• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of jbacterPermissionsJournals.ASM.orgJournalJB ArticleJournal InfoAuthorsReviewers
J Bacteriol. Sep 2010; 192(17): 4528–4529.
Published online Jul 2, 2010. doi:  10.1128/JB.00663-10
PMCID: PMC2937367

Complete Genome Sequence of Halalkalicoccus jeotgali B3T, an Extremely Halophilic Archaeon[down-pointing small open triangle]

Abstract

Halalkalicoccus jeotgali B3T, isolated from salt-fermented seafood from South Korea, is an extremely halophilic archaeon belonging to the family Halobacteriaceae. Here, we present the complete genome sequence of the type strain H. jeotgali B3T (3,698,650 bp, with a G+C content of 62.5%), which consists of one chromosome and six plasmids. This is the first complete genome sequence of the Halalkalicoccus species.

Extremely halophilic archaea (haloarchaea) are adapted to hypersaline environments and grow optimally in NaCl solutions of 2.6 M or higher (12). These haloarchaea are classified within the family Halobacteriaceae in the order Halobacteriales; currently, this family comprises 28 genera (3), and only 11 complete genome sequences in Halobacteriaceae have been reported. In a study of archaeal diversity in salt-fermented small shrimp or shellfish from South Korea, our laboratory isolated and characterized 5 novel, extremely halophilic archaeal strains of Halobacteriaceae. These strains included Natronococcus jeotgali (9), Halalkalicoccus jeotgali (11), Halorubrum cibi (7), Haloterrigena jeotgali (10) and Haladaptatus cibarius (8). We have now sequenced the genome of Halalkalicoccus jeotgali B3T; genome sequencing had not been completed or initiated for any strain in this genus when our sequencing project was begun. The genus Halalkalicoccus currently contains only two species, Halalkalicoccus tibetensis (13) and H. jeotgali, and these species exhibit 98.6% gene sequence similarity in their 16S rRNA. The genome of H. jeotgali B3T is the first of this genus to be sequenced.

The complete genome sequence of H. jeotgali B3T was determined by a whole-genome shotgun strategy using Roche 454 GS (FLX Titanium) pyrosequencing (898,168 reads totaling ~348 Mb; ~94-fold coverage of the genome) and a fosmid library (514 reads totaling ~680 kb) at the Genome Resource Center, KRIBB (Korea Research Institute of Bioscience and Biotechnology). Genome sequences from pyrosequencing were processed by Roche's software according to the manufacturer's instructions, and sequences from the fosmid library were processed by PESTAS (6). A total of 898,196 reads were assembled using Newbler Assembler 2.3 (454 Life Science), which generated 54 large contigs (>100 bp in size) with bases having quality scores of 40 and above. The gaps between contigs were closed by primer walking and sequencing of PCR products across the gaps. The annotation was done by merging results obtained from the RAST (Rapid Annotation using Subsystem Technology) pipeline (1), Glimmer 3.02 (2), tRNAscan-SE 1.21 (5), and RNAmmer 1.2 (4).

The H. jeotgali B3T genome is 3,698,650 bases long with a 62.5% G+C content. The chromosome consists of a single circular chromosome (2,809,118 bp, with a G+C content of 65.0%) and six plasmids (406,285 bp, 55.3%; 363,534 bp, 54.2%; 44,576 bp, 58.9%; 44,459 bp, 54.9%; 23,727 bp, 47.6%; 6,951 bp, 60.6%). The genome contains 3,860 predicted coding sequences and 52 RNA genes (determined using RAST). The chromosome is predicted to contain 3,101 coding sequences with a coding intensity of 90.0%, including 47 tRNA genes, 1 5S rRNA gene, 1 16S rRNA gene, and 1 23S rRNA gene. The largest plasmid contains 466 coding sequences with a coding intensity of 81.2% and 2 tRNA genes, while the other five plasmids contain 425, 44, 48, 29, and 5 coding sequences with coding intensities of 80.2%, 84.2%, 83.0%, 69.6%, and 22.8%, respectively (determined using Glimmer3). More detailed analysis of this genome and comparative analysis with other haloarchaea will provide further insight into the genomic differences and metabolism of the extremely halophilic archaea.

Acknowledgments

This work was supported by NMC0300837 and TDPAF (Technology Development Program for Agriculture and Forestry).

Footnotes

[down-pointing small open triangle]Published ahead of print on 2 July 2010.

REFERENCES

1. Aziz, R. K., D. Bartels, A. A. Best, M. DeJongh, T. Disz, R. A. Edwards, K. Formsma, S. Gerdes, E. M. Glass, M. Kubal, F. Meyer, G. J. Olsen, R. Olson, A. L. Osterman, R. A. Overbeek, L. K. McNeil, D. Paarmann, T. Paczian, B. Parrello, G. D. Pusch, C. Reich, R. Stevens, O. Vassieva, V. Vonstein, A. Wilke, and O. Zagnitko. 2008. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75. [PMC free article] [PubMed]
2. Delcher, A. L., K. A. Bratke, E. C. Powers, and S. L. Salzberg. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673-679. [PMC free article] [PubMed]
3. Euzeby, J. P. 1997. List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet. Int. J. Syst. Bacteriol. 47:590-592. [PubMed]
4. Lagesen, K., P. Hallin, E. A. Rodland, H. H. Staerfeldt, T. Rognes, and D. W. Ussery. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35:3100-3108. [PMC free article] [PubMed]
5. Lowe, T. M., and S. R. Eddy. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955-964. [PMC free article] [PubMed]
6. Nam, S. H., D. W. Kim, T. S. Jung, Y. S. Choi, H. S. Choi, S. H. Choi, and H. S. Park. 2009. PESTAS: a web server for EST analysis and sequence mining. Bioinformatics 25:1846-1848. [PubMed]
7. Roh, S. W., and J. W. Bae. 2009. Halorubrum cibi sp. nov., an extremely halophilic archaeon from salt-fermented seafood. J. Microbiol. 47:162-166. [PubMed]
8. Roh, S. W., M. L. Lee, and J. W. Bae. 2010. Haladaptatus cibarius sp. nov., an extremely halophilic archaeon from seafood, and emended description of the genus Haladaptatus. Int. J. Syst. Evol. Microbiol. 60:1187-1190. [PubMed]
9. Roh, S. W., Y.-D. Nam, H.-W. Chang, K.-H. Kim, H.-J. Lee, H.-M. Oh, and J.-W. Bae. 2007. Natronococcus jeotgali sp. nov., a halophilic archaeon isolated from shrimp jeotgal, a traditional fermented seafood from Korea. Int. J. Syst. Evol. Microbiol. 57:2129-2131. [PubMed]
10. Roh, S. W., Y. D. Nam, H. W. Chang, K. H. Kim, Y. Sung, M. S. Kim, H. M. Oh, and J. W. Bae. 2009. Haloterrigena jeotgali sp. nov., an extremely halophilic archaeon from salt-fermented food. Int. J. Syst. Evol. Microbiol. 59:2359-2363. [PubMed]
11. Roh, S. W., Y. D. Nam, H. W. Chang, Y. Sung, K. H. Kim, H. M. Oh, and J. W. Bae. 2007. Halalkalicoccus jeotgali sp. nov., a halophilic archaeon from shrimp jeotgal, a traditional Korean fermented seafood. Int. J. Syst. Evol. Microbiol. 57:2296-2298. [PubMed]
12. Ventosa, A., J. J. Nieto, and A. Oren. 1998. Biology of moderately halophilic aerobic bacteria. Microbiol. Mol. Biol. Rev. 62:504-544. [PMC free article] [PubMed]
13. Xue, Y., H. Fan, A. Ventosa, W. D. Grant, B. E. Jones, D. A. Cowan, and Y. Ma. 2005. Halalkalicoccus tibetensis gen. nov., sp. nov., representing a novel genus of haloalkaliphilic archaea. Int. J. Syst. Evol. Microbiol. 55:2501-2505. [PubMed]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...