title: Development and validation of a mixed-tissue oligonucleotide DNA microarray for Atlantic bluefin tuna, Thunnus thynnus (Linnaeus, 1758).
abstract: BACKGROUND
  The largest of the tuna species, Atlantic bluefin tuna (Thunnus thynnus), inhabits the North Atlantic Ocean and the Mediterranean Sea and is considered to be an endangered species, largely a consequence of overfishing. T. thynnus aquaculture, referred to as fattening or farming, is a capture based activity dependent on yearly renewal from the wild. Thus, the development of aquaculture practices independent of wild resources can provide an important contribution towards ensuring security and sustainability of this species in the longer-term. The development of such practices is today greatly assisted by large scale transcriptomic studies.
  
  
  RESULTS
  We have used pyrosequencing technology to sequence a mixed-tissue normalised cDNA library, derived from adult T. thynnus. A total of 976,904 raw sequence reads were assembled into 33,105 unique transcripts having a mean length of 893 bases and an N50 of 870. Of these, 33.4% showed similarity to known proteins or gene transcripts and 86.6% of them were matched to the congeneric Pacific bluefin tuna (Thunnus orientalis) genome, compared to 70.3% for the more distantly related Nile tilapia (Oreochromis niloticus) genome. Transcript sequences were used to develop a novel 15 K Agilent oligonucleotide DNA microarray for T. thynnus and comparative tissue gene expression profiles were inferred for gill, heart, liver, ovaries and testes. Functional contrasts were strongest between gills and ovaries. Gills were particularly associated with immune system, signal transduction and cell communication, while ovaries displayed signatures of glycan biosynthesis, nucleotide metabolism, transcription, translation, replication and repair.
  
  
  CONCLUSIONS
  Sequence data generated from a novel mixed-tissue T. thynnus cDNA library provide an important transcriptomic resource that can be further employed for study of various aspects of T. thynnus ecology and genomics, with strong applications in aquaculture. Tissue-specific gene expression profiles inferred through the use of novel oligo-microarray can serve in the design of new and more focused transcriptomic studies for future research of tuna physiology and assessment of the welfare in a production environment.
authors.affiliation: University Department of Marine Studies, University of Split, Split, Croatia. ztrumbic@unist.hr.
authors.forename: Željka
authors.initials: Ž
authors.lastname: Trumbić
authors.affiliation: Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, Scotland, UK. michael.bekaert@stir.ac.uk.
authors.forename: Michaël
authors.initials: M
authors.lastname: Bekaert
authors.affiliation: Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, Scotland, UK. j.b.taggart@stir.ac.uk.
authors.forename: John B
authors.initials: JB
authors.lastname: Taggart
authors.affiliation: Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, Scotland, UK. j.e.bron@stir.ac.uk.
authors.forename: James E
authors.initials: JE
authors.lastname: Bron
authors.affiliation: Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, Scotland, UK. Karim.Gharbi@ed.ac.uk.
authors.forename: Karim
authors.initials: K
authors.lastname: Gharbi
authors.affiliation: Institute of Oceanography and Fisheries, Split, Croatia. mladineo@izor.hr.
authors.forename: Ivona
authors.initials: I
authors.lastname: Mladineo
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D018076:DNA, Complementary; D020869:Gene Expression Profiling; D015723:Gene Library; D023281:Genomics; D058977:Molecular Sequence Annotation; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D009928:Organ Specificity / Q000235:genetics; D015203:Reproducibility of Results; D059467:Transcriptome; D014413:Tuna / Q000235:genetics*
chemical_list: D018076:DNA, Complementary