Genomic insights of Vibrio harveyi RT-6 strain, from infected “Whiteleg shrimp” (Litopenaeus vannamei) using Illumina platform

Abstract

The pathogenicity of “Vibriosis” in shrimps imposes prominent menace to the sustainable growth of mariculture economy. Often the disease outbreak is associated speciously with Vibrio harveyi and its closely related species. The present study investigated the complete genome of the strain V. harveyi RT-6 to explore the molecular mechanism of pathogenesis. The genome of V. harveyi possesses a single chromosome of 6,374,398 bp in size, G + C content (44.7%) and 5730 protein coding genes. The reads of 1.3 Gb were retained from Illumina Hiseq 2500 sequencing method, assembled into 5912 predicted genes, 114 tRNAs genes, and 11 rRNAs genes. Unigenes were annotated by matching against Clusters of Orthologous Groups of proteins (COG)-5730, Gene ontology (GO)-1088, and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases-3401. Furthermore, 13 insertion sequences-(IS), virulence factors and prophage regions were also identified. A total of 94 pathogenic genes and 36 virulence factor genes were mainly identified using Virulence Factors Database (VFDB). Out of the 36 virulence factors, 23 genes responsible for encoding flagella-based motility protein were exclusively predicted to take part in pathogenic mechanism. The Whole Genome Sequencing (WGS) of the strain RT-6 (accession number: SRR5410471) highlighted the underlying genes and specifically accountable functional genes that were responsible for pathogenic infections in shrimps.