Abstract
Pectobacterium carotovorum is known to cause serious damage to various major crops worldwide. Here, we report the draft genome of Pectobacterium carotovorum strain M022, a freshwater isolate from a Malaysian waterfall, which has been reported as a plant pathogen and is able to communicate with N-acylhomoserine lactone-mediated quorum sensing.
GENOME ANNOUNCEMENT
Plant pathogens have been a threat to crops and pose a danger to food security. Potato blackleg, which is caused by various soft rot coliforms such as Pectobacterium (1), is one of the major concerns worldwide. Plant pathogenic characteristics, such as production of virulence factors, can be regulated from their communication, which is also known as quorum sensing (QS) (2, 3). QS is the ability of bacteria to express orchestrated physiological activities when a quorate is reached. The plant pathogen, Pectobacterium carotovorum, is a Gram-negative bacteria that destroys various commercially important crops via the production of cell-wall-degrading enzymes (4, 5). In this study, P. carotovorum strain M022 was isolated from a waterfall source. The whole-genome sequencing was conducted for a deeper molecular understanding of this strain.
Initially, a MasterPure DNA purification kit (Epicentre, Inc., Madison, WI, USA) was used to extract the genomic DNA of strain M022 and its quality was checked by a NanoDrop spectrophotometer (Thermo Scientific, Waltham, MA, USA) and a Qubit version 2.0 fluorometer (Life Technologies, Carlsbad, CA, USA). Whole-genome shotgun sequencing of the purified DNA was then performed on an Illumina MiSeq personal sequencer (Illumina Inc., CA, USA), which generated 4,151,785 paired-end reads. Next, the sequences were trimmed and de novo assembled with CLC Genomics Workbench version 5.1 (CLC Bio, Denmark), which produced 1,101,735 quality reads (6). The assembly of trimmed reads generated a total of 105 contigs and an N50 of approximately 126,203.
The draft genome of strain M022 consisted of 4,151,564 bases with an average coverage of 53.3-fold and a G+C content of 51%. Prodigal version 2.60 (7) was used for gene prediction with the prokaryote gene prediction algorithm. In addition, the amounts of tRNAs and rRNAs were predicted using tRNAscanSE version 1.21 (8) and RNAmmer (9), respectively. The strain was then annotated using RAST (10), and 3,600 open reading frames were predicted. In the genomic makeup of strain M022, there are 7 copies of rRNAs and 69 copies of tRNAs.
From the annotation results, the luxI and luxR homologues of strain M022 were predicted to be located at contigs 33 and 11, respectively. The whole-genome sequence allows deeper understanding of the genetic makeup of P. carotovorum and may help in identifying the link between QS ability with pathogenicity and production of virulence factors (11, 12). It will contribute to an understanding of the mechanism of plant-pathogen interaction and benefit the management of crop disease.
Nucleotide sequence accession numbers.
This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number JSXC00000000. The version described in this paper is the first version, JSXC01000000.
ACKNOWLEDGMENTS
This work was supported by the University of Malaya via High Impact Research Grants (UM.C/625/1/HIR/MOHE/CHAN/01, grant no. A-000001-50001 and UM-MOHE HIR Grant UM.C/625/1/HIR/MOHE/CHAN/14/1, grant no. H-50001-A000027) awarded to K.-G.C.
Footnotes
Citation Chan K-G, Tan W-S. 2015. Genomic insights of Pectobacterium carotovorum strain M022 quorum-sensing activity through whole-genome sequencing. Genome Announc 3(1):e01554-14. doi:10.1128/genomeA.01554-14.
REFERENCES
- 1.Kettani-Halabi M, Terta M, Amdan M, El Fahime EM, Bouteau F, Ennaji MM. 2013. An easy, simple inexpensive test for the specific detection of Pectobacterium carotovorum subsp. carotovorum based on sequence analysis of the pmrA gene. BMC Microbiol 13:176. doi: 10.1186/1471-2180-13-176. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Williams P, Winzer K, Chan WC, Camara M. 2007. Look who’s talking: communication and quorum sensing in the bacterial world. Philos Trans R Soc Lond B Biol Sci 362:1119–1134. doi: 10.1098/rstb.2007.2039. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Chong TM, Koh CL, Sam CK, Choo YM, Yin WF, Chan KG. 2012. Characterization of quorum sensing and quorum quenching soil bacteria isolated from Malaysian tropical montane forest. Sensors 12:4846–4859. doi: 10.3390/s120404846. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Nunes Leite L, de Haan EG, Krijger M, Kastelein P, van der Zouwen PS, van den Bovenkamp GW, Tebaldi ND, van der Wolf JM. 2014. First report of potato blackleg caused by Pectobacterium carotovorum subsp. brasiliensis in the Netherlands. New Dis Rep 29:24. doi: 10.5197/j.2044-0588.2014.029.024. [DOI] [Google Scholar]
- 5.Park TH, Choi BS, Choi AY, Choi I-Y, Heu S, Park BS. 2012. Genome sequence of Pectobacterium carotovorum subsp. carotovorum strain PCC21, a pathogen causing soft rot in Chinese cabbage. J Bacteriol 194:6345–6346. doi: 10.1128/JB.01583-12. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Chan KG, Wong CS, Yin WF, Chan XY. 2014. Draft genome sequence of quorum-sensing and quorum-quenching Pseudomonas aeruginosa strain MW3a. Genome Announc 2(2):e00258-14. doi: 10.1128/genomeA.00258-14. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119. doi: 10.1186/1471-2105-11-119. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.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: 10.1093/nar/25.5.0955. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108. doi: 10.1093/nar/gkm160. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.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. doi: 10.1186/1471-2164-9-75. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Molina L, Constantinescu F, Michel L, Reimmann C, Duffy B, Défago G. 2003. Degradation of pathogen quorum-sensing molecules by soil bacteria: a preventive and curative biological control mechanism. FEMS Microbiol Ecol 45:71–81. doi: 10.1016/S0168-6496(03)00125-9. [DOI] [PubMed] [Google Scholar]
- 12.Tan WS, Muhamad Yunos NY, Tan PW, Mohamad NI, Adrian TGS, Yin WF, Chan KG. 2014. Pantoea sp. isolated from tropical fresh water exhibiting N-acyl homoserine lactone production. ScientificWorldJournal 1–5:828971. doi: 10.1155/2014/828971. [DOI] [PMC free article] [PubMed] [Google Scholar]