Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome Sequences of Poaceae-Associated Gemycircularviruses from the Pacific Ocean Island of Tonga.

ABSTRACT: We sampled and analyzed 43 Poaceae plants from the Pacific Ocean island of Tonga for the presence of circular DNA viruses. From these samples, we recovered three gemycircularvirus genomes, which share >99% identity, from Brachiaria deflexa (n = 2) and sugarcane (n = 1). These genomes share <61% genome-wide identity with other gemycircularvirus sequences in public databases.

SUBMITTER: Male MF

PROVIDER: S-EPMC4611678 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Genome Sequences of Poaceae-Associated Gemycircularviruses from the Pacific Ocean Island of Tonga.

Male Maketalena F MF Kami Viliami V Kraberger Simona S Varsani Arvind A

Genome announcements 20151015 5

We sampled and analyzed 43 Poaceae plants from the Pacific Ocean island of Tonga for the presence of circular DNA viruses. From these samples, we recovered three gemycircularvirus genomes, which share >99% identity, from Brachiaria deflexa (n = 2) and sugarcane (n = 1). These genomes share <61% genome-wide identity with other gemycircularvirus sequences in public databases. ...[more]

PMID: 26472826

Similar Datasets

Genome Sequence of Banana Streak MY Virus from the Pacific Ocean Island of Tonga.

Project description:Banana streak disease is caused by a variety of banana-infecting badnaviruses. A genome of the episomal form of a banana streak MY virus was recovered from an infected banana plant sampled on Vava'u Island, Tonga, and shares >98% pairwise identity with the six other genomes available in public databases.

| S-EPMC4447910 | biostudies-literature

Complete Genome Sequences of Two Pseudomonas Species Isolated from Marine Environments of the Pacific Ocean.

Project description:Pseudomonas marincola YsY11 and Pseudomonas oleovorans T9AD were both isolated from marine environments of the Pacific Ocean. Here, we report the whole-genome sequences of these two organisms. Pseudomonas marincola YsY11 consists of a single 4.77-Mb chromosome, and Pseudomonas oleovorans T9AD consists of a 5.57-Mb chromosome and a 2.8-kb plasmid.

| S-EPMC8063651 | biostudies-literature

Pacific Ocean

Project description:California Current Ecosystem Bacterial Iron Limitation

| PRJNA1071118 | ENA

Identifying key demographic parameters of a small island-associated population of Indo-Pacific bottlenose dolphins (Reunion, Indian Ocean).

Project description:Photo-identification surveys of Indo-Pacific bottlenose dolphins were conducted from 2009 to 2014 off Reunion Island (55°E33'/21°S07'), in the Indian Ocean. Robust Design models were applied to produce the most reliable estimate of population abundance and survival rate, while accounting for temporary emigration from the survey area (west coast). The sampling scheme consisted of a five-month (June-October) sampling period in each year of the study. The overall population size at Reunion was estimated to be 72 individuals (SE = 6.17, 95%CI = 61-85), based on a random temporary emigration (γ") of 0.096 and a proportion of 0.70 (SE = 0.03) distinct individuals. The annual survival rate was 0.93 (±0.018 SE, 95%CI = 0.886-0.958) and was constant over time and between sexes. Models considering gender groups indicated different movement patterns between males and females. Males showed null or quasi-null temporary emigration (γ" = γ' < 0.01), while females showed a random temporary emigration (γ") of 0.10, suggesting that a small proportion of females was outside the survey area during each primary sampling period. Sex-specific temporary migration patterns were consistent with movement and residency patterns observed in other areas. The Robust Design approach provided an appropriate sampling scheme for deriving island-associated population parameters, while allowing to restrict survey effort both spatially (i.e. west coast only) and temporally (five months per year). Although abundance and survival were stable over the six years, the small population size of fewer than 100 individuals suggested that this population is highly vulnerable. Priority should be given to reducing any potential impact of human activity on the population and its habitat.

| S-EPMC5480988 | biostudies-literature

Draft Genome Sequences of Two Bacterial Strains, Muricauda sp. 72 and NH166, Isolated from the South China Sea and West Pacific Ocean.

Project description:Here, we report the whole-genome sequences of two bacterial strains, Muricauda sp. 72 and NH166, isolated from the South China Sea and West Pacific Ocean, respectively. These two strains may represent a novel species of the genus Muricauda, and the features of their genome sequences will enrich our understandings of strains in the genus Muricauda.

| S-EPMC6953513 | biostudies-literature

Complete chloroplast genome sequences of two <i>Alloteropsis</i> species (Poaceae) from China.

Project description:Alloteropsis is a widely-distributed genus with C3 and C4 photosynthetic species belonging to the Poaceae family. This study characterized the complete chloroplast genomes of two Alloteropsis species from Chinese mainland, i.e. Alloteropsis semialata with C4 photosynthetic type and Alloteropsis cimicina with C3 photosynthetic type. The chloroplast genomes of A. semialata and A. cimicina are 138,188 bp and 139,335 bp in length, with 38.48% and 38.59% GC contents, respectively. These two chloroplast genomes contain the same number of genes, i.e. 107 unique genes including 27 tRNA, 4 rRNA, and 76 protein-coding genes. Phylogenomic analysis confirmed the species identity of A. semialata and A. cimicina and supported a close relationship of Alloteropsis with species of Setaria and Panicum in grass family.

| S-EPMC7872562 | biostudies-literature

South Pacific ocean microbiome

Project description:Bacterial and fungal amplicon sequencing to understand the microbial communities of the South Pacific ocean

| PRJEB42801 | ENA

Draft Genome Sequence of Brucella ceti Isolated in the Western Pacific Ocean.

Project description:In 2018, Brucella ceti was isolated from a bottlenose dolphin from the western Pacific Ocean. Here, we report a draft genome sequence of the isolate BD1442 of sequence type 27, which is the only sequence type known to have been isolated from human clinical cases.

| S-EPMC7516157 | biostudies-literature

Southwest Pacific Absolute Plate Kinematic Reconstruction Reveals Major Cenozoic Tonga-Kermadec Slab Dragging.

Project description:Tectonic plates subducting at trenches having strikes oblique to the absolute subducting plate motion undergo trench-parallel slab motion through the mantle, recently defined as a form of "slab dragging." We investigate here long-term slab-dragging components of the Tonga-Kermadec subduction system driven by absolute Pacific plate motion. To this end we develop a kinematic restoration of Tonga-Kermadec Trench motion placed in a mantle reference frame and compare it to tomographically imaged slabs in the mantle. Estimating Tonga-Kermadec subduction initiation is challenging because another (New Caledonia) subduction zone existed during the Paleogene between the Australia and Pacific plates. We test partitioning of plate convergence across the Paleogene New Caledonia and Tonga-Kermadec subduction zones against resulting mantle structure and show that most, if not all, Tonga-Kermadec subduction occurred after ca. 30 Ma. Since then, Tonga-Kermadec subduction has accommodated 1,700 to 3,500 km of subduction along the southern and northern ends of the trench, respectively. When placed in a mantle reference frame, the predominantly westward directed subduction evolved while the Tonga-Kermadec Trench underwent ~1,200 km of northward absolute motion. We infer that the entire Tonga-Kermadec slab was laterally transported through the mantle over 1,200 km. Such slab dragging by the Pacific plate may explain observed deep-slab deformation and may also have significant effects on surface tectonics, both resulting from the resistance to slab dragging by the viscous mantle.

| S-EPMC6175462 | biostudies-literature

Distinctive microbial community and genome structure in coastal seawater from a human-made port and nearby offshore island in northern Taiwan facing the Northwestern Pacific Ocean.

Project description:Pollution in human-made fishing ports caused by petroleum from boats, dead fish, toxic chemicals, and effluent poses a challenge to the organisms in seawater. To decipher the impact of pollution on the microbiome, we collected surface water from a fishing port and a nearby offshore island in northern Taiwan facing the Northwestern Pacific Ocean. By employing 16S rRNA gene amplicon sequencing and whole-genome shotgun sequencing, we discovered that Rhodobacteraceae, Vibrionaceae, and Oceanospirillaceae emerged as the dominant species in the fishing port, where we found many genes harboring the functions of antibiotic resistance (ansamycin, nitroimidazole, and aminocoumarin), metal tolerance (copper, chromium, iron and multimetal), virulence factors (chemotaxis, flagella, T3SS1), carbohydrate metabolism (biofilm formation and remodeling of bacterial cell walls), nitrogen metabolism (denitrification, N2 fixation, and ammonium assimilation), and ABC transporters (phosphate, lipopolysaccharide, and branched-chain amino acids). The dominant bacteria at the nearby offshore island (Alteromonadaceae, Cryomorphaceae, Flavobacteriaceae, Litoricolaceae, and Rhodobacteraceae) were partly similar to those in the South China Sea and the East China Sea. Furthermore, we inferred that the microbial community network of the cooccurrence of dominant bacteria on the offshore island was connected to dominant bacteria in the fishing port by mutual exclusion. By examining the assembled microbial genomes collected from the coastal seawater of the fishing port, we revealed four genomic islands containing large gene-containing sequences, including phage integrase, DNA invertase, restriction enzyme, DNA gyrase inhibitor, and antitoxin HigA-1. In this study, we provided clues for the possibility of genomic islands as the units of horizontal transfer and as the tools of microbes for facilitating adaptation in a human-made port environment.

| S-EPMC10256201 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data