Abstract
Vibrio tubiashii strain T33 was isolated from the coastal waters of Morib, Malaysia, and was shown to possess quorum-sensing activity similar to that of its famous relative Vibrio fischeri. Here, the assembly and annotation of its genome are presented.
GENOME ANNOUNCEMENT
In 1965, Tubiash, Chanley, and Leifson (1) first discovered pathogenic bacteria that infect the mollusk, and these were classified as Vibrio anguillarum. However, due to the advancement of molecular taxonomical approaches, further work done in 1984 by Hada and colleagues (2) confirmed that the bacterium isolated in 1965 by Tubiash, Chanley, and Leifson is a new species, which was named Vibrio tubiashii. Isolated in 2014, V. tubiashii strain T33 forms a round yellow colony on Luria-Bertani agar (LBA) with 3% (wt/vol) NaCl concentration. Here, we sequenced the whole genome of V. tubiashii strain T33, as this will contribute to the understanding of its pathogenic properties and pave the way to solutions to combat severe vibriosis in mollusks, such as clams, oysters, and shellfish.
By using the QIAamp DNA minikit (Qiagen, Germany), the genomic DNA of V. tubiashii strain T33 was isolated according to the manufacturer’s recommendations. DNA quality was checked via a NanoDrop spectrophotometer (Thermo Scientific) and Qubit 2.0 fluorometer (Life Technologies). Using the platform Illumina MiSeq personal sequencer (Illumina, Inc., CA), the whole genome of V. tubiashii strain T33 was sequenced. The number of calculated filtered reads was 1,308,193, with approximately 60.05-fold coverage. Assembly of the filtered reads was done using CLC Genomics Workbench version 5.1 (CLC bio, Denmark) (3) and resulted in 46 contig numbers, with an N50 value of 410,629. A total of 4,144,653 bp makes up the draft genome of V. tubiashii strain T33, with a G+C content of 45%. Annotation was done using the Rapid Annotations using Subsystems Technology (RAST) server (4). The number of open reading frames (ORFs) of strain T33 is 3,815, and the number of tRNAs predicted using tRNAscan-SE (version 1.21) (5) is 76. There are 5 main housekeeping genes in strain T33, which consist of three copies of 5S rRNA genes, one copy of 23S rRNA gene, and one copy of 16S rRNA gene, which was characterized using RNAmmer (6).
From the RAST server annotation, we discovered a protein that was responsible for the N-acyl homoserine lactone (AHL), LuxM, in contig number 8. AHL is a quorum-sensing (QS) signaling molecule that has been reported in many proteobacteria, including marine vibrios (7, 8). LuxM is a homologue to LuxI, which is a protein responsible for the production of signal molecules, namely, AHLs (9, 10). The QS signaling system, which consists of genes and regulators, may play a key role in the pathogenic properties of V. tubiashii. Therefore, this study may provide insight to better understand the virulence factors of V. tubiashii, hence leading to an effective solution for severe vibriosis.
Nucleotide sequence accession number.
This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. JRWQ00000000. The version described in this paper is the first version.
ACKNOWLEDGMENT
This work was supported by a High Impact Research Grant (A000001-50001; awarded to K.-G. Chan) from the University of Malaya.
Footnotes
Citation Izzati Mohamad N, Yin W-F, Chan K-G. 2015. Whole-genome sequence of quorum-sensing Vibrio tubiashii strain T33. Genome Announc. 3(1):e01362-14. doi:10.1128/genomeA.01362-14.
REFERENCES
- 1.Tubiash HS, Chanley PE, Leifson E. 1965. Bacillary necrosis, a disease or larval and juvenile bivalve mollusks. I. Etiology and epizootiology. J Bacteriol 90:1036–1044. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Hada HS, West PA, Lee JV, Stemmler J, Colwell RR. 1984. Vibrio tubiashii sp. nov., a pathogen of bivalve mollusks. Int J Syst Bacteriol 34:1–4. doi: 10.1099/00207713-34-1-1. [DOI] [Google Scholar]
- 3.Chan XY, Chua KH, Puthucheary SD, Yin WF, Chan KG. 2012. Draft genome sequence of an Aeromonas sp. strain 159 clinical isolate that shows quorum-sensing activity. J Bacteriol 194:6350–6350. doi: 10.1128/JB.01642-12. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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, 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]
- 5.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]
- 6.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]
- 7.Tan WS, Yunos NYM, Tan PW, Mohamad NI, Adrian TGS, Yin WF, Chan KG. 2014. Characterisation of a marine bacterium Vibrio brasiliensis T33 producing N-acyl homoserine lactone quorum sensing molecules. Sensors 14:12104–12113. doi: 10.3390/s140712104. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Cámara M, Hardman A, Williams P, Milton D. 2002. Quorum sensing in Vibrio cholerae. Nat Genet 32:217–218. doi: 10.1038/ng1002-217. [DOI] [PubMed] [Google Scholar]
- 9.Engebrecht J, Nealson K, Silverman M. 1983. Bacterial bioluminescence: isolation and genetic analysis of functions from Vibrio fischeri. Cell 32:773–781. doi: 10.1016/0092-8674(83)90063-6. [DOI] [PubMed] [Google Scholar]
- 10.Hong KW, Koh CL, Sam CK, Yin WF, Chan KG. 2012. Whole-genome sequence of N-acylhomoserine lactone-synthesizing and-degrading Acinetobacter sp. strain GG2. J Bacteriol 194:6318–6318. doi: 10.1128/JB.01579-12. [DOI] [PMC free article] [PubMed] [Google Scholar]