A first generation Atlantic halibut Hippoglossus hippoglossus (L.) microarray: application to developmental studies

ABSTRACT

An oligonucleotide microarray containing 50-mer oligonucleotides representing 9277 unique Atlantic halibut Hippoglossus hippoglossus genes has been designed, printed and is currently being used for the study of gene expression in developing halibut. The oligonucleotides are based on all the Atlantic halibut data available at the time of printing, these included expressed sequence tags (ESTs) and complete cDNAs derived from the Pleurogene sequencing project as well as sequences deposited in GenBank by other groups as of September 2006. Of the Pleurogene ESTs, 5040 are functionally annotated; the remainder are unknown (1016) or are similar to unannotated sequences in GenBank (1626). In addition to Atlantic halibut features, several control features have been incorporated, including an oligonucleotide representing a heterologous plant gene (92 spots) and empty spots containing buffer only (1344). The array contains 48 subgrids, each comprised of 32 columns and 26 rows. Every feature is printed at least four times as side-by-side quadruplicates, resulting in a microarray containing 39 936 features. This microarray has been utilized to identify genes differentially expressed in larval Atlantic halibut during the developmental period from post-hatch to post-metamorphosis. Early in development, transcription of the gene for hatching enzyme was down-regulated, whereas a gene involved in eye development was up-regulated. Midway to metamorphosis, transcription of genes encoding several key digestive enzymes was up-regulated, and in pre-metamorphic larvae, transcription of genes encoding muscle proteins was prominent.