Molecular characterization of cDNA's obtained from black tiger shrimp (Penaeus monodon) haemocytes through the use of degenerate primers

The black tiger shrimp (Penaeus monodon) is an economically important species for several countries in the Asia-Pacific region and the intensive aquaculture practiced in these countries may promote the spread of pathogens, often causing significant economic loss. In the absence of effective treatment or control strategies for Penaeid shrimp viruses, attention has turned to understanding the mechanism of shrimp diseases and shrimp viral immunity. This project sought to isolate shrimp homologues of proteins from a key defense tissue, the hemocyte. Degenerate primers were designed based on the conserved Rel homology domain of NF-κB proteins, and RT-PCR was used on total RNA extracted from healthy black tiger shrimp haemocytes. A total of 28 cDNA fragments were isolated and characterized. Sequence search analysis showed that these clones fell in to three classes. Six clones showed significant amino acid identity (>90%) to 14-3-3 (3 clones) and α-tubulin (3 clones). A further 16 clones showed homology of 25% to 45% with other characterized genes, while 6 clones showed no homology to either each other or to sequences in databases. All sequences were submitted to the Genbank sequence database, adding significantly to the reported sequences for the black tiger shrimp.