An Oligonucleotide Fingerprint Normalized and Expressed Sequence Tag Characterized Zebrafish cDNA Library

Abstract

The zebrafish is a powerful system for understanding the vertebrate genome, allowing the combination of genetic, molecular, and embryological analysis. Expressed sequence tags (ESTs) provide a rapid means of identifying an organism's genes for further analysis, but any EST project is limited by the availability of suitable libraries. Such cDNA libraries must be of high quality and provide a high rate of gene discovery. However, commonly used normalization and subtraction procedures tend to select for shorter, truncated, and internally primed inserts, seriously affecting library quality. An alternative procedure is to use oligonucleotide fingerprinting (OFP) to precluster clones before EST sequencing, thereby reducing the re-sequencing of common transcripts. Here, we describe the use of OFP to normalize and subtract 75,000 clones from two cDNA libraries, to a minimal set of 25,102 clones. We generated 25,788 ESTs (11,380 3′ and 14,408 5′) from over 16,000 of these clones. Clustering of 10,654 high-quality 3′ ESTs from this set identified 7232 clusters (likely genes), corresponding to a 68% gene diversity rate, comparable to what has been reported for the best normalized human cDNA libraries, and indicating that the complete set of 25,102 clones contains as many as 17,000 genes. Yet, the library quality remains high. The complete set of 25,102 clones is available for researchers as glycerol stocks, filters sets, and as individual EST clones. These resources have been used for radiation hybrid, genetic, and physical mapping of the zebrafish genome, as well as positional cloning and candidate gene identification, molecular marker, and microarray development.[The sequence data described in this paper have been submitted to the dbEST/GenBank data library under accession nos. AA497144–AA497369, AA542435–AA542678,AA545709–AA545724, AI384176–AI384205, AI384761–AI384796,AI396646–AI396663, AI396733–AI396777, AI396895–AI396938,AI397015–AI397130, AI397219–AI397252, AI397388–AI397484,AI415743–AI416403, AI436854–AI437493, AI444118–AI444540,AI461280–AI461395, AI476823–AI478024, AI496677–AI497576,AI522337–AI522810, AI544445–AI546083, AI558267–AI558995,AI584192–AI585023, AI585025–AI585238, AI588088–AI588836,AI601277–AI601868, AI626134–AI626875, AI629052–AI629398,AI641018–AI641780, AI657549–AI658347, AI666929–AI667197,AI667264–AI667414, AI667488–AI667567, AI721460–AI721747,AI721839–AI721978, and AI722283–AI722483.]