Thesis

Evidence of multiple retrotransposons in two litopenaeid species

Retrotransposons encompass a specific class of mobile genetic elements that are widespread across eukaryotic genomes, the impact of which are just beginning to be deciphered. In a step towards understanding their role in litopenaied shrimp, we have herein identified ten non-LTR retrotransposons and their putative phylogenetic placement. Two Litopenaeus stylirostris elements were discovered through standard and degenerate PCR amplification using previously defined non-L TR primers. A third genomic L. stylirostris element was identified using specific priming from an amplification protocol. These three PCR-derived sequences showed conserved domains of the non-LTR reverse transcriptase gene. A degenerate, 3' located non-L TR retrotransposon showing homology to ZEPP elements was isolated through screening of an L. stylirostris genomic library. In silica searching of genome databases and subsequent contig construction yielded six non-LTR retrotransposons (both genomic and expressed) in the Litopenaeus vannamei genome that also exhibited the highly conserved domains. Phylogenetic placement among representatives from all non-LTR clades showed a possibly novel monophyletic group. This group included elements from both L. stylirostris and L. vannamei and appeared most closely related to the highly active R TE clade. Our remaining four sequences placed in the CRl and I clades of retrotransposons, with one showing high similarity to ancient Penelope elements. This research identifies active retrotransposons in litopenaied genomes. Keywords: retrotransposon, litopenaied, penaied, non-LTR, IHHNV

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