{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T02:25:14Z","timestamp":1775096714092,"version":"3.50.1"},"reference-count":86,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2019,5,3]],"date-time":"2019-05-03T00:00:00Z","timestamp":1556841600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Canadian Regulatory System for Biotechnology","award":["NA"],"award-info":[{"award-number":["NA"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"published-print":{"date-parts":[[2019,12]]},"DOI":"10.1186\/s12864-019-5655-8","type":"journal-article","created":{"date-parts":[[2019,5,3]],"date-time":"2019-05-03T16:04:18Z","timestamp":1556899458000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Effect of triploidy on liver gene expression in coho salmon (Oncorhynchus kisutch) under different metabolic states"],"prefix":"10.1186","volume":"20","author":[{"given":"Kris A.","family":"Christensen","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dionne","family":"Sakhrani","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric B.","family":"Rondeau","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeffery","family":"Richards","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ben F.","family":"Koop","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert H.","family":"Devlin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2019,5,3]]},"reference":[{"key":"5655_CR1","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1038\/nrm3756","volume":"15","author":"BA Edgar","year":"2014","unstructured":"Edgar BA, Zielke N, Gutierrez C. Endocycles: a recurrent evolutionary innovation for post-mitotic cell growth. Nat Rev Mol Cell Biol. 2014;15:197\u2013210.","journal-title":"Nat Rev Mol Cell Biol."},{"key":"5655_CR2","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1126\/science.264.5157.421","volume":"264","author":"J Masterson","year":"1994","unstructured":"Masterson J. Stomatal size in fossil plants: evidence for polyploidy in majority of angiosperms. Science. 1994;264:421\u20134.","journal-title":"Science."},{"key":"5655_CR3","doi-asserted-by":"publisher","first-page":"150","DOI":"10.1042\/BST0390150","volume":"39","author":"J Soppa","year":"2011","unstructured":"Soppa J. Ploidy and gene conversion in archaea. Biochem Soc Trans. 2011;39:150\u20134.","journal-title":"Biochem Soc Trans."},{"key":"5655_CR4","doi-asserted-by":"publisher","first-page":"a019216","DOI":"10.1101\/cshperspect.a019216","volume":"7","author":"PA Levin","year":"2015","unstructured":"Levin PA, Angert ER. Small but mighty: cell size and Bacteria. Cold Spring Harb Perspect Biol. 2015;7:a019216.","journal-title":"Cold Spring Harb Perspect Biol."},{"key":"5655_CR5","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1159\/000368855","volume":"24","author":"J Soppa","year":"2014","unstructured":"Soppa J. Polyploidy in archaea and Bacteria: about desiccation resistance, Giant cell size, long-term survival, enforcement by a eukaryotic host and additional aspects. J Mol Microbiol Biotechnol. 2014;24:409\u201319.","journal-title":"J Mol Microbiol Biotechnol."},{"key":"5655_CR6","doi-asserted-by":"publisher","first-page":"855","DOI":"10.1016\/j.pt.2016.08.006","volume":"32","author":"SK Maciver","year":"2016","unstructured":"Maciver SK. Asexual amoebae escape Muller\u2019s ratchet through polyploidy. Trends Parasitol. 2016;32:855\u201362.","journal-title":"Trends Parasitol."},{"key":"5655_CR7","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1146\/annurev.genet.34.1.401","volume":"34","author":"SP Otto","year":"2000","unstructured":"Otto SP, Whitton J. Polyploid incidence and evolution. Annu Rev Genet. 2000;34:401\u201337.","journal-title":"Annu Rev Genet."},{"key":"5655_CR8","doi-asserted-by":"publisher","first-page":"R1121","DOI":"10.1016\/j.cub.2008.09.039","volume":"18","author":"SP Otto","year":"2008","unstructured":"Otto SP, Gerstein AC. The evolution of haploidy and diploidy. Curr Biol CB. 2008;18:R1121\u20134.","journal-title":"Curr Biol CB."},{"key":"5655_CR9","doi-asserted-by":"publisher","first-page":"453","DOI":"10.1002\/(SICI)1521-1878(199806)20:6<453::AID-BIES3>3.0.CO;2-N","volume":"20","author":"BK Mable","year":"1998","unstructured":"Mable BK, Otto SP. The evolution of life cycles with haploid and diploid phases. BioEssays. 1998;20:453\u201362.","journal-title":"BioEssays."},{"key":"5655_CR10","doi-asserted-by":"publisher","first-page":"1423","DOI":"10.1242\/dev.102202","volume":"141","author":"A Wutz","year":"2014","unstructured":"Wutz A. Haploid animal cells. Development. 2014;141:1423\u20136.","journal-title":"Development."},{"key":"5655_CR11","doi-asserted-by":"publisher","first-page":"322","DOI":"10.1016\/j.ajpath.2013.06.035","volume":"184","author":"G Gentric","year":"2014","unstructured":"Gentric G, Desdouets C. Polyploidization in liver tissue. Am J Pathol. 2014;184:322\u201331.","journal-title":"Am J Pathol."},{"key":"5655_CR12","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1126\/science.285.5425.251","volume":"285","author":"T Galitski","year":"1999","unstructured":"Galitski T, Saldanha AJ, Styles CA, Lander ES, Fink GR. Ploidy regulation of gene expression. Science. 1999;285:251\u20134.","journal-title":"Science."},{"key":"5655_CR13","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1016\/j.ygeno.2006.08.014","volume":"89","author":"OV Anatskaya","year":"2007","unstructured":"Anatskaya OV, Vinogradov AE. Genome multiplication as adaptation to tissue survival: evidence from gene expression in mammalian heart and liver. Genomics. 2007;89:70\u201380.","journal-title":"Genomics."},{"key":"5655_CR14","doi-asserted-by":"publisher","first-page":"485","DOI":"10.1083\/jcb.201502016","volume":"209","author":"KP Schoenfelder","year":"2015","unstructured":"Schoenfelder KP, Fox DT. The expanding implications of polyploidy. J Cell Biol. 2015;209:485\u201391.","journal-title":"J Cell Biol."},{"key":"5655_CR15","doi-asserted-by":"crossref","first-page":"1349","DOI":"10.1093\/genetics\/142.4.1349","volume":"142","author":"M Guo","year":"1996","unstructured":"Guo M, Davis D, Birchler JA. Dosage effects on gene expression in a maize ploidy series. Genetics. 1996;142:1349\u201355.","journal-title":"Genetics."},{"key":"5655_CR16","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1016\/j.molcel.2015.01.027","volume":"58","author":"KB Halpern","year":"2015","unstructured":"Halpern KB, Tanami S, Landen S, Chapal M, Szlak L, Hutzler A, et al. Bursty gene expression in the intact mammalian liver. Mol Cell. 2015;58:147\u201356.","journal-title":"Mol Cell."},{"key":"5655_CR17","doi-asserted-by":"publisher","first-page":"617","DOI":"10.1007\/s00335-007-9048-y","volume":"18","author":"P Lu","year":"2007","unstructured":"Lu P, Prost S, Caldwell H, Tugwood JD, Betton GR, Harrison DJ. Microarray analysis of gene expression of mouse hepatocytes of different ploidy. Mamm Genome. 2007;18:617.","journal-title":"Mamm Genome."},{"key":"5655_CR18","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1038\/sj.hdy.6800941","volume":"98","author":"RM Johnson","year":"2007","unstructured":"Johnson RM, Shrimpton JM, Cho GK, Heath DD. Dosage effects on heritability and maternal effects in diploid and triploid Chinook salmon (Oncorhynchus tshawytscha). Heredity. 2007;98:303\u201310.","journal-title":"Heredity."},{"key":"5655_CR19","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1186\/s12863-017-0502-x","volume":"18","author":"AC Harvey","year":"2017","unstructured":"Harvey AC, Fjelldal PG, Solberg MF, Hansen T, Glover KA. Ploidy elicits a whole-genome dosage effect: growth of triploid Atlantic salmon is linked to the genetic origin of the second maternal chromosome set. BMC Genet. 2017;18:34.","journal-title":"BMC Genet."},{"key":"5655_CR20","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1007\/s10695-007-9138-5","volume":"33","author":"JM Shrimpton","year":"2007","unstructured":"Shrimpton JM, Sentlinger AMC, Heath JW, Devlin RH, Heath DD. Biochemical and molecular differences in diploid and triploid ocean-type Chinook salmon (Oncorhynchus tshawytscha) smolts. Fish Physiol Biochem. 2007;33:259\u201368.","journal-title":"Fish Physiol Biochem."},{"key":"5655_CR21","doi-asserted-by":"publisher","first-page":"1200","DOI":"10.1073\/pnas.79.4.1200","volume":"79","author":"RH Devlin","year":"1982","unstructured":"Devlin RH, Holm DG, Grigliatti TA. Autosomal dosage compensation Drosophila melanogaster strains trisomic for the left arm of chromosome 2. Proc Natl Acad Sci U S A. 1982;79:1200\u20134.","journal-title":"Proc Natl Acad Sci U S A."},{"key":"5655_CR22","doi-asserted-by":"publisher","first-page":"2461","DOI":"10.1093\/gbe\/evx154","volume":"9","author":"L Gu","year":"2017","unstructured":"Gu L, Walters JR. Evolution of sex chromosome dosage compensation in animals: a beautiful theory, undermined by facts and bedeviled by details. Genome Biol Evol. 2017;9:2461\u201376.","journal-title":"Genome Biol Evol."},{"key":"5655_CR23","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1016\/j.semcdb.2013.02.004","volume":"24","author":"JA Birchler","year":"2013","unstructured":"Birchler JA. Aneuploidy in plants and flies: the origin of studies of genomic imbalance. Semin Cell Dev Biol. 2013;24:315\u20139.","journal-title":"Semin Cell Dev Biol."},{"key":"5655_CR24","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1093\/genetics\/118.1.87","volume":"118","author":"RH Devlin","year":"1988","unstructured":"Devlin RH, Holm DG, Grigliatti TA. The influence of whole-arm trisomy on gene expression in Drosophila. Genetics. 1988;118:87\u2013101.","journal-title":"Genetics."},{"key":"5655_CR25","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1093\/genetics\/74.2.331","volume":"74","author":"G Maroni","year":"1973","unstructured":"Maroni G, Plaut W. Dosage compensation in DROSOPHILA MELANOGASTER triploids. II. Glucose-6-phosphate dehydrogenase activity. Genetics. 1973;74:331\u201342.","journal-title":"Genetics."},{"key":"5655_CR26","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1007\/BF00485589","volume":"9","author":"JC Lucchesi","year":"1973","unstructured":"Lucchesi JC, Rawls JM. Regulation of gene function: a comparison of enzyme activity levels in relation to gene dosage in diploids and triploids of Drosophila melanogaster. Biochem Genet. 1973;9:41\u201351.","journal-title":"Biochem Genet."},{"key":"5655_CR27","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1534\/genetics.105.047894","volume":"172","author":"J Wang","year":"2006","unstructured":"Wang J, Tian L, Lee H-S, Wei NE, Jiang H, Watson B, et al. Genomewide nonadditive gene regulation in Arabidopsis Allotetraploids. Genetics. 2006;172:507\u201317.","journal-title":"Genetics."},{"key":"5655_CR28","doi-asserted-by":"publisher","first-page":"2055","DOI":"10.1534\/genetics.107.074286","volume":"176","author":"RM Stupar","year":"2007","unstructured":"Stupar RM, Bhaskar PB, Yandell BS, Rensink WA, Hart AL, Ouyang S, et al. Phenotypic and transcriptomic changes associated with potato Autopolyploidization. Genetics. 2007;176:2055\u201367.","journal-title":"Genetics."},{"key":"5655_CR29","doi-asserted-by":"publisher","first-page":"17809","DOI":"10.1073\/pnas.1000852107","volume":"107","author":"Z Yu","year":"2010","unstructured":"Yu Z, Haberer G, Matthes M, Rattei T, Mayer KFX, Gierl A, et al. Impact of natural genetic variation on the transcriptome of autotetraploid Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2010;107:17809\u201314.","journal-title":"Proc Natl Acad Sci U S A."},{"key":"5655_CR30","doi-asserted-by":"publisher","first-page":"e314","DOI":"10.1371\/journal.pbio.0030314","volume":"3","author":"P Dehal","year":"2005","unstructured":"Dehal P, Boore JL. Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol. 2005;3:e314.","journal-title":"PLoS Biol."},{"key":"5655_CR31","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1007\/978-3-642-31442-1_16","volume-title":"Polyploidy and Genome Evolution","author":"Cristian Ca\u00f1estro","year":"2012","unstructured":"Ca\u00f1estro C. Two rounds of whole-genome duplication: evidence and impact on the evolution of vertebrate innovations. In: Polyploidy and genome evolution. Berlin: Springer; 2012. p. 309\u201339. https:\/\/doi.org\/10.1007\/978-3-642-31442-1_16 ."},{"key":"5655_CR32","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0173053","volume":"12","author":"KA Christensen","year":"2017","unstructured":"Christensen KA, Davidson WS. Autopolyploidy genome duplication preserves other ancient genome duplications in Atlantic salmon (Salmo salar). PLoS One. 2017;12:e0173053.","journal-title":"PLoS One."},{"key":"5655_CR33","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/978-1-4684-4652-4_1","volume-title":"Evolutionary genetics of fishes. Monographs in Evolutionary Biology","author":"FW Allendorf","year":"1984","unstructured":"Allendorf FW, Thorgaard GH. Tetraploidy and the evolution of salmonid fishes. In: Turner BJ, editor. Evolutionary genetics of fishes. Monographs in Evolutionary Biology. Boston: Springer; 1984. p. 1\u201353. https:\/\/doi.org\/10.1007\/978-1-4684-4652-4_1 . Online ISBN 978-1-4684-4652-4, Print ISBN 978-1-4684-4654-8."},{"key":"5655_CR34","doi-asserted-by":"publisher","unstructured":"Berthelot C, Brunet F, Chalopin D, Juanchich A, Bernard M, No\u00ebl B, et al. The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nat Commun. 2014;5(3657) https:\/\/doi.org\/10.1038\/ncomms4657 .","DOI":"10.1038\/ncomms4657"},{"key":"5655_CR35","doi-asserted-by":"publisher","first-page":"e0195461","DOI":"10.1371\/journal.pone.0195461","volume":"13","author":"KA Christensen","year":"2018","unstructured":"Christensen KA, Leong JS, Sakhrani D, Biagi CA, Minkley DR, Withler RE, et al. Chinook salmon (Oncorhynchus tshawytscha) genome and transcriptome. PLoS One. 2018;13:e0195461.","journal-title":"PLoS One."},{"key":"5655_CR36","doi-asserted-by":"publisher","first-page":"200","DOI":"10.1038\/nature17164","volume":"533","author":"S Lien","year":"2016","unstructured":"Lien S, Koop BF, Sandve SR, Miller JR, Kent MP, Nome T, et al. The Atlantic salmon genome provides insights into rediploidization. Nature. 2016;533:200\u20135.","journal-title":"Nature."},{"key":"5655_CR37","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1093\/jhered\/esv015","volume":"106","author":"FW Allendorf","year":"2015","unstructured":"Allendorf FW, Bassham S, Cresko WA, Limborg MT, Seeb LW, Seeb JE. Effects of crossovers between Homeologs on inheritance and population genomics in Polyploid-derived salmonid fishes. J Hered. 2015;106:217\u201327.","journal-title":"J Hered."},{"key":"5655_CR38","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1111\/1755-0998.12394","volume":"16","author":"RK Waples","year":"2016","unstructured":"Waples RK, Seeb LW, Seeb JE. Linkage mapping with paralogs exposes regions of residual tetrasomic inheritance in chum salmon (Oncorhynchus keta). Mol Ecol Resour. 2016;16:17\u201328.","journal-title":"Mol Ecol Resour."},{"key":"5655_CR39","doi-asserted-by":"publisher","first-page":"727","DOI":"10.1051\/rnd:19800415","volume":"20","author":"D Chourrout","year":"1980","unstructured":"Chourrout D. Thermal induction of diploid gynogenesis and triploidy in the eggs of the rainbow trout (Salmo gairdneri Richardson). Reprod Nutr D\u00e9v. 1980;20:727\u201333.","journal-title":"Reprod Nutr D\u00e9v."},{"key":"5655_CR40","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1016\/0044-8486(83)90080-7","volume":"35","author":"FM Utter","year":"1983","unstructured":"Utter FM, Johnson OW, Thorgaard GH, Rabinovitch PS. Measurement and potential applications of induced triploidy in Pacific salmon. Aquaculture. 1983;35:125\u201335.","journal-title":"Aquaculture."},{"key":"5655_CR41","doi-asserted-by":"publisher","first-page":"359","DOI":"10.1016\/0044-8486(84)90328-4","volume":"36","author":"TJ Benfey","year":"1984","unstructured":"Benfey TJ, Sutterlin AM. Triploidy induced by heat shock and hydrostatic pressure in landlocked Atlantic salmon (Salmo salar L.). Aquaculture. 1984;36:359\u201367.","journal-title":"Aquaculture."},{"key":"5655_CR42","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1080\/10641269991319162","volume":"7","author":"TJ Benfey","year":"1999","unstructured":"Benfey TJ. The physiology and behavior of triploid fishes. Rev Fish Sci. 1999;7:39\u201367.","journal-title":"Rev Fish Sci."},{"key":"5655_CR43","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1051\/alr:1991016","volume":"4","author":"E McLean","year":"1991","unstructured":"McLean E, Sadar MD, Delvin RH, Souza LM, Donaldson EM. Promotion of growth in diploid and triploid coho salmon with parenteral delivery of a recombinant porcine somatotropin. Aquat Living Resour. 1991;4:155\u201360.","journal-title":"Aquat Living Resour."},{"key":"5655_CR44","doi-asserted-by":"publisher","first-page":"112","DOI":"10.1016\/j.ygcen.2013.11.023","volume":"196","author":"RH Devlin","year":"2014","unstructured":"Devlin RH, Sakhrani D, Biagi CA, Smith JL, Fujimoto T, Beckman B. Growth and endocrine effect of growth hormone transgene dosage in diploid and triploid coho salmon. Gen Comp Endocrinol. 2014;196:112\u201322.","journal-title":"Gen Comp Endocrinol."},{"key":"5655_CR45","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1007\/s10126-017-9730-3","volume":"19","author":"S Chatchaiphan","year":"2017","unstructured":"Chatchaiphan S, Srisapoome P, Kim J-H, Devlin RH, Na-Nakorn U. De novo transcriptome characterization and growth-related gene expression profiling of diploid and triploid bighead catfish (Clarias macrocephalus G\u00fcnther, 1864). Mar Biotechnol N Y. 2017;19:36\u201348.","journal-title":"Mar Biotechnol N Y."},{"key":"5655_CR46","doi-asserted-by":"publisher","first-page":"224","DOI":"10.1038\/hdy.2009.108","volume":"104","author":"B Ching","year":"2010","unstructured":"Ching B, Jamieson S, Heath JW, Heath DD, Hubberstey A. Transcriptional differences between triploid and diploid Chinook salmon (Oncorhynchus tshawytscha) during live Vibrio anguillarum challenge. Heredity. 2010;104:224\u201334.","journal-title":"Heredity."},{"key":"5655_CR47","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1186\/s13059-016-0881-8","volume":"17","author":"A Conesa","year":"2016","unstructured":"Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, et al. A survey of best practices for RNA-seq data analysis. Genome Biol. 2016;17:13.","journal-title":"Genome Biol."},{"key":"5655_CR48","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1016\/j.cbd.2017.02.005","volume":"22","author":"WG Nuez-Ort\u00edn","year":"2017","unstructured":"Nuez-Ort\u00edn WG, Carter CG, Wilson R, Cooke IR, Amoroso G, Cobcroft JM, et al. Triploid Atlantic salmon shows similar performance, fatty acid composition and proteome response to diploids during early freshwater rearing. Comp Biochem Physiol Part D Genomics Proteomics. 2017;22:67\u201377.","journal-title":"Comp Biochem Physiol Part D Genomics Proteomics."},{"key":"5655_CR49","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1016\/j.bbrc.2004.01.044","volume":"315","author":"ID Kerr","year":"2004","unstructured":"Kerr ID. Sequence analysis of twin ATP binding cassette proteins involved in translational control, antibiotic resistance, and ribonuclease L inhibition. Biochem Biophys Res Commun. 2004;315:166\u201373.","journal-title":"Biochem Biophys Res Commun."},{"key":"5655_CR50","doi-asserted-by":"publisher","first-page":"7088","DOI":"10.1128\/MCB.17.12.7088","volume":"17","author":"T Gautier","year":"1997","unstructured":"Gautier T, Berg\u00e8s T, Tollervey D, Hurt E. Nucleolar KKE\/D repeat proteins Nop56p and Nop58p interact with Nop1p and are required for ribosome biogenesis. Mol Cell Biol. 1997;17:7088\u201398.","journal-title":"Mol Cell Biol."},{"key":"5655_CR51","doi-asserted-by":"publisher","first-page":"484","DOI":"10.1021\/bi00350a031","volume":"25","author":"MOJ Olson","year":"1986","unstructured":"Olson MOJ, Wallace MO, Herrera AH, Marshall-Carlson L, Hunt RC. Preribosomal ribonucleoprotein particles are a major component of a nucleolar matrix fraction. Biochemistry. 1986;25:484\u201391.","journal-title":"Biochemistry."},{"key":"5655_CR52","doi-asserted-by":"publisher","first-page":"529","DOI":"10.1038\/ncb814","volume":"4","author":"E Colombo","year":"2002","unstructured":"Colombo E, Marine J-C, Danovi D, Falini B, Pelicci PG. Nucleophosmin regulates the stability and transcriptional activity of p53. Nat Cell Biol. 2002;4:529\u201333.","journal-title":"Nat Cell Biol."},{"key":"5655_CR53","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1186\/s12864-017-3837-9","volume":"18","author":"P-Y Rescan","year":"2017","unstructured":"Rescan P-Y, Le Cam A, Ralli\u00e8re C, Montfort J. Global gene expression in muscle from fasted\/refed trout reveals up-regulation of genes promoting myofibre hypertrophy but not myofibre production. BMC Genomics. 2017;18:447.","journal-title":"BMC Genomics."},{"key":"5655_CR54","doi-asserted-by":"publisher","first-page":"E28","DOI":"10.1152\/ajpendo.90897.2008","volume":"297","author":"CM Paton","year":"2009","unstructured":"Paton CM, Ntambi JM. Biochemical and physiological function of stearoyl-CoA desaturase. Am J Physiol - Endocrinol Metab. 2009;297:E28\u201337.","journal-title":"Am J Physiol - Endocrinol Metab."},{"key":"5655_CR55","doi-asserted-by":"publisher","first-page":"522","DOI":"10.1186\/1471-2164-12-522","volume":"12","author":"F Geay","year":"2011","unstructured":"Geay F, Ferraresso S, Zambonino-Infante JL, Bargelloni L, Quentel C, Vandeputte M, et al. Effects of the total replacement of fish-based diet with plant-based diet on the hepatic transcriptome of two European sea bass (Dicentrarchus labrax) half-sibfamilies showing different growth rates with the plant-based diet. BMC Genomics. 2011;12:522.","journal-title":"BMC Genomics."},{"key":"5655_CR56","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1677\/jme.1.02031","volume":"37","author":"ML Rise","year":"2006","unstructured":"Rise ML, Douglas SE, Sakhrani D, Williams J, Ewart KV, Rise M, et al. Multiple microarray platforms utilized for hepatic gene expression profiling of GH transgenic coho salmon with and without ration restriction. J Mol Endocrinol. 2006;37:259\u201382.","journal-title":"J Mol Endocrinol."},{"key":"5655_CR57","doi-asserted-by":"publisher","first-page":"3047","DOI":"10.1073\/pnas.0809798106","volume":"106","author":"RH Devlin","year":"2009","unstructured":"Devlin RH, Sakhrani D, Tymchuk WE, Rise ML, Goh B. Domestication and growth hormone transgenesis cause similar changes in gene expression in coho salmon (Oncorhynchus kisutch). Proc Natl Acad Sci. 2009;106:3047\u201352.","journal-title":"Proc Natl Acad Sci."},{"key":"5655_CR58","doi-asserted-by":"publisher","first-page":"5247","DOI":"10.2527\/jas.2013-6612","volume":"91","author":"RH Devlin","year":"2013","unstructured":"Devlin RH, Sakhrani D, White S, Overturf K. Effects of domestication and growth hormone transgenesis on mRNA profiles in rainbow trout (Oncorhynchus mykiss). J Anim Sci. 2013;91:5247\u201358.","journal-title":"J Anim Sci."},{"key":"5655_CR59","doi-asserted-by":"publisher","first-page":"545","DOI":"10.1093\/jxb\/erl228","volume":"58","author":"W Tang","year":"2007","unstructured":"Tang W, Newton RJ, Weidner DA. Genetic transformation and gene silencing mediated by multiple copies of a transgene in eastern white pine. J Exp Bot. 2007;58:545\u201354.","journal-title":"J Exp Bot."},{"key":"5655_CR60","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1046\/j.1365-313X.2003.01746.x","volume":"34","author":"B Lechtenberg","year":"2003","unstructured":"Lechtenberg B, Schubert D, Forsbach A, Gils M, Schmidt R. Neither inverted repeat T-DNA configurations nor arrangements of tandemly repeated transgenes are sufficient to trigger transgene silencing. Plant J Cell Mol Biol. 2003;34:507\u201317.","journal-title":"Plant J Cell Mol Biol."},{"key":"5655_CR61","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1007\/BF00286486","volume":"91","author":"RH Devlin","year":"1984","unstructured":"Devlin RH, Grigliatti TA, Holm DG. Dosage compensation is transcriptionally regulated in autosomal trisomies of Drosophila. Chromosoma. 1984;91:65\u201373.","journal-title":"Chromosoma."},{"key":"5655_CR62","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1002\/dvg.1020060104","volume":"6","author":"RH Devlin","year":"1985","unstructured":"Devlin RH, Grigliatti TA, Holm DG. Gene dosage compensation in trisomies of Drosophila melanogaster. Dev Genet. 1985;6:39\u201358.","journal-title":"Dev Genet."},{"key":"5655_CR63","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1017\/S001667230001507X","volume":"24","author":"JM Rawls","year":"1974","unstructured":"Rawls JM, Lucchesi JC. Regulation of enzyme activities in Drosophila: I. The detection of regulatory loci by gene dosage responses. Genet Res. 1974;24:59\u201372.","journal-title":"Genet Res."},{"key":"5655_CR64","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1042\/bj3620513","volume":"362","author":"E van Schaftingen","year":"2002","unstructured":"van Schaftingen E, Gerin I. The glucose-6-phosphatase system. Biochem J. 2002;362(Pt 3:513\u201332.","journal-title":"Biochem J."},{"key":"5655_CR65","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1016\/j.aquaculture.2008.08.036","volume":"286","author":"DA Higgs","year":"2009","unstructured":"Higgs DA, Sutton JN, Kim H, Oakes JD, Smith J, Biagi C, et al. Influence of dietary concentrations of protein, lipid and carbohydrate on growth, protein and energy utilization, body composition, and plasma titres of growth hormone and insulin-like growth factor-1 in non-transgenic and growth hormone transgenic coho salmon, Oncorhynchus kisutch (Walbaum). Aquaculture. 2009;286:127\u201337.","journal-title":"Aquaculture."},{"key":"5655_CR66","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1016\/j.cbpa.2014.01.013","volume":"170","author":"S Panserat","year":"2014","unstructured":"Panserat S, Kamalam BS, Fournier J, Plagnes-Juan E, Woodward K, Devlin RH. Glucose metabolic gene expression in growth hormone transgenic coho salmon. Comp Biochem Physiol A Mol Integr Physiol. 2014;170:38\u201345.","journal-title":"Comp Biochem Physiol A Mol Integr Physiol."},{"key":"5655_CR67","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1016\/j.cbpb.2009.05.010","volume":"154","author":"RA Leggatt","year":"2009","unstructured":"Leggatt RA, Raven PA, Mommsen TP, Sakhrani D, Higgs D, Devlin RH. Growth hormone transgenesis influences carbohydrate, lipid and protein metabolism capacity for energy production in coho salmon (Oncorhynchus kisutch). Comp Biochem Physiol B Biochem Mol Biol. 2009;154:121\u201333.","journal-title":"Comp Biochem Physiol B Biochem Mol Biol."},{"key":"5655_CR68","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1016\/j.fsi.2016.03.016","volume":"52","author":"Y Wang","year":"2016","unstructured":"Wang Y, Bu L, Yang L, Li H, Zhang S. Identification and functional characterization of fish-egg lectin in zebrafish. Fish Shellfish Immunol. 2016;52:23\u201330.","journal-title":"Fish Shellfish Immunol."},{"key":"5655_CR69","doi-asserted-by":"publisher","first-page":"1201","DOI":"10.1016\/j.fsi.2011.10.024","volume":"31","author":"B-S Kim","year":"2011","unstructured":"Kim B-S, Nam B-H, Kim J-W, Park H-J, Song J-H, Park C-I. Molecular characterisation and expression analysis of a fish-egg lectin in rock bream, and its response to bacterial or viral infection. Fish Shellfish Immunol. 2011;31:1201\u20137.","journal-title":"Fish Shellfish Immunol."},{"key":"5655_CR70","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1186\/s12864-015-1427-2","volume":"16","author":"L He","year":"2015","unstructured":"He L, Pei Y, Jiang Y, Li Y, Liao L, Zhu Z, et al. Global gene expression patterns of grass carp following compensatory growth. BMC Genomics. 2015;16:184.","journal-title":"BMC Genomics."},{"key":"5655_CR71","doi-asserted-by":"publisher","first-page":"418","DOI":"10.1186\/1471-2164-11-418","volume":"11","author":"SA Martin","year":"2010","unstructured":"Martin SA, Douglas A, Houlihan DF, Secombes CJ. Starvation alters the liver transcriptome of the innate immune response in Atlantic salmon (Salmo salar). BMC Genomics. 2010;11:418.","journal-title":"BMC Genomics."},{"key":"5655_CR72","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1186\/1471-2164-9-299","volume":"9","author":"MJ Leaver","year":"2008","unstructured":"Leaver MJ, Villeneuve LA, Obach A, Jensen L, Bron JE, Tocher DR, et al. Functional genomics reveals increases in cholesterol biosynthetic genes and highly unsaturated fatty acid biosynthesis after dietary substitution of fish oil with vegetable oils in Atlantic salmon (Salmo salar). BMC Genomics. 2008;9:299.","journal-title":"BMC Genomics."},{"key":"5655_CR73","doi-asserted-by":"publisher","first-page":"607","DOI":"10.1016\/j.aquaculture.2004.02.026","volume":"236","author":"RH Devlin","year":"2004","unstructured":"Devlin RH, Biagi CA, Yesaki TY. Growth, viability and genetic characteristics of GH transgenic coho salmon strains. Aquaculture. 2004;236:607\u201332.","journal-title":"Aquaculture."},{"key":"5655_CR74","doi-asserted-by":"publisher","first-page":"711","DOI":"10.1007\/s11248-006-9016-4","volume":"15","author":"M Uh","year":"2006","unstructured":"Uh M, Khattra J, Devlin RH. Transgene constructs in coho salmon (Oncorhynchus kisutch) are repeated in a head-to-tail fashion and can be integrated adjacent to horizontally-transmitted parasite DNA. Transgenic Res. 2006;15:711\u201327.","journal-title":"Transgenic Res."},{"key":"5655_CR75","unstructured":"QIAGEN Bioinformatics - sample to insight. QIAGEN Bioinformatics https:\/\/www.qiagenbioinformatics.com\/ . Accessed 16 Jan 2018."},{"key":"5655_CR76","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","volume":"26","author":"MD Robinson","year":"2010","unstructured":"Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinforma Oxf Engl. 2010;26:139\u201340.","journal-title":"Bioinforma Oxf Engl."},{"key":"5655_CR77","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1093\/biostatistics\/kxm030","volume":"9","author":"MD Robinson","year":"2008","unstructured":"Robinson MD, Smyth GK. Small-sample estimation of negative binomial dispersion, with applications to SAGE data. Biostat Oxf Engl. 2008;9:321\u201332.","journal-title":"Biostat Oxf Engl."},{"key":"5655_CR78","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","volume":"57","author":"Y Benjamini","year":"1995","unstructured":"Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol. 1995;57:289\u2013300.","journal-title":"J R Stat Soc Ser B Methodol."},{"key":"5655_CR79","unstructured":"Calc | LibreOffice - Free Office Suite - Fun Project - Fantastic People. https:\/\/www.libreoffice.org\/discover\/calc\/ . Accessed 16 Jan 2018."},{"key":"5655_CR80","doi-asserted-by":"publisher","first-page":"3420","DOI":"10.1093\/nar\/gkn176","volume":"36","author":"S G\u00f6tz","year":"2008","unstructured":"G\u00f6tz S, Garc\u00eda-G\u00f3mez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, et al. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res. 2008;36:3420\u201335.","journal-title":"Nucleic Acids Res."},{"issue":"Database issue","key":"5655_CR81","doi-asserted-by":"publisher","first-page":"D115","DOI":"10.1093\/nar\/gkh131","volume":"32","author":"R Apweiler","year":"2004","unstructured":"Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, et al. UniProt: the universal protein knowledgebase. Nucleic Acids Res. 2004;32(Database issue):D115\u20139.","journal-title":"Nucleic Acids Res."},{"key":"5655_CR82","doi-asserted-by":"publisher","first-page":"2949","DOI":"10.1093\/bioinformatics\/btm479","volume":"23","author":"SA Shiryev","year":"2007","unstructured":"Shiryev SA, Papadopoulos JS, Sch\u00e4ffer AA, Agarwala R. Improved BLAST searches using longer words for protein seeding. Bioinforma Oxf Engl. 2007;23:2949\u201351.","journal-title":"Bioinforma Oxf Engl."},{"key":"5655_CR83","doi-asserted-by":"publisher","first-page":"3045","DOI":"10.1093\/bioinformatics\/btp536","volume":"25","author":"D Binns","year":"2009","unstructured":"Binns D, Dimmer E, Huntley R, Barrell D, O\u2019Donovan C, Apweiler R. QuickGO: a web-based tool for gene ontology searching. Bioinformatics. 2009;25:3045\u20136.","journal-title":"Bioinformatics."},{"key":"5655_CR84","doi-asserted-by":"publisher","first-page":"e21800","DOI":"10.1371\/journal.pone.0021800","volume":"6","author":"F Supek","year":"2011","unstructured":"Supek F, Bo\u0161njak M, \u0160kunca N, \u0160muc T. REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS One. 2011;6:e21800.","journal-title":"PLoS One."},{"key":"5655_CR85","unstructured":"R Core Team. R: a language and environment for statistical computing. R Foundation for statistical Computing. 2017; https:\/\/www.R-project.org ."},{"key":"5655_CR86","volume-title":"Gplots: various R programming tools for plotting data","author":"GR Warnes","year":"2016","unstructured":"Warnes GR, Bolker B, Bonebakker L, Gentleman R, Liaw WHA, Lumley T, et al. Gplots: various R programming tools for plotting data. 2016. https:\/\/CRAN.R-project.org\/package=gplots . Accessed 23 Apr 2018."}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-019-5655-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12864-019-5655-8\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-019-5655-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,17]],"date-time":"2024-07-17T16:23:28Z","timestamp":1721233408000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/s12864-019-5655-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,5,3]]},"references-count":86,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2019,12]]}},"alternative-id":["5655"],"URL":"https:\/\/doi.org\/10.1186\/s12864-019-5655-8","relation":{},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,5,3]]},"assertion":[{"value":"7 November 2018","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 March 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 May 2019","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Fish husbandry and euthanasia followed guidelines from the Canadian Council for Animal Care under permit from Fisheries and Oceans Canada\u2019s Pacific Regional Animal Care Committee (Ex.7.1, Pacific Region Animal Care Committee management procedure 3.7).","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"336"}}