Abstract
BackgroundAn essential first step in the genomic characterisation of a new species, in this case Atlantic halibut (Hippoglossus hippoglossus), is the generation of EST information. This forms the basis for subsequent microarray design, SNP detection and the placement of novel markers on genetic linkage maps.ResultsNormalised directional cDNA libraries were constructed from five different larval stages (hatching, mouth-opening, midway to metamorphosis, premetamorphosis, and post-metamorphosis) and eight different adult tissues (testis, ovary, liver, head kidney, spleen, skin, gill, and intestine). Recombination efficiency of the libraries ranged from 91–98% and insert size averaged 1.4 kb. Approximately 1000 clones were sequenced from the 5'-end of each library and after trimming, 12675 good sequences were obtained. Redundancy within each library was very low and assembly of the entire EST collection into contigs resulted in 7738 unique sequences of which 6722 (87%) had matches in Genbank. Removal of ESTs and contigs that originated from bacteria or food organisms resulted in a total of 7710 unique halibut sequences.ConclusionA Unigene collection of 7710 functionally annotated ESTs has been assembled from Atlantic halibut. These have been incorporated into a publicly available, searchable database and form the basis for an oligonucleotide microarray that can be used as a tool to study gene expression in this economically important aquacultured fish.
Highlights
An essential first step in the genomic characterisation of a new species, in this case Atlantic halibut (Hippoglossus hippoglossus), is the generation of Expressed sequence tag (EST) information
Results cDNA libraries and ESTs Normalized cDNA libraries were constructed from eight Atlantic halibut tissues and five developmental stages
The 7710 remaining unique ESTs consisted of 2556 unique clusters and 5154 singletons
Summary
An essential first step in the genomic characterisation of a new species, in this case Atlantic halibut (Hippoglossus hippoglossus), is the generation of EST information. This forms the basis for subsequent microarray design, SNP detection and the placement of novel markers on genetic linkage maps. Flatfish have long been a choice food fish, with many members of the group e.g., halibuts, flounders, soles, turbot, and plaice, having great commercial value especially in Asia. Aquaculture production of Japanese flounder, turbot, Atlantic halibut and others has been successfully achieved, improvements in efficiency are still clearly required. Production of Atlantic halibut is relatively recent and is currently underway in Norway, Iceland, Scotland and Canada.
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