Genomic characterization of Ralstonia solanacearum phage ϕRS138 of the family Siphoviridae

2015 ◽  
Vol 161 (2) ◽  
pp. 483-486 ◽  
Author(s):  
Bich Van Truong Thi ◽  
Nguyen Huan Pham Khanh ◽  
Ryuta Namikawa ◽  
Kaito Miki ◽  
Akihiro Kondo ◽  
...  
Keyword(s):  
Ralstonia Solanacearum ◽  
The Family ◽  
Genomic Characterization

scholarly journals Rediscovery and genomic characterization of bovine astroviruses

2011 ◽  
Vol 92 (8) ◽  
pp. 1888-1898 ◽  
Author(s):  
Herman Tse ◽  
Wan-Mui Chan ◽  
Hoi-Wah Tsoi ◽  
Rachel Y. Y. Fan ◽  
Candy C. Y. Lau ◽  
...  
Keyword(s):  
Roe Deer ◽  
Mammalian Species ◽  
Capreolus Capreolus ◽  
Genetic Distances ◽  
Genome Sequences ◽  
Sea Lions ◽  
The Family ◽  
Genomic Characterization ◽  
Similar Organization

The genus Mamastrovirus belongs to the family Astroviridae and consists of at least six members infecting different mammalian hosts, including humans, cattle and pigs. In recent years, novel astroviruses have been identified in other mammalian species like roe deer, bats and sea lions. While the bovine astrovirus was one of the earliest astroviruses to have been studied, no further research has been performed recently and its genome sequence remains uncharacterized. In this report, we describe the detection and genomic characterization of astroviruses in bovine faecal specimens obtained in Hong Kong. Five of 209 specimens were found to be positive for astrovirus by RT-PCR. Two of the positive specimens were found to contain sequences from two different astrovirus strains. Complete genome sequences of approximately 6.3 kb in length were obtained for four strains, which showed similar organization of the genome compared to other astroviruses. Phylogenetic analysis confirmed their identities as members of the genus Mamastrovirus, and showed them to be most closely related to the Capreolus capreolus astrovirus. Based on the pairwise genetic distances among their full-length ORF2 sequences, these bovine astroviruses may be assigned into at least three different genotype species. Sequence analysis revealed evidence of potential recombination in ORF2. In summary, we report the first genome sequences of bovine astroviruses and clearly establish the species status of the virus. Additionally, our study is among the first to report co-infection by different astrovirus genotypes in the same host, which is an essential step for recombination to occur.

Genomic characterization of covert mortality nodavirus from farming shrimp: Evidence for a new species within the family Nodaviridae

2020 ◽  
Vol 286 ◽  
pp. 198092
Author(s):  
Tingting Xu ◽  
Shuang Liu ◽  
Xiaoping Li ◽  
Qingli Zhang
Keyword(s):  
New Species ◽  
The Family ◽  
Genomic Characterization ◽  
A New Species

scholarly journals Genomic characterization of the unclassified bovine enteric virus Newbury agent-1 (Newbury1) endorses a new genus in the family Caliciviridae

Virology ◽  
2006 ◽  
Vol 350 (1) ◽  
pp. 240-250 ◽  
Author(s):  
S.L. Oliver ◽  
E. Asobayire ◽  
A.M. Dastjerdi ◽  
J.C. Bridger
Keyword(s):  
New Genus ◽  
Enteric Virus ◽  
The Family ◽  
Genomic Characterization

scholarly journals Genomic Characterization of Ralstonia solanacearum Phage φRSB1, a T7-Like Wide-Host-Range Phage

2008 ◽  
Vol 191 (1) ◽  
pp. 422-427 ◽  
Author(s):  
Takeru Kawasaki ◽  
Mio Shimizu ◽  
Hideki Satsuma ◽  
Akiko Fujiwara ◽  
Makoto Fujie ◽  
...  
Keyword(s):  
Host Range ◽  
Ralstonia Solanacearum ◽  
Open Reading Frames ◽  
Phytopathogenic Bacterium ◽  
Strong Activity ◽  
Double Stranded Dna ◽  
Wide Host Range ◽  
Genomic Characterization ◽  
Reading Frames

ABSTRACT φRSΒ1 is a wide-host-range, T7-like bacteriophage that infects and efficiently lyses the phytopathogenic bacterium Ralstonia solanacearum. The φRSB1 genome comprises 43,079 bp of double-stranded DNA (61.7% G+C) with 325-bp terminal repeats and contains 47 open reading frames. Strong activity of tandem early promoters and wide specificity of phage promoters of φRSB1 were demonstrated.

Identification, transmission and genomic characterization of a new member of the family Caulimoviridae causing a flower distortion disease of Rudbeckia hirta

2017 ◽  
Vol 241 ◽  
pp. 62-67 ◽  
Author(s):  
Benham Lockhart ◽  
Dimitre Mollov ◽  
Neil Olszewski ◽  
Nicholas Goldsmith
Keyword(s):  
Rudbeckia Hirta ◽  
The Family ◽  
Genomic Characterization

scholarly journals Co-cultivation of microbial sub-communities in microfluidic droplets facilitates high-resolution genomic dissection of microbial ‘dark matter’

2020 ◽  
Vol 12 (11) ◽  
pp. 263-274
Author(s):  
James Y Tan ◽  
Sida Wang ◽  
Gregory J Dick ◽  
Vincent B Young ◽  
David H Sherman ◽  
...  
Keyword(s):  
Dark Matter ◽  
Microbial Communities ◽  
Ecological Interactions ◽  
Healthy Human ◽  
Encapsulated Cells ◽  
Microfluidic Droplets ◽  
The Family ◽  
Culture Independent ◽  
Genomic Characterization

Abstract While the ‘unculturable’ majority of the bacterial world is accessible with culture-independent tools, the inability to study these bacteria using culture-dependent approaches has severely limited our understanding of their ecological roles and interactions. To circumvent cultivation barriers, we utilize microfluidic droplets as localized, nanoliter-size bioreactors to co-cultivate subsets of microbial communities. This co-localization can support ecological interactions between a reduced number of encapsulated cells. We demonstrated the utility of this approach in the encapsulation and co-cultivation of droplet sub-communities from a fecal sample collected from a healthy human subject. With the whole genome amplification and metagenomic shotgun sequencing of co-cultivated sub-communities from 22 droplets, we observed that this approach provides accessibility to uncharacterized gut commensals for study. The recovery of metagenome-assembled genomes from one droplet sub-community demonstrated the capability to dissect the sub-communities with high-genomic resolution. In particular, genomic characterization of one novel member of the family Neisseriaceae revealed implications regarding its participation in fatty acid degradation and production of atherogenic intermediates in the human gut. The demonstrated genomic resolution and accessibility to the microbial ‘dark matter’ with this methodology can be applied to study the interactions of rare or previously uncultivated members of microbial communities.

Identification and genomic characterization of a novel fish reovirus, Hubei grass carp disease reovirus, isolated in 2009 in China

2013 ◽  
Vol 94 (10) ◽  
pp. 2266-2277 ◽  
Author(s):  
Yuding Fan ◽  
Shujing Rao ◽  
Lingbing Zeng ◽  
Jie Ma ◽  
Yong Zhou ◽  
...  
Keyword(s):  
Amino Acid ◽  
Grass Carp ◽  
Sequence Similarity ◽  
Amino Acid Level ◽  
Amino Acid Sequences ◽  
Full Genome Sequence ◽  
Total Size ◽  
The Family ◽  
Genomic Characterization

A novel fish reovirus, Hubei grass carp disease reovirus (HGDRV; formerly grass carp reovirus strain 104, GCRV104), was isolated from diseased grass carp in China in 2009 and the full genome sequence was determined. This reovirus was propagated in a grass carp kidney cell line with a typical cytopathic effect. The total size of the genome was 23 706 bp with a 51 mol% G+C content, and the 11 dsRNA segments encoded 12 proteins (two proteins encoded by segment 11). A nucleotide sequence similarity search using blastn found no significant matches except for segment 2, which partially matched that of the RNA-dependent RNA polymerase (RdRp) from several viruses in the genera Aquareovirus and Orthoreovirus of the family Reoviridae. At the amino acid level, seven segments (Seg-1 to Seg-6, and Seg-8) matched with species in the genera Aquareovirus (15–46 % identities) and Orthoreovirus (12–44 % identities), while for four segments (Seg-7, Seg-9, Seg-10 and Seg-11) no similarities in these genera were found. Conserved terminal sequences, 5′-GAAUU----UCAUC-3′, were found in each HGDRV segment at the 5′ and 3′ ends, and the 5′-terminal nucleotides were different from any known species in the genus Aquareovirus. Phylogenetic analysis based on RdRp amino acid sequences from members of the family Reoviridae showed that HGDRV clustered with aquareoviruses prior to joining a branch common with orthoreoviruses. Based on these observations, we propose that HGDRV is a new species in the genus Aquareovirus that is distantly related to any known species within this genus.

scholarly journals Genomic Characterization of a Novel Virus of the Family Tymoviridae Isolated from Mosquitoes

PLoS ONE ◽  
2012 ◽  
Vol 7 (7) ◽  
pp. e39845 ◽  
Author(s):  
Lihua Wang ◽  
Xinjun Lv ◽  
Yougang Zhai ◽  
Shihong Fu ◽  
David Wang ◽  
...  
Keyword(s):  
The Family ◽  
Genomic Characterization ◽  
Novel Virus

scholarly journals Genomic characterization of three novel Pseudomonas phages within the subfamily of Autographivirinae isolated from organic waste

2020 ◽  
Author(s):  
Jacob B Jørgensen ◽  
Amaru M Djuurhus ◽  
Alexander B. Carstens ◽  
Witold Kot ◽  
Cindy E. Morris ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Organic Waste ◽  
New Genus ◽  
Open Reading Frames ◽  
Genomic Comparison ◽  
Double Stranded Dna ◽  
The Family ◽  
Genomic Characterization ◽  
Reading Frames

AbstractThree phages targeting Pseudomonas syringae GAW0113 have been isolated from organic waste samples: Pseudomonas phage Bertil, Misse and Strit. The phages have double-stranded DNA genomes ranging from 41342 to 41374 bp in size comprising 50 to 51 open reading frames. The three phages genomes are highly similar and genomic comparison analyses shows that they all belong to the Autographivirinae subfamily of the family Podoviridae. The phages are however only distantly related to other members of this family, and have limited gene synteny with type-phages of other genera within Autographivirinae, suggesting that the newly isolated phages could represent a new genus.

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