Rimmer MA, Glamuzina B. A review of grouper (Family Serranidae: Subfamily Epinephelinae) aquaculture from a sustainability science perspective. Rev Aquac. 2019;11:58–87.
Article
Google Scholar
Zeller DC. Home range and activity patterns of the coral trout Plectropomus leopardus (Serranidae). Mar Ecol Prog Ser. 1997;154:65–77.
Article
Google Scholar
Cai X, Qu M, Ding S, Wang H, Wang H, Hu L, et al. Differentiation of coral trout (Plectropomus leopardus) based on an analysis of morphology and complete mitochondrial DNA: are cryptic species present? Acta Oceanol Sin. 2013;32:40–6.
Article
CAS
Google Scholar
Maoka T, Sato W, Nagai H, Takahashi T. Carotenoids of red, brown, and black specimens of plectropomus leopardus, the coral trout (Suziara in Japanese). J Oleo Sci. 2017;66:579–84.
Article
CAS
Google Scholar
Yang Y, Wu LN, Chen JF, Wu X, Xia JH, Meng ZN, et al. Whole-genome sequencing of leopard coral grouper (Plectropomus leopardus) and exploration of regulation mechanism of skin color and adaptive evolution. Zool Res. 2020;41:328–40.
Article
CAS
Google Scholar
Padilla JE, Mamauag S, Braganza G, Brucal N, Yu D, Morales A. Sustainability Assessment of the live reef-fish for Food Industry in Palawan, Philippines. Quezon City: WWF-Philippines; 2003.
Mclean DL, Harvey ES, Meeuwig JJ. Declines in the abundance of coral trout (Plectropomus leopardus) in areas closed to fishing at the Houtman Abrolhos Islands, Western Australia. J Exp Mar Bio Ecol. 2011;406:71–8.
Article
Google Scholar
Yin X. Sustainability of Coral Trout (Plectropomus leopardus) Fisheries in the Philippines and Indonesia (MSc thesis). Hong Kong: University of Hong Kong; 2014.
Choat JH, Samoilys M.A. “Plectropomus leopardus,” The IUCN Red List of Threatened Species. 2018. Available online: http://www.iucnredlist.org/details/44684/0. Accessed 25 June 2019.
Cheney KL, Grutter AS, Marshall NJ. Facultative mimicry: cues for colour change and colour accuracy in a coral reef fish. Proc R Soc B Biol Sci. 2008;275:117–22.
Article
Google Scholar
Sun J, Bhushan B, Tong J. Structural coloration in nature. RSC Adv. 2013;3:14862–89.
Article
CAS
Google Scholar
Fujii R. The regulation of motile activity in fish chromatophores. Pigment Cell Res. 2000;13:300–19.
Article
CAS
Google Scholar
Braasch I, Schartl M, Volff JN. Evolution of pigment synthesis pathways by gene and genome duplication in fish. BMC Evol Biol. 2007;7:1–18.
Article
Google Scholar
Kelsh RN, Inoue C, Momoi A, Kondoh H, Furutani-Seiki M, Ozato K, et al. The Tomita collection of medaka pigmentation mutants as a resource for understanding neural crest cell development. Mech Dev. 2004;121:841–59.
Article
CAS
Google Scholar
Henning F, Jones JC, Franchini P, Meyer A. Transcriptomics of morphological color change in polychromatic Midas cichlids. BMC Genomics. 2013;14:1–14.
Article
Google Scholar
Jiang Y, Zhang S, Xu J, Feng J, Mahboob S, Al-Ghanim KA, et al. Comparative transcriptome analysis reveals the genetic basis of skin color variation in common carp. PLoS ONE. 2014;9:e108200.
Article
Google Scholar
Wang C, Wachholtz M, Wang J, Liao X, Lu G. Analysis of the skin transcriptome in two Oujiang color varieties of common carp. PLoS ONE. 2014;9:1–8.
Google Scholar
Oka M, Nagai H, Ando H, Fukunaga M, Matsumura M, Araki K, et al. Regulation of melanogenesis through phosphatidylinositol 3-kinase-akt pathway in human G361 melanoma cells. J Invest Dermatol. 2000;115:699–703.
Article
CAS
Google Scholar
Fabinyi M. Historical, cultural and social perspectives on luxury seafood consumption in China. Environ Conserv. 2012;39:83–92.
Article
Google Scholar
Kingsford MJ. Spatial and temporal variation in predation on reef fishes by coral trout (Plectropomus leopardus, Serranidae). Coral Reefs. 1992;11:193–8.
Article
Google Scholar
Lerebours A, Chapman EC, Sweet MJ, Heupel MR, Rotchell JM. Molecular changes in skin pigmented lesions of the coral trout Plectropomus leopardus. Mar Environ Res. 2016;120:130–5.
Article
CAS
Google Scholar
Wang L, Yu C, Guo L, Lin H, Meng Z. In silico comparative transcriptome analysis of two color morphs of the common coral trout (Plectropomus leopardus). PLoS ONE. 2015;10:1–15.
Article
Google Scholar
Kelsh RN. Genetics and evolution of pigment patterns in fish. Pigment Cell Res. 2004;17:326–36.
Article
CAS
Google Scholar
Melianawati R, Astuti NWW, Suwirya K. The use of copepods to improve juveniles production of coral trout Plectropomus leopardus (Lacepède, 1802). Middle East J Sci Res. 2013;16:237–44.
Google Scholar
Liu X, Wang H, Chen Z. Effect of carotenoids on body colour of discus fish (Symphysodon aequifasciatus axelrodi Schultz, 1960). Aquac Res. 2016;47:1309–14.
Article
CAS
Google Scholar
Kusumawati D, Setiawati KM. The use of carotene materials as the source of red color pigmentation on leopard grouper larvae (Plectropomus leopardus). Aquac Indones. 2017;17:35.
Article
Google Scholar
Zhu X, Hao R, Tian C, Zhang J, Zhu C, Li G. Integrative transcriptomics and metabolomics analysis of body color formation in the Leopard Coral Grouper (Plectropomus leopardus). Front Mar Sci. 2021;8:726102.
Article
Google Scholar
Hao R, Zhu X, Tian C, Zhu C, Li G. Analysis of body color formation of leopard coral grouper Plectropomus leopardus. Front Mar Sci. 2022;9:964774.
Article
Google Scholar
Hao R, Zhu X, Tian C, Jiang M, Huang Y, Zhu C. Integrated analysis of the role of miRNA-mRNA in determining different body colors of leopard coral grouper (Plectropomus leopardus). Aquaculture. 2022;548:737575.
Article
CAS
Google Scholar
Zhou Q, Guo X, Huang Y, Gao H, Xu H, Liu S, et al. De novo sequencing and chromosomal-scale genome assembly of leopard coral grouper, Plectropomus leopardus. Mol Ecol Resour. 2020;20:1403–13.
Article
CAS
Google Scholar
Wang Y, Wen X, Zhang X, Fu S, Liu J, Tan W, et al. Chromosome Genome Assembly of the Leopard Coral Grouper (Plectropomus leopardus) with Nanopore and Hi-C sequencing data. Front Genet. 2020;11:876.
Article
Google Scholar
Ding SX, Zeng HS, Wang Y, Pan Y, Shi XF. Characterization of eight polymorphic microsatellite loci for the leopard coral grouper (Plectropomus leopardus Lacepède). Mol Ecol Resour. 2009;9:1485–7.
Article
CAS
Google Scholar
Van Herwerden L, Howard Choat J, Newman SJ, Leray M, Hillersøy G. Complex patterns of population structure and recruitment of Plectropomus leopardus (Pisces: Epinephelidae) in the Indo-West Pacific: implications for fisheries management. Mar Biol. 2009;156:1595–607.
Article
Google Scholar
Zhang J, Liu H, Song Y. Development and characterization of polymorphic microsatellite loci for a threatened reef fish Plectropomus leopardus. Conserv Genet Resour. 2010;2:101–3.
Article
Google Scholar
Ma KY, Van Herwerden L, Newman SJ, Berumen ML, Howard Choat J, Chu KH, et al. Contrasting population genetic structure in three aggregating groupers (Percoidei: Epinephelidae) in the Indo-West Pacific: the importance of reproductive mode. BMC Evol Biol. 2018;18:1–15.
Article
Google Scholar
Ge H, Lin K, Shen M, Wu S, Wang Y, Zhang Z, et al. De novo assembly of a chromosome-level reference genome of red-spotted grouper (Epinephelus akaara) using nanopore sequencing and Hi-C. Mol Ecol Resour. 2019;19:1461–9.
Article
CAS
Google Scholar
Austin CM, Tan MH, Harrisson KA, Lee YP, Croft LJ, Sunnucks P, et al. De novo genome assembly and annotation of Australia’s largest freshwater fish, the Murray cod (Maccullochella peelii), from Illumina and Nanopore sequencing read. Gigascience. 2017;6:1–6.
Article
Google Scholar
Nguinkal JA, Brunner RM, Verleih M, Rebl A, Ríos-Pérez L de los, Schäfer N, et al. The first highly contiguous genome assembly of pikeperch (Sander lucioperca), an emerging aquaculture species in Europe. Genes. 2019;10:708.
Yang X, Liu H, Ma Z, Zou Y, Zou M, Mao Y, et al. Chromosome-level genome assembly of Triplophysa tibetana, a fish adapted to the harsh high‐altitude environment of the Tibetan Plateau. Mol Ecol Resour. 2019;19:1027–36.
Article
CAS
Google Scholar
Li X, Song YN, Xiao GB, Zhu BH, Xu GC, Sun MY, et al. Gene expression variations of red—white skin coloration in common carp (Cyprinus carpio). Int J Mol Sci. 2015;16:21310–29.
Article
CAS
Google Scholar
Du J, Chen X, Wang J, Chen H, Yue W, Lu G, et al. Comparative skin transcriptome of two Oujiang color common carp (Cyprinus carpio var. Color) varieties. Fish Physiol Biochem. 2019;45:177–85.
Article
CAS
Google Scholar
Zhang Y, Liu J, Peng L, Ren L, Zhang H, Zou L, et al. Comparative transcriptome analysis of molecular mechanism underlying gray-to-red body color formation in red crucian carp (Carassius auratus, red var.). Fish Physiol Biochem. 2017;43:1387–98.
Article
CAS
Google Scholar
Zhang YP, Wang ZD, Guo YS, Liu L, Yu J, Zhang S, et al. Morphological characters and transcriptome profiles associated with black skin and red skin in crimson snapper (Lutjanus erythropterus). Int J Mol Sci. 2015;16:26991–7004.
Article
CAS
Google Scholar
Chen Y, Gong Q, Lai J, Song M, Liu Y, Wu Y, et al. Transcriptome analysis identifies candidate genes associated with skin color variation in Triplophysa siluroides. Comp Biochem Physiol - Part D Genomics Proteomics. 2020;35:100682.
Article
CAS
Google Scholar
Fang W, Huang J, Li S, Lu J. Identification of pigment genes (melanin, carotenoid and pteridine) associated with skin color variant in red tilapia using transcriptome analysis. Aquaculture. 2021;547:737429.
Article
Google Scholar
Wang Z, Jia Y, Huang X, Zhu D, Liu H, Wang W. Transcriptome profiling towards understanding of the morphogenesis in the scale development of blunt snout bream (Megalobrama amblycephala). Genomics. 2021;113:983–91.
Article
CAS
Google Scholar
Huang D, Lewis VM, Toomey MB, Corbo JC, Parichy DM. Development and genetics of red coloration in the zebrafish relative Danio albolineatus. Elife. 2021;10:e70253.
Article
CAS
Google Scholar
Yan X, Wei L, Huang J, Wang J, Yang Z, Gan B, et al. Comparative skin transcriptome between common carp and the variety jinbian carp (Cyprinus carpio v. jinbian). Aquac Res. 2020;51:187–96.
Article
CAS
Google Scholar
Tsetskhladze ZR, Canfield VA, Ang KC, Wentzel SM, Reid KP, Berg AS, et al. Functional Assessment of Human coding mutations affecting skin pigmentation using zebrafish. PLoS One. 2012;7:e47398.
Hirata M, Nakamura K, Kanemaru T, Shibata Y, Kondo S. Pigment cell organization in the hypodermis of zebrafish. Dev Dyn. 2003;227:497–503.
Article
Google Scholar
Zhu W, Wang L, Dong Z, Chen X, Song F, Liu N, et al. Comparative transcriptome analysis identifies candidate genes related to skin color differentiation in red tilapia. Sci Rep. 2016;6:1–12.
Google Scholar
Xu P, Zhang X, Wang X, Li J, Liu G, Kuang Y, et al. Genome sequence and genetic diversity of the common carp, Cyprinus carpio. Nat Genet. 2014;46:1212–9.
Article
CAS
Google Scholar
Lamason RL, Mohideen MPK, Mest JR, Wong AC, Norton HL, Aros MC, et al. SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. Science. 2005;310:1782–7.
Article
CAS
Google Scholar
Yu L, Chen H, Hu X, Chen X, Liu Z, Wang J, et al. SLC24A5 plays fundamental roles in regulating melanophore development in Cyprinidae fish. Reprod Breed. 2021;1:167–73.
Article
Google Scholar
Graf J, Voisey J, Hughes I, Daal A. Promoter polymorphisms in the MATP (SLC45A2) gene are associated with normal human skin color variation. Hum Mutat. 2006;28:710–7.
Article
Google Scholar
Li C, Chen H, Lan Z, He S, Chen R, Wang F, et al. mTOR-dependent upregulation of xCT blocks melanin synthesis and promotes tumorigenesis. Cell Death Differ. 2019;26:2015–28.
Article
CAS
Google Scholar
Ruprecht JJ, Kunji ERS. The SLC25 mitochondrial carrier family: structure and mechanism. Trends Biochem Sci. 2020;45:244–58.
Article
CAS
Google Scholar
Huo SM, Zhang YY, Song ZR, Xiong XH, Hong XY. The potential pigmentation-related genes in spider mites revealed by comparative transcriptomes of the red form of Tetranychus urticae. Insect Mol Biol. 2021;30:580–93.
Article
CAS
Google Scholar
Ma X, Ma Z, Jiao X, Hejtmancik JF. Functional non-coding polymorphism in an EPHA2 promoter PAX2 binding site modifies expression and alters the MAPK and AKT pathways. Sci Rep. 2017;7:1–15.
Google Scholar
Mashek DG, Li LO, Coleman RA. Future Lipidology Long-Chain acyl-coa synthetases and fatty acid channeling. Future Lipidol. 2017;2:465–76.
Article
Google Scholar
Wu X, Jin S, Yang Y, Lu X, Dai X, Xu Z, et al. Altered expression of ferroptosis markers and iron metabolism reveals a potential role of ferroptosis in vitiligo. Pigment Cell Melanoma Res. 2022;35:328–41.
Article
CAS
Google Scholar
Hirobe T. Role of keratinocyte-derived factors involved in regulating the proliferation and differentiation of mammalian epidermal melanocytes. Pigment Cell Res. 2005;18:2–12.
Article
CAS
Google Scholar
Costin G-E, Hearing VJ. Human skin pigmentation: melanocytes modulate skin color in response to stress. FASEB J. 2007;21:976–94.
Article
CAS
Google Scholar
Cheng KC. Skin color in Fish and humans: impacts on Science and Society. Zebrafish. 2008;5:242.
Article
Google Scholar
Chen S, Zhou Y, Chen Y, Gu J. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34:i884–90.
Article
Google Scholar
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29:15–21.
Article
CAS
Google Scholar
Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Philip D, Bowden J, et al. De novo transcript sequence recostruction from RNA-Seq: reference generation and analysis with Trinity. Nat Protoc. 2013;8:1494–512.
Article
CAS
Google Scholar
Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28:3150–2.
Article
CAS
Google Scholar
Kanehisa M, Furumichi M, Sato Y, Kawashima M, Ishiguro-Watanabe M. KEGG for taxonomy-based analysis of pathways and genomes. Nucleic Acids Res. 2022;27:gkac963.
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9.
Article
CAS
Google Scholar
Li B, Dewey CN. RSEM. Accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011;12:1–16.
Article
Google Scholar
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2009;26:139–40.
Article
Google Scholar
Bu D, Luo H, Huo P, Wang Z, Zhang S, He Z, et al. KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis. Nucleic Acids Res. 2021;49:W317–25.
Article
CAS
Google Scholar
Ye J, Coulouris G, Zaretskaya I, Cutcutache I, Rozen S, Madden TL. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics. 2012;13:134.
Article
CAS
Google Scholar
Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2 – ∆∆CT method. Methods. 2001;25:402–8.
Article
CAS
Google Scholar