Abstract
Burkholderia species are ubiquitous in soil environments. Many Burkholderia species isolated from various environments have the potential to biodegrade man-made chemicals. Burkholderia sp. strain YI23 was isolated from a golf course soil and identified as a fenitrothion-degrading bacterium. In this study, we report the complete genome sequence of Burkholderia sp. strain YI23.
GENOME ANNOUNCEMENT
Man-made organophosphorus insecticides inhibit the normal activity of the acetylcholine esterase in insects and mammals (8). Many bacterial strains capable of completely or partially degrading organophosphorus pesticides have been isolated from soils (4, 8, 11). Their insecticide-degradative genes, pathways, metabolites, and bioremediation potential have been researched (3, 9, 10). However, there have been no reports on genomic analyses of these insecticide-degrading bacteria. Therefore, we have analyzed the whole-genome sequence of Burkholderia sp. strain YI23, which was isolated as a fenitrothion (O,O-dimethyl-O-[p-nitro-m-tolyl]phosphorothioate)-degrading bacterium from a golf course soil and is able to quickly degrade diverse organophosphorus pesticides (4).
Whole-genome DNA sequencing was performed using the pyrosequencing method on an FLX Titanium genome sequencer system. In total, 271,089,161 and 177,899,085 bases were analyzed in single reads and paired-end reads, respectively. The sequence data were assembled with Newbler (version 2.5.3; 454 Life Sciences). In total, 138 contigs were produced in 14 scaffolds through de novo assembly. Gaps among the contigs were closed by primer walking on standard PCR products. Coding genes and pseudogenes across the genome were predicted using Glimmer (2) and annotated by comparison with the NCBI-NR database (1). Our annotation results were verified using Artemis (7).
The Burkholderia sp. strain YI23 genome is 8.89 Mb and consists of three chromosomes and three plasmids. Chromosome 1 (BYI23_A) contains 3,131,280 bp with a G+C content of 63.5% and 2,769 predicted coding sequences (CDS). Chromosome 2 (BYI23_B) contains 1,773,019 bp with a G+C content of 63.7% and 1,539 CDS. Chromosome 3 (BYI23_C) contains 1,569,570 bp with a G+C content of 63.7% and 1,364 CDS. Plasmid 1 (BYI23_D) contains 1,951,047 bp (63% G+C content and 1,651 CDS), plasmid 2 (BYI23_E) contains 356,263 bp (58.7% G+C content and 390 CDS), and plasmid 3 (BYI23_F) contains 115,232 bp (59.4% G+C content and 91 CDS). Four, one, and one rRNA operons were located on chromosome 1 (BYI23_A), chromosome 2 (BYI23_B), and chromosome 3 (BYI23_C), respectively (5). Chromosome 1 (BYI23_A), chromosome 2 (BYI23_B), chromosome 3 (BYI23_C), and plasmid 1 (BYI23_D) have 56, 4, 3, and 1 tRNA genes, respectively (6). The fenitrothion-degradative genes are located on plasmids BYI23_E and BYI23_F. The whole-genome sequences of Burkholderia sp. strain YI23 can provide valuable information on organophosphorus insecticide-degradative genes, including fenitrothion-degradative genes.
Nucleotide sequence accession numbers.
The complete genome sequence of Burkholderia sp. YI23 has been assigned GenBank accession numbers CP003087, CP003088, CP003089, CP003090, CP003091, and CP003092.
ACKNOWLEDGMENTS
This study was supported by National Instrumentation Center for Environmental Management and the RDA GenBank Management Program from the Genetic Resources Division, National Institute of Agricultural Biotechnology.
REFERENCES
- 1. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. 2008. GenBank. Nucleic Acids Res. 36:D25–D30 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 274:4636–4641 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3. Hong Q, Zhang Z, Hong Y, Li S. 2007. A microcosm study on bioremediation of fenitrothion-contaminated soil using Burkholderia sp. FDS-1. Int. Biodeterioration Biodegradation 59:55–61 [Google Scholar]
- 4. Kim KD, et al. 2009. Genetic and phenotypic diversity of fenitrothion-degrading bacteria isolated from soils. J. Microbiol. Biotechnol. 19:113–120 [DOI] [PubMed] [Google Scholar]
- 5. Lagesen K, et al. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35:3100–3108 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6. 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 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7. Rutherford K, et al. 2000. Artemis: sequence visualization and annotation. Bioinformatics 16:944–955 [DOI] [PubMed] [Google Scholar]
- 8. Singh B, Walker A. 2006. Microbial degradation of organophosphorus compounds. FEMS Microbiol. Rev. 30:428–471 [DOI] [PubMed] [Google Scholar]
- 9. Tago K, Sato J, Takesa H, Kawagishi H, Hayatsu M. 2005. Characterization of methylhydroquinone-metabolizing oxygenase genes encoded on plasmid in Burkholderia sp. NF100. J. Biosci. Bioeng. 100:517–523 [DOI] [PubMed] [Google Scholar]
- 10. Tago K, et al. 2007. Diversity of fenitrothion-degrading bacteria in soils from distant geographical areas. Microbes Environ. 21:58–64 [Google Scholar]
- 11. Zhang Z, Hong Q, Xu J, Zhang X, Li S. 2006. Isolation of fenitrothion-degrading strain Burkholderia sp. FDS-1 and cloning of mpd gene. Biodegradation 17:275–283 [DOI] [PubMed] [Google Scholar]