scholarly journals Genome Sequence of a Novel Kunsagivirus (Picornaviridae: Kunsagivirus) from a Wild Baboon (Papio cynocephalus)

2017 ◽  
Vol 5 (18) ◽  
Author(s):  
Connor R. Buechler ◽  
Adam L. Bailey ◽  
Michael Lauck ◽  
Anna Heffron ◽  
Joshua C. Johnson ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genomic Sequence ◽  
Migratory Bird ◽  
Papio Cynocephalus ◽  
Bird Feces

ABSTRACT The picornaviral genus Kunsagivirus has a single member, kunsagivirus A, which was discovered in migratory bird feces. We report here the discovery of a novel kunsagivirus in wild yellow baboon (Papio cynocephalus) blood. The genomic sequence of this virus indicates the probable need for the establishment of a second kunsagivirus species.

scholarly journals Complete Genome Sequence of a Vampire Bat Rabies Virus from French Guiana

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Anne Lavergne ◽  
Edith Darcissac ◽  
Hervé Bourhy ◽  
Sourakhata Tirera ◽  
Benoît de Thoisy ◽  
...  
Keyword(s):  
Rabies Virus ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
French Guiana ◽  
Genomic Sequence ◽  
Amazon Region ◽  
Desmodus Rotundus ◽  
Bat Rabies ◽  
Vampire Bat

A rabies virus was detected in a common vampire bat ( Desmodus rotundus ) in French Guiana. Its genomic sequence was obtained and found to be closely related to other hematophagous bat-related viruses that widely circulate in the northern Amazon region. This virus is named AT6.

scholarly journals Complete Genome Sequence of Potato Virus T from Bolivia, Obtained from a 33-Year-Old Sample

2018 ◽  
Vol 7 (18) ◽  
Author(s):  
Ian P. Adams ◽  
Jorge Abad ◽  
Cesar E. Fribourg ◽  
Neil Boonham ◽  
Roger A. C. Jones
Keyword(s):  
Genome Sequence ◽  
Potato Virus ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Genomic Sequence ◽  
Complete Genomic Sequence ◽  
Potato Sample ◽  
Type Isolate ◽  
Andean Potato ◽  
Complete Genomic

We present the complete genomic sequence of a Potato virus T (PVT) isolate originally obtained from a Bolivian potato sample collected in 1976, and we compare it with the genome of the PVT type isolate from Peru. There is an 81% nucleotide identity between the two genomes of this Andean potato virus.

scholarly journals Identification of Concomitant Infection with Chlamydia trachomatis IncA-Negative Mutant and Wild-Type Strains by Genomic, Transcriptional, and Biological Characterizations

2008 ◽  
Vol 76 (12) ◽  
pp. 5438-5446 ◽  
Author(s):  
Robert J. Suchland ◽  
Brendan M. Jeffrey ◽  
Minsheng Xia ◽  
Ajay Bhatia ◽  
Hencelyn G. Chu ◽  
...  
Keyword(s):  
Chlamydia Trachomatis ◽  
Genome Sequence ◽  
Type Strain ◽  
Wild Type Strain ◽  
Genomic Sequence ◽  
Genomic Structure ◽  
Transcriptional Analysis ◽  
Clinical Samples ◽  
Wild Type

ABSTRACT Clinical isolates of Chlamydia trachomatis that lack IncA on their inclusion membrane form nonfusogenic inclusions and have been associated with milder, subclinical infections in patients. The molecular events associated with the generation of IncA-negative strains and their roles in chlamydial sexually transmitted infections are not clear. We explored the biology of the IncA-negative strains by analyzing their genomic structure, transcription, and growth characteristics in vitro and in vivo in comparison with IncA-positive C. trachomatis strains. Three clinical samples were identified that contained a mixture of IncA-positive and -negative same-serovar C. trachomatis populations, and two more such pairs were found in serial isolates from persistently infected individuals. Genomic sequence analysis of individual strains from each of two serovar-matched pairs showed that these pairs were very similar genetically. In contrast, the genome sequence of an unmatched IncA-negative strain contained over 5,000 nucleotide polymorphisms relative to the genome sequence of a serovar-matched but otherwise unlinked strain. Transcriptional analysis, in vitro culture kinetics, and animal modeling demonstrated that IncA-negative strains isolated in the presence of a serovar-matched wild-type strain are phenotypically more similar to the wild-type strain than are IncA-negative strains isolated in the absence of a serovar-matched wild-type strain. These studies support a model suggesting that a change from an IncA-positive strain to the previously described IncA-negative phenotype may involve multiple steps, the first of which involves a translational inactivation of incA, associated with subsequent unidentified steps that lead to the observed decrease in transcript level, differences in growth rate, and differences in mouse infectivity.

scholarly journals Human Herpesvirus 6B Genome Sequence: Coding Content and Comparison with Human Herpesvirus 6A

1999 ◽  
Vol 73 (10) ◽  
pp. 8040-8052 ◽  
Author(s):  
Geraldina Dominguez ◽  
Timothy R. Dambaugh ◽  
Felicia R. Stamey ◽  
Stephen Dewhurst ◽  
Naoki Inoue ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Genome Sequence ◽  
Nucleotide Sequence Identity ◽  
Genomic Sequence ◽  
Human Herpesvirus ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Sequence Identity ◽  
T Cell Lines ◽  
The Right

ABSTRACT Human herpesvirus 6 variants A and B (HHV-6A and HHV-6B) are closely related viruses that can be readily distinguished by comparison of restriction endonuclease profiles and nucleotide sequences. The viruses are similar with respect to genomic and genetic organization, and their genomes cross-hybridize extensively, but they differ in biological and epidemiologic features. Differences include infectivity of T-cell lines, patterns of reactivity with monoclonal antibodies, and disease associations. Here we report the complete genome sequence of HHV-6B strain Z29 [HHV-6B(Z29)], describe its genetic content, and present an analysis of the relationships between HHV-6A and HHV-6B. As sequenced, the HHV-6B(Z29) genome is 162,114 bp long and is composed of a 144,528-bp unique segment (U) bracketed by 8,793-bp direct repeats (DR). The genomic sequence allows prediction of a total of 119 unique open reading frames (ORFs), 9 of which are present only in HHV-6B. Splicing is predicted in 11 genes, resulting in the 119 ORFs composing 97 unique genes. The overall nucleotide sequence identity between HHV-6A and HHV-6B is 90%. The most divergent regions are DR and the right end of U, spanning ORFs U86 to U100. These regions have 85 and 72% nucleotide sequence identity, respectively. The amino acid sequences of 13 of the 17 ORFs at the right end of U differ by more than 10%, with the notable exception of U94, the adeno-associated virus type 2 rep homolog, which differs by only 2.4%. This region also includes putative cis-acting sequences that are likely to be involved in transcriptional regulation of the major immediate-early locus. The catalog of variant-specific genetic differences resulting from our comparison of the genome sequences adds support to previous data indicating that HHV-6A and HHV-6B are distinct herpesvirus species.

scholarly journals Genomic sequence of yellow fever virus from a Dutch traveller returning from the Gambia-Senegal region, the Netherlands, November 2018

2019 ◽  
Vol 24 (4) ◽  
Author(s):  
My VT Phan ◽  
Sarwa Darwish Murad ◽  
Annemiek A van der Eijk ◽  
Herold J. Metselaar ◽  
Hermien Hartog ◽  
...  
Keyword(s):  
The Netherlands ◽  
Yellow Fever ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Yellow Fever Virus ◽  
Genomic Sequence ◽  
Public Awareness ◽  
The Gambia ◽  
Fever Virus

In November 2018, yellow fever was diagnosed in a Dutch traveller returning from a bicycle tour in the Gambia-Senegal region. A complete genome sequence of yellow fever virus (YFV) from the case was generated and clustered phylogenetically with YFV from the Gambia and Senegal, ruling out importation into the Netherlands from recent outbreaks in Brazil or Angola. We emphasise the need for increased public awareness of YFV vaccination before travelling to endemic countries.

scholarly journals Genome sequencing and transcriptome analysis of Geotrichum citri-aurantii on citrus reveal the potential pathogenic- and guazatine resistance-related genes

2019 ◽  
Author(s):  
Juan Zhao ◽  
DeYao Zhang ◽  
Zhe Wang ◽  
Zhonghuan Tian ◽  
Fan Yang ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Genome Sequence ◽  
Genomic Sequence ◽  
Resistance Mechanism ◽  
Effective Control ◽  
Postharvest Disease ◽  
Economic Losses ◽  
Sequencing Analysis ◽  
Transporter Family ◽  
High Quality Genome

Abstract Background: Citrus grow in more than 100 countries and is one of the most produced fruit genus. Sour rot, caused by Geotrichum citri-aurantii , is a major postharvest disease of citrus，and it causes economic losses. In recent years, the disease had a rising trend year by year. In this study, the genome sequence of G. citri-aurantii and transcriptome sequence of pathogenic- and guazatine resistance were sequenced with a view to explore the potential pathogenic mechanism and drug resistance mechanism of G. citri-aurantii on citrus. Results: We sequenced a high-quality genome sequence of G. citri-aurantii by SMRT. This sequence encodes 6,783 predicted genes of the 28.1-Mb G. citri-aurantii genome. Approximately 5.43 Gb of clean data were obtained after Hi-C sequencing, and a 27.94-Mb genomic sequence was positioned to the 10 chromosome groups after Hi-C assembly , accounting for 99.43% of the previously measured G. citri-aurantii genome. In the process of studying pathogenic mechanisms, the content of polygalacturonase (PG) and polymethylgalacturonase (PMG) was considerably increased in the Newhall navel orange infected by G. citri-aurantii. Then, three polygalacturonase (PG) genes (EVM0005942, EVM0004416, EVM0002276) related to pathogenicity were identified and the expression level was significantly increased during the infection by quantitative RT-PCR. Additionally, G. citri-aurantii is only sensitive to the chemical fungicide guazatine. Massive guazatine use has led to evolution of the wild G. citri-aurantii in citrus-producing areas. Owing to its uniqueness, RNA sequencing analysis of guazatine-resistance showed that the guazatine-resistance of G. citri-aurantii is may related to two ABC transporter family genes, six MFS transporter family genes and two MATE transporter family genes. Conclusions: We found three polygalacturonase (PG) genes related to pathogenicity and ten genes related to guazatine-resistance from molecular level. Our research may provide novel insights into the effective control of this pathogen. Keywords: Geotrichum citri-aurantii , citrus, genome, pathogenicity, guazatine, drug resistance

scholarly journals A 33-Year-Old Plant Sample Contributes the First Complete Genomic Sequence of Potato Virus U

2018 ◽  
Vol 7 (23) ◽  
Author(s):  
Ian P. Adams ◽  
Neil Boonham ◽  
Roger A. C. Jones
Keyword(s):  
Amino Acid ◽  
Genome Sequence ◽  
Potato Virus ◽  
Genomic Sequence ◽  
Amino Acid Sequences ◽  
Plant Sample ◽  
Complete Genomic Sequence ◽  
Potato Sample ◽  
Complete Genomic

A Potato virus U isolate detected in a Peruvian potato sample collected in 1977 produced the first genome sequence of this virus. When this genome sequence was compared with those of other nepoviruses, the amino acid sequences of RNA1 and RNA2 were most similar to those of subgroup C nepoviruses.

scholarly journals Genomic Sequence of the Prophage-Free Lactococcus lactis Strain IL6288

2019 ◽  
Vol 8 (1) ◽  
Author(s):  
Alexander Bolotin ◽  
Anne Aucouturier ◽  
Alexei Sorokin ◽  
Elena Bidnenko
Keyword(s):  
Lactococcus Lactis ◽  
Genome Sequence ◽  
Genomic Sequence ◽  
Content Type ◽  
Lactis Strain

We report here the genome sequence of IL6288, a prophage-free derivative of Lactococcus lactis subsp. lactis strain IL1403, and confirm precise deletion of all prophages.

scholarly journals Genomic Sequence of the Strain Enterococcus faecium ICIS 18

2020 ◽  
Vol 9 (2) ◽  
Author(s):  
M. V. Sycheva ◽  
L. P. Popova ◽  
T. M. Pashkova ◽  
Y. A. Khlopko ◽  
O. L. Kartashova ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Enterococcus Faecium ◽  
Genomic Sequence ◽  
Draft Genome ◽  
Beta Lactam ◽  
Human Feces ◽  
Content Type ◽  
Beta Lactam Antibiotics ◽  
Genes Encoding ◽  
Feces Analysis

We report here the draft genome sequence of Enterococcus faecium strain ICIS 18, which was isolated from human feces. Analysis of the E. faecium ICIS 18 genome revealed genes encoding resistance to metals, fluoroquinolones, and beta-lactam antibiotics.

scholarly journals Genome Sequence of Trypanosoma cruzi Strain Bug2148

2018 ◽  
Vol 6 (3) ◽  
Author(s):  
Francisco Callejas-Hernández ◽  
Núria Gironès ◽  
Manuel Fresno
Keyword(s):  
Gene Expression ◽  
Trypanosoma Cruzi ◽  
Vertical Transmission ◽  
Genome Sequence ◽  
Genomic Sequence ◽  
Gene Organization ◽  
Polycistronic Transcription ◽  
Complex Mechanisms ◽  
Plastic Genome

ABSTRACT Trypanosoma cruzi belongs to the group of mitochondrion-containing eukaryotes and has a highly plastic genome, unusual gene organization, and complex mechanisms for gene expression (polycistronic transcription). We report here the genome sequence of strain Bug2148, the first genomic sequence belonging to cluster TcV, which has been related to vertical transmission.

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