Development of a halibut (Hippoglossus hippoglossus) oligonucleotide microarray

Summary

Atlantic halibut (Hippoglossus hippoglossus) is an important species in commercial fisheries and aquaculture in Norway. In recent years there has been an increasing focus on developing molecular tools for this species, resulting in the sequencing of a high number of ESTs made available through Genbank. The aims of the present work were to develop a 44k custom oligonucleotide array (oligoarray) for Atlantic halibut and to use this oligoarray for characterizing the transcriptional profiles of maternal transcripts during embryonic development. The oligoarray design was based on the available ~20 000 NCBI Genbank ESTs after vector removal, repeat masking, clustering and contig assembly using a locally installed version of the ESTexplorer assembly and annotation platform. The resulting 3105 contigs and 7114 single ESTs were functionally annotation by the blast2Go pipeline and high quality 60-mere probes designed and printed in triplicates on an Agilent 4x44k oligoarray. Of the total 10 219 sequences, 5046 (49%) were successfully annotated. Future work involves characterizing the performance of the oligoarray with the aim to investigate transcriptional events occurring in halibut during embryonic/ larval development and to correlate the data to egg and larval quality.