Standards in Genomic Sciences

http://link.springer.com/journal/40793

List of Papers (Total 748)

Genome sequence of the white-rot fungus Irpex lacteus F17, a type strain of lignin degrader fungus

Irpex lacteus, a cosmopolitan white-rot fungus, degrades lignin and lignin-derived aromatic compounds. In this study, we report the high-quality draft genome sequence of I. lacteus F17, isolated from a decaying hardwood tree in the vicinity of Hefei, China. The genome is 44,362,654 bp, with a GC content of 49.64% and a total of 10,391 predicted protein-coding genes. In addition, a ...

Draft genome sequence of the cellulolytic endophyte Chitinophaga costaii A37T2T

Here we report the draft genome sequence of Chitinophaga costai A37T2T (=CIP 110584T, =LMG 27458T), which was isolated from the endophytic community of Pinus pinaster tree. The total genome size of C. costaii A37T2T is 5.07 Mbp, containing 4204 coding sequences. Strain A37T2T encoded multiple genes likely involved in cellulolytic, chitinolytic and lipolytic activities. This genome ...

Complete genome of Arthrobacter alpinus strain R3.8, bioremediation potential unraveled with genomic analysis

Arthrobacter alpinus R3.8 is a psychrotolerant bacterial strain isolated from a soil sample obtained at Rothera Point, Adelaide Island, close to the Antarctic Peninsula. Strain R3.8 was sequenced in order to help discover potential cold active enzymes with biotechnological applications. Genome analysis identified various cold adaptation genes including some coding for anti-freeze ...

Complete genome sequence of the sulfur-oxidizing chemolithoautotrophic Sulfurovum lithotrophicum 42BKTT

A sulfur-oxidizing chemolithoautotrophic bacterium, Sulfurovum lithotrophicum 42BKTT, isolated from hydrothermal sediments in Okinawa, Japan, has been used industrially for CO2 bio-mitigation owing to its ability to convert CO2 into C5H8NO4 − at a high rate of specific mitigation (0.42 g CO2/cell/h). The genome of S. lithotrophicum 42BKTT comprised of a single chromosome of ...

Permanent draft genome sequence of Frankia sp. NRRL B-16219 reveals the presence of canonical nod genes, which are highly homologous to those detected in Candidatus Frankia Dg1 genome

Frankia sp. NRRL B-16219 was directly isolated from a soil sample obtained from the rhizosphere of Ceanothus jepsonii growing in the USA. Its host plant range includes members of Elaeagnaceae species. Phylogenetically, strain NRRL B-16219 is closely related to “Frankia discariae” with a 16S rRNA gene similarity of 99.78%. Because of the lack of genetic tools for Frankia, our ...

Genome sequence of the sulfur-oxidizing Bathymodiolus thermophilus gill endosymbiont

Bathymodiolus thermophilus, a mytilid mussel inhabiting the deep-sea hydrothermal vents of the East Pacific Rise, lives in symbiosis with chemosynthetic Gammaproteobacteria within its gills. The intracellular symbiont population synthesizes nutrients for the bivalve host using the reduced sulfur compounds emanating from the vents as energy source. As the symbiont is uncultured, ...

Draft genome sequences of two opportunistic pathogenic strains of Staphylococcus cohnii isolated from human patients

Herein, we report the draft-genome sequences and annotation of two opportunistic pathogenic strains of Staphylococcus cohnii isolated from humans. One strain (SC-57) was isolated from blood from a male patient in May 2006 and the other (SC-532) from a catheter from a male patient in June 2006. Similar to other genomes of Staphylococcus species, most genes (42%) of both strains are ...

Complete Genome sequence of the nematicidal Bacillus thuringiensis MYBT18246

Bacillus thuringiensis is a rod-shaped facultative anaerobic spore forming bacterium of the genus Bacillus . The defining feature of the species is the ability to produce parasporal crystal inclusion bodies, consisting of δ-endotoxins, encoded by cry-genes. Here we present the complete annotated genome sequence of the nematicidal B. thuringiensis strain MYBT18246. The genome ...

The draft genome of the hyperthermophilic archaeon Pyrodictium delaneyi strain hulk, an iron and nitrate reducer, reveals the capacity for sulfate reduction

Pyrodictium delaneyi strain Hulk is a newly sequenced strain isolated from chimney samples collected from the Hulk sulfide mound on the main Endeavour Segment of the Juan de Fuca Ridge (47.9501 latitude, −129.0970 longitude, depth 2200 m) in the Northeast Pacific Ocean. The draft genome of strain Hulk shared 99.77% similarity with the complete genome of the type strain Su06T, which ...

The complete genome sequence of the cold adapted crude-oil degrader: Pedobacter steynii DX4

Pedobacter steynii DX4 was isolated from the soil of Tibetan Plateau and it can use crude oil as sole carbon and energy source at 15 °C. The genome of Pedobacter steynii DX4 has been sequenced and served as basis for analysis its metabolic mechanism. It is the first genome of crude oil degrading strain in Pedobacter genus. The 6.58 Mb genome has an average G + C content of 41.31% ...

High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460

The genetic platforms of Deinococcus species remain the only systems in which massive ionizing radiation (IR)-induced genome damage can be investigated in vivo at exposures commensurate with cellular survival. We report the whole genome sequence of the extremely IR-resistant rod-shaped bacterium Deinococcus ficus KS 0460 and its phenotypic characterization. Deinococcus ficus KS ...

Complete genome sequence of the sand-sediment actinobacterium Nocardioides dokdonensis FR1436T

Nocardioides dokdonensis, belonging to the class Actinobacteria, was first isolated from sand sediment of a beach in Dokdo, Korea, in 2005. In this study, we determined the genome sequence of FR1436, the type strain of N. dokdonensis, and analyzed its gene contents. The genome sequence is the second complete one in the genus Nocardioides after that of Nocardioides sp. JS614. It is ...

The genome of the cotton bacterial blight pathogen Xanthomonas citri pv. malvacearum strain MSCT1

Xanthomonas citri pv. malvacearum is a major pathogen of cotton, Gossypium hirsutum L.. In this study we report the complete genome of the X. citri pv. malvacearum strain MSCT1 assembled from long read DNA sequencing technology. The MSCT1 genome is the first X. citri pv. malvacearum genome with complete coding regions for X. citri pv. malvacearum transcriptional activator-like ...

Neisseria lactamica Y92–1009 complete genome sequence

We present the high quality, complete genome assembly of Neisseria lactamica Y92–1009 used to manufacture an outer membrane vesicle (OMV)-based vaccine, and a member of the Neisseria genus. The strain is available on request from the Public Health England Meningococcal Reference Unit. This Gram negative, dipplococcoid bacterium is an organism of worldwide clinical interest because ...

First draft genome sequence of a strain from the genus Fusibacter isolated from Salar de Ascotán in Northern Chile

Fusibacter sp. 3D3 (ATCC BAA-2418) is an arsenate-reducing halotolerant strain within the Firmicutes phylum, isolated from the Salar de Ascotán, a hypersaline salt flat in Northern Chile. This high-Andean closed basin is an athalassohaline environment located at the bottom of a tectonic basin surrounded by mountain range, including some active volcanoes. This landscape can be an ...

High-quality draft genome sequence of a biofilm forming lignocellulolytic Aspergillus niger strain ATCC 10864

Filamentous fungus Aspergillus niger has high industrial value due to their lignocellulolytic enzyme activities and ATCC 10864 is one of the few type strains of A. niger which has a unique biofilm forming capability. Here we report the first draft genome sequence of A. niger ATCC 10864 strain. The genome of A. niger ATCC 10864 is 36,172,237 bp long and comprise of 310 scaffolds ...

Complete genome sequence of Leuconostoc suionicum DSM 20241T provides insights into its functional and metabolic features

The genome of Leuconostoc suionicum DSM 20241T (=ATCC 9135T = LMG 8159T = NCIMB 6992T) was completely sequenced and its fermentative metabolic pathways were reconstructed to investigate the fermentative properties and metabolites of strain DSM 20241T during fermentation. The genome of L. suionicum DSM 20241T consists of a circular chromosome (2026.8 Kb) and a circular plasmid (21.9 ...

Draft genome sequences of strains Salinicola socius SMB35T, Salinicola sp. MH3R3–1 and Chromohalobacter sp. SMB17 from the Verkhnekamsk potash mining region of Russia

Halomonads are moderately halophilic bacteria that are studied as models of prokaryotic osmoadaptation and sources of enzymes and chemicals for biotechnological applications. Despite the progress in understanding the diversity of these organisms, our ability to explain ecological, metabolic, and biochemical traits of halomonads at the genomic sequence level remains limited. This ...

Insights into Cedecea neteri strain M006 through complete genome sequence, a rare bacterium from aquatic environment

Cedecea neteri M006 is a rare bacterium typically found as an environmental isolate from the tropical rainforest Sungai Tua waterfall (Gombak, Selangor, Malaysia). It is a Gram-reaction-negative, facultative anaerobic, bacillus. Here, we explore the features of Cedecea neteri M006, together with its genome sequence and annotation. The genome comprised 4,965,436 bp with 4447 ...

Draft genome sequence of Desulfoplanes formicivorans Pf12BT, a sulfate-reducing bacterium of the family Desulfomicrobiaceae

Desulfoplanes formicivorans strain Pf12BT is the type strain of the type species in the genus Desulfoplanes, which is the one of the genera in the family Desulfomicrobiaceae within the order Desulfovibrionales. This deltaproteobacterium was isolated from a blackish meromictic lake sediment. D. formicivorans strain Pf12BT is a Gram-negative, motile and sulfate-reducing bacterium. ...

Genomics insights into production of 2-methylisoborneol and a putative cyanobactin by Planktothricoides sp. SR001

Planktothricoides is a free-living filamentous cyanobacterium belonging to the order Oscillatoriales and the family Phormidiaceae, capable of forming bloom in fresh and brackish waters. A unicyanobacterial non-axenic culture dominated by Planktothricoides sp. SR001 was obtained from a freshwater reservoir in Singapore. The draft genome presented here is the first tropical ...

High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482T, isolated from raw cow milk

Chryseobacterium bovis DSM 19482T (Hantsis-Zacharov et al., Int J Syst Evol Microbiol 58:1024-1028, 2008) is a Gram-negative, rod shaped, non-motile, facultative anaerobe, chemoorganotroph bacterium. C. bovis is a member of the Flavobacteriaceae, a family within the phylum Bacteroidetes. It was isolated when psychrotolerant bacterial communities in raw milk and their proteolytic ...

Complete genome sequence of bacteriochlorophyll-synthesizing bacterium Porphyrobacter neustonensis DSM 9434

The genus Porphyrobacter belongs to aerobic anoxygenic phototrophic bacteria cluster. Porphyrobacter neustonensis DSM 9434 was isolated from a eutrophic freshwater pond in Australia, and is able to synthesize Bacteriochlorophyll a as well as grow under aerobic conditions. It is the type species of the genus Porphyrobacter. Here we describe the characteristics of the strain DSM ...

Chromosomal features of Escherichia coli serotype O2:K2, an avian pathogenic E. coli

Escherichia coli causing infection outside the gastrointestinal system are referred to as extra-intestinal pathogenic E. coli. Avian pathogenic E. coli is a subgroup of extra-intestinal pathogenic E. coli and infections due to avian pathogenic E. coli have major impact on poultry production economy and welfare worldwide. An almost defining characteristic of avian pathogenic E. coli ...