Browse
Submit Data
Databases
API
Help

Dataset Information

9 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Closed Genome Sequence of Octadecabacter temperatus SB1, the First Mesophilic Species of the Genus Octadecabacter.

ABSTRACT: The Gram-negative alphaproteobacterium Octadecabacter temperatus SB1 (DSM 26878) belongs to the marine Roseobacter clade. The genome of this strain is the smallest closed genome of the Roseobacter clade. O. temperatus SB1 is the first described nonpolar mesophilic isolate of the genus Octadecabacter and the type strain of the species.

SUBMITTER: Voget S

PROVIDER: S-EPMC4566189 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Closed Genome Sequence of Octadecabacter temperatus SB1, the First Mesophilic Species of the Genus Octadecabacter.

Voget Sonja S Billerbeck Sara S Simon Meinhard M Daniel Rolf R

Genome announcements 20150910 5

The Gram-negative alphaproteobacterium Octadecabacter temperatus SB1 (DSM 26878) belongs to the marine Roseobacter clade. The genome of this strain is the smallest closed genome of the Roseobacter clade. O. temperatus SB1 is the first described nonpolar mesophilic isolate of the genus Octadecabacter and the type strain of the species. ...[more]

PMID: 26358607

Similar Datasets

First Closed Genome Sequence of Campylobacter fetus subsp. venerealis bv. intermedius.

Project description:Campylobacter fetus subsp. venerealis bv. intermedius is a variant of C. fetus subsp. venerealis, the causative agent of bovine genital campylobacteriosis, a venereal disease associated with abortion and infertility in cattle. We report the first closed whole-genome sequence of this biovar.

| S-EPMC3916489 | biostudies-literature

Genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultivated representative of the order Methanocellales.

Project description:We report complete genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultured representative of the order Methanocellales once recognized as an uncultured key archaeal group for methane emission in rice fields. The genome sequence of M. paludicola consists of a single circular chromosome of 2,957,635 bp containing 3004 protein-coding sequences (CDS). Genes for most of the functions known in the methanogenic archaea were identified, e.g. a full complement of hydrogenases and methanogenesis enzymes. The mixotrophic growth of M. paludicola was clarified by the genomic characterization and re-examined by the subsequent growth experiments. Comparative genome analysis with the previously reported genome sequence of RC-I(MRE50), which was metagenomically reconstructed, demonstrated that about 70% of M. paludicola CDSs were genetically related with RC-I(MRE50) CDSs. These CDSs included the genes involved in hydrogenotrophic methane production, incomplete TCA cycle, assimilatory sulfate reduction and so on. However, the genetic components for the carbon and nitrogen fixation and antioxidant system were different between the two Methanocellales genomes. The difference is likely associated with the physiological variability between M. paludicola and RC-I(MRE50), further suggesting the genomic and physiological diversity of the Methanocellales methanogens. Comparative genome analysis among the previously determined methanogen genomes points to the genome-wide relatedness of the Methanocellales methanogens to the orders Methanosarcinales and Methanomicrobiales methanogens in terms of the genetic repertoire. Meanwhile, the unique evolutionary history of the Methanocellales methanogens is also traced in an aspect by the comparative genome analysis among the methanogens.

| S-EPMC3146512 | biostudies-literature

First <i>de novo</i> draft genome sequence of <i>Oryza coarctata</i>, the only halophytic species in the genus Oryza.

Project description:Oryza coarctata plant, collected from Sundarban delta of West Bengal, India, has been used in the present study to generate draft genome sequences, employing the hybrid genome assembly with Illumina reads and third generation Oxford Nanopore sequencing technology. We report for the first time the draft genome with the coverage of 85.71 % and deposited the raw data in NCBI SRA, with BioProject ID PRJNA396417.

| S-EPMC5657017 | biostudies-literature

Chromosome-scale genome assembly of Eustoma grandiflorum, the first complete genome sequence in the genus Eustoma.

Project description:Eustoma grandiflorum (Raf.) Shinn. is an annual herbaceous plant native to the southern United States, Mexico, and the Greater Antilles. It has a large flower with a variety of colors and is an important flower crop. In this study, we established a chromosome-scale de novo assembly of E. grandiflorum genome sequences by integrating four genomic and genetic approaches: (1) Pacific Biosciences (PacBio) Sequel deep sequencing, (2) error correction of the assembly by Illumina short reads, (3) scaffolding by chromatin conformation capture sequencing (Hi-C), and (4) genetic linkage maps derived from an F2 mapping population. Thirty-six pseudomolecules and 64 unplaced scaffolds were created, with a total length of 1,324.8 Mb. A total of 36,619 genes were predicted on the genome as high-confidence genes. A comparison of genome structure between E. grandiflorum and C. canephora or O. pumila suggested whole-genome duplication after the divergence between the families Gentianaceae and Rubiaceae. Phylogenetic analysis with single-copy genes suggested that the divergence time between Gentianaceae and Rubiaceae was 74.94 MYA. Genetic diversity analysis was performed for nine commercial E. grandiflorum varieties bred in Japan, from which 254,205 variants were identified. This first report on the construction of a reference genome sequence in the genus Eustoma is expected to contribute to genetic and genomic studies in this genus and in the family Gentianaceae.

| S-EPMC9911058 | biostudies-literature

Genome sequence of the cellulosome-producing mesophilic organism Clostridium cellulovorans 743B.

Project description:Clostridium cellulovorans 743B was isolated from a wood chip pile and is an anaerobic and mesophilic spore-forming bacterium. This organism degrades native substrates in soft biomass such as corn fiber and rice straw efficiently by producing an extracellular enzyme complex called the cellulosome. Here we report the genome sequence of C. cellulovorans 743B.

| S-EPMC2812471 | biostudies-literature

Closed Genome Sequence of Clostridium pasteurianum ATCC 6013.

Project description:We report here the closed genome of Clostridium pasteurianum ATCC 6013, a saccharolytic, nitrogen-fixing, and spore-forming Gram-positive obligate anaerobe. The organism is of biotechnological interest due to the production of solvents (butanol and 1,3-propanediol) but can be associated with food spoilage. The genome comprises a total of 4,351,223 bp.

| S-EPMC4335343 | biostudies-literature

First draft genome sequence from a member of the genus agrococcus, isolated from modern microbialites.

Project description:We report the first draft genome sequence from a member of the genus Agrococcus, isolated from cold thrombolytic microbialites within Pavilion Lake, British Columbia, Canada. The draft genome assembly for Agrococcus pavilionensis strain RW-1 has a size of 2,878,403 bp with a G+C content of 72.56%.

| S-EPMC3695436 | biostudies-literature

Insight into the First Draft Genome Sequence of the Genus Sediminibacillus, Sediminibacillus halophilus Strain NSP9.3.

Project description:We report the 3.98-Mbp first draft genome sequence of Sediminibacillus halophilus strain NSP9.3, a moderate halophile isolated from a seasonal salt marsh of the Great Rann of Kutch, India. Exploring the genome of this organism will facilitate the understanding of the mechanism(s) of osmotolerance and survival in differential osmolarity.

| S-EPMC3886954 | biostudies-literature

Genome sequence of the fungus Glarea lozoyensis: the first genome sequence of a species from the Helotiaceae family.

Project description:The anamorphic fungus Glarea lozoyensis mutant strain 74030 is an overproducer of pneumocandin B(0), which is chemically converted into Cancidas, a potent antibiotic against clinically important fungal pathogens. Pneumocandins are acylated, cyclic hexapeptides with unusual hydroxylated amino acids. With the Glarea lozoyensis genome, the first species from the large polyphyletic family Helotiaceae has been sequenced.

| S-EPMC3272893 | biostudies-literature

Genus-wide Yersinia core-genome multilocus sequence typing for species identification and strain characterization.

Project description:The genus Yersinia comprises species that differ widely in their pathogenic potential and public-health significance. Yersinia pestis is responsible for plague, while Yersinia enterocolitica is a prominent enteropathogen. Strains within some species, including Y. enterocolitica, also vary in their pathogenic properties. Phenotypic identification of Yersinia species is time-consuming, labour-intensive and may lead to incorrect identifications. Here, we developed a method to automatically identify and subtype all Yersinia isolates from their genomic sequence. A phylogenetic analysis of Yersinia isolates based on a core subset of 500 shared genes clearly demarcated all existing Yersinia species and uncovered novel, yet undefined Yersinia taxa. An automated taxonomic assignment procedure was developed using species-specific thresholds based on core-genome multilocus sequence typing (cgMLST). The performance of this method was assessed on 1843 isolates prospectively collected by the French National Surveillance System and analysed in parallel using phenotypic reference methods, leading to nearly complete (1814; 98.4 %) agreement at species and infra-specific (biotype and serotype) levels. For 29 isolates, incorrect phenotypic assignments resulted from atypical biochemical characteristics or lack of phenotypic resolution. To provide an identification tool, a database of cgMLST profiles and reference taxonomic information has been made publicly accessible (https://bigsdb.pasteur.fr/yersinia). Genomic sequencing-based identification and subtyping of any Yersinia is a powerful and reliable novel approach to define the pathogenic potential of isolates of this medically important genus.

| S-EPMC6861861 | 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