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Draft Genome Sequence of Psychrobacter aquaticus Strain CMS 56T, Isolated from a Cyanobacterial Mat Sample Collected from Water Bodies in the McMurdo Dry Valley Region of Antarctica.
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PMID:  24201199     Owner:  NLM     Status:  PubMed-not-MEDLINE    
Abstract/OtherAbstract:
We report the 3.2-Mb draft genome sequence of Psychrobacter aquaticus strain CMS 56(T), isolated from a cyanobacterial mat sample collected from a water body in the McMurdo Dry Valley region of Antarctica.
Authors:
Gundlapally Satyanarayana Reddy; Sreenivas Ara; Aditya Singh; Anil Kumar Pinnaka; S Shivaji
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Publication Detail:
Type:  Journal Article     Date:  2013-11-07
Journal Detail:
Title:  Genome announcements     Volume:  1     ISSN:  2169-8287     ISO Abbreviation:  Genome Announc     Publication Date:  2013  
Date Detail:
Created Date:  2013-11-08     Completed Date:  2013-11-08     Revised Date:  2013-11-15    
Medline Journal Info:
Nlm Unique ID:  101595808     Medline TA:  Genome Announc     Country:  United States    
Other Details:
Languages:  eng     Pagination:  -     Citation Subset:  -    
Affiliation:
CSIR-Centre for Cellular and Molecular Biology, Habsiguda, Hyderabad, Andhra Pradesh, India.
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Journal Information
Journal ID (nlm-ta): Genome Announc
Journal ID (iso-abbrev): Genome Announc
Journal ID (hwp): ga
Journal ID (pmc): ga
Journal ID (publisher-id): GA
ISSN: 2169-8287
Publisher: American Society for Microbiology, 1752 N St., N.W., Washington, DC
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Copyright © 2013 Reddy et al.
open-access:
Received Day: 1 Month: 10 Year: 2013
Accepted Day: 2 Month: 10 Year: 2013
Electronic publication date: Day: 7 Month: 11 Year: 2013
collection publication date: Season: Nov-Dec Year: 2013
Volume: 1 Issue: 6
E-location ID: e00918-13
PubMed Id: 24201199
ID: 3820780
Publisher Id: genomeA00918-13
DOI: 10.1128/genomeA.00918-13

Draft Genome Sequence of Psychrobacter aquaticus Strain CMS 56T, Isolated from a Cyanobacterial Mat Sample Collected from Water Bodies in the McMurdo Dry Valley Region of Antarctica
Gundlapally Satyanarayana Reddya
Sreenivas Araa
Aditya Singhb
Anil Kumar Pinnakab
S. Shivajia
CSIR—Centre for Cellular and Molecular Biology, Habsiguda, Hyderabad, Andhra Pradesh, Indiaa
CSIR—Institute of Microbial Technology, Sector 39A, Chandigarh, Indiab
Correspondence: Address correspondence to S. Shivaji, shivas@ccmb.res.in.

GENOME ANNOUNCEMENT

Psychrobacter aquaticus strain CMS 56T is a Gram-negative, nonmotile, halotolerant, psychrophilic bacterium, isolated from a cyanobacterial mat sample collected from various water bodies in the McMurdo Dry Valley region of Antarctica (1). Based on the 16S rRNA gene sequence similarity, the closest neighbor of Psychrobacter aquaticus CMS 56T is Psychrobacter vallis CMS 39T, isolated at the same time, with a similarity score of 99.59%, followed by other members of the genus Psychrobacter, with similarity scores ranging from 99.05 to 89.41%.

Whole-genome sequencing of Psychrobacter aquaticus CMS 56T was performed using the Roche 454 (FLX Titanium) pyrosequencing platform, which yielded a raw sequence of 136,405,203 bp in 411,734 reads, which is 40× coverage of the genome. Assembly of the raw sequencing data was carried out using GS De Novo Assembler (v 2.8), which yielded a genome sequence of 3,216,409 bp in 38 contigs. All of the contigs were larger than 561 bp, with the longest contig being 535,134 bp long with a G+C mol% of 42.63%. Annotation of the assembled genome was performed using RAST (Rapid Annotation using Subsystem Technology) (2), tRNA was predicted by tRNAscan-SE (v. 1.23) (3), and rRNA genes were predicted by RNAmmer (v. 1.2) (4).

The Psychrobacter aquaticus CMS 56T draft genome sequence has 2,814 predicted coding regions, including one 5S rRNA, one 23S rRNA, one 16S rRNA, and 43 tRNA genes. In the annotation there are 41 genes encoding resistance against antibiotics and toxic compounds, including 6 genes for arsenic resistance, 2 genes for mercuric resistance, 4 genes for fluoroquinolone resistance, 5 genes for cobalt-zinc-cadmium resistance, and 12 genes for copper homeostasis. There are 80 genes for membrane transport, including 88 Ton and Tol transport systems. Several stress response genes (97 genes) were also predicted in the annotation.

The functional comparison of the genome sequence, performed using the SEED framework for comparative genomics (http://www.theseed.org), revealed that Psychrobacter arcticus 273-4, Psychrobacter cryohalolentis K5, Moraxella catarrhalis RH4, and Enhydrobacter aerosaccus SK60, with similarity score values of 542, 521, 368, and 281, respectively, are the closest neighbors of Psychrobacter aquaticus CMS-56T. The whole-genome sequence of Psychrobacter aquaticus CMS-56T, isolated from Antarctica, will help in our understanding of the adaptation of psychrophiles to harsh conditions.

Nucleotide sequence accession numbers.

The draft genome sequence of Psychrobacter aquaticus strain CMS 56T has been deposited in DDBJ/EMBL/GenBank under the accession number AUSW00000000. The version described in this paper is version AUSW01000000.


Notes

Citation Reddy GS, Ara S, Singh A, Kumar Pinnaka A, Shivaji S. 2013. Draft genome sequence of Psychrobacter aquaticus strain CMS 56T, isolated from a cyanobacterial mat sample collected from water bodies in the McMurdo dry valley region of Antarctica. Genome Announc. 1(6):e00918-13. doi:10.1128/genomeA.00918-13.

ACKNOWLEDGMENTS

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


REFERENCES
1.. Shivaji S,Reddy GS,Suresh K,Gupta P,Chintalapati S,Schumann P,Stackebrandt E,Matsumoto GI. Year: 2005Psychrobacter vallis sp. nov. and Psychrobacter aquaticus sp. nov., from Antarctica. Int. J. Syst. Evol. Microbiol.55:757–76215774658
2.. Aziz RK,Bartels D,Best AA,DeJongh M,Disz T,Edwards RA,Formsma K,Gerdes S,Glass EM,Kubal M,Meyer F,Olsen GJ,Olson R,Osterman AL,Overbeek RA,McNeil LK,Paarmann D,Paczian T,Parrello B,Pusch GD,Reich C,Stevens R,Vassieva O,Vonstein V,Wilke A,Zagnitko O. Year: 2008The RAST server: rapid annotations using subsystems technology. BMC Genomics9:7518261238
3.. Lowe TM,Eddy SR. Year: 1997tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res.25:955–9649023104
4.. Lagesen K,Hallin P,Rødland EA,Staerfeldt HH,Rognes T,Ussery DW. Year: 2007RNAmmer: consistent and rapid annotation of ribosomal rRNA genes. Nucleic Acids Res.35:3100–310817452365

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  • Prokaryotes


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