Weighted correlation network analysis of the genes in the eyes of juvenile Plectropomus leopardus provide novel insights into the molecular mechanisms of the adaptation to the background color

Anders, 2010, Differential expression analysis for sequence count data, Genome Biol., 11, R106, 10.1186/gb-2010-11-10-r106 Aspengren, 2009, Different strategies for color change, Cell. Mol. Life Sci., 66, 187, 10.1007/s00018-008-8541-0 Bertolesi, 2015, Melanopsin photoreceptionin the eye regulates light-induced skin colour changes through the production of α-MSH in the pituitary gland, Pigm. Cell Melan. Res., 28, 559, 10.1111/pcmr.12387 Boaventura, 2021, Cultivation of juvenile Colossoma macropomum in different colored tanks in recirculating aquaculture system (RAS): effects on performance, metabolism and skin pigmentation, Aquaculture., 532, 10.1016/j.aquaculture.2020.736079 Braissant, 2011, Creatine deficiency syndromes and the importance of creatine synthesis in the brain, Amino Acids, 40, 1315, 10.1007/s00726-011-0852-z Cal, 2017, Fish pigmentation and the melanocortin system, Comp. Biochem. Physiol. A Mol. Integr. Physiol., 211, 26, 10.1016/j.cbpa.2017.06.001 Caves, 2018, Visual acuity and the evolution of signals, Trends Ecol. Evol., 33, 358, 10.1016/j.tree.2018.03.001 Chen, 2011, KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases, Nucleic Acids Res., 39, 316, 10.1093/nar/gkr483 Dillon, 2004, Interleukin 31, a cytokine produced by activated T cells, induces dermatitis in mice, Nat. Immunol., 5, 752, 10.1038/ni1084 Drosten, 2014, Loss of p53 induces cell proliferation via Ras-independent activation of the Raf/Mek/Erk signaling pathway, Proc. Natl. Acad. Sci. U. S. A., 111, 15155, 10.1073/pnas.1417549111 Evans, 2004, Variation in the development of the fish retina, Am. Fish. Soc. Symp., 40, 145 Ghoreschi, 2009, Janus kinases in immune cell signaling, Immunol. Rev., 228, 273, 10.1111/j.1600-065X.2008.00754.x Giorgianni, 2022, Oxidized low-density lipoprotein causes ribosome reduction and inhibition of protein synthesis in retinal pigment epithelial cells, Biochem. Biophys. Rep., 32 Gouveia, 2005, Effect of microalgal biomass concentration and temperature on ornamental goldfish (Carassius auratus) skin pigmentation, Aquac. Nutr., 11, 19, 10.1111/j.1365-2095.2004.00319.x Haimo, 1994, Regulation of organelle transport: lessons from color change in fish, BioEssays, 16, 727, 10.1002/bies.950161007 Hao, 2022, Analysis of body color formation of leopard coral grouper Plectropomus leopardus, Front. Mar. Sci., 9, 10.3389/fmars.2022.964774 Hao, 2022, Integrated analysis of the role of miRNA-mRNA in determining different body colors of leopard coral grouper (Plectropomus leopardus), Aquaculture., 548, 10.1016/j.aquaculture.2021.737575 Haque, 2016, Evaluation of production performance and profitability of hybrid red tilapia and genetically improved farmed tilapia (GIFT) strains in the carbon/nitrogen controlled periphyton-based (C/N-CP) on-farm prawn culture system in Bangladesh, Aquacult. Rep., 4, 101 Jiang, 2022, Transcriptome analysis of skin color variation during and after overwintering of Malaysian red tilapia, Fish Physiol. Biochem., 48, 669, 10.1007/s10695-022-01073-5 Jomura, 2022, SLC6A and SLC16A family of transporters: contribution to transport of creatine and creatine precursors in creatine biosynthesis and distribution, BBA Biomembr., 1864, 10.1016/j.bbamem.2021.183840 Kanehisa, 2017, KEGG: new perspectives on genomes, pathways, diseases and drugs, Nucleic Acids Res., 45, D353, 10.1093/nar/gkw1092 Kim, 2019, Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype, Nat. Biotechnol., 37, 907, 10.1038/s41587-019-0201-4 Kiu, 2012, Biology and significance of the JAK/STAT signalling pathways, Growth Factors, 30, 88, 10.3109/08977194.2012.660936 Kramer, 2003, Alpha-melanophore-stimulating hormone in the brain, cranial placode derivatives, and retina of Xenopus laevis during development in relation to background adaptation, J. Comp. Neurol., 456, 73, 10.1002/cne.10513 Lan, 2015 Langfelder, 2008, WGCNA: an R package for weighted correlation network analysis, BMC Bioinf., 9, 559, 10.1186/1471-2105-9-559 Laskowski, 2017, Insulin during in vitro oocyte maturation has an impact on development, mitochondria, and cytoskeleton in bovine day 8 blastocysts, Theriogenology., 101, 15, 10.1016/j.theriogenology.2017.06.002 Laura, 2017, Fish pigmentation and the melanocortin system, Comp. Biochem. Physiol. A Mol. Integr. Physiol., 211, 26, 10.1016/j.cbpa.2017.06.001 Leclercq, 2009, Morphological skin colour changes in teleosts, Fish Fish., 11, 159, 10.1111/j.1467-2979.2009.00346.x Li, 2011, Diverse energy metabolism patterns in females in Neodon fuscus, Lasiopodomys brandtii, and Mus musculus revealed by comparative transcriptomics under hypoxic conditions, Sci. Total Environ., 783 Livak, 2001, Analysis of relative gene expression data using real-time quantitative PCR and the 2-∆∆Ct method, Methods, 25, 402, 10.1006/meth.2001.1262 Luo, 2021, Fish pigmentation and coloration: molecular mechanisms and aquaculture perspectives, Rev. Aquacult., 13, 2395, 10.1111/raq.12583 Maoka, 2017, Carotenoids of red, brown, and black specimens of Plectropomus leopardus, the coral trout (Suziara in Japanese), J. Oleo Sci., 66, 579, 10.5650/jos.ess16179 Mayor, 2013, The neural crest, Development, 140, 2247, 10.1242/dev.091751 Mehere, 2010, Tyrosine aminotransferase: biochemical and structural properties and molecular dynamics simulations, Prot. Cell., 1, 1023, 10.1007/s13238-010-0128-5 Minakhina, 2011, JAK/STAT and the GATA factor Pannier control hemocyte maturation and differentiation in Drosophila, Dev. Biol., 352, 308, 10.1016/j.ydbio.2011.01.035 Mizusawa, 2013, Interrelation between melanocyte-stimulating hormone and melanin-concentrating hormone in physiological body color change: roles emerging from barfin flounder Verasper moseri, Gen. Comp. Endocrinol., 181, 229, 10.1016/j.ygcen.2012.09.026 Mizusawa, 2018, Melanin-concentrating hormone is a major substance mediating light wavelength-dependent skin color change in larval zebrafish, Gen. Comp. Endocrinol., 269, 141, 10.1016/j.ygcen.2018.09.006 Nüsslein-Volhard, 2017, How fish color their skin: a paradigm for development and evolution of adult patterns: multipotency, plasticity, and cell competition regulate proliferation and spreading of pigment cells in zebrafish coloration, BioEssays, 39, 1600231, 10.1002/bies.201600231 Opiyo, 2014, Combined effects of stocking density and background colour on growth performance and survival of nile tilapia (Oreochromis niloticus, L.) fry reared in aquaria, J. Fish. Sci., 8, 228 Oshima, 2016, Fish skin color and its changes: mechanisms and ethological significance, J. Jpn. Soc. Colour Mater., 89, 178, 10.4011/shikizai.89.178 Pavlidis, 2008, Environmental control of skin color in the red porgy, Pagrus pagrus, Aquac. Res., 39, 837, 10.1111/j.1365-2109.2008.01937.x Pertea, 2015, StringTie enables improved reconstruction of a transcriptome from RNA-seq reads, Nat. Biotechnol., 33, 290, 10.1038/nbt.3122 Rawlings, 2004, The JAK/STAT signaling pathway, J. Cell Sci., 117, 1281, 10.1242/jcs.00963 Sandner, 2021, The tyrosine kinase tec regulates effector Th17 differentiation, pathogenicity, and plasticity in T-cell-driven intestinal inflammation, Front. Immunol., 21 Schmieder, 2011, Quality control and preprocessing of metagenomic datasets, Bioinformatics, 27, 863, 10.1093/bioinformatics/btr026 Shannon, 2003, Cytoscape: a software environment for integrated models of biomolecular interaction networks, Genome Res., 13, 2498, 10.1101/gr.1239303 Shin, 2014, The stimulatory effect of LED light spectra on genes related to photoreceptors and skin pigmentation in goldfish (Carassius auratus), Fish Physiol. Biochem., 40, 1229 Shiraki, 2010, Light-induced body color change in developing zebrafish, Photochem. Photobiol. Sci., 9, 1498, 10.1039/c0pp00199f Sköld, 2013, Rapid color change in fish and amphibians-function, regulation, and emerging applications, Pigm. Cell Melan. Res., 26, 29, 10.1111/pcmr.12040 Song, 2022, The effect of background color on skin color variation of juvenile Plectropomus leopardus, Animals, 12, 3349, 10.3390/ani12233349 Song, 2022, Transcriptome analysis reveals the complex regulatory pathway of background color in juvenile Plectropomus leopardus skin color variation, Int. J. Mol. Sci., 23, 11186, 10.3390/ijms231911186 Sugimoto, 2002, Morphological color changes in fish: regulation of pigment cell density and morphology, Microsc. Res. Tech., 58, 496, 10.1002/jemt.10168 Sun, 2017, Binding of a C-type lectin’s coiled-coil domain to the Domeless receptor directly activates the JAK/STAT pathway in the shrimp immune response to bacterial infection, PLoS Pathog., 13, 1006, 10.1371/journal.ppat.1006626 Sun, 2020, Environmental estrogen exposure converts lipid metabolism in male fish to a female pattern mediated by AMPK and mTOR signaling pathways, J. Hazard. Mater., 406 Tian, 2022, Dynamic transcriptome and LC-MS/MS analysis revealed the important roles of taurine and glutamine metabolism in response to environmental salinity changes in gills of rainbow trout (Oncorhynchus mykiss), Int. J. Biol. Macromol., 16, 1545, 10.1016/j.ijbiomac.2022.09.124 Tujebajeva, 2000, Expression and characterization of nonmammalian selenoprotein P in the zebrafish, Danio rerio, Genes Cells., 5, 897, 10.1046/j.1365-2443.2000.00375.x Wang, 2020, Effects of background adaptation on the skin color of Malaysian red tilapia, Aquaculture, 521, 10.1016/j.aquaculture.2020.735061 Wang, 2020, Expression characteristics of opsin genes in different developmental stages of Scophthalmus maximus, Oceanol. Limnol. Sin., 51, 186 Wen, 2022, Transcriptomic and proteomic analyses reveal the common and unique pathway(s) underlying different skin colors of leopard coral grouper (Plectropomus leopardus), J. Proteome, 266 Wyss, 2000, Creatine and creatinine metabolism, Physiol. Rev., 80, 1107, 10.1152/physrev.2000.80.3.1107 Zhou, 2021, Analysis of pigment cells difference in body color variation of Plectropomus leopardus, Acta Hydrobiol. Sin., 45, 1164