Expressed Sequence Tags — A Snapshot of the Fish Genome

Expressed Sequence Tags (ESTs) represent the transcribed portion of an organism's genome and as such provide a snapshot of the expression of that genome at a particular time. Since non-coding DNA such as introns, intergenic spacers, repeat elements, etc. which comprise the bulk of the genome, is not sequenced, ESTs provide an information-rich source of data that is relatively easily interpreted and managed. EST surveys of non-normalized libraries can also provide an estimate of the abundance of particular transcripts. At the Institute for Marine Biosciences, we have optimized inexpensive template preparation and automated sequencing methodologies to produce large numbers of ESTs in an efficient and cost-effective manner. Tissue-specific EST libraries for winter flounder, our model system for studying flatfish biology, have been generated both for gene discovery purposes and for comparative purposes with other organisms. We have also produced an EST database from liver, head kidney and spleen of Atlantic salmon that will aid in genome mapping, identification of duplicated genes and DNA microarray construction, as well as providing information on genes critical to the fish immune system. An EST approach is also being used with subtractive libraries constructed from salmon infected with the pathogen Aeromonas salmonicida in order to focus on transcripts that are differentially regulated in response to disease.