Sequencing and characterization of a multi-organ Arctic charr transcriptome: A toolbox for investigating polymorphism and seasonal life in a high Arctic fish.
The Arctic charr (Salvelinus alpinus L.) inhabits fresh water ecosystems of the high North. The species has developed a strong phenotypic plasticity and variability in life history characteristics which has made this species an attractive model for investigations on phenotype plasticity, morph formation and ecological speciation. Further, the extreme seasonal variations in environmental conditions (e.g. food availability) in the high North induce seasonal changes in phenotype, which require precise timing mechanisms and physiological preparations. Individual gating of life-history strategies (e.g. formation of resident and sea-migrating morphs) and transitions (e.g. maturation) depends on conditional traits (size/energy status) at specific assessment time windows, and complex neuroendocrine regulation, which so far is poorly understood. In the absence of a reference genome, and in order to facilitate the investigation of the complex biological mechanisms of this unique fish model, the present study reveals a reference transcriptome for the Arctic charr. Using Roche 454 GS FLX+, we targeted various organs being either at the crossroads of many key pathways (neuroendocrine, metabolic, behavioral), of different ontological origins or displaying complementary physiological functions. The assemblage yielded 34,690 contigs greater than 1000bp with an average length (1690bp) and annotation rate (52%) within the range, or even higher, than what has been previously obtained with other teleost de novo transcriptomes. We dramatically improve the publically available transcript data on this species that may indeed be useful for various disciplines, from basic research to applied aspects related to conservation issues and aquaculture.
Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650, Banyuls/Mer, France. Electronic address: elodie.magnanou@obs-banyuls.fr.
Elodie
E
Magnanou
INRA, Plateforme bioinformatique Toulouse Midi-Pyrénées, UR875 Biométrie et Intelligence Artificielle, BP 52627, 31326 Castanet-Tolosan Cedex, France.
Celine
C
Noirot
Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650, Banyuls/Mer, France.
Jack
J
Falcón
Faculty of Biosciences, Fisheries and Economy, Department of Arctic and Marine Biology, UiT the Arctic University of Norway, NO-9037 Tormsø, Norway. Electronic address: even.jorgensen@uit.no.
Even Hjalmar
EH
Jørgensen
D000818:Animals; D001110:Arctic Regions; D005260:Female; D008297:Male; D009664:Norway; D011110:Polymorphism, Genetic; D012621:Seasons; D013538:Svalbard; D059467:Transcriptome; D014337:Trout / Q000235:genetics*
454 sequencing; Contig; Life-history; Phenotype; Physiology; Salvelinus alpinus