Subtracted Transcriptome Profile of Tiger Shrimp (Penaeus monodon) That Survived WSSV Challenge

Abstract

There is increased interest in the development of virus-resistant or improved shrimp stock because production is currently hindered by outbreaks and limited understanding of shrimp defense. Recent advancement now allows for high-throughput molecular studies on shrimp immunity. We used next-generation sequencing (NGS) coupled with suppression subtractive hybridization (SSH) to generate a transcriptome database of genes from tiger shrimp that survived White spot syndrome virus (WSSV) challenge. A total of 9,597 unique sequences were uploaded to NCBI Sequence Read Archive with accession number SRR577080. Sixty-five unique sequences, 6% of the total, were homologous to genes of Penaeus monodon. Genes that were initially related to bacterial infection and environmental stress such as 14-3-3 gene, heat shock protein 90, and calreticulin were also found including a few full-length gene sequences. Initial analysis of the expression of some genes was done. Hemocyanin, ferritin, and fortilin-binding protein exhibited differential expression between survivor and control tiger shrimps. Furthermore, candidate microsatellite markers for brood stock selection were mined and tested. Four trinucleotide and one dinucleotide microsatellites were successfully amplified. The study highlights the advantage of the NGS platform coupled with SSH in terms of gene discovery and marker generation.

The State of “Omics” Research for Farmed Penaeids: Advances in Research and Impediments to Industry Utilization

“…In particular, EST studies have been conducted to identify potential genes of interest related to male (Leelatanawit et al, 2008 , 2009 ) and female (Yamano and Unuma, 2006 ; Preechaphol et al, 2007 , 2010 ) reproductive functions. Likewise, comparisons of EST libraries between challenged individuals (i.e., exposed to stress and pathogens), and non-challenged individuals, have allowed the identification of genes with putative roles in virally-induced immune response (Gross et al, 2001 ; Rojtinnakorn et al, 2002 ; Shen et al, 2004 ; Clavero-Salas et al, 2007 ; Dong and Xiang, 2007 ; Leu et al, 2007 ; Pongsomboon et al, 2008b ; Maralit et al, 2014 ) and bacterial resistance (Bartlett et al, 2002 ; Supungul et al, 2002 , 2004 ; de Lorgeril et al, 2005 ; Somboonwiwat et al, 2006 ). While these studies were effective in the initial discovery of a small number of penaeid genes (Table 3 ), alone they provide an incomplete view of the transcriptionally active genes in each biological situation investigated.…”

Reviving the Philippine shrimp industry: molecular diagnostics and therapeutics

“…A transcriptome database of genes from tiger shrimp that survived WSSV challenged was generated by Maralit [40], who also unveiled a ubiquitin conjugating enzyme-like gene that renders protective effect to WSSV challenged M. rosenbergii [unpublished data]. Table 2 summarizes the genes utilized by RNA interference discussed in this review.…”

Molecular cloning and expression of chitin deacetylase 1 gene from the gills of Penaeus monodon (black tiger shrimp)

“…More 74 so when there is differential gene expression analysis between healthy and infected organism. 75 In this study, a partial fragment obtained from a transcriptome database extracted from the 76 gills of black tiger shrimp (P. monodon) that survived WSSV challenge (Maralit et al 2014 suggesting that it is CDA1 hence it is named here as PmCDA1. Differences in motifs from CDAs 238 of different groups are further exemplified in multiple alignment of CDA sequences (Fig.…”