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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #160693


item Gahr, Scott
item Keele, John
item Palti, Yniv
item Rexroad, Caird

Submitted to: Plant and Animal Genome VX Conference Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: 1/11/2003
Publication Date: 1/11/2003
Citation: Gahr, S.A., Keele, J.W., Palti, Y., Rexroad III, C.E. 2003. Sequence analysis and utilization of rainbow trout expressed sequence tags (est's). Plant and Animal Genome Abstracts. Abstract P667. p.241.

Interpretive Summary:

Technical Abstract: Current research efforts at NCCCWA are focused on the utilization of molecular genetic technologies development improving rainbow trout aquaculture production efficiency. To this end, an expressed sequence tag (EST) project was initiated to: 1) identify as many unique rainbow trout transcripts as possible, 2) functionally annotate ESTs using comparative genome information from public databases, 3) target EST sequences of interest for genetic mapping, and 4) identify ESTs for utilization with technologies developed for high throughput studies of gene expression. A single normalized cDNA library was constructed from pooled rainbow trout brain, liver, gill, spleen, kidney, and white muscle tissue mRNA. Five prime end sequencing of 61,188 clones from the library yielded 46,792 with PHRED>20 over 100 bp averaging read length 521.5 bp. Analysis of redundancy revealed that only 4.55% of the 46,792 clones had a match within those sequences yielding approximately 44,662 unique sequences. Comparative genome analysis included the following using GenBank: blastx on the protein database, blastn on the non-redundant database, blastn on the zebrafish genome, and blastn on dbEST. Using the results of these analyses, ESTs are being identified as candidates for microarrays based on association with functional annotation. Eleven of the cDNAs were selected based on interest in the EST BLAST match for screening the NCCCWA BAC library. The results of analysis of two cDNA sequences representing the Inhibitor of Differentiation (Id) protein family are presented to demonstrate the usefulness of the ESTs for gene family identification, SNP discovery and gene expression data.