Open access
5 March 2015

Draft Genome Sequence of Aeromonas caviae Strain L12, a Quorum-Sensing Strain Isolated from a Freshwater Lake in Malaysia


Here, we present the draft genome sequence of Aeromonas caviae strain L12, which shows quorum-sensing activity. The availability of this genome sequence is important to the research of the quorum-sensing regulatory system in this isolate.


Aeromonads are Gram-negative, non-spore-forming, facultative anaerobic, rod-shaped bacteria. Members of Aeromonas can be found in aquatic environments. Aeromonas caviae is a motile mesophilic species in the Aeromonas genus, which is often associated with human infections (1). A. caviae has been isolated from patients with sepsis and wounds, gastroenteritis, and systemic infections (24). A process known as quorum sensing was described to be responsible for the regulation of virulence factors (58). In this work, A. caviae strain L12 was isolated from a freshwater lake in Malaysia and subjected to whole-genome sequencing.
Genomic DNA of A. caviae strain L12 was extracted using a MasterPure DNA purification kit (Epicentre, Madison, WI, USA) according to the manufacturer's recommended protocol. The quality of the purified genomic DNA was determined using a NanoDrop spectrophotometer (Thermo Scientific) and Qubit 2.0 fluorometer (Life Technologies) (9). Whole-genome sequencing was done using a paired-end sequencing method with the HiSeq 2500 platform (Illumina, Inc., San Diego, CA, USA) (10). The sequences were trimmed with a quality threshold of Q30 and de novo assembly was done using CLC Genomics Workbench version 7.0 (CLC Bio, Aarhus, Denmark) (11). The quality trimming yielded a total count of 4,908,771 paired-end reads with an average read length of 80.8 bp. The draft genome size of A. caviae strain L12 is 4,376,717 bp with 91 contigs with an average coverage of 100.6-fold. The mean contig read length is 126,255-bp and the maximum contig read length is 294,904 bp. Its G+C content is 61.7%, consisting of 30.7% cytosine and 31.0% guanine. Gene prediction and annotation was done using PROKKA version 1.10 resulting in 3,958 open reading frames (ORFs) and 4,089 genes (12). The number of RNAs was also predicted using PROKKA version 1.10. There were 3 rRNAs and 84 tRNAs identified.
Genes that were annotated were then searched against the NCBI database using BLAST (13) to confirm their identity and searched against the UniProt database (14) to further understand their functions and characteristics. From the annotated genes of the draft genome of strain L12, several putative quorum-sensing related genes were found, such as transcriptional activator protein LuxR, homoserine and homoserine lactone efflux proteins, regulatory protein LuxO, and autoinducer 2 sensor kinase/phosphatase LuxQ. It is hoped that this genome sequence will provide a better understanding of quorum-sensing regulation in this isolate.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under accession no. JWJP00000000. The version described in this paper is version JWJP01000000.


This work was financially supported by High Impact Research Grants from the University of Malaya (A000001-50001; UM-MOHE HIR Grant UM C/625/1/HIR/MOHE/CHAN/14/1, H-50001-A000027), which were awarded to K.-G.C.


Figura N, Guglielmetti P. 1987. Differentiation of motile and mesophilic Aeromonas strains into species by testing for a camp-like factor. J Clin Microbiol 25:1341–1342.
Beatson SA, das Graças de Luna M, Bachmann NL, Alikhan NF, Hanks KR, Sullivan MJ, Wee BA, Freitas-Almeida AC, Dos Santos PA, de Melo JT, Squire DJ, Cunningham AF, Fitzgerald JR, Henderson IR. 2011. Genome sequence of the emerging pathogen Aeromonas caviae. J Bacteriol 193:1286–1287.
Janda JM, Abbott SL. 2010. The genus Aeromonas: taxonomy, pathogenicity, and infection. Clin Microbiol Rev 23:35–73.
Tang HJ, Lai CC, Lin HL, Chao CM. 2014. Clinical manifestations of bacteremia caused by Aeromonas species in southern Taiwan. PLoS One 9:e91642.
Lim YL, Ee R, Yin WF, Chan KG. 2014. Quorum sensing activity of Aeromonas caviae strain YL12, a bacterium isolated from compost. Sensors (Basel) 14:7026–7040.
Tan WS, Yin WF, Chan KG. 2015. Insights into the quorum-sensing activity in Aeromonas hydrophila strain m013 as revealed by whole-genome sequencing. Genome Announc 3(1):e01372-14.
Chan XY, Chua KH, Yin WF, Puthucheary SD, Chan KG. 2014. Whole-genome analysis of Aeromonas hydrophila strain 187, exhibiting quorum-sensing activity. Genome Announc 2(6):e01360-14.
Chan KG, Puthucheary SD, Chan XY, Yin WF, Wong CS, Too WS, Chua KH. 2011. Quorum sensing in Aeromonas species isolated from patients in Malaysia. Curr Microbiol 62:167–172.
Mohamad NI, Yin WF, Chan KG. 2015. Whole-genome sequence of quorum-sensing Vibrio tubiashii strain t33. Genome Announc 3(1):e01362-14.
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.
Chong TM, Yin WF, Mondy S, Grandclément C, Dessaux Y, Chan KG. 2012. Heavy-metal resistance of a France vineyard soil bacterium, Pseudomonas mendocina strain S5.2, revealed by whole-genome sequencing. J Bacteriol 194:6366.
Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069.
Tatusova T, Ciufo S, Fedorov B, O’Neill K, Tolstoy I. 2014. RefSeq microbial genomes database: new representation and annotation strategy. Nucleic Acids Res 42:D553–D559.
Leinonen R, Nardone F, Zhu W, Apweiler R. 2006. UniSave: the UniProtKB sequence/annotation version database. Bioinformatics 22:1284–1285.

Information & Contributors


Published In

cover image Genome Announcements
Genome Announcements
Volume 3Number 230 April 2015
eLocator: e00079-15
PubMed: 25745006


Received: 21 January 2015
Accepted: 28 January 2015
Published online: 5 March 2015



Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
Pui-San Chin
Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
Kok Keng Tee
Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
Chien-Yi Chang
Interdisciplinary Computing and Complex BioSystems (ICOS) research group, School of Computing Science, Claremont Tower, Newcastle University, Newcastle upon Tyne, United Kingdom
The Centre for Bacterial Cell Biology, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne, United Kingdom
Wai-Fong Yin
Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
Kit-Yeng Sheng
Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia


Address correspondence to Kok-Gan Chan, [email protected].

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