Transcriptional shifts during juvenile Coho salmon (Oncorhynchus kisutch) life stage changes in freshwater and early marine environments

André, 2012, Coupling nutrient sensing to metabolic homeostasis: the role of the mammalian target of rapamycin complex 1 pathway, Proc. Nutr. Soc., 71, 502, 10.1017/S0029665112000754 Aubin-Horth, 2005, Alternative life histories shape brain gene expression profiles in males of the same population, Proc. R. Soc. Lond., 272, 1655 Backman, 2016, systemPipeR: NGS workflow and report generation environment, BMC Bioinforma., 17, 10.1186/s12859-016-1241-0 Bassett, 2015 Beacham, 2012, Microsatellite mixed-stock identification of Coho salmon in British Columbia, Mar. Coast. Fish., 4, 85, 10.1080/19425120.2012.661393 Beacham, 2014, Stock-specific migration pathways of juvenile Sockeye salmon in British Columbia waters and in the Gulf of Alaska, Trans. Am. Fish. Soc., 143, 1386, 10.1080/00028487.2014.935476 Beacham, 2016, Stock-specific size and migration of juvenile Coho salmon in British Columbia and Southeast Alaska Waters, Mar. Coast. Fish., 8, 292, 10.1080/19425120.2016.1161683 Beamish, 2003, A history of the research on the early marine life of Pacific salmon off Canada's Pacific coast, 3, 1 Beamish, 2012, The synchronous failure of juvenile Pacific salmon and herring production in the Strait of Georgia in 2007 and the poor return of Sockeye salmon to the Fraser River in 2009, Mar. Coast. Fish., 4, 403, 10.1080/19425120.2012.676607 Benjamini, 2001, The control of the false discovery rate in multiple testing under dependency, Ann. Stat., 29, 1165, 10.1214/aos/1013699998 Björnsson, 2011, Environmental endocrinology of salmon smoltification, Gen. Comp. Endocrinol., 170, 290, 10.1016/j.ygcen.2010.07.003 Bond, 1996 Buchfink, 2015, Fast and sensitive protein alignment using DIAMOND, Nat. Methods, 12, 59, 10.1038/nmeth.3176 Chittenden, 2009, The use of acoustic tags to determine the timing and location of the juvenile Coho salmon migration out of the Strait of Georgia, Canada, Trans. Am. Fish. Soc., 138, 1220, 10.1577/T09-037.1 Chittenden, 2010, Recent salmon declines: a result of lost feeding opportunities due to bad timing?, PLoS One, 5, 10.1371/journal.pone.0012423 Churova, 2017, Activity of metabolic enzymes and muscle-specific gene expression in parr and smolts Atlantic salmon Salmo salar L. of different age groups, Fish Physiol. Biochem., 43, 1117, 10.1007/s10695-017-0357-0 Coughlin, 2002, A molecular mechanism for variations in muscle function in Rainbow trout, Integr. Comp. Biol., 42, 190, 10.1093/icb/42.2.190 Coughlin, 2001, Thyroxine induces transitions in red muscle kinetics and steady swimming kinematics in Rainbow trout (Oncorhynchus mykiss), J. Exp. Zool., 290, 115, 10.1002/jez.1041 Cui, 2005, Improved statistical tests for differential gene expression by shrinking variance components estimates, Biostatistics, 6, 59, 10.1093/biostatistics/kxh018 Davie, 2009, Seasonal variations in clock-gene expression in Atlantic salmon (Salmo salar), Chronobiol. Int., 26, 379, 10.1080/07420520902820947 Díaz, 2016, Melanopsin and the non-visual photochemistry in the inner retina of vertebrates, Photochem. Photobiol., 92, 29, 10.1111/php.12545 Dobin, 2013, STAR: ultrafast universal RNA-seq aligner, Bioinformatics, 29, 15, 10.1093/bioinformatics/bts635 Drenner, 2012, A synthesis of tagging studies examining the behaviour and survival of anadromous salmonids in marine environments, PLoS One, 7, 10.1371/journal.pone.0031311 Ebbesson, 2012, Environmental effects on fish neural plasticity and cognition, J. Fish Biol., 81, 2151, 10.1111/j.1095-8649.2012.03486.x Ebbesson, 2003, Neural circuits and their structural and chemical reorganization in the light-brain-pituitary axis during parr-smolt transformation in salmon, Aquaculture, 222, 59, 10.1016/S0044-8486(03)00102-9 Ebbesson, 2011, Corticotropin-releasing factor neurogenesis during midlife development in salmon: genetic, environmental and thyroid hormone regulation, J. Neuroendocrinol., 23, 733, 10.1111/j.1365-2826.2011.02164.x Efron, 1993 Fernald, 1991, Teleost vision: seeing while growing, J. Exp. Zool., 256, 167, 10.1002/jez.1402560521 Ferriss, 2014, Regional and inter-annual trends in marine growth of juvenile salmon in coastal pelagic ecosystems of British Columbia, Canada, Mar. Ecol. Prog. Ser., 503, 247, 10.3354/meps10726 Fuentes, 2013, Regulation of skeletal muscle growth in fish by the growth hormone - insulin-like growth factor system, Gen. Comp. Endocrinol., 192, 136, 10.1016/j.ygcen.2013.06.009 Gallagher, 2008, Hepatic expression profiling in smolting and adult Coho salmon (Onchorhynchus kisutch), Environ. Res., 106, 365, 10.1016/j.envres.2007.10.001 Groot, 1991 Hale, 2016, RNA-seq reveals differential gene expression in the brains of juvenile resident and migratory smolt Rainbow trout (Oncorhynchus mykiss), Comp. Biochem. Physiol. D Genomics Proteomics, 20, 136, 10.1016/j.cbd.2016.07.006 Huang, 2009, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources, Nat. Protoc., 4, 44, 10.1038/nprot.2008.211 Hughes, 1984, General anatomy of the gills, Fish Physiol., 10, 1, 10.1016/S1546-5098(08)60317-9 Jürss, 1995, Amino acid metabolism in fish, vol. 4, 159, 10.1016/S1873-0140(06)80010-X Kaslin, 2008, Proliferation, neurogenesis and regeneration in the non-mammalian vertebrate brain, Philos. Trans. R. Soc. Lond. Ser. B Biol. Sci., 363, 101, 10.1098/rstb.2006.2015 Kolditz, 2008, Liver and muscle metabolic changes induced by dietary energy content and genetic selection in Rainbow trout (Oncorhynchus mykiss), Am. J. Phys. Regul. Integr. Comp. Phys., 294, R1154 Koop, 2008, A salmonid EST genomic study: genes, duplications, phylogeny and microarrays, BMC Genomics, 9, 10.1186/1471-2164-9-545 Lemmetyinen, 2013, Comparison of gene expression in the gill of salmon (Salmo salar) smolts from anadromous and landlocked populations, Ann. Zool. Fenn., 50, 16, 10.5735/086.050.0102 Leonard, 2001, Metabolic enzyme activity during smolting in stream- and hatchery-reared Atlantic salmon (Salmo salar), Can. J. Fish. Aquat. Sci., 58, 1585, 10.1139/f01-105 Liao, 2014, featureCounts: an efficient general purpose program for assigning sequence reads to genomic features, Bioinformatics, 30, 923, 10.1093/bioinformatics/btt656 Lien, 2016, The Atlantic salmon genome provides insights into rediploidization, Nature, 533, 200, 10.1038/nature17164 MacKinlay, 2004, Pacific salmon hatcheries in British Columbia, 44, 57 Magnoni, 2013, Effects of sustained swimming on the red and white muscle transcriptome of Rainbow trout (Oncorhynchus mykiss) fed a carbohydrate-rich diet, Comp. Biochem. Physiol. A Mol. Integr. Physiol., 166, 510, 10.1016/j.cbpa.2013.08.005 Martin, 2003, Proteomic sensitivity to dietary manipulations in Rainbow trout, Biochim. Biophys. Acta Protein Proteomics, 1651, 17, 10.1016/S1570-9639(03)00231-0 Martin, 2010, Starvation alters the liver transcriptome of the innate immune response in Atlantic salmon (Salmo salar), BMC Genomics, 11, 10.1186/1471-2164-11-418 Masson, 2009, Chlorophyll distribution in a temperate estuary: the Strait of Georgia and Juan de Fuca Strait, Estuar. Coast. Shelf Sci., 82, 19, 10.1016/j.ecss.2008.12.022 Maynard, 2004, A review of recent studies investigating seminatural rearing strategies as a tool for increasing Pacific salmon postrelease survival, 44, 573 McCormick, 1998, Movement, migration, and smolting of Atlantic salmon (Salmo salar), Can. J. Fish. Aquat. Sci., 55, 77, 10.1139/d98-011 McCormick, 2013, Physiological and endocrine changes in Atlantic salmon smolts during hatchery rearing, downstream migration, and ocean entry, Can. J. Fish. Aquat. Sci., 70, 105, 10.1139/cjfas-2012-0151 McKinney, 2015, Ontogenetic changes in embryonic and brain gene expression in progeny produced from migratory and resident Oncorhynchus mykiss, Mol. Ecol., 24, 1792, 10.1111/mec.13143 Melnychuk, 2010, Spatio-temporal migration patterns of Pacific salmon smolts in rivers and coastal marine waters, PLoS One, 5, 10.1371/journal.pone.0012916 Miller, 2009, Salmon spawning migration: metabolic shifts and environmental triggers, Comp. Biochem. Physiol. D Genomics Proteomics, 4, 75, 10.1016/j.cbd.2008.11.002 Moriyama, 2000, Growth regulation by insulin-like growth factor-I in fish, Biosci. Biotechnol. Biochem., 64, 1553, 10.1271/bbb.64.1553 Moyes, 1995, Exercise metabolism in fish, Biochem. Mol. Biol., 4, 367, 10.1016/S1873-0140(06)80019-6 Navarro, 1995, Fasting and starvation, vol. 4, 393, 10.1016/S1873-0140(06)80020-2 Nilsen, 2007, Differential expression of gill Na+, K+-ATPase α- and β-subunits, Na+, K+, 2Cl− cotransporter and CFTR anion channel in juvenile anadromous and landlocked Atlantic salmon Salmo salar, J. Exp. Biol., 210, 2885, 10.1242/jeb.002873 Quinn, 2005 Repérant, 2006, The centrifugal visual system of vertebrates: a comparative analysis of its functional anatomical organization, Brain Res. Rev., 52, 1, 10.1016/j.brainresrev.2005.11.008 Roberge, 2006, Rapid parallel evolutionary changes of gene transcription profiles in farmed Atlantic salmon, Mol. Ecol., 15, 9, 10.1111/j.1365-294X.2005.02807.x Robertson, 2012, Transcriptional profiling of the parr-smolt transformation in Atlantic salmon, Comp. Biochem. Physiol. D Genomics Proteomics, 7, 351, 10.1016/j.cbd.2012.07.003 Salem, 2007, Effect of starvation on global gene expression and proteolysis in Rainbow trout (Oncorhynchus mykiss), BMC Genomics, 8, 10.1186/1471-2164-8-328 Sandercock, 1991, Life history of Coho Salmon Seear, 2010, Differential gene expression during smoltification of Atlantic salmon (Salmo salar L.): a first large-scale microarray study, Mar. Biotechnol., 12, 126, 10.1007/s10126-009-9218-x Segner, 1994, Enzymes of lipogenesis, vol. 3, 313, 10.1016/B978-0-444-82033-4.50033-7 Shephard, 1994, Functions for fish mucus, Rev. Fish Biol. Fish., 4, 401, 10.1007/BF00042888 Shrimpton, 1996, Relationship between size, gill corticosteroid receptors, Na+-K+ ATPase activity and smolting in juvenile Coho salmon (Oncorhynchus kisutch) in autumn and spring, Aquaculture, 147, 127, 10.1016/S0044-8486(96)01390-7 Smith, 2015, Ultrasonic telemetry reveals seasonal variation in depth distribution and diel vertical migrations of sub-adult Chinook and Coho salmon in Puget Sound, Mar. Ecol. Prog. Ser., 532, 227, 10.3354/meps11360 Sutherland, 2014, Divergent immunity and energetic programs in the gills of migratory and resident Oncorhynchus mykiss, Mol. Ecol., 23, 1952, 10.1111/mec.12713 Totland, 1987, Growth and composition of the swimming muscle of adult Atlantic salmon (Salmo salar L.) during long-term sustained swimming, Aquaculture, 66, 299, 10.1016/0044-8486(87)90115-3 Wang, 2009, Intra-retinal visual cycle required for rapid and complete cone dark adaptation, Nat. Neurosci., 12, 295, 10.1038/nn.2258 Wegner, 2006, Gill specializations in high-performance pelagic teleosts, with reference to striped marlin (Tetrapturus audax) and wahoo (Acanthocybilim solandri), Bull. Mar. Sci., 79, 747 Welch, 2011, In situ measurement of coastal ocean movements and survival of juvenile Pacific salmon, Proc. Natl. Acad. Sci. U. S. A., 108, 8708, 10.1073/pnas.1014044108 White, 2013, Influence of developmental stage and genotype on liver mRNA levels among wild, domesticated, and hybrid Rainbow trout (Oncorhynchus mykiss), BMC Genomics, 14, 10.1186/1471-2164-14-673 Wijngaarden, 2014, Regulation of skeletal muscle energy/nutrient-sensing pathways during metabolic adaptation to fasting in healthy humans, Am. J. Physiol. Endocrinol. Metab., 307, E885, 10.1152/ajpendo.00215.2014 Wu, 2018