scholarly journals Genome Sequence Resource of Burkholderia glumae UAPB13

2021 ◽  
Author(s):  
Juanita Gil ◽  
Laura Ortega ◽  
J Alejandro Rojas ◽  
Clemencia M Rojas
Keyword(s):  
Genome Sequence ◽  
Genomic Sequence ◽  
Burkholderia Glumae ◽  
Genomic Complexity ◽  
Panicle Blight

Burkholderia glumae causes Bacterial Panicle Blight of rice. Here, we report the genomic sequence of B. glumae strain UAPB13 isolated from fields in Arkansas. The assembled genome consists of 123 scaffolds totaling 6,504,483 bp representing two chromosomes and two plasmids. The genomic complexity of B. glumae warrants the sequencing of additional strains. This additional genomic sequence will enable us to further understand this pathogen and the disease it causes.

scholarly journals Genome Sequence and Adaptation Analysis of the Human and Rice Pathogenic Strain Burkholderia glumae AU6208

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 87
Author(s):  
Zhouqi Cui ◽  
Sai Wang ◽  
Kaleem Ullah Kakar ◽  
Guanglin Xie ◽  
Bin Li ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Type Strain ◽  
Antibiotic Biosynthesis ◽  
Chronic Infections ◽  
Burkholderia Glumae ◽  
Niche Adaptation ◽  
History Of ◽  
Clinical Conditions ◽  
Important Disease ◽  
Panicle Blight

Burkholderia glumae causes rice (Oryza sativa) bacterial panicle blight, which is an increasingly economically important disease worldwide. As the first B. glumae strain isolated from patients with chronic infections, AU6208 has been reported as an opportunistic clinic pathogen. However, our understanding of the molecular mechanism underlying human pathogenesis by B. glumae remains rudimentary. In this study, we report the complete genome sequence of the human-isolated B. glumae strain AU6208 and compare this to the genome of the rice-pathogenic B. glumae type strain LMG 2196T. Analysis of the average nucleotide identity demonstrated 99.4% similarity between the human- and plant-pathogenic strains. However, the phenotypic results from this study suggest a history of niche adaptation and divergence. In particular, we found 44 genes were predicted to be horizontally transferred into AU6208, and most of these genes were upregulated in conditions that mimic clinical conditions. In these, the gene pair sbnAB encodes key enzymes in antibiotic biosynthesis. These results suggest that horizontal gene transfer in AU6208 may be responsible for selective advantages in its pathogenicity in humans. Our analysis of the AU6208 genome and comparison with that of LMG 2196T reveal the evolutionary signatures of B. glumae in the process of switching niches from plants to humans.

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 Chemical or genetic alteration of proton motive force results in loss of virulence of Burkholderia glumae , the cause of rice bacterial panicle blight.

2021 ◽  
Author(s):  
Asif Iqbal ◽  
Pradip R. Panta ◽  
John Ontoy ◽  
Jobelle Bruno ◽  
Jong Hyun Ham ◽  
...  
Keyword(s):  
Sodium Bicarbonate ◽  
Wild Type Strain ◽  
Proton Motive Force ◽  
Membrane Transporters ◽  
Motive Force ◽  
Wild Type ◽  
Bacterial Genomes ◽  
Burkholderia Glumae ◽  
Sheath Rot ◽  
Panicle Blight

Rice is an important source of food for more than half the world’s population. Bacterial panicle blight (BPB) is a disease of rice characterized by grain discoloration or sheath rot caused mainly by Burkholderia glumae . B. glumae synthesizes toxoflavin, an essential virulence factor, that is required for symptoms of the disease. The products of the tox operons, ToxABCDE and ToxFGHI, are responsible for the synthesis and the proton motive force (PMF)-dependent secretion of toxoflavin, respectively. The DedA family is a highly conserved membrane protein family found in most bacterial genomes that likely function as membrane transporters. Our previous work has demonstrated that absence of certain DedA family members results in pleiotropic effects, impacting multiple pathways that are energized by PMF. We have demonstrated that a member of the DedA family from Burkholderia thailandensis , named DbcA, is required for the extreme polymyxin resistance observed in this organism. B. glumae encodes a homolog of DbcA with 73% amino acid identity to Burkholderia thailandensis DbcA. Here, we created and characterized a B. glumae Δ dbcA strain. In addition to polymyxin sensitivity, B. glumae Δ dbcA is compromised for virulence in several BPB infection models and secretes only low amounts of toxoflavin (∼15% of wild type levels). Changes in membrane potential in B. glumae Δ dbcA were reproduced in the wild type strain by the addition of sub-inhibitory concentrations of sodium bicarbonate, previously demonstrated to cause disruption of PMF. Sodium bicarbonate inhibited B. glumae virulence in rice suggesting a possible non-toxic chemical intervention for bacterial panicle blight. IMPORTANCE Bacterial panicle blight (BPB) is a disease of rice characterized by grain discoloration or sheath rot caused mainly by Burkholderia glumae . The DedA family is a highly conserved membrane protein family found in most bacterial genomes that likely function as membrane transporters. Here, we constructed a B. glumae mutant with a deletion in a DedA family member named dbcA and report a loss of virulence in models of BPB. Physiological analysis of the mutant shows that the proton motive force is disrupted, leading to reduction of secretion of the essential virulence factor toxoflavin. The mutant phenotypes are reproduced in the virulent wild type strain without an effect on growth using sodium bicarbonate, a nontoxic buffer that has been reported to disrupt the PMF. The results presented here suggest that bicarbonate may be an effective antivirulence agent capable of controlling BPB without imposing an undue burden on the environment.

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 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 Complete Genome Sequence of Burkholderia glumae BGR1

2009 ◽  
Vol 191 (11) ◽  
pp. 3758-3759 ◽  
Author(s):  
JaeYun Lim ◽  
Tae-Ho Lee ◽  
Baek Hie Nahm ◽  
Yang Do Choi ◽  
Minkyun Kim ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Causative Agent ◽  
Bacterial Wilt ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Burkholderia Glumae ◽  
Field Crops ◽  
Seedling Rot

ABSTRACT Burkholderia glumae is the causative agent of grain and seedling rot in rice and of bacterial wilt in many field crops. Here, we report the complete genome sequence of B. glumae BGR1 isolated from a diseased rice panicle in Korea.

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

Sign in / Sign up

Export Citation Format

Share Document