186
Views
2
CrossRef citations to date
0
Altmetric
Research articles

Cutaneous transcriptomic profiling and candidate pigment genes in the wild discus (Symphysodon spp.)

, ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon & ORCID Icon show all
Pages 478-496 | Received 31 Oct 2022, Accepted 12 Feb 2023, Published online: 06 Mar 2023

References

  • Ahi EP, Lecaudey LA, Ziegelbecker A, Steiner O, Glabonjat R, Goessler W, Hois V, Wagner C, Lass A, Sefc KM. 2020. Comparative transcriptomics reveals candidate carotenoid color genes in an East African cichlid fish. BMC Genomics. 21(1):1–15. doi:10.1016/j.aquaculture.2021.736979.
  • Ahi EP, Lecaudey LA, Ziegelbecker A, Steiner O, Goessler W, Sefc KM. 2020. Expression levels of the tetratricopeptide repeat protein gene ttc39b covary with carotenoid-based skin colour in cichlid fish. Biol Lett. 16(11):20200629.
  • Ahi EP, Sefc KM. 2017a. A gene expression study of dorso-ventrally restricted pigment pattern in adult fins of Neolamprologus meeli, an African cichlid species. PeerJ. 5:e2843. doi:10.7717/peerj.2843.
  • Ahi EP, Sefc KM. 2017b. Anterior-posterior gene expression differences in three Lake Malawi cichlid fishes with variation in body stripe orientation. PeerJ. 5:e4080. doi:10.7717/peerj.4080.
  • Aspengren S, Sköld HN, Wallin M. 2009. Different strategies for color change. Cell Mol Life Sci. 66(2):187–191. doi:10.1007/s00018-008-8541-0.
  • Barro O, Joly C, Condamine H, Boulekbache H. 1994. Widespread expression of the Xenopus homeobox gene Xhox3 in zebrafish eggs causes a disruption of the anterior-posterior axis. Int J Dev Biol. 38(4):613–622.
  • Baxter LL, Watkins-Chow DE, Pavan WJ, Loftus SK. 2019. A curated gene list for expanding the horizons of pigmentation biology. Pigment Cell Melanoma Res. 32(3):348–358. doi:10.1111/pcmr.12743.
  • Braasch I, Schartl M, Volff JN. 2007. Evolution of pigment synthesis pathways by gene and genome duplication in fish. BMC Evol Biol. 7(1):74. doi:10.1186/1471-2148-7-74.
  • Cal L, Suarez-Bregua P, Cerdá-Reverter JM, Braasch I, Rotllant J. 2017. Fish pigmentation and the melanocortin system. Comp Biochem Physiol A Mol Integr Physiol. 211:26–33. doi:10.1016/j.cbpa.2017.06.001.
  • Chevalier D, Morris ER, Walker JC. 2009. 14-3-3 and FHA domains mediate phosphoprotein interactions. Annu Rev Plant Biol. 60(1):67–91. doi:10.1146/annurev.arplant.59.032607.092844.
  • Curran K, Lister JA, Kunkel GR, Prendergast A, Parichy DM, Raible DW. 2010. Interplay between Foxd3 and Mitf regulates cell fate plasticity in the zebrafish neural crest. Dev Biol. 344(1):107–118. doi:10.1016/j.ydbio.2010.04.023.
  • Dijkstra PD, Maguire SM, Harris RM, Rodriguez AA, DeAngelis RS, Flores SA, Hofmann HA. 2017. The melanocortin system regulates body pigmentation and social behaviour in a colour polymorphic cichlid fish. Proc Biol Sci. 284(1851):20162838. doi:10.1098/rspb.2016.2838.
  • Fang W, Huang J, Li S, Lu J. 2022. Identification of pigment genes (melanin, carotenoid and pteridine) associated with skin color variant in red tilapia using transcriptome analysis. Aquaculture. 547:737429. doi:10.1016/j.aquaculture.2021.737429.
  • Farias IP, Hrbek T. 2008. Patterns of diversification in the discus fishes (Symphysodon spp. Cichlidae) of the Amazon basin. Mol Phylogenet Evol. 49(1):32–43. doi:10.1016/j.ympev.2008.05.033.
  • Galas L, Lamacz M, Garnier M, Roubos EW, Tonon MC, Vaudry H. 1999. Involvement of protein kinase c and protein tyrosine kinase in thyrotropin-releasing hormone-induced stimulation ofα -melanocyte-stimulating hormone secretion in frog melanotrope cells. Endocrinology. 140(7):3264–3272. doi:10.1210/endo.140.7.6772.
  • Goralczyk R, Wertz K. 2009. Skin photoprotection by carotenoids. In: G. Britton, H. Pfander, S. Liaaen-Jensen, editor. Carotenoids: volume 5: nutrition and health. Basel: Birkhäuser Basel; p. 335–362.
  • Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, et al. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 29(7):644–652. doi:10.1038/nbt.1883.
  • Han Z, Firtel RA. 1998. The homeobox-containing gene Wariai regulates anterior-posterior patterning and cell-type homeostasis in Dictyostelium. Development. 125(2):313–325. doi:10.1242/dev.125.2.313.
  • Henle AM, Muske J, Poplawski M, Perlmutter T. 2018. The development of pigmentation in new tissue arises from precursor and not migratory melanocytes in a transgenic GNAQQ209L zebrafish model of uveal melanoma. Invest Ophthalmol Visual Sci. 59(9):3177–3177.
  • Hoey T, Doyle HJ, Harding K, Levine M. 1986. Homeo box gene expression in anterior and posterior regions of the Drosophila embryo. Proc Natl Acad Sci U S A. 83(13):4809–4813. doi:10.1073/pnas.83.13.4809.
  • Inoue S, Kondo S, Parichy DM, Watanabe M. 2014. Tetraspanin 3c requirement for pigment cell interactions and boundary formation in zebrafish adult pigment stripes. Pigment Cell Melanoma Res. 27(2):190–200. doi:10.1111/pcmr.12192.
  • Irion U, Nüsslein-Volhard C. 2019. The identification of genes involved in the evolution of color patterns in fish. Curr Opin Genet Dev. 57:31–38. doi:10.1016/j.gde.2019.07.002.
  • Kawakami K, Amsterdam A, Shimoda N, Becker T, Mugg J, Shima A, Hopkins N. 2000. Proviral insertions in the zebrafish hagoromo gene, encoding an F-box/WD40-repeat protein, cause stripe pattern anomalies. Curr Biol. 10(8):463–466. doi:10.1016/S0960-9822(00)00444-9.
  • Kelsh RN. 2004. Genetics and evolution of pigment patterns in fish. Pigment Cell Res. 17(4):326–336. doi:10.1111/j.1600-0749.2004.00174.x.
  • Kobayashi Y, Mizusawa K, Saito Y, Takahashi A. 2012. Melanocortin systems on pigment dispersion in fish chromatophores. Front Endocrinol (Lausanne). 3:9. doi:10.3389/fendo.2012.00009.
  • Koskinen H, Krasnov A, Rexroad C, Gorodilov Y, Afanasyev S, Mölsä H. 2004. The 14-3-3 proteins in the teleost fish rainbow trout (Oncorhynchus mykiss). J Exp Biol. 207(19):3361–3368. doi:10.1242/jeb.01165.
  • Kratochwil CF, Liang Y, Gerwin J, Woltering JM, Urban S, Henning F, Machado-Schiaffino G, Hulsey CD, Meyer A. 2018. Agouti-related peptide 2 facilitates convergent evolution of stripe patterns across cichlid fish radiations. Science. 362(6413):457–460. doi:10.1126/science.aao6809.
  • Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods. 9(4):357–359. doi: 10.1038/nmeth.1923.
  • Liang Y, Gerwin J, Meyer A, Kratochwil CF. 2020. Developmental and cellular basis of vertical bar color patterns in the east African cichlid fish Haplochromis latifasciatus. Front Cell Dev Biol. 8:62. doi:10.3389/fcell.2020.00062.
  • Liao Y, Smyth GK, Shi W. 2013. Featurecounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 30(7):923–930. doi:10.1093/bioinformatics/btt656.
  • Liu J, Ma J. 2011. Fates-shifted is an F-box protein that targets Bicoid for degradation and regulates developmental fate determination in Drosophila embryos. Nat Cell Biol. 13:22–29. doi:10.1038/ncb2141.
  • Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15(12):550. doi:10.1186/s13059-014-0550-8.
  • Luo M, Lu G, Yin H, Wang L, Atuganile M, Dong ZJRiA. 2021. Fish pigmentation and coloration: molecular mechanisms and aquaculture perspectives. Rev Aquacult. 13(4):2395–2412. doi:10.1111/raq.12583.
  • Mackintosh C. 2004. Dynamic interactions between 14-3-3 proteins and phosphoproteins regulate diverse cellular processes. Biochem J. 381(2):329–342. doi:10.1042/BJ20031332.
  • MacMicking JD. 2004. IFN-inducible GTPases and immunity to intracellular pathogens. Trends Immunol. 25(11):601–609. doi:10.1016/j.it.2004.08.010.
  • Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM. 2021. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol Biol Evol. 38(10):4647–4654. doi:10.1093/molbev/msab199.
  • Mellerick DM, Nirenberg M. 1995. Dorsal-ventral patterning genes restrict NK-2 homeobox gene expression to the ventral half of the central nervous system of Drosophila embryos. Dev Biol. 171(2):306–316. doi:10.1006/dbio.1995.1283.
  • Mo ES, Cheng Q, Reshetnyak AV, Schlessinger J, Nicoli S. 2017. Alk and Ltk ligands are essential for iridophore development in zebrafish mediated by the receptor tyrosine kinase Ltk. Proc Natl Acad Sci USA. 114(45):12027–12032. doi:10.1073/pnas.1710254114.
  • Natarajan VT, Ganju P, Singh A, Vijayan V, Kirty K, Yadav S, Puntambekar S, Bajaj S, Dani PP, Kar HK, et al. 2014. IFN-γ signaling maintains skin pigmentation homeostasis through regulation of melanosome maturation. Proc Natl Acad Sci USA. 111(6):2301–2306. doi:10.1073/pnas.13049881.
  • Ng TT, Sung YY, Danish-Daniel M, Sorgeloos P, de Peer YV, Wong LL, Tan MP. 2021. Genetic variation of domesticated discus (Symphysodon spp.). Aquacult Aquarium Conserv Legis. 14(2):832–840.
  • Nishimura O, Hara Y, Kuraku S. 2017. Gvolante for standardizing completeness assessment of genome and transcriptome assemblies. Bioinformatics. 33(22):3635–3637. doi:10.1093/bioinformatics/btx445.
  • Nüsslein-Volhard C, Singh AP. 2017. How fish color their skin: A paradigm for development and evolution of adult patterns. Bioessays. 39(3):1600231. doi:10.1002/bies.201600231.
  • Otręba M, Rok J, Buszman E, Wrzesniok D. 2012. Regulation of melanogenesis: the role of cAMP and MITF. Postepy Hig Med Dosw. 66:33–40.
  • Saito Y, Hojo Y, Tanimoto T, Abe J-i, Berk BC. 2002. Protein kinase C-α and protein kinase C-ϵ are required for grb2-associated binder-1 tyrosine phosphorylation in response to platelet-derived growth factor. J Biol Chem. 277(26):23216–23222. doi:10.1074/jbc.M200605200.
  • Szklarczyk D, Gable AL, Nastou KC, Lyon D, Kirsch R, Pyysalo S, Doncheva NT, Legeay M, Fang T, Bork P, et al. 2020. The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Res. 49(D1):D605–D612. doi:10.1093/nar/gkaa1074.
  • Tripathy PS, Devi NC, Parhi J, Priyadarshi H, Patel AB, Pandey PK, Mandal SC. 2019. Molecular mechanisms of natural carotenoid-based pigmentation of queen loach, Botia dario (Hamilton, 1822) under captive condition. Sci Rep. 9(1):12585. doi:10.1038/s41598-019-48982-9.
  • Wang TZ, Wu Q, Zhang N, Wang DJ, Xu Z, Luo W, Du ZJ. 2020. Advances in research on melanin synthesis and signaling pathway in fish. China Biotech. 40(5):84–93.
  • Wang X, Li D, Song S, Zhang Y, Li Y, Wang X, Liu D, Zhang C, Cao Y, Fu Y, et al. 2019. Combined transcriptomics and proteomics forecast analysis for potential genes regulating the Columbian plumage color in chickens. PLoS One. 14(11):e0210850. doi:10.1371/journal.pone.0210850.
  • Wu S, Huang J, Li Y, Zhao L, Liu Z. 2022. Analysis of yellow mutant rainbow trout transcriptomes at different developmental stages reveals dynamic regulation of skin pigmentation genes. Sci Rep. 12(1):256. doi:10.1038/s41598-021-04255-y.
  • Yan K, Gao LN, Cui YL, Zhang Y, Zhou X. 2016. The cyclic AMP signaling pathway: exploring targets for successful drug discovery (Review). Mol Med Rep. 13(5):3715–3723. doi:10.3892/mmr.2016.5005.
  • Yang BT, Wen B, Ji Y, Wang Q, Zhang H-R, Zhang Y, Gao J-Z, Chen ZZ. 2021. Comparative metabolomics analysis of pigmentary and structural coloration in discus fish (Symphysodon haraldi). J Proteomics. 233:104085. doi:10.1016/j.jprot.2020.104085.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.