Browse > Article
http://dx.doi.org/10.35399/ISK.32.3.1

Skin Transcriptome Profiling of the Blass Bloched Rockfish (Sebastes pachycephalus) with Different Body Color Patterns  

Jang, Yo-Soon (East Sea Environment Research Center, Korea Institute of Ocean Science & Technology)
Publication Information
Korean Journal of Ichthyology / v.32, no.3, 2020 , pp. 117-129 More about this Journal
Abstract
The body color pattern in fish is a distinctive feature for species identification. The blass bloched rockfish Sebastes pachycephalus is a commercially important marine fish species, distributed in the central and southern parts of Korea and south Hokkaido of Japan. It has a morphological feature divided into four subspecies according to with or lacking distinct spots on the body surface, and to the location of markings on the body surface. However, the genetic basis of body color pattern of S. pachycephalus is still unknown. Thus we analyzed the transcriptome of S. pachycephalus skin samples using RNA-seq analysis to investigate functional genes related to body color patterns. The experimental skin samples were prepared by classified into 'Wild type' (lacking distinct spots and markings) and 'Color type' (with distinct spots and marking). Two skin sample transcriptomes were compared pairwise and the results revealed that were 164 differentially expressed unigenes in the skin samples of 'Wild type' and 'Color type'. Gene Ontology analysis of 164 differentially expressed unigenes showed that these genes were included in the functional group of molecular function (2 genes), biological process (46 genes), and cellular component (6 genes). There were several genes that body color type skin specific expression and the genes were CTL (Galactose-specific lectin nattectin), CUL1 (Cullin-1), CMAS (N-acylneuraminate cytidylyltransferase), NMRK2 (Nicotinamide riboside kinase 2), ALOXE3 (Hydroperoxide isomerase ALOXE3), SLC4A7 (sodium bicarbonate cotransporter 3). Our study is the first attempt to search for functional genes involved in the formation of body color patterns in S. pachycephalus. The differentially expressed unigenes obtained in this study can be used as candidate genes for functional gene study related to body coloration of fish.
Keywords
Transcriptome; body color; RNA-seq; differentially expressed gene; Sebastes pachycephalus;
Citations & Related Records
Times Cited By KSCI : 1  (Citation Analysis)
연도 인용수 순위
1 Kai, Y., K. Nakayama and T. Nakabo. 2011. Genetic and morphological divergence within the Sebastes pachycephalus complex (Scorpaeniformes: Scorpaenidae). Ichthyol. Res., 58: 333-343. https://doi.org/10.1007/s10228-011-0236-0.   DOI
2 Kai, Y. and T. Nakabo. 2013. Taxonomic review of the Sebastes pachycephalus complex (Scorpaeniformes: Scorpaenidae). Zootaxa, 3637: 541-560. https://doi.org/10.11646/zootaxa.3637.5.3.   DOI
3 Kelsh, R.N., M. Brand, Y.J. Jiang, C.P. Heisenberg, S. Lin, P. Haffter, J. Odenthal, M.C. Mullins, F.J. M. van Eeden, M. Furutani-Seiki, M. Granato, M. Hammerschmidt, D.A. Kane, R.M. Warga, D. Beuchle, L. Vogelsang and C. Nusslein-Volhard. 1996. Zebrafish pigmentation mutations and the processes of neural crest development. Development, 123: 369-389. https://dev.biologists.org/content/develop/123/1/369.   DOI
4 Kelsh, R.N., C. Inoue, A. Momoi, H. Kondoh, M. Furutani-Seiki, K. Ozato and Y. Wakamatsu. 2004. The Tomita collection of medaka pigmentation mutants as a resource for understanding neural crest cell development. Mech. Dev., 121: 841-859. https://doi.org/10.1016/j.mod.2004.01.004.   DOI
5 Lamason, R.L., M-A.P.K. Mohideen, J.R. Mest, A.C. Wong, H.L. Norton, M.C. Aros, M.J. Jurynec, X. Mao, V.R. Humphreville, J.E. Humbert, S. Sinha, J.L. Moore, P. Jagadeeswaran, W. Zhao, G. Ning, I. Makalowska, P.M. McKeigue, D. O'Donnell, R. Kittles, E.J. Parra, N.J. Mangini, D.J. Grunwald, M.D. Shriver, V.A. Canfield, K.C. Cheng. 2005. SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. Science, 310: 1782-1786. https://doi.org/10.1126/science.1116238.   DOI
6 Leclercq, E., J.F. Taylor and H. Migaud. 2010. Morphological skin colour changes in teleosts. Fish Fish., 11: 159-193. https://doi.org/10.1111/j.1467-2979.2009.00346.x.   DOI
7 Li, B. and C.N. Dewey. 2011. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics, 12: 323. https://doi.org/10.1186/1471-2105-12-323.   DOI
8 Liao, X., L. Cheng, P. Xu, G. Lu, M. Wachholtz, X. Sun and S. Chen. 2013. Transcriptome analysis of crucian carp (Carassius auratus), an important aquaculture and hypoxia-tolerant species. PLoS One, 8: e62308. https://doi.org/10.1371/journal.pone.0062308.   DOI
9 Matsubara, K. 1943. Studies on the scorpaenoid fishes of Japan. Anatomy, phylogeny and taxonomy II. Trans. Sigenkagaku Kenkyusyo, 2: 171-486.
10 Medina, I., J. Carbonell, L. Pulido, S.C. Madeira, S. Goetz, A. Conesa, J. Tarraga, A. Pascual-Montano, R. Nogales-Cadenas, J. Santoyo, F. García, M. Marba, D. Montaner and J. Dopazo. 2010. Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Nucleic Acids Res., 38: W210-213. https://doi.org/10.1093/nar/gkq388.   DOI
11 Mellgren, E.M. and S.L. Johnson. 2002. The evolution of morphological complexity in zebrafish stripes. Trends Genet., 18: 128-134. https://doi.org/10.1016/s0168-9525(01)02614-2.   DOI
12 Parichy, D.M. 2006. Evolution of danio pigment pattern development. Heredity, 97: 200-210. https://doi.org/10.1038/sj.hdy.6800867.   DOI
13 Miller, C.T., S. Beleza, A.A. Pollen, D. Schluter, R.A. Kittles, M.D. Shriver and D.M. Kingsley. 2007. Cis-regulatory changes in Kit ligand expression and parallel evolution of pigmentation in sticklebacks and humans. Cell, 131: 1179-1189. https://doi.org/10.1016/j.cell.2007.10.055.   DOI
14 Mortazavi, A., B.A. Williams, K. McCue, L. Schaeffer and B. Wold. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods, 5: 1-8. https://doi.org/10.1038/nmeth.1226.   DOI
15 Nakabo, T. 2002. Scorpaenidae. In: Nakabo, T. (ed.), Fishes of Japan with pictorial keys to the species, English ed. Tokai Univ. Press, Tokyo, Japan, pp. 565-595, 1524-1528.
16 Pertea, G., X. Huang, F. Liang, V. Antonescu, R. Sultana, S. Karamycheva, Y. Lee, J. White, F. Cheung, B. Parvizi, J. Tsai and J. Quackenbush. 2003. TIGR Gene indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics, 19: 651-652. https://doi.org/10.1093/bioinformatics/btg034.   DOI
17 Protas, M.E. and N.H. Patel. 2008. Evolution of coloration patterns. Annu. Rev. Cell Dev. Biol., 24: 425-446. https://doi.org/10.1146/annurev.cellbio.24.110707.175302.   DOI
18 Roberts, R.B., J.R. Ser and T.D. Kocher. 2009. Sexual conflict resolved by invasion of a novel sex determiner in Lake Malawi cichlid fishes. Science, 326: 998-1001. https://doi.org/10.1126/science.1174705.   DOI
19 Rodgers, G.M., J.L. Kelley and L.J. Morrell. 2010. Colour change and assortment in the western rainbowfish. Anim. Behav., 79: 1025-1030. https://doi.org/10.1016/j.anbehav.2010.01.017.   DOI
20 Rodionov, V.I., J. Yi, A. Kashina, A. Oladipo and S.P. Gross. 2003. Switching between microtubule- and actin-based transport systems in melanophores is controlled by cAMP levels. Curr. Biol., 13: 1837-1847. https://doi.org/10.1016/j.cub.2003.10.027.   DOI
21 Samanta, M.P., W. Tongprasit, S. Istrail, R.A. Cameron, Q. Tu, E.H. Davidson and V. Stolc. 2006. The transcriptome of the sea urchin embryo. Science, 314: 960-962. https://doi.org/10.1126/science.1131898.   DOI
22 Sims, D., I. Sudbery, N.E. Ilott, A. Heger, and C.P. Ponting. 2014. Sequencing depth and coverage: key considerations in genomic analyses. Nat. Rev. Genet., 15: 121-132. https://doi.org/10.1038/nrg3642.   DOI
23 Sun, J., T. Nishiyama, K. Shimizu and K. Kadota. 2013. TCC: an R package for comparing tag count data with robust normalization strategies. BMC Bioinformatics, 14: 219. https://doi.org/10.1186/1471-2105-14-219.   DOI
24 Tarazona, S., F. Garcia-Alcalde, J. Dopazo, A. Ferrer and A. Conesa. 2011. Differential expression in RNA-seq: a matter of depth. Genome Res., 21: 2213-2223. https://doi.org/10.1101/gr.124321.111.   DOI
25 Ashburner, M., C.A. Ball, J.A. Blake, D. Botstein, H. Butler, J.M. Cherry, A.P. Davis, K. Dolinski, S.S. Dwight, J.T. Eppig, M.A. Harris, D.P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J.C. Matese, J.E. Richardson, M. Ringwald, G.M. Rubin and G. Sherlock. 2000. Gene Ontology: tool for the unification of biology. Nat. Genet., 25: 25-29. https://doi.org/10.1038/75556.   DOI
26 Bagnara, J.T., P.J. Fernandez and R. Fujii. 2007. On the blue coloration of vertebrates. Pigment Cell Res., 20: 14-26. https://doi.org/10.1111/j.1600-0749.2006.00360.x.   DOI
27 Bairoch, A., B. Boeckmann, S. Ferro and E. Gasteiger. 2004. Swiss-Prot: juggling between evolution and stability. Brief Bioinformatics, 5: 39-55. https://doi.org/10.1093/bib/5.1.39.   DOI
28 Blanco, E., G. Parra and R. Guigo. 2007. Using geneid to identify genes. Curr. Protoc. Bioinformatics, 18: 4.3.1-4.3.28. https://doi.org/10.1002/0471250953.bi0403s18.
29 Braasch, I., M. Schart and J.N. Volff. 2007. Evolution of pigment synthesis pathways by gene and genome duplication in fish. BMC Evol. Biol., 7: 74. https://doi.org/10.1186/1471-2148-7-74.   DOI
30 Braasch, I., F. Brunet, J.N. Volff and M. Schart. 2009. Pigmentation pathway evolution after whole-genome duplication in fish. Genome Biol. Evol., 1: 479-493. https://doi.org/10.1093/gbe/evp050.   DOI
31 Huang, D.W., B.T. Sherman and R.A. Lempicki. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc., 4: 44-57. https://doi.org/10.1038/nprot.2008.211.   DOI
32 Trapnell, C., B.A. Williams, G. Pertea, A. Mortazavi, G. Kwan, M.J. van Baren, S.L. Salzberg, B.J. Wold and L. Pachter. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol., 28: 511-515. https://doi.org/doi.org/10.1038/nbt.1621.   DOI
33 Wang, C., M. Wachholtz, J. Wang, X. Liao and G. Lu. 2014. Analysis of the skin transcriptome in two oujiang color varieties of common carp. PLoS One, 9: e90074. https://doi.org/10.1371/journal.pone.0090074.   DOI
34 Yu, H.J. and J.K. Kim. 2014. New record of Sebastes nudus and redescription of Sebastes pachycephalus (Pisces: Scorpaenidae) from Korea. Fish Aquat. Sci., 17: 129-136. https://doi.org/10.5657/FAS.2014.0129.   DOI
35 Zhu, W., L. Wang, Z. Dong, X. Chen, F. Song, N. Liu, H. Yang and J. Fu. 2016. Comparative transcriptome analysis identifies candidate genes related to skin color differentiation in red tilapia. Sci. Rep., 6: 31347 https://doi.org/10.1038/srep31347.   DOI
36 Conesa, A., P. Madrigal, S. Tarazona, D. Gomez-Cabrero, A. Cervera, A. McPherson, M.W. Szczesniak, D.J. Gaffney, L.L. Elo, X. Zhang and A. Mortazavi. 2016. A survey of best practices for RNA-seq data analysis. Genome Biol., 17: 13. https://doi.org/10.1186/s13059-016-0881-8.   DOI
37 Grabherr, M.G., B.J. Haas, M. Yassour, J.Z. Levin, D.A. Thompson, I. Amit, X. Adiconis, L. Fan, R. Raychowdhury, Q. Zeng, Z. Chen, E. Mauceli, N. Hacohen, A. Gnirke, N. Rhind, F. di Palma, B.W. Birren, C. Nusbaum, K. Lindblad-Toh, N. Friedman and A. Regev. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol., 29: 644-652. https://doi.org/10.1038/nbt.1883.   DOI
38 Haas, B.J., A. Papanicolaou, M. Yassour, M. Grabher, P.D. Blood, J. Bowden, M.B. Couger, D. Eccles, B. Li, M. Lieber, M.D. MacManes, M. Ott, J. Orvis, N. Pochet, F. Strozzi, N. Weeks, R. Westerman, T. William, C.N. Dewey, R. Henschel, R.D. LeDuc, N. Friedman and A. Regev. 2013. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat. Protoc., 8: 1494-1512. https://doi.org/10.1038/nprot.2013.084.   DOI
39 Hoekstra, H.E. 2006. Genetics, development and evolution of adaptive pigmentation in vertebrates. Heredity, 97: 222-234. https://doi.org/10.1038/sj.hdy.6800861.   DOI
40 Huan, P., H. Wang and B. Liu. 2012. Transcriptomic analysis of the clam meretrix meretrix on different larval stages. Mar. Biotechnol., 14: 69-78. https://doi.org/10.1007/s10126-011-9389-0.   DOI
41 Hubbard, J.K., J.A.C. Uy, M.E. Hauber, H.E. Hoekstra and R.J. Safran. 2010. Vertebrate pigmentation: from underlying genes to adaptive function. Trends Genet., 26: 231-239. https://doi.org/10.1016/j.tig.2010.02.002.   DOI
42 Jiang, Y., S. Zhang, J. Xu, J. Feng, S. Mahboob, K.A. Al-Ghanim, X. Sun and P. Xu. 2014. Comparative transcriptome analysis reveals the genetic basis of skin color variation in common carp. PLoS ONE, 9: e108200. https://doi.org/10.1371/journal.pone.0108200.   DOI
43 Huber, W., V.J. Carey, R. Gentleman, S. Anders, M. Carlson, B.S. Carvalho, H.C. Bravo, S. Davis, L. Gatto, T. Girke, R. Gottardo, F. Hahne, K.D. Hansen, R.A. Irizarry, M. Lawrence, M.I. Love, J. MacDonald, V. Obenchain, A.K. Oles, H. Pagès, A. Reyes, P. Shannon, G.K. Smyth, D. Tenenbaum, L. Waldron and M. Morgan. 2015. Orchestrating high-throughput genomic analysis with Bioconductor. Nat. Methods, 12: 115-121. https://doi.org/10.1038/nmeth.3252.   DOI
44 Hunter, S., P. Jones, A. Mitchell, R. Apweiler, T.K. Attwood, A. Bateman, T. Bernard, D. Binns, P. Bork, S. Burge, E. de Castro, P. Coggill, M. Corbett, U. Das, L. Daugherty, L. Duquenne, R.D. Finn, M. Fraser, J. Gough, D. Haft, N. Hulo, D. Kahn, E. Kelly, I. Letunic, D. Lonsdale, R. Lopez, M. Madera, J. Maslen, C. McAnulla, J. McDowall, C. McMenamin, H. Mi, P. Mutowo-Muellenet, N. Mulder, D. Natale, C. Orengo, S. Pesseat, M. Punta, A.F. Quinn, C. Rivoire, A. Sangrador-Vegas, J.D. Selengut, C.J.A. Sigrist, M. Scheremetjew, J. Tate, M. Thimmajanarthanan, P.D. Thomas, C.H. Wu, C. Yeats and S.-Y. Yong. 2011. InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res., 40 (Database issue): D306-312. https://doi.org/10.1093/nar/gkr948.   DOI
45 Jaitin, D.A., E. Kenigsberg, H. Keren-Shaul, N. Elefant, F. Paul, I. Zaretsky, A. Mildner, N. Cohen, S. Jung, A. Tanay and I. Amit. 2015. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science, 343: 776-779. https://doi.org/10.1126/science.1247651.   DOI
46 Ji, P., G. Liu, J. Xu, X. Wang, J. Li, Z. Zhao, X. Zhang, Y. Zhang, P. Xu and X. Sun. 2012. Characterization of common carp transcriptome: sequencing, de novo assembly, annotation and comparative genomics. PLoS One, 7: e35152. https://doi.org/10.1371/journal.pone.0035152.   DOI