scholarly journals Genome Sequences of Gordonia terrae Bacteriophages Phinally and Vivi2

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
Welkin H. Pope ◽  
Kaitlyn C. Anderson ◽  
Charu Arora ◽  
Michael E. Bortz ◽  
George Burnet ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Genome Sequences ◽  
Share Sequence Similarity

Bacteriophages Phinally and Vivi2 were isolated from soil from Pittsburgh, Pennsylvania, USA, using host Gordonia terrae 3612. The Phinally and Vivi2 genomes are 59,265 bp and 59,337 bp, respectively, and share sequence similarity with each other and with GTE6. Fewer than 25% of the 87 to 89 putative genes have predictable functions.

scholarly journals Identification of Epidemiological Traits by Analysis of SARS−CoV−2 Sequences

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 764
Author(s):  
Bohu Pan ◽  
Zuowei Ji ◽  
Sugunadevi Sakkiah ◽  
Wenjing Guo ◽  
Jie Liu ◽  
...  
Keyword(s):  
Clustering Analysis ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Host Age ◽  
Hierarchical Clustering Analysis ◽  
Genome Sequences ◽  
Geographic Patterns ◽  
Rapid Spread ◽  
Pairwise Sequence Similarity ◽  
Sequence Similarity Analysis

Severe acute respiratory syndrome coronavirus 2 (SARS−CoV−2) has caused the ongoing global COVID-19 pandemic that began in late December 2019. The rapid spread of SARS−CoV−2 is primarily due to person-to-person transmission. To understand the epidemiological traits of SARS−CoV−2 transmission, we conducted phylogenetic analysis on genome sequences from >54K SARS−CoV−2 cases obtained from two public databases. Hierarchical clustering analysis on geographic patterns in the resulting phylogenetic trees revealed a co-expansion tendency of the virus among neighboring countries with diverse sources and transmission routes for SARS−CoV−2. Pairwise sequence similarity analysis demonstrated that SARS−CoV−2 is transmitted locally and evolves during transmission. However, no significant differences were seen among SARS−CoV−2 genomes grouped by host age or sex. Here, our identified epidemiological traits provide information to better prevent transmission of SARS−CoV−2 and to facilitate the development of effective vaccines and therapeutics against the virus.

scholarly journals Complete Genome Sequences of Six Legionella pneumophila Isolates from Two Collocated Outbreaks of Legionnaires’ Disease in 2005 and 2008 in Sarpsborg/Fredrikstad, Norway

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Marius Dybwad ◽  
Tone Aarskaug ◽  
Else-Marie Fykse ◽  
Elisabeth Henie Madslien ◽  
Janet Martha Blatny
Keyword(s):  
Comparative Genomics ◽  
Genetic Relationship ◽  
Legionella Pneumophila ◽  
Complete Genome ◽  
Sequence Similarity ◽  
Secretion Systems ◽  
Environmental Isolates ◽  
Genome Sequences ◽  
High Sequence Similarity ◽  
Legionnaires Disease

Here, we report the complete genome sequences of Legionella pneumophila isolates from two collocated outbreaks of Legionnaires’ disease in 2005 and 2008 in Sarpsborg/Fredrikstad, Norway. One clinical and two environmental isolates were sequenced from each outbreak. The genome of all six isolates consisted of a 3.36 Mb-chromosome, while the 2005 genomes featured an additional 68 kb-episome sharing high sequence similarity with the L. pneumophila Lens plasmid. All six genomes contained multiple mobile genetic elements including novel combinations of type-IVA secretion systems. A comparative genomics study will be launched to resolve the genetic relationship between the L. pneumophila isolates.

scholarly journals The SARS-CoV-2 ORF10 is not essential in vitro or in vivo in humans

2020 ◽  
Author(s):  
Katarzyna Pancer ◽  
Aleksandra Milewska ◽  
Katarzyna Owczarek ◽  
Agnieszka Dabrowska ◽  
Wojciech Branicki ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Hypothetical Protein ◽  
Open Reading Frames ◽  
N Gene ◽  
Coding Region ◽  
Protein Coding ◽  
Share Sequence Similarity ◽  
Genome Annotations

AbstractSARS-CoV-2 genome annotation revealed the presence of 10 open reading frames (ORFs), of which the last one (ORF10) is positioned downstream the N gene. It is a hypothetical gene, which was speculated to encode a 38 aa protein. This hypothetical protein does not share sequence similarity with any other known protein and cannot be associated with a function. While the role of this ORF10 was proposed, there is a growing evidence showing that the ORF10 is not a coding region.Here, we identified SARS-CoV-2 variants in which the ORF10 gene was prematurely terminated. The disease was not attenuated, and the transmissibility between humans was not hampered. Also in vitro, the strains replicated similarly, as the related viruses with the intact ORF10. Altogether, based on clinical observation and laboratory analyses, it appears that the ORF10 protein is not essential in humans. This observation further proves that the ORF10 should not be treated as the protein-coding gene, and the genome annotations should be amended.

scholarly journals Identification and capsular serotype sequetyping ofStreptococcus pneumoniaestrains

2018 ◽  
Author(s):  
Lucia Gonzales-Siles ◽  
Francisco Salvà-Serra ◽  
Anna Degerman ◽  
Rickard Nordén ◽  
Magnus Lindh ◽  
...  
Keyword(s):  
Related Species ◽  
Sequence Similarity ◽  
Culture Collection ◽  
Pcr Analysis ◽  
Correct Identification ◽  
Genome Sequences ◽  
Distance Method ◽  
Specific Product ◽  
Serotype Identification ◽  
Type Strains

ABSTRACTCorrect identification ofStreptococcus pneumoniae(pneumococcus) and differentiation from the closely related species of the Mitis group of the genusStreptococcus, as well as serotype identification, is important for monitoring disease epidemiology and assessing the impacts of pneumococcal vaccines. In this study, we assessed the taxonomic identifications of 422 publicly available genome sequences ofS. pneumoniae, S. pseudopneumoniaeandS. mitis, using different methods. Identification ofS. pneumoniae, by comparative analysis of thegroELpartial sequence, was possible and accurate, whereasS. pseudopneumoniaeandS. mitiscould be misclassified asS. pneumoniae, suggesting thatgroELis unreliable as a biomarker for differentiatingS. pneumoniaefrom its closest related species. The genome sequences ofS. pneumoniaeandS. pseudopneumoniaefulfilled the suggested thresholds of average nucleotide identity (ANI), i.e., > 95% genome sequence similarity to the sequence of respective type strains for identification of species, whereas none of theS. mitisgenome sequences fulfilled this criterion. However, ANI analyses of all sequencesversusall sequences allowed discrimination of the different species by clustering, with respect to species type strains. Thein silicoDNA-DNA distance method was also inconclusive for identification ofS. mitisgenome sequences, whereas presence of the “Xisco” gene proved to be a reliable biomarker forS. pneumoniaeidentification. Furthermore, we present an improved sequetyping protocol including two newly-designed internal sequencing primers with two PCRs, as well as an improved workflow for differentiation of serogroup 6 types. The proposed sequetyping protocol generates a more specific product by generating the whole gene PCR-product for sequencing, which increases the resolution for identification of serotypes. Validations of both protocols were performed with publicly availableS. pneumoniaegenome sequences, reference strains at the Culture Collection University of Gothenburg (CCUG), as well as with clinical isolates. The results were compared with serotype identifications, using real-time Q-PCR analysis, as well as the Quellung reaction or antiserum panel gel-precipitation. Our protocols provide a reliable diagnostic tool for taxonomic identification as well as serotype identification ofS. pneumoniae.

scholarly journals Taxonomy-aware, sequence similarity ranking reliably predicts phage-host relationships

2021 ◽  
Author(s):  
Andrzej Zielezinski ◽  
Jakub Barylski ◽  
Wojciech M. Karlowski
Keyword(s):  
Prediction Accuracy ◽  
Phage Genome ◽  
Sequence Similarity ◽  
Area Under The Curve ◽  
Genome Sequences ◽  
Host Interactions ◽  
Host Interaction ◽  
Percentage Points ◽  
Host Relationships ◽  
Blast Alignment

ABSTRACTMotivationSimilar regions in virus and host genomes provide strong evidence for phage-host interaction, and BLAST is one of the leading tools to predict hosts from phage sequences. However, BLAST-based host prediction has three limitations: (i) top-scoring prokaryotic sequences do not always point to the actual host, (ii) mosaic phage genomes may produce matches to many, typically related, bacteria, and (iii) phage and host sequences may diverge beyond the point where their relationship can be detected by a BLAST alignment.ResultsWe created an extension to BLAST, named Phirbo, that improves host prediction quality beyond what is obtainable from standard BLAST searches. The tool harnesses information concerning sequence similarity and bacteria relatedness to predict phage-host interactions. Phirbo was evaluated on two benchmark sets of known phage-host pairs, and it improved precision and recall by 25 percentage points, as well as the discriminatory power for the recognition of phage-host relationships by 10 percentage points (Area Under the Curve = 0.95). Phirbo also yielded a mean host prediction accuracy of 60% and 70% at the genus and family levels, respectively, representing a 5% improvement over BLAST. When using only a fraction of phage genome sequences (3 kb), the prediction accuracy of Phirbo was 5-11% higher than BLAST at all taxonomic levels.ConclusionOur results suggest that Phirbo is an effective, unsupervised tool for predicting phage-host relationships.AvailabilityPhirbo is available at https://github.com/aziele/phirbo.

scholarly journals Molecular Characterization of Novel Cucurbit Aphid Borne Yellows Virus Strains Infecting Squash and Watermelon in India

2022 ◽  
Author(s):  
Nagendran Krishnan ◽  
Shweta Kumari ◽  
Koshlendra Kumar Pandey ◽  
Sudhakar Pandey ◽  
Tusar Kanti Behera ◽  
...  
Keyword(s):  
Asian American ◽  
Recombinant Strain ◽  
Sequence Similarity ◽  
Uttar Pradesh ◽  
Amino Acid Sequences ◽  
Full Length ◽  
Rt Pcr ◽  
Genome Sequences ◽  
Species Demarcation Threshold ◽  
Full Length Genome

Abstract The pathogen responsible for yellowing and downward rolling of leaves of squash and watermelon plants from Uttar Pradesh state, India, was identified as probably strains of Cucurbit aphid-borne yellows virus (CABYV) through RT-PCR using universal Polerovirus primers followed by sequencing. The full-length genome sequences of an isolate from squash (POL-SQ - 5650 nt) and one from watermelon (POL-WM - 5647nt) were determined by sequencing the products from RT-PCR with six sets of primers with overlapping products. Sequence comparison and phylogenetic analysis showed that these isolates had closest identity with a recombinant strain obtained between CABYV and Melon aphid-borne yellows virus (MABYV) reported from Taiwan infecting Luffa aegyptiaca (CABYV-R-TW82) rather than other Asian, American, or European isolates. The deduced amino acid sequences of the P0, P1 and P1-P2 proteins showed >10% variation, whereas the P3, P4 and P3-P5 proteins showed <10% variation when compared to the corresponding proteins of other strains of CABYV worldwide. Thus, according to the Polerovirus species demarcation threshold, these new sequences should be regarded as representing strains of a novel previously undescribed Polerovirus species. However, based on their sequence similarity and phylogenetic grouping with the recombinant strain from Taiwan we suggest these sequences represent recombinant strains of CABYV. These are the first full-length genome sequences for CABYV strains from India and this study adds watermelon as host for CABYV in India.

scholarly journals The SARS-CoV-2 ORF10 is not essential in vitro or in vivo in humans

2020 ◽  
Vol 16 (12) ◽  
pp. e1008959
Author(s):  
Katarzyna Pancer ◽  
Aleksandra Milewska ◽  
Katarzyna Owczarek ◽  
Agnieszka Dabrowska ◽  
Michał Kowalski ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Hypothetical Protein ◽  
Open Reading Frames ◽  
N Gene ◽  
Coding Region ◽  
Protein Coding ◽  
Share Sequence Similarity ◽  
Genome Annotations

SARS-CoV-2 genome annotation revealed the presence of 10 open reading frames (ORFs), of which the last one (ORF10) is positioned downstream of the N gene. It is a hypothetical gene, which was speculated to encode a 38 aa protein. This hypothetical protein does not share sequence similarity with any other known protein and cannot be associated with a function. While the role of this ORF10 was proposed, there is growing evidence showing that the ORF10 is not a coding region. Here, we identified SARS-CoV-2 variants in which the ORF10 gene was prematurely terminated. The disease was not attenuated, and the transmissibility between humans was maintained. Also, in vitro, the strains replicated similarly to the related viruses with the intact ORF10. Altogether, based on clinical observation and laboratory analyses, it appears that the ORF10 protein is not essential in humans. This observation further proves that the ORF10 should not be treated as the protein-coding gene, and the genome annotations should be amended.

scholarly journals Genome Sequences of 19 Rhodococcus erythropolis Cluster CA Phages

2017 ◽  
Vol 5 (49) ◽  
Author(s):  
J. Alfred Bonilla ◽  
Sharon Isern ◽  
Ann M. Findley ◽  
Karen K. Klyczek ◽  
Scott F. Michael ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Complete Genome ◽  
Environmental Samples ◽  
Sequence Similarity ◽  
Rhodococcus Erythropolis ◽  
Genome Sequences ◽  
Content Type ◽  
Nucleotide Sequence Similarity

ABSTRACT We report the complete genome sequences of 19 cluster CA bacteriophages isolated from environmental samples using Rhodococcus erythropolis as a host. All of the phages are Siphoviridae, have similar genome lengths (46,314 to 46,985 bp) and G+C contents (58.5 to 58.8%), and share nucleotide sequence similarity.

scholarly journals Transcriptional Regulation of the virR Operon of the Intracellular Pathogen Rhodococcus equi

2007 ◽  
Vol 189 (14) ◽  
pp. 5082-5089 ◽  
Author(s):  
Gavin A. Byrne ◽  
Dean A. Russell ◽  
Xiaoxiao Chen ◽  
Wim G. Meijer
Keyword(s):  
Response Regulator ◽  
Sequence Similarity ◽  
High Growth ◽  
Rhodococcus Equi ◽  
Low Ph ◽  
Initiation Codon ◽  
Virulence Plasmid ◽  
Intracellular Pathogen ◽  
Share Sequence Similarity ◽  
A Site

ABSTRACT The virR operon, located on the virulence plasmid of the intracellular pathogen Rhodococcus equi, contains five genes, two of which (virR and orf8) encode transcriptional regulators. The first gene of the operon (virR), encoding a LysR-type transcriptional regulator, is transcribed at a constitutive low level, whereas the four downstream genes are induced by low pH and high growth temperature. Differential regulation of the virR operon genes could not be explained by differential mRNA stability, as there were no major differences in mRNA half-lives of the transcripts representing each of the five genes within the virR operon. Transcription of virR is driven by the P virR promoter, with a transcription start site 53 bp upstream of the virR initiation codon. The four genes downstream of virR are transcribed from P virR and from a second promoter, P orf5 , located 585 bp downstream of the virR initiation codon. VirR binds to a site overlapping the initiation codon of virR, resulting in negative autoregulation of the virR gene, explaining its low constitutive transcription level. The P orf5 promoter is induced by high temperature and low pH, thus explaining the observed differential gene expression of the virR operon. VirR has a positive effect on P orf5 activity, whereas the response regulator encoded by orf8 is not involved in regulating transcription of the virR operon. The P virR promoter is strikingly similar to those recognized by the principal sigma factors of Streptomyces and Mycobacterium, whereas the P orf5 promoter does not share sequence similarity with P virR . This suggests that P orf5 is recognized by an alternative sigma factor.

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