J Genomics 2017; 5:48-50. doi:10.7150/jgen.16163

Short Research Communication

Whole-genome Sequencing of Vibrio sinaloensis T47, a Tropical Marine Isolate with Quorum Sensing Properties

Nur Izzati Mohamad, Kah Yan How, Wai-Fong Yin, Kok-Gan Chan Corresponding address

Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 50603 Malaysia.

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How to cite this article:
Mohamad NI, How KY, Yin WF, Chan KG. Whole-genome Sequencing of Vibrio sinaloensis T47, a Tropical Marine Isolate with Quorum Sensing Properties. J Genomics 2017; 5:48-50. doi:10.7150/jgen.16163. Available from http://www.jgenomics.com/v05p0048.htm

Abstract

A large number of Vibrio sp. thrive in the marine environment and they are notable to cause food borne infection associated with undercooked seafood. In this study, we report the whole genome sequence of Vibrio sinaloensis T47 which was isolated from coastal marine water in Morib Beach, Hulu Selangor. The genome is made up of approximately 4.59 Mbp with 80 contigs and 46% G+C content. From the annotated genome, genes associated with quorum sensing (QS) were identified. This research provides a genetic basis for better understanding of QS pathway which contributes to the physiological traits of strain T47 to thrive in the marine environment.

Keywords: Vibrio sinaloensis, whole genome sequencing, quorum sensing, autoinducer synthase, virulence factor

Introduction

Vibrio sp. is a very common bacterium which can be found in almost all water-borne environments including sea, estuary and fresh water. Vibrio sp. first made its debut into the scientific world through the discovery of bioluminescence properties. It was reported that Vibrio fischeri forms a symbiotic relationship with its host, the Hawaiian bobtail squid (Euprymna scolopes) and this underlying symbiosis is associated with quorum sensing (QS) [1]. QS is well known as a mechanism of virulence and colonization when the population in bacteria surpasses a threshold. This feature seems to be a common trait in the members of the genus Vibrio.

Since the development of advance taxonomical tools such as DNA-DNA hybridization, fluorescent amplified fragment length polymorphism and multilocus sequence analysis, the number of novel species from Vibrio family being discovered is constantly expanding [2, 3]. Among the vast members of Vibrio genus, a number of them were demonstrated to possess QS abilities such as V. harveyi [4], V. cholera [5], and V. anguillarum [6]. There is mounting data suggesting that QS is responsible for many unique traits such as pathogenicity, swarming abilities and biofilm production [7, 8, 9]. In this work, we study on V. sinaloensis strain T47 which was isolated from a tropical marine in Morib Beach, Selangor (2ᵒ 45' 2.7" N, 101ᵒ 26' 34.7" E). A water sample was collected approximately 15 cm from the water surface.

V. sinaloensis was first documented by Gomez-Gil and colleagues [10] from the spotted rose snapper (Lutjanus guttatus) which causes infection and vibriosis. In fact, this bacterium is a major threat to the aquaculture sector due to its pathogenicity properties. The colonization of V. sinaloensis has been reported in crustaceans, for example, the white-leg shrimp, Litopenaeus vannamei [11]. Here, the sequencing strategy and data of the whole genome of strain T47 is presented to provide better understanding of the marine bacterium as well as insights to the physiological behaviors associated to QS activity.

V. sinaloensis strainT47 was cultured in aseptic condition on Luria Bertani Agar (LBA) with 3% NaCl concentration (w/v) and incubated at 28°C overnight. The genomic DNA of strain T47 was extracted using QIAamp DNA Minikit (Qiagen, Germany) according to the manufacturer's instructions. The quality of the extracted DNA was measured using NanoDrop Spectrophotometer (Thermo Scientific) and Qubit 2.0 fluorometer (Life Technologies). Next, Nextera DNA Prep Kit (Illumina Inc., CA) was used to prepare the sequencing library followed by whole genome sequencing using a personal sequencer, Illumina MiSeq (Illumina Inc., CA). The total reads were assembled into 80 contigs with 43.8 × coverage using CLC Genomic Workbench version 5.1 (CLC Bio, Denmark). The draft genome of strain T47 is made up of 4,599,504 bp with G+C content of 46.12%. The genome sequence has been deposited into GenBank under the accession number JXBJ00000000. The 16S rDNA sequence used in identification of strain T47 [12] was also deposited into NCBI under accession number KR058860.

Based on 16S rDNA sequence, strain T47 was found to have more than 99% similarity to several Vibrio sp. such as V. variabilis, V. caribbeanicus, and V. sinaloensis. On the other hand, annotations of both functional and predicted genes were performed using the Integrated Microbial Genomes (IMG-ER) platform and with GOLD-ID Ga0063884 [13]. As shown in Table 1, the genome was resolved into 4,105 protein coding genes (CDs) and a total of 127 RNA genes which consist of 8 genes responsible for 5S rRNA synthesis, 5 genes for 16S rRNA synthesis, 6 genes for 23S rRNA synthesis and 107 genes for tRNA. From the IMG-ER platform, cluster of orthologous groups (COG) categories showed that a large number of genes are responsible for basic life-sustaining needs of the bacterium. It was found that 310 genes were predicted to contribute to amino acid transport and metabolism, 245 genes are linked to carbohydrate transport and metabolism, 295 involves in signal transduction mechanisms, and 91 genes are related to the virulence and defense regulation (Table 2).

From the annotated genome sequences, a gene associated with QS was found in contig 14. The 1203 bp of luxM homologue is analogous to an N-acyl homoserine lactone (AHL) synthase, AinS, which can be also found in V. fischeri [14, 15]. Hence, it is highly postulated that the autoinducer synthase LuxM is responsible for the production of signaling molecules in strain T47. In this study, the availability of the sequence could contribute to a better understanding of QS system and its role in V. sinaloensis.

 Table 1 

Genome features of V. sinaloensis strain T47

AttributesNumber% of Total
DNA, total number of bases4, 599, 504100.00
DNA coding number of bases4, 053, 74788.13
DNA G + C number of bases2, 121, 49446.12 1
DNA scaffolds80100.00
Genes total number4232100.00
Protein coding genes410597.00
RNA genes1273.00
rRNA genes190.45
5S rRNA80.19
16S rRNA50.12
23S rRNA60.14
tRNA genes1062.50
Other RNA genes20.05
Protein coding genes with function prediction342881.00
Pseudo genes651.54
Without function prediction67716.00
Protein coding genes with enzymes112426.56
Without enzymes but with candidate KO based enzymes50.12
Protein coding genes connected to Transporter Classification61414.51
Protein coding genes connected to KEGG pathways131030.95
Not connected to KEGG pathways279566.04
Protein coding genes connected to KEGG Orthology (KO)244857.84
Not connected to KEGG Orthology (KO)165739.15
Protein coding genes connected to MetaCyc pathways95422.54
Not connected to MetaCyc pathways315174.46
Protein coding genes with COGs308572.90
Chromosomal Cassettes392-
Biosynthetic Clusters8-
Genes in Biosynthetic Clusters1252.95
Fused Protein coding genes1363.21
Protein coding genes coding signal peptides44510.52
Protein coding genes coding transmembrane proteins103424.43
 Table 2 

Cluster of orthologous groups for strain T47 IMG-ER platform

NameCountPercentage (%)
Amino acid transport and metabolism3108.8
Carbohydrate transport and metabolism2456.95
Cell cycle control, cell division, chromosome partitioning391.11
Cell motility1353.83
Cell wall/ membrane/ envelope biogenesis2206.24
Chromatin structure and dynamics10.03
Coenzyme transport and metabolism1734.91
Defense mechanisms912.58
Energy production and conversion1985.58
Extracellular structures491.39
Function unknown2075.87
General function prediction only2386.75
Inorganic ion transport and metabolism1775.02
Intracellular trafficking, secretion and vesicular transport772.19
Lipid transport and metabolism1223.48
Mobilome: prophages and transposons120.34
Nucleotide transport and metabolism932.64
Posttranslational modification, protein turnover, chaperones1624.6
RNA processing and modification10.03
Replication, recombination and repair1203.41
Secondary metabolites biosynthesis, transport and catabolism641.82
Signal transduction mechanisms2958.37
Transcription2577.29
Translation, ribosomal structure and biogenesis2406.81
Not in COG114727.1

Nucleotide sequence accession numbers

The draft genome sequence of V. sinaloensis strain T47 can be obtained from GenBank under the accession number JXBJ00000000. This version described in the paper is the first version, JXBJ00000000. The GenBank accession number for 16S rDNA nucleotide sequence for strain T47 is KR058860. This version described in the paper is the first version, KR058860.

Acknowledgements

This work was supported by the High Impact Research Grants, University of Malaya (UM-MOHE HIR Grant UM.C/625/1/HIR/MOHE/CHAN/14/1, No. H-50001-A000027; UM-MOHE HIR Grant UM.C/625/1/HIR/MOHE/CHAN/01, No. A000001-50001) awarded to Kok-Gan Chan which are gratefully acknowledged.

Competing Interests

The authors have declared that no competing interest exists.

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Author contact

Corresponding address Corresponding author: Kok-Gan Chan, Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia. Email address: kokganedu.my


Published 2017-3-9