scholarly journals Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Novel Tern Atadenovirus

2021 ◽  
Vol 10 (1) ◽  
pp. 31
Author(s):  
Alina Matsvay ◽  
Marina Dyachkova ◽  
Ivan Mikhaylov ◽  
Daniil Kiselev ◽  
Anna Say ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Migratory Birds ◽  
Nucleotide Composition ◽  
Open Reading Frames ◽  
Common Tern ◽  
Base Pairs ◽  
Separate Species ◽  
Taxonomic Affiliation

Discovery and study of viruses carried by migratory birds are tasks of high importance due to the host’s ability to spread infectious diseases over significant distances. With this paper, we present and characterize the first complete genome sequence of atadenovirus from a tern bird (common tern, Sterna hirundo) preliminarily named tern atadenovirus 1 (TeAdV-1). TeAdV-1 genome is a linear double-stranded DNA molecule, 31,334 base pairs which contain 30 methionine-initiated open reading frames with gene structure typical for Atadenovirus genus, and the shortest known inverted terminal repeats (ITRs) within the Atadenovirus genus consisted of 25 bases. The nucleotide composition of the genome is characterized by a low G + C content (33.86%), which is the most AT-rich genome of known avian adenoviruses within Atadenovirus genus. The nucleotide sequence of the TeAdV-1 genome shows high divergence compared to known representatives of the Atadenovirus genus with the highest similarity to the duck atadenovirus 1 (53.7%). Phylogenetic analysis of the protein sequences of core genes confirms the taxonomic affiliation of the new representative to the genus Atadenovirus with the degree of divergence from the known representatives exceeding the interspecies distance within the genus. Thereby we proposed a novel TeAdV-1 to be considered as a separate species.

scholarly journals Complete Genome Sequence of Stenotrophomonas Phage Mendera

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Kameron D. Garza ◽  
Heather Newkirk ◽  
Russell Moreland ◽  
Carlos F. Gonzalez ◽  
Mei Liu ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Stenotrophomonas Maltophilia ◽  
Human Pathogen ◽  
Base Pairs ◽  
Content Type ◽  
Genomic Annotation ◽  
Opportunistic Human Pathogen

Stenotrophomonas maltophilia is an emerging opportunistic human pathogen. In this report, we describe the isolation and genomic annotation of the S. maltophilia-infecting bacteriophage Mendera. A myophage of 159,961 base pairs, Mendera is T4-like and related most closely to Stenotrophomonas phage IME-SM1.

scholarly journals Complete Genome Sequence of Streptococcus pneumoniae Strain Rx1, a Hex Mismatch Repair-Deficient Standard Transformation Recipient

2021 ◽  
Vol 10 (41) ◽  
Author(s):  
Anna Maria Cuppone ◽  
Lorenzo Colombini ◽  
Valeria Fox ◽  
David Pinzauti ◽  
Francesco Santoro ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Mismatch Repair ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Gc Content ◽  
Open Reading Frames ◽  
Circular Chromosome ◽  
Content Type ◽  
Sequencing Technologies

The complete genome sequence of Streptococcus pneumoniae strain Rx1, a Hex mismatch repair-deficient standard transformation recipient, was obtained by combining Nanopore and Illumina sequencing technologies. The genome consists of a 2.03-Mb circular chromosome, with 2,054 open reading frames and a GC content of 39.72%.

scholarly journals Complete genome sequence of GII.9 norovirus

2021 ◽  
Author(s):  
Zilong Zhang ◽  
Danlei Liu ◽  
Zilei Zhang ◽  
Peng Tian ◽  
Shenwei Li ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
High Throughput Sequencing ◽  
Open Reading Frames ◽  
Viral Sequence ◽  
Sequence Comparisons ◽  
Rapid Amplification ◽  
Genome Level ◽  
Reading Frames

AbstractNorovirus is recognized as one of the leading causes of acute gastroenteritis outbreaks. Genotype GII.9 was first detected in Norfolk, VA, USA, in 1997. However, the complete genome sequence of this genotype has not yet been determined. In this study, a complete genome sequence of GII.9[P7] norovirus, SCD1878_GII.9[P7], from a patient was determined using high-throughput sequencing and rapid amplification of cDNA ends (RACE) technology. The complete genome sequence of SCD1878_GII.9[P7] is 7544 nucleotides (nt) in length with a 3’ poly(A) tail and contains three open reading frames. Sequence comparisons indicated that SCD1878_GII.9[P7] shares 92.1%-92.3% nucleotide sequence identity with GII.P7 (AB258331 and AB039777) and 96.7%-97.4% identity with GII.9 (AY038599 and DQ379715). The results suggested that SCD1878_GII.9[P7] is a member of P genotype GII.P7 and G genotype GII.9. This viral sequence fills a gap at the whole-genome level for the GII.9 genotype.

scholarly journals Complete Genome Sequence of theBacillus pumilusPhage Leo2

2018 ◽  
Vol 6 (7) ◽  
Author(s):  
Sondos Badran ◽  
Nathanael Morales ◽  
Phillip Schick ◽  
Brandon Jacoby ◽  
William Villella ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Bacillus Pumilus ◽  
Open Reading Frames ◽  
Gram Positive ◽  
Coding Regions ◽  
Symbiotic Interactions ◽  
Associated Functions ◽  
Reading Frames

ABSTRACTBacillusspp. are ubiquitous Gram-positive microbes with many ecological and symbiotic interactions and can be pathogens. Phage Leo2 was found to infect aBacillus pumilusstrain isolated from soil. The sequence of phage Leo2 revealed 74 genes; 31% of the genes have associated functions, and 67% of coding regions are unidentified open reading frames.

scholarly journals Complete Genome Sequence of a Novel Satellite Virus Associated with Cassava Plants

2017 ◽  
Vol 5 (16) ◽  
Author(s):  
Adriana N. Souza ◽  
Fábio N. Silva ◽  
Claudine M. Carvalho
Keyword(s):  
Amino Acids ◽  
Coat Protein ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Open Reading Frames ◽  
Putative Protein ◽  
Satellite Virus ◽  
Cassava Plant ◽  
Reading Frames

ABSTRACT A novel satellite virus of 1,228 bp in length was found in a single cassava plant. Bioinformatic analyses show that it has two open reading frames (ORFs) in its genome, probably encoding a coat protein of 156 and a putative protein of 90 amino acids.

scholarly journals Complete Genome Sequence of a Renamed Isolate, Trichoplusia ni Ascovirus 6b, from the United States

2018 ◽  
Vol 6 (10) ◽  
Author(s):  
Yuan-Yuan Liu ◽  
Wen-Fei Xian ◽  
Jin Xue ◽  
Yong-Lu Wei ◽  
Xiao-Wen Cheng ◽  
...  
Keyword(s):  
United States ◽  
Phylogenetic Relationship ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Trichoplusia Ni ◽  
The United States ◽  
Open Reading Frames ◽  
First Time ◽  
Reading Frames

ABSTRACT The complete genome of Trichoplusia ni ascovirus 6b (TnAV-6b) was sequenced for the first time. The TnAV-6b isolate, which has its closest phylogenetic relationship with the TnAV-6a isolate, has a circular genome of 185,664 bp, with a G+C content of 46.0% and 178 predicted open reading frames.

scholarly journals Complete Genome Sequence of the Broad-Host-Range Vibriophage KVP40: Comparative Genomics of a T4-Related Bacteriophage

2003 ◽  
Vol 185 (17) ◽  
pp. 5220-5233 ◽  
Author(s):  
Eric S. Miller ◽  
John F. Heidelberg ◽  
Jonathan A. Eisen ◽  
William C. Nelson ◽  
A. Scott Durkin ◽  
...  
Keyword(s):  
Host Range ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Gene Clusters ◽  
Open Reading Frames ◽  
Broad Host Range ◽  
Group I Introns ◽  
Repair Enzymes ◽  
Group I

ABSTRACT The complete genome sequence of the T4-like, broad-host-range vibriophage KVP40 has been determined. The genome sequence is 244,835 bp, with an overall G+C content of 42.6%. It encodes 386 putative protein-encoding open reading frames (CDSs), 30 tRNAs, 33 T4-like late promoters, and 57 potential rho-independent terminators. Overall, 92.1% of the KVP40 genome is coding, with an average CDS size of 587 bp. While 65% of the CDSs were unique to KVP40 and had no known function, the genome sequence and organization show specific regions of extensive conservation with phage T4. At least 99 KVP40 CDSs have homologs in the T4 genome (Blast alignments of 45 to 68% amino acid similarity). The shared CDSs represent 36% of all T4 CDSs but only 26% of those from KVP40. There is extensive representation of the DNA replication, recombination, and repair enzymes as well as the viral capsid and tail structural genes. KVP40 lacks several T4 enzymes involved in host DNA degradation, appears not to synthesize the modified cytosine (hydroxymethyl glucose) present in T-even phages, and lacks group I introns. KVP40 likely utilizes the T4-type sigma-55 late transcription apparatus, but features of early- or middle-mode transcription were not identified. There are 26 CDSs that have no viral homolog, and many did not necessarily originate from Vibrio spp., suggesting an even broader host range for KVP40. From these latter CDSs, an NAD salvage pathway was inferred that appears to be unique among bacteriophages. Features of the KVP40 genome that distinguish it from T4 are presented, as well as those, such as the replication and virion gene clusters, that are substantially conserved.

scholarly journals Complete Genome Sequence of a Bacteroides fragilis Bacteriophage, vB_BfrS_NCTC

2021 ◽  
Vol 10 (29) ◽  
Author(s):  
Mohammad A. Tariq ◽  
Simon R. Carding
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Bacteroides Fragilis ◽  
Opportunistic Pathogen ◽  
Open Reading Frames ◽  
Obligate Anaerobe ◽  
Commensal Bacterium ◽  
Content Type ◽  
Reading Frames

Bacteroides fragilis is an obligate anaerobe and a common gut commensal bacterium that is also an important opportunistic pathogen. Here, we present the complete genome sequence of the circularly permuted B. fragilis bacteriophage vB_BfrS_NCTC. It comprises 47,160 bp, with 69 open reading frames.

scholarly journals Complete Genome Sequence of a Rhabdovirus Strain from Culex Mosquitos Collected in Southern Switzerland

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Jakub Kubacki ◽  
Isabelle Hardmeier ◽  
Weihong Qi ◽  
Eleonora Flacio ◽  
Mauro Tonolla ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Culex Pipiens ◽  
Full Length ◽  
Open Reading Frames ◽  
Content Type ◽  
Full Length Genome ◽  
Reading Frames

ABSTRACT We report here the full-length genome sequence of a rhabdovirus strain detected in a pool of 21 Culex pipiens and Culex torrentium mosquitos collected in southern Switzerland. The genome has a length of 11,914 nucleotides and encodes five major putative open reading frames.

scholarly journals Complete Genome Sequence of XaF13, a Novel Bacteriophage of Xanthomonas vesicatoria from Mexico

2020 ◽  
Vol 9 (5) ◽  
Author(s):  
Guillermo Alejandro Solís-Sánchez ◽  
Evangelina Esmeralda Quiñones-Aguilar ◽  
Saul Fraire-Velázquez ◽  
Julio Vega-Arreguín ◽  
Gabriel Rincón-Enríquez
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Open Reading Frames ◽  
Phytopathogenic Bacterium ◽  
Content Type ◽  
Bacterial Spot Disease ◽  
Solanaceae Family ◽  
Reading Frames ◽  
Xanthomonas Vesicatoria

The phytopathogenic bacterium Xanthomonas vesicatoria is the causative agent of bacterial spot disease in various Solanaceae family members. Here, we describe the complete genome sequence of XaF13, a novel filamentous phage that infects the phytopathogenic bacterium X. vesicatoria. The 7,045-bp genome is predicted to encode 14 open reading frames, 7 of which are related to those of other filamentous Xanthomonas phages.

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