Burkholderia caribensis MBA4 was isolated from soil for its ability to utilize 2-haloacid. An inducible haloacid operon, encoding for a dehalogenase and a permease, is mainly responsible for the biotransformation. Here, we report the draft genome sequence of this strain.postprin

Kong, KF

Pan, Y

Tsang, JSH

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Title Draft Genome Sequence of the Haloacid-Degrading Burkholderiacaribensis Strain MBA4Author(s) Pan, Y; Kong, KF; Tsang, JSHCitation Genome Announcements, 2014, v. 2 n. 1, p. e00047-14Issued Date 2014URL http://hdl.handle.net/10722/196403Rights Genome Announcements. Copyright © American Society forMicrobiology.Draft Genome Sequence of the Haloacid-Degrading Burkholderiacaribensis Strain MBA4Yanling Pan, Ka Fai Kong, Jimmy S. H. TsangMolecular Microbiology Laboratory, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, ChinaBurkholderia caribensisMBA4 was isolated from soil for its ability to utilize 2-haloacid. An inducible haloacid operon, encodinga dehalogenase and a permease, is mainly responsible for the biotransformation. Here, we report the draft genome sequence ofthis strain.Received 16 January 2014 Accepted 29 January 2014 Published 20 February 2014Citation Pan Y, Kong KF, Tsang JSH. 2014. Draft genome sequence of the haloacid-degrading Burkholderia caribensis strain MBA4. Genome Announc. 2(1):e00047-14. doi:10.1128/genomeA.00047-14.Copyright © 2014 Pan et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.Address correspondence to Jimmy S. H. Tsang, jshtsang@hku.hk.Haloacetates such as monochloroacetate (MCA) are toxic andmutagenic and can be produced incidentally during disinfec-tion of water. Burkholderia caribensis MBA4 is a Gram-negativebacterium that can utilize 2-haloacid as a growth substrate. Thisbacterium was characterized for its production of a dimeric hy-drolytic dehalogenase (Deh4a) (1, 2) that removes the halogenfrom the carbon backbone. Here we describe the draft genomesequence of Burkholderia caribensis MBA4.Analysis of B. caribensis MBA4 with pulsed-field gel electro-phoresis showed that it has a genome size of more than 9 Mbwith at least three replicons (data not shown). Whole-genomicsequencing was obtained with 454 GS FLX Titanium and Illu-mina HiSeq 2000. With low-quality short reads discarded, the454 sequencing has 929,485 reads and 380,525,001 bp aftertrimming. Four sets of Illumina paired-end libraries with insertsizes of 100, 300, 500, and 2,000 bp were constructed and se-quenced. After trimming and filtering, the four libraries have37,483,321, 36,788,695, 23,594,431, and 12,689,821 high-quality paired-end reads, respectively. The average read lengthswere 61, 61, 69, and 39 bp, respectively. The overall coverage isabout 750-fold. Illumina paired-end and 454 reads were denovo assembled using CLC Genomic Workbench 6.0.1 (CLCbio, Aarhus, Denmark) with default settings. SSPACE basic 2.0(3) was used to join contigs into scaffolds with informationderived from paired-end reads. Moreover, 47,627 de novo-assembled transcripts from nine sets of RNA-seq data weremapped to the scaffolds to (i) remove some of the internal gaps,(ii) remove ambiguous base pairs, and (iii) join the scaffoldstogether. Standard PCR and Sanger-sequencing technologywere applied to fill gaps inside the scaffolds. Multiplex PCR wasused to amplify unknown regions between scaffolds, and somescaffolds were linked after subsequent cloning and sequencing.As a result, 14 scaffolds were obtained with 79 component con-tigs of 200 bp. Contig relationships were maintained in theGenBank submission by the inclusion of an AGP (A GoldenPath) file. The total size of the contigs is 9,418,480 bp. The N50of thecontigs is 217,392bpand the longest contig is 1,305,062bp.TheGC content was determined to be 62.48%, which is consistent with aresult obtained from high-performance liquid chromatography(HPLC) analysis.The draft genome was annotated automatically with the RapidAnnotations using Subsystems Technology (RAST) server (4) andthe Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP)fromNCBI (5). The draft genome contains 9,082 genes, including 8rRNA and 52 tRNA genes. Furthermore, there were 624 tandem re-peats identified by Tandem Repeats Finder (6). Among the 9,022protein-coding sequences, 76% were annotated as encoding knownproteins while the remaining 24% encode hypothetical products.Among these RAST-annotated genes, 3,666 coding DNA sequences(CDS) were assigned to 27 subsystems. Analysis of the CDS with theKEGGAutomatic Annotation Server (version 1.6a) (7) has specified34 groups with 191 pathways.Nucleotide sequence accessionnumbers.Thiswhole-genomeshotgun project has been deposited at DDBJ/EMBL/GenBank un-der the accession number AXDD00000000. The version describedin this paper is version AXDD01000000.ACKNOWLEDGMENTSWe thank S. Lok, A. Tong, N. Lin, J. Jiang, F. C. C. Leung, and the Uni-versity Centre for Genomic Sciences for advice.This work has been supported by grants from the University SmallProject Funding 2010 and the General Research Fund (project numberHKU 780511) of the Research Grants Council of the Hong Kong SpecialAdministrative Region, China.REFERENCES1. Tsang JSH, Pang BCM. 2000. Identification of the dimerization domain ofdehalogenase IVa ofBurkholderia cepaciaMBA4. Appl. Environ.Microbiol.66:3180–3186. http://dx.doi.org/10.1128/AEM.66.8.3180-3186.2000.2. Tsang JSH, Sallis PJ, Bull AT, Hardman DJ. 1988. A monobromoacetatedehalogenase from Pseudomonas cepacia MBA4. Arch. Microbiol. 150:441–446. http://dx.doi.org/10.1007/BF00422284.3. Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. 2011. Scaf-folding pre-assembled contigs using SSPACE. Bioinformatics 27:578–579.http://dx.doi.org/10.1093/bioinformatics/btq683.4. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA,Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, OlsonR, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T,Genome AnnouncementsJanuary/February 2014 Volume 2 Issue 1 e00047-14 genomea.asm.org 1Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V,Wilke A, Zagnitko O. 2008. The RAST server: rapid annotations usingsubsystems technology. BMC Genomics 9:75. http://dx.doi.org/10.1186/1471-2164-9-75.5. Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, Garrity G,Kodira CD, Kyrpides N, Madupu R, Markowitz V, Tatusova T, Thom-son N, White O. 2008. Toward an online repository of standard operatingprocedures (SOPs) for (meta)genomic annotation. Omics 12:137–141.http://dx.doi.org/10.1089/omi.2008.0017.6. Benson G. 1999. Tandem repeats finder: a program to analyze DNA sequences.NucleicAcidsRes. 27:573–580. http://dx.doi.org/10.1093/nar/27.2.573.7. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. 2007. KAAS: anautomatic genome annotation and pathway reconstruction server. NucleicAcids Res. 35:W182–W185. http://dx.doi.org/10.1093/nar/gkm321.Pan et al.Genome Announcements2 genomea.asm.org January/February 2014 Volume 2 Issue 1 e00047-14

Draft Genome Sequence of the Haloacid-Degrading Burkholderia caribensis Strain MBA4

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Draft Genome Sequence of the Haloacid-Degrading Burkholderia caribensis Strain MBA4

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