clusters

2021 ◽  
Author(s):  
Patrick D. Schloss
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Genome ◽  
Full Length ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Bacterial Genomes ◽  
A Genome ◽  
The 16S Rrna Gene

AbstractAmplicon sequencing variants (ASVs) have been proposed as an alternative to operational taxonomic units (OTUs) for analyzing microbial communities. ASVs have grown in popularity, in part, because of a desire to reflect a more refined level of taxonomy since they do not cluster sequences based on a distance-based threshold. However, ASVs and the use of overly narrow thresholds to identify OTUs increase the risk of splitting a single genome into separate clusters. To assess this risk, I analyzed the intragenomic variation of 16S rRNA genes from the bacterial genomes represented in a rrn copy number database, which contained 20,427 genomes from 5,972 species. As the number of copies of the 16S rRNA gene increased in a genome, the number of ASVs also increased. There was an average of 0.58 ASVs per copy of the 16S rRNA gene for full length 16S rRNA genes. It was necessary to use a distance threshold of 5.25% to cluster full length ASVs from the same genome into a single OTU with 95% confidence for genomes with 7 copies of the 16S rRNA, such as E. coli. This research highlights the risk of splitting a single bacterial genome into separate clusters when ASVs are used to analyze 16S rRNA gene sequence data. Although there is also a risk of clustering ASVs from different species into the same OTU when using broad distance thresholds, those risks are of less concern than artificially splitting a genome into separate ASVs and OTUs.

Molecular Assessment of Microbial Diversity and Community Structure at Uranium Mines of Jaduguda, India

2007 ◽  
Vol 20-21 ◽  
pp. 413-416 ◽  
Author(s):  
Pinaki Sar ◽  
Paltu K. Dhal ◽  
Ekramul Islam ◽  
Sufia K. Kazy
Keyword(s):  
16S Rrna ◽  
Microbial Diversity ◽  
Molecular Level ◽  
Restriction Analysis ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Uranium Mine ◽  
Rrna Gene ◽  
Wide Range ◽  
Mine Sites

Microbial diversity associated with uranium mine areas of Jaduguda, India has been investigated using a culture independent molecular approach. Soil samples collected from existing and proposed mine sites were analyzed for physicochemical parameters. Community DNA was extracted from five samples. Small subunit rRNA gene (16S rRNA) was PCR amplified using bacterial primers. The diversity of the total bacterial community was described at molecular level by amplified ribosomal DNA restriction analysis (ARDRA). Dominant bacterial groups (represents by OTUs) selected by ARDRA were identified by sequencing the 16S rRNA genes. From the bacterial rDNA clone library around 230 clones were used for further analysis. The unique OTUs and number of clones representing such OTUs were determined. Dominant OTUs were sequenced and identified. These phylotypes spanned a wide range within the bacterial domain occupying Proteobacteria, Acidobacteria, Bacteroidetes, Firmicutes, Cyanobacteria as major phyla. About 46 % of clones sequenced from various sites were identified as Proteobacteria. The present findings on microbial diversity at the molecular level are the first of its kind for uranium mine sites of India. Around 20 % of the clone sequences showed little affiliation with known taxa and probably represent new organisms adapted to this habitat.

Differentiation Of Clarias Batrachus, C. Gariepinus And Heteropneustes Fossilis By Pcr-Sequencing Of Mitochondrial 16s Rrna Gene

2015 ◽  
Vol 41 (1) ◽  
pp. 51-58
Author(s):  
Mohammad Shamimul Alam ◽  
Hawa Jahan ◽  
Rowshan Ara Begum ◽  
Reza M Shahjahan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Fish Larva ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Valuable Insight ◽  
Multiple Sequence ◽  
Pcr Rflp ◽  
Alternative Means

Heteropneustesfossilis, Clariasbatrachus and C. gariepinus are three major catfishes ofecological and economic importance. Identification of these fish species becomes aproblem when the usual external morphological features of the fish are lost or removed,such as in canned fish. Also, newly hatched fish larva is often difficult to identify. PCRsequencingprovides accurate alternative means of identification of individuals at specieslevel. So, 16S rRNA genes of three locally collected catfishes were sequenced after PCRamplification and compared with the same gene sequences available from othergeographical regions. Multiple sequence alignment of the 16S rRNA gene fragments ofthe catfish species has revealed polymorphic sites which can be used to differentiate thesethree species from one another and will provide valuable insight in choosing appropriaterestriction enzymes for PCR-RFLP based identification in future. Asiat. Soc. Bangladesh, Sci. 41(1): 51-58, June 2015

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