Differential gene expression in healthy and infectious hypodermal and hematopoietic necrosis virus (IHHNV) infected shrimp, Litopenaeus stylirostris

Two serial analyses of gene expression (SAGE) libraries of healthy and infectious hypodermal and hematopoietic necrosis virus (IHHNV) infected shrimp species, Litopenaeus stylirostris, were constructed to identify genes associated with immune response. Invertebrates rely on the innate immune system when under a pathogenesis attack due to the lack of an adaptive immune response. Therefore, we are interested in genes involved in innate immune defense. The healthy library had 287,139 total tags and the infected library had 300,858 tags. 2,839 tags were differentially expressed of which 2% of these tags mapped to immune related genes. Of these 2,839 tags 35% of these tags were unmatched. The major problem with SAGE tags is their short length which often leads to inability to match SAGE tags to specific genes in databases. In an effort to better understand the innate response, those unknown genes were addressed. Through the rapid amplification of complementary DNA ends (RACE) in the 3' and 5' direction, a portion ofthese genes were successfully extended and matched. In total, 61 immune related genes were identified through SAGE and 3' and 5' RACE. These immune related genes coded for proteins whose function includes antimicrobial peptides, apoptosis, stress response and phagocytosis. One of the most interesting genes identified was the gene that encodes for the protein, Tripartite Motif -Containing Protein 5 (TRIM5alpha). TRIMS alpha serves an important role in inhibiting viral infectivity. Keywords: SAGE, innate, shrimp, Litopenaeus stylirostris, TRIM