Draft Genome Sequence of Environmental Bacterium Vibrio vulnificus CladeA-yb158

Abstract

We report the genome sequence of the environmental Vibrio vulnificus biotype 1_cladeA. This draft genome of the CladeA-yb158 strain, isolated in Israel, represents this newly emerged clonal group that contains both clinical and environmental strains.

GENOME ANNOUNCEMENT

Vibrio vulnificus is an aquatic bacterium and an important human pathogen (1–4). Strains of V. vulnificus are biochemically divided into three biotypes. Biotype 1 is a worldwide distributed pathogen and highly varied (5, 6). Recently, we found a new phylogroup, clade_A, which includes both environmental and clinical isolates and presents biochemical characteristics that differ from those of biotypes 1 and 3 (7, 8). Here, we describe the draft genome sequence of the environmental V. vulnificus biotype 1 strain CladeA-yb158, isolated in 2005 from tilapia fish grown at aquaculture ponds in northern Israel (9, 10) and subjected to whole-genome shotgun sequencing.

The 300-bp library (233 to 414 bp) was sequenced using Illumina HiSeq 2000, generating 82,200,000 past-filtered 100-bp paired-end reads, with a coverage of 500×. Reads were de novo assembled with Velvet 1/1/06, SOAPdenovo 0.9.5, and GapCloser 1.10 (11–13) (without filtering) generating 448 segments (kmer = 83) using reads with a minimum quality of 30 for each base. The assembly that contains 76 scaffolds of ≥200 bp, covers 5,294,657 bp, with an N₅₀ of 543,331 bp and a longest segment of 1,472,236 bp and second longest segment of 635,056 bp. Mapping was done using BWA 0.9.5 with a maximum of two differences from the reference sequence per paired-end read and a maximum of one gap not in the 5 bp of the read. A total of 97.96% of the single reads were mapped to the assembly (with 0.37% singletons), and 68% of the single reads were mapped to the V. vulnificus YJ016 genome (14). There is evidence for the presence of a plasmid related to pYJ016 (scaffold_27 and contig_C1443).

Various bioinformatics approaches were applied with the aim of reducing the number of contigs without any success, maybe due to the genome complexity of CladeA-yb158(BT1), derived from the high rates of horizontal gene transfer in the Vibrio species (5, 6, 15) and the presence of multiple repetitive regions. However, there are three scaffolds that account for more than 50% of the assembly (L50), indicating the high quality of the assembly taking into consideration the genome complexity of this phylogroup.

The draft genome of CladeA-yb158(BT1) consists of 76 segments covering 2 chromosomes and a plasmid (5.29 Mbp; 46.7% G+C content). A total of 4,574 coding sequences (CDS), 82 pseudo genes, 7 rRNAs, 94 tRNAs, and 1 non-coding RNA (ncRNA) were predicted and annotated by the NCBI Prokaryotic Genome Annotation Pipeline (16), similar to the annotation predicted by RAST (17).

Genome comparison of the CladeA-yb158 genome to two published V. vulnificus biotype I genomes using the SEED viewer in RAST (17, 18) revealed 88.32% (2,847 I chromosomes, 1,473 II chromosomes, and 34 plasmids) and 91.54% (2,685 I chromosomes and 1,448 II chromosomes) common genes to YJ016 (14) and CMCP6 (5, 19), respectively, suggesting higher resemblance to the CMCP6 strain.

Since clade_A is highly clonal, the genome of the CladeA-yb158 strain provides a representation of this phylogroup, contributing to the understanding of the evolution of this human pathogen in the environment.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. LBNN00000000. The version described in this paper is version LBNN01000000.