GENOME ANNOUNCEMENT
Genome Sequence of the Alkaliphilic Bacterium Nitritalea halalkaliphila Type Strain LW7, Isolated from Lonar Lake, India Pramod Kumar Jangir,a Ajit Singh,a S. Shivaji,b and Rakesh Sharmaa,c Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research (CSIR), Delhi, Indiaa; Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research (CSIR), Hyderabad, Indiab; and National Chemical Laboratory, Council of Scientific and Industrial Research (CSIR), Pune, Indiac
An alkaliphilic bacterium, Nitritalea halalkaliphila LW7, which belongs to the family Cyclobacteriacae in the phylum Bacteroidetes, was isolated from Lonar Lake in Maharastra, India. Here we announce the draft genome sequence of the type strain LW7, which contains 3,633,701 bp with a GⴙC content of 48.58%.
N
itritalea halalkaliphila LW7 is a Gram-negative, rod-shaped, nonmotile bacterium that was isolated from a water sample collected at a depth of 4.5 m from Lonar Lake, Buldana District, Maharastra, India (2). The strain grows within a pH range of 7.5 to 12 and a salinity range of 1 to 22% (NaCl [wt/vol]), with an optimum growth at pH 10 and salinity between 2 and 5% (NaCl [wt/ vol]) (2). The bacterium is a type strain of a novel species, as well as a novel genus in the family Cyclobacteriaceae in phylum Bacteroidetes (2). Here we report genome sequence of the type strain LW7 of N. halalkaliphila. The genomic DNA of N. halalkaliphila LW7 was extracted from a culture grown on Zobell marine broth (pH 10.0) at 30°C. The genome of N. halalkaliphila LW7 was sequenced by using a whole-genome shotgun strategy with Ion Torrent, which produced a total of 732,711 reads with an average read length of 239 bp. Assembly was performed by MIRA software (version 3.4.0), and a total number of 140 contigs were generated. The contigs were used for gene prediction and annotation by the automatic Prokaryotic Genomes Annotation Pipeline at NCBI, which uses GeneMark and Glimmer (4, 5, 9) for gene prediction and compares the translated proteins with the Nonredundant Proteins (NR) database at GenBank, Entrez Protein Clusters (7), the Conserved Domain Database (10), and the Cluster of Orthologous Groups (COGs) database (12) for annotation. The draft genome was also uploaded to the IMG (11) and the RAST (3) servers for annotation, identification of metabolic pathways, and comparative analysis with other bacterial genomes. The unclosed draft genome sequence of the strain LW7 contains 3,633,701 bp with a G⫹C content of 48.58%. The genome contains 3,103 protein-coding genes and 38 tRNA genes. The RAST server revealed that Algoriphagus sp. strain PR1 (score, 531) and Cytophaga hutchinsonii ATCC 33406 (score, 344) were the closest neighbors of N. halalkaliphila LW7. The genome is predicted to have genes for glycolysis, the tricarboxylic acid (TCA) cycle, the pentose phosphate pathway, and trehalose uptake and utilization. The genes were also present for high-affinity phosphate transporter and phosphate metabolism, inorganic sulfur assimilation, ammonia assimilation, and biotin, thiamine, and coenzyme A biosynthesis. Similar to the genomes of many other members of the phylum Bacteroidetes, the genes for ABC transporters were missing in the genome of strain LW7, and it contained large numbers of genes for the Ton and Tol types of transporters. The N. halalkaliphila LW7 genome possess genes for the Na⫹/H⫹ transporter, multisubunit cation transporter, sodium-
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dependent phosphate transporters, and proton-dependent peptide transporter, which were absent in the Algoriphagus sp. strain PR1 genome (1). The Na⫹/H⫹ transporter and multisubunit cation transporter play important role in bacterial growth in alkaline and saline conditions (6, 8) and might be responsible for the adaptation of strain LW7 to alkaline and saline environments. Nucleotide sequence accession numbers. This Whole Genome Shotgun project has been deposited in DDBJ/EMBL/ GenBank under accession no. AJYA00000000. The version described in this paper is the first version, AJYA01000000. The 140 contigs have been deposited under accession no. AJYA01000001 to AJYA01000140. ACKNOWLEDGMENTS We thank the Director of I.G.I.B. for encouragement and support. We thank Atima Agarwal and Ashish George (Invitrogen Bioservices India, Pvt., Ltd.) for help in sequencing and assembly. A.S. acknowledges CSIR for a senior research fellowship. R.S. thanks CSIR—Institute of Genomics and Integrative Biology for funding. S.S. thanks the Department of Biotechnology, New Delhi, and the CSIR Network Project on Biodiversity for funding.
REFERENCES 1. Alegado RA, et al. 2011. Complete genome sequence of Algoriphagus sp. PR1, bacterial prey of a colony-forming choanoflagellate. J. Bacteriol. 193: 1485–1486. 2. Anil KP, Srinivas TN, Pavan KP, Madhu S, Shivaji S. 2010. Nitritalea halalkaliphila gen. nov., sp. nov., an alkaliphilic bacterium of the family ’Cyclobacteriaceae’, phylum Bacteroidetes. Int. J. Syst. Evol. Microbiol. 60: 2320 –2325. 3. Aziz R, et al. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. doi:10.1186/1471-2164-9-75. 4. Borodovsky M, McIninch J. 1993. GeneMark: parallel gene recognition for both DNA strands. Comput. Chem. 17:123–133. 5. Delcher AL, Hormon D, Kasif S, White O, Salzberg SL. 1999. Improved microbialgeneidentificationwithGLIMMER.NucleicAcidsRes.27:4636–4641. 6. Hiramatsu T, Kodama K, Kuroda T, Mizushima T, Tsuchiya T. 1998. A putative multisubunit Na⫹/H⫹ antiporter from Staphylococcus aureus. J. Bacteriol. 180:6642– 6648.
Received 20 July 2012 Accepted 27 July 2012 Address correspondence to Rakesh Sharma,
[email protected]. P.K.J. and A.S. contributed equally to this article. Copyright © 2012, American Society for Microbiology. All Rights Reserved. doi:10.1128/JB.01302-12
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7. Klimke, W, et al. 2009. The National Center for Biotechnology Information’s Protein Clusters Database. Nucleic Acids Research. 37(Database issue):D32–D36. 8. Krulwich TA, Sachs G, Padan E. 2011. Molecular aspects of bacterial pH sensing and homeostasis Nat. Rev. Microbiol. 9:330 –343. 9. Lukashin A, Borodovsky M. 1998. GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res. 26:1107–1115. 10. Marchler-Bauer A, et al. 2011. CDD: a Conserved Domain Database for
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the functional annotation of proteins. Nucleic Acids Res. 39(Database issue):D225–D229. 11. Markowitz VM, et al. 2009. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 25:2271–2278. 12. Tatusov RL, Galperin MY, Natle DA, Koonin EV. 2000. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28:33–36.
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