Skip to main content
Journal of Bacteriology logoLink to Journal of Bacteriology
. 2011 Apr;193(8):2074–2075. doi: 10.1128/JB.00121-11

Genome Sequence of Citromicrobium Strain JLT1363, Isolated from the South China Sea

Qiang Zheng 1, Rui Zhang 1, Nianzhi Jiao 1,*
PMCID: PMC3133042  PMID: 21317332

Abstract

Citromicrobium is a member of the alpha-4 subcluster in the Alphaproteobacteria and is identified as a typical aerobic anoxygenic phototrophic bacterium (AAPB). Here we report the draft genome sequence of a non-AAPB strain, Citromicrobium sp. JLT1363. The genome sequence reveals a multimechanism of horizontal gene transfer, as well.


The genus Citromicrobium was first named by Yurkov et al. in 1999, and it is one clade of the alpha-4 subcluster in the Alphaproteobacteria (14). Currently, this genus contains only one species, Citromicrobium bathyomarinum. The type strain C. bathyomarinum JF-1 was isolated from deep-sea hydrothermal vent plume waters. C. bathyomarinum JF-1 and other Citromicrobium spp. were identified as aerobic anoxygenic phototrophic bacteria (AAPB) (6, 11, 14). We isolated a Citromicrobium sp. strain, JLT1363 (98.0% sequence similarity of 16S rRNA gene with that of JF-1), not showing phototrophic growth, from the surface water of the South China Sea. Here we report the whole-genome sequence of Citromicrobium sp. JLT1363.

Whole-genome shotgun sequencing was performed on JLT1363 using 454 pyrosequencing technologies, which produced 362,544 reads and 154,451,585 bp sequences. We used 355,141 high-quality reads to assemble the genome and obtained a 49.5-fold coverage of the genome. The complete sequence was analyzed using the Glimmer 3.02 software program (4) for the protein-coding genes, tRNAscan-SE (9) for the tRNA, and RNAmmer (8) for the rRNA. The functions of predicted protein-coding genes were then annotated through comparisons with the NCBI-NR (1), COG (12), and KEGG (7) databases.

The Citromicrobium sp. JLT1363 draft genome sequence has a total of 3,117,324 bp (3,198 open reading frames [ORFs]) distributed in 26 contigs with an average GC content of 64.9%. One 16S-23S-5S operon and 46 tRNAs on the draft assembly were identified, as were complete sets of genes for the synthesis of amino acids and nucleotides. A detailed inspection of the genome sequence revealed the presence of complete sets of genes encoding flagellum formation and the complete tricarboxylic acid cycle.

In particular, the Citromicrobium sp. JLT1363 genome showed various mechanisms for horizontal gene transfer. An integrative conjugative element (ICE) (about 100 kb) was observed in the Citromicrobium sp. JLT1363 genome (2, 5). Two regions carrying exogenous DNA were discovered in the ICE. We further found a nearly complete gene transfer agent (GTA) (about 15 kb) gene cluster. In addition, seven genes (virB2B3B4-virB6-virB9B10B11) of the type IV secretion system (T4SS) (about 7 kb) existed in the genome.

In the JLT1363 genome, we found exactly the same genes as those located upstream and downstream of the photosynthetic gene cluster (PGC) of JL354 (6). Their order and direction are the same as well. This suggests a loss of PGC in Citromicrobium sp. JLT1363 (10). So far, JLT1363 is the only isolate in the Citromicrobium genus without phototrophic capability.

The exchange of genetic information by horizontal gene transfer plays important roles in the evolution of bacteria (3, 13). A multimechanism of horizontal gene transfer and the loss of PGC in Citromicrobium sp. JLT1363 may give us some clues for further studies on the evolution of the photosynthesis gene of AAPB.

Nucleotide sequence accession number.

The data from this whole-genome shotgun project have been deposited at DDBJ/EMBL/GenBank under accession number AEUE01000000.

ACKNOWLEDGMENTS

This work was supported by the 973 Program (2011 CB808800), the NSFC project (91028001), the SOA project (201105021), and the NSFC project (40821063, 41076063).

All authors contributed equally.

Footnotes

Published ahead of print on 11 February 2011.

REFERENCES

  • 1. Benson D. A., Karsch-Mizrachi I., Lipman D. J., Ostell J., Wheeler D. L. 2008. GenBank. Nucleic Acids Res. 36:D25–D30 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 2. Boltner D., MacMahon C., Pembroke J. T., Strike P., Osborn A. M. 2002. R391: a conjugative integrating mosaic comprised of phage, plasmid, and transposon elements. J. Bacteriol. 184:5158–5169 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 3. Burrus V., Marrero J., Waldor M. K. 2006. The current ICE age: biology and evolution of SXT-related integrating conjugative elements. Plasmid 55:173–183 [DOI] [PubMed] [Google Scholar]
  • 4. Delcher A. L., Bratke K. A., Powers E. C., Salzberg S. L. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673–679 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 5. Hochhut B., Beaber J. W., Woodgate R., Waldor M. K. 2001. Formation of chromosomal tandem arrays of the SXT element and R391, two conjugative chromosomally integrating elements that share an attachment site. J. Bacteriol. 183:1124–1132 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 6. Jiao N. Z., Zhang R., Zheng Q. 2010. Coexistence of two different photosynthetic operons in Citromicrobium bathyomarinum JL354 as revealed by whole-genome sequencing. J. Bacteriol. 192:1169–1170 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 7. Kanehisa M., et al. 2008. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 36:D480–D484 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 8. Lagesen K., et al. 2007. RNammer: consistent annotation of rRNA genes in genomic sequences. Nucleic Acids Res. 35:3100–3108 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 9. Lowe T. M., Eddy S. R. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955–964 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 10. Oh H. M., Giovannoni S. J., Ferriera S., Johnson J., Cho J. C. 2009. Complete genome sequence of Erythrobacter litoralis HTCC2594. J. Bacteriol. 191:2419–2420 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 11. Rathgeber C., et al. 2008. Vertical distribution and characterization of aerobic phototrophic bacteria at the Juan de Fuca Ridge in the Pacific Ocean. Photosynth. Res. 97:235–244 [DOI] [PubMed] [Google Scholar]
  • 12. Tatusov R. L., Koonin E. V., Lipman D. J. 1997. A genomic perspective on protein families. Science 278:631–637 [DOI] [PubMed] [Google Scholar]
  • 13. Wozniak R. A. F., et al. 2009. Comparative ICE genomics: insights into the evolution of the SXT/R391 family of ICEs. Plos Genet. 5:e1000786. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 14. Yurkov V. V., Krieger S., Stackebrandt E., Beatty J. T. 1999. Citromicrobium bathyomarinum, a novel aerobic bacterium isolated from deep-sea hydrothermal vent plume waters that contains photosynthetic pigment-protein complexes. J. Bacteriol. 181:4517–4525 [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES