Research article

An EST-based approach for identifying genes expressed in the intestine and gills of pre-smolt Atlantic salmon (Salmo salar)

Heidi Hagen-Larsen¹ , Jon K Laerdahl² , Frank Panitz³ , Alexei Adzhubei² and Bjørn Høyheim^1,4

¹Norwegian School of Veterinary Science, Department of Basic Sciences and Aquatic Medicine. PO Box 8146 Dep., NO-0033 Oslo, Norway

²Biotechnology Centre of Oslo (BIO), University of Oslo, PO Box 1125 Blindern, 0317 Oslo, Norway

³Danish Institute of Agricultural Sciences, Department of Animal Breeding and Genetics, PO Box 50, DK-8830 Tjele, Denmark

⁴Rikshospitalet University Hospital, Department of Dermatology, NO-0027 Oslo, Norway

author email corresponding author email

BMC Genomics 2005, 6:171doi:10.1186/1471-2164-6-171

Published:	1 December 2005

Abstract

Background

The Atlantic salmon is an important aquaculture species and a very interesting species biologically, since it spawns in fresh water and develops through several stages before becoming a smolt, the stage at which it migrates to the sea to feed. The dramatic change of habitat requires physiological, morphological and behavioural changes to prepare the salmon for its new environment. These changes are called the parr-smolt transformation or smoltification, and pre-adapt the salmon for survival and growth in the marine environment. The development of hypo-osmotic regulatory ability plays an important part in facilitating the transition from rivers to the sea. The physiological mechanisms behind the developmental changes are largely unknown. An understanding of the transformation process will be vital to the future of the aquaculture industry. A knowledge of which genes are expressed prior to the smoltification process is an important basis for further studies.

Results

In all, 2974 unique sequences, consisting of 779 contigs and 2195 singlets, were generated for Atlantic salmon from two cDNA libraries constructed from the gills and the intestine, accession numbers [Genbank: CK877169-CK879929, CK884015-CK886537 and CN181112-CN181464]. Nearly 50% of the sequences were assigned putative functions because they showed similarity to known genes, mostly from other species, in one or more of the databases used. The Swiss-Prot database returned significant hits for 1005 sequences. These could be assigned predicted gene products, and 967 were annotated using Gene Ontology (GO) terms for molecular function, biological process and/or cellular component, employing an annotation transfer procedure.

Conclusion

This paper describes the construction of two cDNA libraries from pre-smolt Atlantic salmon (Salmo salar) and the subsequent EST sequencing, clustering and assigning of putative function to 1005 genes expressed in the gills and/or intestine.