Abstract
Burkholderia sp. K24 is an aniline-degrading soil bacterium that utilizes aniline and its analogues as sole carbon and nitrogen sources. Here, we report the draft genome sequence of this strain that consists of 8,344,181 bp, with a G+C content of 61.7%.
GENOME ANNOUNCEMENT
Burkholderia sp. K24, formerly known as Acinetobacter lwoffii K24, was screened from an herbicide-contaminated field in Gyeonggi province in Korea (1). The biodegradation activities of Burkholderia sp. K24 include various monocyclic aromatic compounds. Burkholderia sp. K24 can use aniline and aniline analogues as its sole carbon and energy source. Aniline is predominantly used as a chemical intermediate in dye, agricultural, and rubber industries. Although it is not considered carcinogenic, continuous inhalation of aniline or water contaminated with aniline produces acute or chronic toxic effects. Many aniline-degrading bacteria have large plasmids containing biodegradation gene clusters. Burkholderia sp. K24 uses the β-ketoadipate pathway to degrade aromatic compounds (2, 3). Genome data can provide comprehensive information on the biodegradation of many monocyclic or polycyclic aromatic compounds by Burkholderia sp. K24 and the metabolic activities of the bacterium. The data can also be used to confirm the identity of metabolic enzymes screened by proteomic studies because previous studies were performed using a public bacterial genome database (4–6).
The draft genome of Burkholderia sp. K24 was generated using the Illumina MiSeq platform (San Diego, CA). A paired-end library with an insert size of 250 to 350 bp resulted in 4,701,300 reads, with a read length of 150 bp. From a mate-paired library with an insert size of 5 kb, we obtained 33,144,478 reads, with a read length of 37 bp.
The sequencing data were assembled with CLC Genomics Workbench (CLC bio, Aarhus, Denmark) version 6.0.2 after data quality control using PrinSeq-lite, version 0.20.3 (7). Genome annotation was performed with the RAST (Rapid Annotation using Subsystem Technology) annotation server (8), Integrated Microbial Genomes/Expert Review (IMG/ER, https://img.jgi.doe.gov/cgi-bin/er/main.cgi) (9), and the NCBI Prokaryotic Genomes Annotation Pipeline (PGAP, http://www.ncbi.nlm.nih.gov/genome/annotation_prok/). Sequencing reads of Burkholderia sp. K24 were assembled into 33 scaffolds. The total length of the scaffolds was 8,344,181 bp, with a G+C content of 61.7% and an N50 contig length of 217,840 bp. A total of 7,033 genes were annotated, including 6,904 protein coding genes and 55 RNA genes.
Nucleotide sequence accession numbers.
This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. JMIK00000000. The version described in this paper is version JMIK01000000.
ACKNOWLEDGMENT
This work was supported by KBSI grants C34112 and T34414.
Footnotes
Citation Lee S-Y, Yun SH, Choi C-W, Lee D-G, Choi JS, Kahng H-Y, Kim SI. 2014. Draft genome sequence of an aniline-degrading bacterium, Burkholderia sp. K24. Genome Announc. 2(6):e01250-14. doi:10.1128/genomeA.01250-14.
REFERENCES
- 1. Kahng HY, Kim SI, Woo MJ, Park YK, Lee YL. 1992. Isolation and characterization of aniline-degrading bacteria. Kor. J. Microbiol. 30:199–206. [Google Scholar]
- 2. Kim SI, Leem SH, Choi JS, Chung YH, Kim S, Park YM, Park YK, Lee YN, Ha KS. 1997. Cloning and characterization of two catA genes in Acinetoacter lwoffii K24. J. Bacteriol. 179:5226–5231. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3. Yoon YH, Yun SH, Park SH, Seol SY, Leem SH, Kim SI. 2007. Characterization of a new catechol branch of the beta-ketoadipate pathway induced for benzoate degradation in Acinetobacter lwoffii K24. Biochem. Biophys. Res. Commun. 360:513–519. 10.1016/j.bbrc.2007.05.132. [DOI] [PubMed] [Google Scholar]
- 4. Kim SI, Kim SJ, Nam MH, Kim S, Ha KS, Oh KH, Yoo JS, Park YM. 2002. Proteome analysis of aniline-induced proteins in Acinetobacter lwoffii K24. Curr. Microbiol. 44:61–66. 10.1007/s00284-001-0075-8. [DOI] [PubMed] [Google Scholar]
- 5. Kahng HY, Cho K, Song SY, Kim SJ, Leem SH, Kim SI. 2002. Enhanced detection and characterization of protocatechuate 3,4-dioxygenase in Acinetobacter lwoffii K24 by proteomics using a column separation. Biochem. Biophys. Res. Commun. 295:903–909. 10.1016/S0006-291X(02)00778-7. [DOI] [PubMed] [Google Scholar]
- 6. Kim EA, Kim JY, Kim SJ, Park KR, Chung HJ, Leem SH, Kim SI. 2004. Proteomic analysis of Acinetobacter lwoffii K24 by 2-D gel electrophoresis and electrospray ionization quadrupole-time of flight mass spectrometry. J. Micrbiol. Methods 57:337–349. 10.1016/j.mimet.2004.02.007. [DOI] [PubMed] [Google Scholar]
- 7. Schmieder R, Edwards R. 2011. Quality control and preprocessing of metagenomic datasets. Bioinformatics 27:863–864. 10.1093/bioinformatics/btr026. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. 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 9:75–89. 10.1186/1471-2164-9-75. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9. Markowitz VM, Mavromatis K, Ivanova NN, Chen IM, Chu K, Kyrpides NC. 2009. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 25:2271–2278. 10.1093/bioinformatics/btp393. [DOI] [PubMed] [Google Scholar]