Draft Genome Sequence of Leifsonia rubra Strain CMS 76RT, Isolated from a Cyanobacterial Mat Sample from a Pond in Wright Valley, McMurdo, Antarctica Anil Kumar Pinnaka,a Aditya Singh,a Sreenivas Ara,b Zareena Begum,b Gundlapally Satyanaryana Reddy,b S. Shivajib CSIR—Institute of Microbial Technology, Chandigarh, Indiaa; CSIR—Centre for Cellular and Molecular Biology, Hyderabad, Andhra Pradesh, Indiab
The 2.7-Mb draft genome sequence of Leifsonia rubra strain CMS 76RT, isolated from a cyanobacterial mat sample from a pond in Wright Valley, McMurdo, Antarctica, is reported. Received 18 July 2013 Accepted 22 July 2013 Published 15 August 2013 Citation Kumar Pinnaka A, Singh A, Ara S, Begum Z, Reddy GS, Shivaji S. 2013. Draft genome sequence of Leifsonia rubra strain CMS 76RT, isolated from a cyanobacterial mat sample from a pond in Wright Valley, McMurdo, Antarctica. Genome Announc. 1(4):e00633-13. doi:10.1128/genomeA.00633-13. Copyright © 2013 Kumar Pinnaka et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to S. Shivaji,
[email protected].
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eifsonia rubra strain CMS 76RT was isolated from a cyanobacterial mat sample collected from a pond in Wright Valley, McMurdo, Antarctica. It is a Gram-positive, nonmotile, curved-rodshaped bacterium. At the level of the 16S rRNA gene, members of the genus Leifsonia exhibited 95 to 96% similarity (1) with Leifsonia rubra strain CMS 76RT. Whole-genome sequencing of Leifsonia rubra strain CMS 76RT was performed using the Roche 454 (FLX Titanium) pyrosequencing platform. The sequencing yielded 127,864,390 bases in 307,943 reads, which is 46⫻ coverage of the genome. Assembly of the raw sequencing data was performed using the GS De Novo Assembler (v 2.8), which yielded a genome of 2,775,399 bp in 207 contigs, with a G⫹C of 44.31%. All contigs were larger than 500 bp, with the longest contig being 307,711 bp long. Annotation of the assembly data 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). There are a total of 2,672 protein-coding genes and 51 RNA features in the annotated genome sequence of Leifsonia rubra strain CMS 76RT. There are 96 genes for membrane transport, including 53 ABC transporters. Twenty-two genes were found to be associated with resistance to antibiotics and toxic compounds. We found 6 genes involved in the synthesis of proteorhodopsin in the annotation of the genome sequence of Leifsonia rubra strain CMS 76RT; these may be responsible for the yellow coloration of the bacterial colonies. The whole-genome sequencing of the bac-
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terium will help us in understanding the adaptation and evolution of bacteria under adverse climatic condition like the very low temperature conditions of Antarctica. Nucleotide sequence accession numbers. The draft genome sequence of Leifsonia rubra strain CMS 76RT has been deposited in DDBJ/EMBL/GenBank under the accession number ATIA00000000. The version described in this paper is version ATIA01000000. 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. Reddy GS, Prakash JS, Srinivas R, Matsumoto GI, Shivaji S. 2003. Leifsonia rubra sp. nov. and Leifsonia aurea sp. nov., psychrophiles from a pond in Antarctica. Int. J. Syst. Evol. Microbiol. 53:977–984. 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. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. 3. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955–964. 4. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35:3100 –3108.
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