Abstract
Mycobacterium bovis W-1171 was isolated from a wild boar living in a free-ranging field in Gyeonggido, South Korea. The whole-genome sequence of this strain was determined in 50 contigs, which was 4,304,865 bp with a 65.57% G+C content. In total 3,945 protein-coding genes were predicted from this assembly.
GENOME ANNOUNCEMENT
Wildlife, including raccoon dogs, water deer, and wild boar, is an important reservoir of Mycobacterium bovis, the causal agent of bovine tuberculosis (bTB). Wild animals are also capable of transmitting the disease to livestock such as cattle (1, 2). To understand the transmission and maintenance of M. bovis in various animal species, its pathogenicity mechanism should be determined through comparisons to other sequenced strains (3). Here, we present the whole-genome sequence of M. bovis strain W-1171 to provide additional information about M. bovis strains isolated from wild animals and to better understand their characteristics. W-1171 was isolated from the laryngopharyngeal lymph node of a bTB-infected wild boar captured near cattle herds in Gyeonggido, South Korea. This strain has the SB1040 spoligotype, which is one of the most commonly found types in South Korea, and has a 53375431052 mycobacterial interspersed repetitive unit-variable-number tandem-repeat pattern.
The genome sequence was obtained using a combination of the 300-bp pair-ended Illumina MiSeq (13,110.87 reads; 670.52× coverage) and Roche 454 GS FLX Titanium systems with an 8-kb paired-end library (310,165.58 reads; 13.83× coverage). Sequencing analysis was performed by Chunlab, Inc. (Seoul, Republic of Korea). The hybrid genome assembly was achieved using GS Assembler 2.6 (Roche), CLC Genomics Workbench 7.0.4 (CLCbio), and CodonCode Aligner (CodonCode Co.). Gene annotation was performed using the NCBI Prokaryotic Genomes Annotation Pipeline (http://www.ncbi.nlm.nih.gov/genome/annotation_prok/) (4).
The final assembly contains 50 contigs (3,945 protein-coding sequences, 4,304,865 bp with a 65.57% G+C ratio), 46 tRNA genes, and 3 rRNA operons. Except for the genes predicted to be related to general and unknown functions, most of the open reading frames (ORFs) matched genes related to “transcription” (233 ORFs, 6.57%) according to eggNOG functional categories (5). Genes related to “lipid transport and metabolism” and “energy production and conversion” ranked the second and third (216 ORFs, 6.09% and 210 ORFs, 5.92%, respectively). Other M. bovis strains such as AF2122/97 (GenBank accession number NC_002945), BCG Pasteur 1173P2 (NC_008769), and Mb1595 (CP012095, previously sequenced in our laboratory) (6) showed the same ranking order of ORFs in eggNOG analysis. Mb1595 additionally showed third-ranked ORFs related to “replication, recombination, and repair.” These strains likely showed a high proportion of lipid-related genes because the mycobacterial cell wall lipids are considered to be important factors for their pathogenesis and virulence (7). For example, the transmembrane transport proteins MmpL and MmpS are responsible for transporting cell wall lipids across the mycobacterial membrane, drug resistance, and iron acquisition (7), which are major virulence factors in mycobacteria that are conserved in M. bovis and M. tuberculosis. In addition, the lipid-rich cell wall enables mycobacteria to survive under adverse conditions such as nutrient shortage and antimicrobial exposure (8, 9). Lastly, clustering analysis based on average nucleotide identity using EzGenome (http://www.ezbiocloud.net/ezgenome/ani) revealed that strain W-1171 was closely related to Mb1595 (99.99%). This genome sequence will serve as a valuable reference for understanding the variation in virulence and epidemiological traits among M. bovis strains.
Nucleotide sequence accession number.
The whole-genome sequence of M. bovis strain W-1171 has been deposited at GenBank under the accession number JXTK00000000.
ACKNOWLEDGMENT
This work was supported by a grant (C-1543081-2014-16-01) from the Animal and Plant Quarantine Agency, Republic of Korea. The funders had no role in the study design, data interpretation, or decision to submit the work for publication.
Footnotes
Citation Kim N, Jang Y, Park S-Y, Song W-S, Kim J-T, Lee HS, Lim Y-H, Kim J-M. 2015. Whole-genome sequence of Mycobacterium bovis W-1171, isolated from the laryngopharyngeal lymph node of a wild boar in South Korea. Genome Announc 3(6):e01464-15. doi:10.1128/genomeA.01464-15.
REFERENCES
- 1.Biek R, O’Hare A, Wright D, Mallon T, McCormick C, Orton RJ, McDowell S, Trewby H, Skuce RA, Kao RR. 2012. Whole genome sequencing reveals local transmission patterns of Mycobacterium bovis in sympatric cattle and badger populations. PLoS Pathog 8:e1003008. doi: 10.1371/journal.ppat.1003008. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Miller RS, Farnsworth ML, Malmberg JL. 2013. Diseases at the livestock-wildlife interface: status, challenges, and opportunities in the United States. Prev Vet Med 110:119–132. doi: 10.1016/j.prevetmed.2012.11.021. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Humblet M, Boschiroli ML, Saegerman C. 2009. Classification of worldwide bovine tuberculosis risk factors in cattle: a stratified approach. Vet Res 40:50. doi: 10.1051/vetres/2009033. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, Garrity GM, Kodira CD, Kyrpides N, Madupu R, Markowitz V, Tatusova T, Thomson N, White O. 2008. Toward an online repository of Standard operating procedures (SOPs) for (meta)genomic annotation. Omics J Integr Biol 12:137–141. doi: 10.1089/omi.2008.0017. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Jensen LJ, Julien P, Kuhn M, von Mering C, Muller J, Doerks T, Bork P. 2008. eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Res 36:D250–D254. doi: 10.1093/nar/gkm796. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Kim N, Jang Y, Kim JK, Ryoo S, Kwon KH, Kang SS, Byeon HS, Lee HS, Lim YH, Kim JM. 2015. Complete genome sequence of Mycobacterium bovis clinical strain 1595, isolated from the laryngopharyngeal lymph node of South Korean cattle. Genome Announc 3(5):e01124-15. doi: 10.1128/genomeA.01124-15. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Bailo R, Bhatt A, Aínsa JA. 2015. Lipid transport in Mycobacterium tuberculosis and its implications in virulence and drug development. Biochem Pharmacol 96:159–167. doi: 10.1016/j.bcp.2015.05.001. [DOI] [PubMed] [Google Scholar]
- 8.Jankute M, Grover S, Birch HL, Besra GS. 2014. Genetics of mycobacterial arabinogalactan and lipoarabinomannan assembly. Microbiol Spectr 2:MGM2-0013-2013. doi: 10.1128/microbiolspec.MGM2-0013-2013. [DOI] [PubMed] [Google Scholar]
- 9.He L, Zhou X, Yin X, Tian L, Yang L, Fan K, Zhao D. 2015. Comparative study of the growth and survival of recombinant Mycobacterium smegmatis expressing Mce4A and Mce4E from Mycobacterium bovis. DNA Cell Biol 34:125–132. doi: 10.1089/dna.2014.2487. [DOI] [PubMed] [Google Scholar]