Korean Journal of Ichthyology (한국어류학회지)

The Ichthyological Society of Korea (한국어류학회)
권호 표지
DOI QR코드

DOI QR Code

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

체색 패턴이 다른 개볼락(Sebastes pachycephalus) 피부 전사체 프로파일링

  • Jang, Yo-Soon (East Sea Environment Research Center, Korea Institute of Ocean Science & Technology)
  • 장요순 (한국해양과학기술원 동해환경연구센터)
  • Received : 2020.08.08
  • Accepted : 2020.09.07
  • Published : 2020.09.30
Download PDF
⟨ Previous Next ⟩

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.

생물의 종 구분에 이용하는 지표 중 체색은 특징이 뚜렷한 형태 지표로서, 어류의 종 동정에 유용한 형태형질이다. 개볼락은 한국 중부와 남부, 일본 홋카이도 남쪽 등지에 분포하는 상업적으로 중요한 어종으로, 피부에 반점의 유무 및 마킹이 있는 위치에 따라 4개의 아종으로 구분하는 복잡한 체색 특성을 갖는다. 그러나 개볼락의 다양한 체색 패턴과 관련된 유전자 탐색 및 유전자 변이 발굴 등 체색 형성에 관여하는 유전자 규명에 관한 연구는 없다. 이에 따라 본 연구에서는 개볼락의 체색 패턴 관련 유전자 발굴 및 유전자 발현 특성을 규명하기 위한 기초 연구로 체색 타입별 피부 전사체를 프로파일링하였다. 개볼락을 Wild type (반점과 marking 없음)과 Color type (반점과 마킹 모두 있음)으로 구분하였고, 피부 전사체를 RNA-seq 방법을 이용하여 분석하였다. 개볼락 피부 전사체의 발현량을 비교하여 체색 타입별 차등발현유전자 164개를 확보하였다. 이들 차등발현유전자의 기능을 Gene ontology(GO) 분석으로 확인한 결과, 2개는 molecular function, 46개는 biological process, 6개는 cellular component 기능그룹에 속하였다. 차등발현유전자 중 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) 등은 특정 체색 타입 특이적인 발현양상을 나타냈다. 이번 연구는 개볼락의 체색 패턴 형성에 관여하는 전사체를 탐색한 첫 번째 연구로, 체색 형성 관련 기능유전자 발굴을 위한 후보유전자로 개볼락의 체색 타입별 차등발현유전자를 확보한 것에 의의가 있다. 향후에는 이들 후보유전자의 발현양상 및 기능을 분석하여 개볼락의 복잡한 체색 패턴과 관련된 기능유전자의 특성을 밝히고자 한다.

Keywords

References

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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. https://doi.org/10.1242/dev.123.1.369
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. Matsubara, K. 1943. Studies on the scorpaenoid fishes of Japan. Anatomy, phylogeny and taxonomy II. Trans. Sigenkagaku Kenkyusyo, 2: 171-486.
  28. 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.
  29. 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.
  30. 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.
  31. 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.
  32. 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.
  33. Parichy, D.M. 2006. Evolution of danio pigment pattern development. Heredity, 97: 200-210. https://doi.org/10.1038/sj.hdy.6800867.
  34. 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.
  35. 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.
  36. 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.
  37. 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.
  38. 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.
  39. 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.
  40. 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.
  41. 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.
  42. 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.
  43. 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.
  44. 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.
  45. 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.
  46. 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.