Abstract
BackgroundThe 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.ResultsWe 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.ConclusionsSequence 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2208-7) contains supplementary material, which is available to authorized users.
Highlights
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
Liver and kidney samples from juvenile moribund fish with signs of septicaemia were available from another study [26] and were included in a normalised Complementary DNA (cDNA) library preparation to increase the diversity of the sequenced transcriptome
Pyrosequencing and transcriptome assembly A total of 976,904 raw sequence reads were generated, with a mean size of 347 bases (b) (Table 1), which is consistent with the sequencing technology used [55]
Summary
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. 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. A key characteristic of tunas is their ability to retain metabolic heat in the brain, red muscle and viscera via vascular specialisations called rete mirabile, which comprise numerous juxtaposed arterial and venous vessels acting as a counter-current heat exchange system [4] This heterothermic physiology shares characteristics of both poikilothermic and homeothermic organisms and is considered to have developed in order to permit thermal niche expansion, especially in correlation with maintenance of central nervous system function [5] or to sustain a rise in aerobic capacity and muscular performance [6]
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