Transcriptome comparison for identification of pigmentation-related genes in different color varieties of Siamese fighting fish Betta splendens

Altschul, 1990, Basic local alignment search tool, J. Mol. Biol., 215, 403, 10.1016/S0022-2836(05)80360-2 Altschul, 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 25, 3389, 10.1093/nar/25.17.3389 Amparyup, 2020, Transcriptome analysis identifies immune-related genes and antimicrobial peptides in siamese fighting fish (Betta splendens), Fish Shellfish Immunol., 99, 403, 10.1016/j.fsi.2020.02.030 Anders, 2010, Differential expression analysis for sequence count data, Genome Biol., 10.1186/gb-2010-11-10-r106 Bagnara, 2007, On the blue coloration of vertebrates, Pigment Cell Res., 20, 14, 10.1111/j.1600-0749.2006.00360.x Bairoch, 1996, The SWISS-PROT protein sequence data bank and its new supplement TREMBL, Nucleic Acids Res., 24, 21, 10.1093/nar/24.1.21 Baxter, 2019, A curated gene list for expanding the horizons of pigmentation biology, Pigment Cell Mel. Res., 32, 348, 10.1111/pcmr.12743 Beier, 2017, MISA-web: a web server for microsatellite prediction, Bioinformatics, 33, 2583, 10.1093/bioinformatics/btx198 Braasch, 2007, Evolution of pigment synthesis pathways by gene and genome duplication in fish, BMC Evol. Biol., 7, 74, 10.1186/1471-2148-7-74 Braasch, 2009, Pigmentation pathway evolution after whole-genome duplication in fish, Genome Biol. Evol., 1, 479, 10.1093/gbe/evp050 Braasch, 2009, Pigmentary function and evolution of tyrp1 gene duplicates in fish, Pigment Cell Melanoma Res., 22, 839, 10.1111/j.1755-148X.2009.00614.x Buchfink, 2014, Fast and sensitive protein alignment using DIAMOND, Nat. Methods Cal, 2017, Fish pigmentation and the melanocortin system, Comp. Biochem. Physiol. A Physiol., 211, 26, 10.1016/j.cbpa.2017.06.001 Carruthers, 2018, De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species, BMC Genomics, 19, 32, 10.1186/s12864-017-4379-x Chailertrit, 2014, Isolation and characterization of novel microsatellite markers from siamese fighting fish (Betta splendens, Osphronemidae, Anabantoidei) and their transferability to related species, B. smaragdina and B. imbellis, Genet. Mol. Res., 13, 7157, 10.4238/2014.September.5.1 Chen, 2021, De novo transcriptomic characterization enables novel microsatellite identification and marker development in Betta splendens, Life, 11, 803, 10.3390/life11080803 Cock, 2010, The sanger FAST Q file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants, Nucleic Acids Res., 38, 1767, 10.1093/nar/gkp1137 Conesa, 2005, Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research, Bioinformatics, 21, 3674, 10.1093/bioinformatics/bti610 Cooksey, 1997, Evidence of the indirect formation of the catecholic intermediate substrate responsible for the autoactivation kinetics of tyrosinase, J. Biol. Chem., 272, 26226, 10.1074/jbc.272.42.26226 Cruz, 2021, Carotenoid coloration and coloration-linked gene expression in red tilapia (Oreochromis sp.) tissues, BMC Vet. Res., 17, 314, 10.1186/s12917-021-03006-5 Curran, 2010, Interplay between Foxd3 and Mitf regulates cell fate plasticity in the zebrafish neural crest, Dev. Biol., 344, 107, 10.1016/j.ydbio.2010.04.023 David, 2004, Aspects of red and black color inheritance in the Japanese ornamental (Koi) carp (Cyprinus Carpio L.), Aquaculture, 233, 129, 10.1016/j.aquaculture.2003.10.033 Dillies, 2013, A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis, Brief. Bioinform., 14, 671, 10.1093/bib/bbs046 Finn, 2008, The pfam protein families database, Nucleic Acids Res., 36, D281, 10.1093/nar/gkm960 Galvan, 2016, Bird integumentary melanins: biosynthesis, forms, function and evolution, Int. J. Mol. Sci., 17, 520, 10.3390/ijms17040520 Götz, 2008, High-throughput functional annotation and data mining with the Blast2GO suite, Nucleic Acids Res., 36, 3420, 10.1093/nar/gkn176 Goyard, 2003, Residual genetic variability in domesticated populations of the Pacific blue shrimp (Litopenaeus stylirostris) of New Caledonia, French Polynesia and Hawaii and some management recommendations, Aquat Living Resour, 16, 501, 10.1016/j.aquliv.2003.07.001 Grabherr, 2011, Full-length transcriptome assembly from RNA-seq data without a reference genome, Nature Biotechnol., 29, 644, 10.1038/nbt.1883 Helgeland, 2019, Genomic and functional gene studies suggest a key role of beta-carotene oxygenase 1 like (bco1l) gene in salmon flesh color, Sci. Rep., 9, 20061, 10.1038/s41598-019-56438-3 Hofreiter, 2010, The genetic and evolutionary basis of colour variation in vertebrates, Cell. Mol. Life Sci., 67, 2591, 10.1007/s00018-010-0333-7 Hou, 2008, Transcriptional and signaling regulation in neural crest stem cell-derived melanocyte development: do all roads lead to Mitf?, Cell Res., 18, 1163, 10.1038/cr.2008.303 Iseli, 1999, ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences, Proc. Int. Conf. Intell. Syst. Mol. Biol., 138 Ji, 2012, Characterization of common carp transcriptome: sequencing, de novo assembly, annotation and comparative genomics, PLoS One, 7, 10.1371/journal.pone.0035152 Jiang, 2014, Comparative transcriptome analysis reveals the genetic basis of skin color variation in common carp, PLoS One, 9 Kanehisa, 2008, KEGG for linking genomes to life and the environment, Nucleic Acids Res., 36, D480, 10.1093/nar/gkm882 Kelsh, 2004, Genetics and evolution of pigment patterns in fish, Pigment Cell Res., 17, 326, 10.1111/j.1600-0749.2004.00174.x Khoo, 1997, Genetic variation in different varieties of siamese fighting fish using isoelectric focusing of sarcoplasmic proteins, Aquac. Inter., 5, 537, 10.1023/A:1018357400571 Khoo, 2012, Ultrastructure of Erythrophores and Xanthophores of the Siamese fighting fish, Betta splendens, Isr. J. Aquacult. Bamidgeh, 64, 775 Khoo, 2014, Cellular basis of metallic iridescence in the Siamese fighting fish, Betta splendens, Isr. J. Aquacult. Bamidgeh, 65, 988 Klinbunga, 2018, Characterization of transforming growth factor beta regulator 1-like and association between its expression levels and growth of the giant tiger shrimp Penaeus monodon, Comp. Biochem. Physiol. B, 225, 38, 10.1016/j.cbpb.2018.06.006 Kobayashi, 2012, Melanocortin systems on pigment dispersion in fish chromatophores, Front. Endocrinol., 3, 9, 10.3389/fendo.2012.00009 Kratochwil, 2018, Agouti-related peptide 2 facilitates convergent evolution of stripe patterns across cichlid fish radiations, Science, 362, 457, 10.1126/science.aao6809 Kumari, 2020, Fish tyrosinase enzyme involved in melanin biosynthesis: insights from physicochemical characterization, homology modeling, and virtual screening studies, Anim. Biotechnol. Kwon, 2022, Genomic consequences of domestication of the siamese fighting fish, Sci. Adv., 8, eabm4950, 10.1126/sciadv.abm4950 Li, 2011, RSEM: accurate transcript quantification from RNA-seq data with or without a reference genome, BMC Bioinformatics Liang, 2021, Functional conservation and divergence of color-patternrelated agouti family genes in teleost fishes, J. Exp. Zool. B (Mol. Dev. Evol.), 336, 443, 10.1002/jez.b.23041 Lister, 1999, Nacre encodes a zebrafish microphthalmia-related protein that regulates neural-crest-derived pigment cell fate, Development, 126, 3757, 10.1242/dev.126.17.3757 Lister, 2014, A conditional zebrafish MITF mutation reveals MITF levels are critical for melanoma promotion vs. regression in vivo, J. Invest. Dermatol., 134, 133, 10.1038/jid.2013.293 Liu, 2001, Tbx19, a tissue-selective regulator of POMC gene expression, Proc. Natl. Acad. Sci. U. S. A., 98, 8674, 10.1073/pnas.141234898 Liu, 2004, DNA marker technologies and their applications in aquaculture genetics, Aquaculture, 238, 1, 10.1016/j.aquaculture.2004.05.027 Livak, 2001, Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT method, Methods, 25, 402, 10.1006/meth.2001.1262 Logan, 2006, Regulation of pigmentation in zebrafish melanophores, Pigment Cell Res., 19, 206, 10.1111/j.1600-0749.2006.00307.x Lucas, 1968, 201 pp. Luo, 2021, Fish pigmentation and coloration: molecular mechanisms and aquaculture perspectives, Rev. Aquac., 10.1111/raq.12583 Maneeruttanarungroj, 2006, Development of polymorphic expressed sequence tag-derived microsatellites for the extension of the genetic linkage map of the black tiger shrimp (Penaeus monodon), Anim. Genet., 37, 363, 10.1111/j.1365-2052.2006.01493.x Mao, 2005, Automated genome annotation and pathway identification using the KEGG orthology (KO) as a controlled vocabulary, Bioinformatics, 21, 3787, 10.1093/bioinformatics/bti430 del Marmol, 1996, Tyrosinase and related proteins in mammalian pigmentation, FEBS Lett., 381, 165, 10.1016/0014-5793(96)00109-3 Meejui, 2005, Allozyme revealed substantial genetic diversity between hatchery stocks of siamese fighting fish, Betta splendens, in the province of nakorn pathom, Thailand, Aquaculture, 250, 110, 10.1016/j.aquaculture.2005.03.020 Minchin, 2008, Sequential actions of Pax3 and Pax7 drive xanthophore development in zebrafish neural crest, Dev. Biol., 317, 508, 10.1016/j.ydbio.2008.02.058 Mo, 2017, Alk and ltk ligands are essential for iridophore development in zebrafish mediated by the receptor tyrosine kinase ltk, Proc. Natl. Acad. Sci. U. S. A., 114, 12027, 10.1073/pnas.1710254114 Mohapatra, 2018, Characterization and expression analysis of nadh dehydrogenase (ubiquinone) iron-sulfur protein-2 in Channa striatus exposed to hypoxia, Res. J. Biotech., 13 Moriya, 2007, KAAS: an automatic genome annotation and pathway reconstruction server, Nucleic Acids Res., 35, W182, 10.1093/nar/gkm321 Nadia, 2014, Corset: enabling differential gene expression analysis for de novo assembled transcriptomes, Genome Biol., 15, 1 Nie, 2020, Transcriptome analysis reveals the pigmentation related genes in four different shell color strains of the Manila clam ruditapes philippinarum, Genomics, 112, 2011, 10.1016/j.ygeno.2019.11.013 Nüsslein-Volhard, 2017, How fish color their skin: a paradigm for development and evolution of adult patterns, Mech. Dev., 39, S2, 10.1016/j.mod.2017.04.519 Page-McCaw, 2004, Retinal network adaptation to bright light requires tyrosinase, Nat. Neurosci., 7, 1329, 10.1038/nn1344 Panijpan, 2020, Wild Betta fighting fish species in Thailand and other Southeast Asian countries, Sci. Asia, 46, 1, 10.2306/scienceasia1513-1874.2020.064 Parichy, 2006, Evolution of danio pigment pattern development, Heredity, 97, 200, 10.1038/sj.hdy.6800867 Prasertlux, 2022, Assessing genetic diversity of wild populations and different color varieties for genetic improvement of Siamese fighting fish Betta splendens in Thailand, Biochem. Genet. Protas, 2008, Evolution of coloration patterns, Annu. Rev. Cell Dev. Biol., 24, 425, 10.1146/annurev.cellbio.24.110707.175302 Punta, 2012, The Pfam protein families database, Nucleic Acids Research, 40, D290, 10.1093/nar/gkr1065 Richardson, 2008, mc1r pathway regulation of zebrafish melanosome dispersion, Zebrafish, 5, 289, 10.1089/zeb.2008.0541 Salem, 2012, RNA-seq identifies SNP markers for growth traits in rainbow trout, PLoS One, 7, 10.1371/journal.pone.0036264 Searfoss, 2001, Linking the 3′ Poly(A) tail to the subunit joining step of translation initiation: relations of Pab1p, eukaryotic translation initiation factor 5B (Fun12p), and Ski2p-Slh1p, Mol. Cell. Biol., 21, 4900, 10.1128/MCB.21.15.4900-4908.2001 Shin, 2012, Zebrafish neurofibromatosis type 1 genes have redundant functions in tumorigenesis and embryonic development, Dis. Model. Mech., 5, 881 Simão, 2015, BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs, Bioinformatics, 31, 3210, 10.1093/bioinformatics/btv351 Sugie, 2004, The evolution of genes for pigmentation in african cichlid fishes, Gene, 343, 337, 10.1016/j.gene.2004.09.019 Tang, 2004, Population structure of tropical abalone (Haliotis asinina) in coastal waters of Thailand determined using microsatellite markers, Mar. Biotechnol., 6, 604, 10.1007/s10126-004-2300-5 Tatusov, 2000, The COG database: a tool for genome-scale analysis of protein functions and evolution, Nucleic Acids Res., 28, 33, 10.1093/nar/28.1.33 Trapnell, 2010, Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation, Nat. Biotech., 28, 511, 10.1038/nbt.1621 Van der Auwera Carneiro, 2013, From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline, Curr. Protoc. Bioinformatics, 43 Wallbrunn, 1957, Genetics of the siamese fighting fish, Betta splendens, Genetics, 43, 281 Wang, 2014, Analysis of the skin transcriptome in two oujiang color varieties of common carp, PLoS ONE, 9 Wang, 2008, Preliminary study on inheritance of red and white color phenotypes in Oujiang color carp, C. carpio var. color, J. Shanghai Fish. Uni., 4, 004 Wang, 2010, DEGseq: an R package for identifying differentially expressed genes from RNA-seq data, Bioinformatics, 26, 136, 10.1093/bioinformatics/btp612 Wang, 2021, Genomic basis of striking fin shapes and colors in the fighting fish, Mol. Biol. Evol., 10.1093/molbev/msab110 Wang, 2009, RNA-seq: a revolutionary tool for transcriptomics, Nat. Rev. Genet., 10, 57, 10.1038/nrg2484 Yang, 2018 Young, 2010, Gene ontology analysis for RNA-seq: accounting for selection bias, Genome Biol., 10.1186/gb-2010-11-2-r14 Zhang, 2022, The genetic architecture of phenotypic diversity in the Betta fish (Betta splendens), Science Advances Zhang, 2018, Molecular cloning and expression analysis of tyr and tyrp1 genes in normal and albino yellow catfish tachysurus fulvidraco, J. Fish Biol., 92, 979, 10.1111/jfb.13556 Zhu, 2016, Comparative transcriptome analysis identifies candidate genes related to skin color differentiation in red tilapia, Sci. Rep., 31347, 10.1038/srep31347