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. 2013 Aug 15;1(4):e00630-13. doi: 10.1128/genomeA.00630-13

Draft Genome Sequence of Winogradskyella psychrotolerans RS-3T, Isolated from the Marine Transect of Kongsfjorden, Ny-Ålesund, Svalbard, Arctic Ocean

Anil Kumar Pinnaka a, Sreenivas Ara b, Aditya Singh a, S Shivaji b,
PMCID: PMC3744688  PMID: 23950132

Abstract

The 4.3-Mb genome of Winogradskyella psychrotolerans strain RS-3T, isolated from a sediment sample of a marine transect of Kongsfjorden, Ny-Ålesund, Svalbard, Arctic Ocean, is reported.

GENOME ANNOUNCEMENT

Winogradskyella psychrotolerans strain RS-3T is a Gram-negative, nonmotile, rod-coccus shaped bacterium. It was isolated from a marine transect sample from Kongsfjorden, Ny-Ålesund, Svalbard, Arctic Ocean. Winogradskyella pacifica and Winogradskyella thalassocola were reported to be the most closely related species by the 16S rRNA gene sequence analysis, with sequence similarities to the type strains of these species of 98.5 and 97.7%, respectively (1).

The Roche 454 (FLX Titanium) pyrosequencing platform was used to sequence the genome of W. psychrotolerans strain RS-3T. The sequencing yielded 121,341,791 bases in 288,329 reads, which is 28× coverage of the genome. The GS de novo assembler (v2.8) was used for the assembly of the raw sequencing data, which yielded a genome of 4,342,100 bp in 219 contigs, with a G+C% mol of 37.70%. The genome annotation was performed using the Rapid Annotations using Subsystems Technology (RAST) server (2), tRNAs were predicted by tRNAscan-SE (v1.23) (3), and rRNA genes were predicted by RNAmmer (v1.2) (4).

The annotation has a total of 4,068 genes, including 44 RNA genes. The annotation has 54 genes providing resistance against different antibiotics and toxic compounds. There are 107 genes for membrane transport, including 5 ABC transporters and 5 cation transporters. The genome also has 67 genes for different stress responses, including 33 genes for oxidative stress, 14 heat shock response genes, and 5 cold shock response genes.

A functional comparison of the genome was performed using the SEED framework (4) which revealed the closest neighbors of W. psychrotolerans RS-3T to be Flavobacteriales bacterium ALC-1, Croceibacter atlanticus HTCC2559, Cellulophaga sp. MED134, Dokdonia donghaensis MED134, and Zunongwangia profunda SM-A87, with similarity score values of 513, 391, 358, 344, and 343, respectively.

Whole-genome sequencing of this bacterium will help in understanding the metabolism and evolution of bacteria under extreme weather conditions, like the Arctic Ocean.

Nucleotide sequence accession numbers.

The draft genome sequence of W. psychrotolerans RS-3T has been deposited in DDBJ/EMBL/GenBank under the accession no. ATMR00000000. The version described in this paper is the first version, ATMR01000000.

ACKNOWLEDGMENTS

This work was funded by the CSIR network project GENESIS to S.S. at CCMB. A.S. is currently a research intern under Diamond Jubilee Scheme of the CSIR at IMTECH.

Footnotes

Citation Kumar Pinnaka A, Ara S, Singh A, Shivaji S. 2013. Draft genome sequence of Winogradskyella psychrotolerans RS-3T, isolated from the marine transect of Kongsfjorden, Ny-Ålesund, Svalbard, Arctic Ocean. Genome Announc. 1(4):e00630-13. doi:10.1128/genomeA.00630-13.

REFERENCES

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