Thesis

Global gene expression profiling in Litopenaeus stylirostris using serial analysis of gene expression (SAGE)

Serial analysis of gene expression (SAGE) was used to examine gene expression profiles of healthy (pathogen-free) Litopenaeus stylirostris. Of the one thousand eight hundred forty-two SAGE clones sequenced, we found seven thousand six hundred and sixtysix SAGE tags. Transcript identification of the healthy L. stylirostris SAGE tags was completed using the reference databases, from SAGEmap. A total of six thousand five hundred forty SAGE tags to gene assignments were matched to a UniGene ID. The set of reliable SAGE tags were used to biologically characterize their function using the Gene Ontology database. SAGE tags that represented transcripts that encode genes found in the Gene Ontology database were divided into seventeen categories according to the major functions of their encoded proteins. From these characterized genes, one hundred four genes were found to be immunity related genes, some which have been seen for the first time in penaeid shrimp, such as neutrophil cytosolic factor 1, and eosonophil peroxidase. The genes identified in this healthy L. stylirostris SAGE library are just the beginning to understanding global gene expression in shrimp. Future research includes sequencing an infectious hypodermal and hematopoietic necrosis virus (lliHNV) infected L. stylirostris SAGE library to compare to the healthy L. stylirostris SAGE library and analyze gene expression of immune related genes including what has been found in this research. Key Words: Litopenaeus. stylirostris, Serial Analysis of Gene Expression; penaeid, innate immunity, ditag, SAGEmap

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