Abdel-Ghany S. E., Hamilton M., Jacobi J. L., Ngam P., Devitt N., Schilkey F. et al. 2016 A survey of the sorghum transcriptome using single-molecule long reads. Nat. Commun. 7, 11706.

Article  PubMed  PubMed Central  Google Scholar 

Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W. et al. 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402.

Article  PubMed  PubMed Central  Google Scholar 

Au K. F., Sebastiano V., Afshar P. T., Durruthy J. D., Lee L., Williams B. A. et al. 2013 Characterization of the human ESC transcriptome by hybrid sequencing. Proc. Natl. Acad. Sci. USA 110, 4821–4830.

Article  Google Scholar 

Braasch I., Schartl M. and Volff J.-N. 2007 Evolution of pigment synthesis pathways by gene and genome duplication in fish. BMC Evol. Biol. 7, 74.

Article  PubMed  PubMed Central  Google Scholar 

Byrne A., Cole C., Volden R. and Vollmers C. 2019 Realizing the potential of full-length transcriptome sequencing. Philos. Trans. R. Soc. Lond. B Biol. Sci. 374, 20190097.

Damek-Poprawa M., Diemer T., Lopes V. S., Lillo C., Harper D. C., Marks M. S. et al. 2009 Melanoregulin (MREG) modulates lysosome function in pigment epithelial cells. J. Biol. Chem. 284, 10877–10889.

Article  PubMed  PubMed Central  Google Scholar 

Deng W., Fernandez A., McLaughlin S. L. and Klinke D. J. 2019 WNT1-inducible signaling pathway protein 1 (WISP1/CCN4) stimulates melanoma invasion and metastasis by promoting the epithelial-mesenchymal transition. J. Biol. Chem. 294, 5261–5280.

Article  PubMed  PubMed Central  Google Scholar 

Dobin A., Davis C. A., Schlesinger F., Drenkow J., Zaleski C., Jha S. et al. 2013 STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21.

Article  PubMed  Google Scholar 

Elkin J., Martin A., Courtier-Orgogozo V. and Santos M. E. 2023 Analysis of the genetic loci of pigment pattern evolution in vertebrates. Biol. Rev. 98, 1250–1277.

Article  PubMed  Google Scholar 

Foissac S. and Sammeth M. 2007 ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets. Nucleic Acids Res. 35, 297–299.

Article  Google Scholar 

Gordon S. P., Tseng E., Salamov A., Zhang J., Meng X., Zhao Z. et al. 2015 Widespread polycistronic transcripts in fungi revealed by single-molecule mRNA sequencing. Plos One 10, e0132628.

Article  PubMed  PubMed Central  Google Scholar 

Guo B., Tang Z., Wu C., Xu K. and Qi P. 2018 Transcriptomic analysis reveal an efficient osmoregulatory system in Siberian sturgeon Acipenser baeri in response to salinity stress. Sci. Rep. 8, 14353.

Article  PubMed  PubMed Central  Google Scholar 

Gutiérrez-Gil B., Wiener P. and Williams J. L. 2007 Genetic effects on coat colour in cattle: dilution of eumelanin and phaeomelanin pigments in an F2-Backcross Charolais x Holstein population. BMC Genet. 8, 56.

Article  PubMed  PubMed Central  Google Scholar 

Haas B. J., Papanicolaou A., Yassour M., Grabherr M., Blood P. D., Bowden J. et al. 2013 De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat. Protoc. 8, 1494–1512.

Article  PubMed  Google Scholar 

Harris M. L., Baxter L. L., Loftus S. K. and Pavan W. J. 2010 Sox proteins in melanocyte development and melanoma. Pigment Cell Melanoma Res. 23, 496–513.

Article  PubMed  PubMed Central  Google Scholar 

Heyn P., Kircher M., Dahl A., Kelso J., Tomancak P., Kalinka A. T. et al. 2014 The earliest transcribed zygotic genes are short, newly evolved, and different across species. Cell Rep. 6, 285–292.

Article  PubMed  Google Scholar 

Huang J., Fang W., Li J., Cai W. and Lu J. 2025 Full-length transcriptome reveals alternative splicing regulation pattern of skin color variant in red tilapia (Oreochromis spp.). Aquaculture 598, 741963.

Hubbard J. K., Uy J. A. C., Hauber M. E., Hoekstra H. E. and Safran R. J. 2010 Vertebrate pigmentation: from underlying genes to adaptive function. Trends Genet. 26, 231–239.

Article  PubMed  Google Scholar 

İbrahim Haliloǧlu H., Bayır A., Necdet Sirkecioǧlu A., Mevlüt Aras N. and Atamanalp M. 2004 Comparison of fatty acid composition in some tissues of rainbow trout (Oncorhynchus mykiss) living in seawater and freshwater. Food Chem. 86, 55–59.

Article  Google Scholar 

Jayaprasad P. P., Srijaya T. C., Jose D., Papini A., Hassan A. and Chatterji A. K. 2011 Identification of Diploid and Triploid Red Tilapia by Using Erythrocyte Indices. Caryologia 64, 485–492.

Google Scholar 

Kelsh R. N., Brand M., Jiang Y. J., Heisenberg C. P., Lin S., Haffter P. et al. 1996 Zebrafish pigmentation mutations and the processes of neural crest development. Development 123, 369–389.

Article  PubMed  Google Scholar 

Klett V. and Meyer A. 2002 What, if anything, is a Tilapia?-mitochondrial ND2 phylogeny of tilapiines and the evolution of parental care systems in the African cichlid fishes. Mol. Biol. Evol. 19, 865–883.

Article  PubMed  Google Scholar 

Kong L., Zhang Y., Ye Z. Q., Liu X. Q., Zhao S. Q., Wei L. et al. 2007 CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res. 35, W345-349.

Article  PubMed  PubMed Central  Google Scholar 

Liao Y., Smyth G. K. and Shi W. 2014 featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930.

Article  PubMed  Google Scholar 

Liu F., Sun F., Kuang G. Q., Wang L. and Yue G. H. 2022 The insertion in the 3′ UTR of Pmel17 is the causal variant for golden skin color in tilapia. Marine Biotech. 24, 566–573.

Article  Google Scholar 

Love M. I., Huber W. and Anders S. 2014 Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550.

Article  PubMed  PubMed Central  Google Scholar 

McAndrew B. J., Roubal F. R., Roberts R. J., Bullock A. M, and McEwen J. H. 1988 The genetics and histology of red, blond and associated variants in Oreochromis niloticus. Genetica 76, 127–137.

McArdle L., Rafferty M., Bergin O., Easty D. J., Mælandsmo G. M., Farr C. J. et al. 2001 Protein tyrosine phosphatase genes downregulated in melanoma. J. Invest. Dermatol. 117, 1255–1260.

Article  PubMed  Google Scholar 

Mistry J., Chuguransky S., Williams L., Qureshi M., Salazar G. A., Sonnhammer E. L. L. et al. 2021 Pfam: The protein families database in 2021. Nucleic Acids Res. 49, D412-d419.

Article  PubMed  Google Scholar 

Nudelman G., Frasca A., Kent B., Sadler K. C., Sealfon S. C., Walsh M. J. et al. 2018 High resolution annotation of zebrafish transcriptome using long-read sequencing. Genome Res. 28, 1415–1425.

Article  PubMed  PubMed Central  Google Scholar 

Ozsolak F. and Milos P. M. 2011 RNA sequencing: advances, challenges and opportunities. Nat. Rev. Genet. 12, 87–98.

Article  PubMed  Google Scholar 

Palmer R. H. and Hallberg B. 2015 The ALK Receptor Family. In: Wheeler D., Yarden Y. (eds) Receptor Tyrosine Kinases: Family and Subfamilies. Springer, Cham.

Parichy D. M. 2006 Evolution of danio pigment pattern development. Heredity (Edinb) 97, 200–210.

Article  PubMed  Google Scholar 

Pauli A., Valen E., Lin M. F., Garber M., Vastenhouw N. L., Levin J. Z. et al. 2012 Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res. 22, 577–591.

Article  PubMed  PubMed Central  Google Scholar 

Pradeep P. J., Srijaya T. C., Hassan A., Chatterji A. K., Withyachumnarnkul B. and Jeffs A. 2014 Optimal conditions for cold-shock induction of triploidy in red tilapia. Aquacult. Int. 22, 1163–1174.

Article  Google Scholar 

Protas M. E. and Patel N. H. 2008 Evolution of coloration patterns. Annu. Rev. Cell Dev. Biol. 24, 425–446.

Article  PubMed  Google Scholar 

Pruitt K. D., Tatusova T., Brown G. R. and Maglott D. R. 2012 NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res. 40, 130–135.

Article  Google Scholar 

Rhoads A. and Au K. F. 2015 PacBio sequencing and its applications. Genomics Proteomics Bioinformatics 13, 278–289.

Article  PubMed  PubMed Central  Google Scholar 

Roberts R. J., Carneiro M. O. and Schatz M. C. 2013 The advantages of SMRT sequencing. Genome Biol. 14, 405.