title: Exploring early micronutrient deficiencies in rainbow Trout (Oncorhynchus mykiss) by next-generation sequencing technology--from black box to functional genomics.
abstract: This work studies final nutritional status and transcriptional responses of rainbow trout (Oncorhynchus mykiss Walbaum 1792) (28 g) after a 10 week feeding experiment designed to elucidate the effect of adding a vitamin and mineral premix on growth, health, and nutritional endpoints. Juvenile fish were fed a either a diet supplemented with a vitamin and mineral premix (Diet S) or the same diet without premix supplementation (Diet U). The analyzed micronutrient composition of diets differed accordingly. Pooled livers from 15 fish from each dietary group were used to create suppression subtractive hybridization (SSH) cDNA libraries that were sequenced with 454 FLX GS Titanium Technology. In total 552 812 reads were sequenced from the two cDNA libraries. Ingenuity pathway analysis (IPA) was then used to characterize the hepatic transcriptome of the two dietary groups of rainbow trout. In the present communication we discuss how selected micronutrients may affect the transcriptome at suboptimal status by directly impacting the cellular metabolism, functions, and structures, and by introducing respective compensatory mechanisms. Processes related to lipid metabolism, peptide hydrolysis, oxygen transportation, and growth development were mostly affected. Considering the transcriptomics data relative to changes in nutritional status from the feeding study and the background phenotypic outcome of growth performance and gill histopathology, the outcome of the transcriptional profiling are suggested to be mainly related to suboptimal pantothenic acid and vitamin C nutrition.
authors.affiliation: National Institute of Nutrition and Seafood Research (NIFES), Bergen, Norway. pal.olsvik@nifes.no
authors.forename: Pål A
authors.initials: PA
authors.lastname: Olsvik
authors.forename: Gro-Ingunn
authors.initials: GI
authors.lastname: Hemre
authors.forename: Rune
authors.initials: R
authors.lastname: Waagbø
mesh_terms: D000818:Animals; D018076:DNA, Complementary / Q000235:genetics; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D018977:Micronutrients / Q000172:deficiency* / Q000502:physiology; D017686:Oncorhynchus mykiss / Q000235:genetics* / Q000502:physiology
chemical_list: D018076:DNA, Complementary; D018977:Micronutrients
references.citation: Genome Biol. 2002 Jun 18;3(7):RESEARCH0034
references.pmid: 12184808
references.citation: Food Chem Toxicol. 2011 Dec;49(12):3258-71
references.pmid: 21967782
references.citation: Mol Aspects Med. 2012 Feb;33(1):14-25
references.pmid: 22061966
references.citation: J Nutr. 2000 Jul;130(7):1800-8
references.pmid: 10867054
references.citation: BMC Genomics. 2010 Oct 08;11:548
references.pmid: 20932299
references.citation: Science. 2008 Jun 6;320(5881):1344-9
references.pmid: 18451266
references.citation: Bioinformatics. 2005 Sep 15;21(18):3674-6
references.pmid: 16081474
references.citation: EMBO Rep. 2008 Aug;9(8):721-4
references.pmid: 18617889
references.citation: Crit Rev Oncol Hematol. 2007 Mar;61(3):222-9
references.pmid: 17092739
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: Fish Physiol Biochem. 1992 Dec;10(4):315-9
references.pmid: 24214328
references.citation: Fish Physiol Biochem. 1994 Jan;12(5):421-9
references.pmid: 24202972
references.citation: Comp Biochem Physiol B Biochem Mol Biol. 2009 May;153(1):81-8
references.pmid: 19416695
references.citation: Biometals. 2011 Dec;24(6):981-92
references.pmid: 21533903
references.citation: J AOAC Int. 2007 May-Jun;90(3):844-56
references.pmid: 17580639
references.citation: J Nutr. 1994 Mar;124(3):430-5
references.pmid: 8120663
references.citation: Cell Mol Life Sci. 2008 Apr;65(7-8):1220-36
references.pmid: 18259688
references.citation: Genome Inform. 2005;16(1):106-15
references.pmid: 16362912
references.citation: J AOAC Int. 2001 Nov-Dec;84(6):1976-83
references.pmid: 11767171
references.citation: J Nutr. 1998 May;128(5):832-8
references.pmid: 9566989
references.citation: J Nutr Biochem. 2012 May;23(5):478-86
references.pmid: 21684137
references.citation: Genome Res. 2007 Mar;17(3):377-86
references.pmid: 17255551
references.citation: Fish Physiol Biochem. 1994 Jul;13(3):241-7
references.pmid: 24198194
references.citation: Fish Shellfish Immunol. 2011 Nov;31(5):704-15
references.pmid: 21377530
references.citation: Nutr Res. 2012 Feb;32(2):124-32
references.pmid: 22348461