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. 1. Introduction Although a lot of best management practices, detection methods, and disease intervention have been developed, shrimp production is still continuously affected by viral infections. Because of this, greater attention has now been placed on molecular studies for application on genetic breeding programs. As seen in recent years, there is an increase in the number of studies that aim to elucidate the function of several previously unknown genes and their viral response pathways. Expression and characterization studies of one or a group of similar genes are currently gaining pace. Likewise, large databases from which immune-related genes may be determined are now publicly available and are continuously generated. Some notable genes that have been recently described from Expressed Sequence Tags (EST) databases are hemocyanin, ferritin, and fortilin-binding protein [1–5]. Many subtraction libraries have also been used to associate mined genes from EST to specific roles in immunity. For instance, cathepsins [1, 6] and penaeidins [7–9] were proven to be immune related based on several separate cDNA library studies [10]. Using the same large-scale sequencing approach, genes
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