Construction of subtracted EST and normalised cDNA libraries from liver of chemical-exposed three-spined stickleback (Gasterosteus aculeatus) containing pollutant-responsive genes as a resource for transcriptome analysis

The three-spined stickleback (Gasterosteus aculeatus) is ideally suited to laboratory studies, while its wide distribution in the northern hemisphere gives it great potential as a sentinel organism. In the setting of a UK-wide collaboration (Fish Toxicogenomics) we have developed a microarray for transcriptomic analysis of chemical responses in populations of G. aculeatus under laboratory and field conditions. Although several EST libraries are available for this species none are from chemical-exposed fish and thus unlikely to include a full set of pollutant-responsive genes. To harvest such transcripts cDNA libraries were produced from liver of chemical-exposed mature males. Two normalised full-length libraries were generated by different methods: (1) partial subtraction of polyA+ RNA against solid-phase cDNA using magnetic bead technology; (2) degradation of double stranded cDNA formed by abundant transcripts. To enrich for pollutant-responsive genes a subtracted EST library was also generated. For each library ∼1.5 K clones were sequenced and characterised using Blast2GO. All libraries contained pollutant-responsive transcripts not previously available while additionally the subtracted library was generally enriched ∼1.2–10-fold for transcripts expected to be induced in response to the pollutants.