Transcriptome analysis identifies candidate genes related to albinism mechanism in the skin of the Picasso clownfish

He Libin; Huang Zhen; Wu Shuiqing; Zheng Leyun

doi:10.12284/hyxb2022050

Volume 44 Issue 2

Feb. 2022

Turn off MathJax

Article Contents

Article Navigation > Haiyang Xuebao > 2022 > 44(2): 67-76

He Libin，Huang Zhen，Wu Shuiqing, et al. Transcriptome analysis identifies candidate genes related to albinism mechanism in the skin of the Picasso clownfish[J]. Haiyang Xuebao，2022, 44(2)：67–76 doi: 10.12284/hyxb2022050

Citation:

PDF( 1297 KB)

Transcriptome analysis identifies candidate genes related to albinism mechanism in the skin of the Picasso clownfish

doi: 10.12284/hyxb2022050

He Libin^{1, 2
,},
Huang Zhen^{2, 3},
Wu Shuiqing¹,
Zheng Leyun¹

1.
Fisheries Research Institute of Fujian, Xiamen 361013, China
2.
College of Life Science, Fujian Normal University, Fuzhou 350117, China
3.
Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization, Fuzhou 350117, China

Received Date: 2021-08-12
Rev Recd Date: 2021-11-10

Available Online: 2021-12-27

Publish Date: 2022-02-01

Abstract

Abstract

Picasso clownfish is named for its disorderly and abstract distribution of white patches in its skin. At the same time, due to the irregular and scarce formation of white patches, it belongs to a valuable clownfish. Therefore, analyzing the formation mechanism of skin white spots in Picasso clownfish can provide a theoretical basis for the artificial breeding of Picasso clownfish. In this study, we sequences the transcriptome of the skin of three color blocks (black, yellow and white） in the same part of the body between the dorsal fin and hip fin of Picasso clownfish. The results show that there are a large number of differentially expressed genes (DEGs） in white skin compared with yellow and black skin. Among them, the genes in the signal pathways related to melanin production (such as melanin production, hedgehog and Wnt signal pathways） show a downward trend in white skin tissue. The expression of upstream regulatory genes (such as ednrba and mitfa） decrease gradually from black to yellow to white skin tissue, but the expression of downstream core genes involved in melanin synthesis (including Tyr, tyrp1b and dct） decreases significantly in white skin assembly. Finally, the validity of transcriptome data is verified by fluorescence quantitative PCR. The results of this study will provide a theoretical basis for future people to interfere with gene expression to regulate clownfish body color.
- albinism,
- Picasso clownfish,
- transcriptome sequencing,
- differentially expressed gene

FullText(HTML)

References(29)

References

[1]	Braasch I, Volff J N, Schartl M. The evolution of teleost pigmentation and the fish-specific genome duplication[J]. Journal of Fish Biology, 2008, 73(8): 1891−1918. doi: 10.1111/j.1095-8649.2008.02011.x
[2]	Hubbard J K, Uy J A C, Hauber M E, et al. Vertebrate pigmentation: from underlying genes to adaptive function[J]. Trends in Genetics, 2010, 26(5): 231−239. doi: 10.1016/j.tig.2010.02.002
[3]	Gordon A K. The effect of diet and age-at-weaning on growth and survival of clownfish Amphiprion percula (Pisces: Pomacentridae)[D]. Grahamstown: Rhodes University, 1999.
[4]	Marcionetti A, Rossier V, Bertrand J A M, et al. First draft genome of an iconic clownfish species (Amphiprion frenatus)[J]. Molecular Ecology Resources, 2018, 18(5): 1092−1101. doi: 10.1111/1755-0998.12772
[5]	He Libin, Wu Shuiqing, Luo Huiyu, et al. The complete mitochondrial genome of the Picasso clownfish: genomic comparisons and phylogenetic inference among Amphiprioninae[J]. Mitochondrial DNA: Part B, 2020, 5(3): 2990−2991. doi: 10.1080/23802359.2020.1797554
[6]	Oetting W S, King R A. Molecular basis of albinism: mutations and polymorphisms of pigmentation genes associated with albinism[J]. Human Mutation, 1999, 13(2): 99−115. doi: 10.1002/(SICI)1098-1004(1999)13:2<99::AID-HUMU2>3.0.CO;2-C
[7]	Oetting W S. Albinism[J]. Current Opinion in Pediatrics, 1999, 11(6): 565−571. doi: 10.1097/00008480-199912000-00016
[8]	Griffiths G M. Albinism and immunity: whats the link?[J]. Current Molecular Medicine, 2002, 2(5): 479−483. doi: 10.2174/1566524023362258
[9]	Xing Lili, Sun Lina, Liu Shilin, et al. Transcriptome analysis provides insights into the mechanism of albinism during different pigmentation stages of the albino sea cucumber Apostichopus japonicus[J]. Aquaculture, 2018, 486: 148−160. doi: 10.1016/j.aquaculture.2017.12.016
[10]	Cox M P, Peterson D A, Biggs P J. SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data[J]. BMC Bioinformatics, 2010, 11(1): 485. doi: 10.1186/1471-2105-11-485
[11]	Kim D, Langmead B, Salzberg S L. HISAT: a fast spliced aligner with low memory requirements[J]. Nature Methods, 2015, 12(4): 357−360. doi: 10.1038/nmeth.3317
[12]	Li Heng, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform[J]. Bioinformatics, 2009, 25(14): 1754−1760. doi: 10.1093/bioinformatics/btp324
[13]	Pertea M, Kim D, Pertea G M, et al. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown[J]. Nature Protocols, 2016, 11(9): 1650−1667. doi: 10.1038/nprot.2016.095
[14]	Young M D, Wakefield M J, Smyth G K, et al. Gene ontology analysis for RNA-seq: accounting for selection bias[J]. Genome Biology, 2010, 11(2): R14. doi: 10.1186/gb-2010-11-2-r14
[15]	Xie Chen, Mao Xizeng, Huang Jiaju, et al. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases[J]. Nucleic Acids Research, 2011, 39(S2): W316−W322.
[16]	Ding Kui, Zhang Libin, Sun Lina, et al. Transcriptome analysis provides insights into the molecular mechanisms responsible for evisceration behavior in the sea cucumber Apostichopus japonicus[J]. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 2019, 30: 143−157. doi: 10.1016/j.cbd.2019.02.008
[17]	Lavado A, Jeffery G, Tovar V, et al. Ectopic expression of tyrosine hydroxylase in the pigmented epithelium rescues the retinal abnormalities and visual function common in albinos in the absence of melanin[J]. Journal of Neurochemistry, 2006, 96(4): 1201−1211. doi: 10.1111/j.1471-4159.2006.03657.x
[18]	Smircich P, Eastman G, Bispo S, et al. Ribosome profiling reveals translation control as a key mechanism generating differential gene expression in Trypanosoma cruzi[J]. BMC Genomics, 2015, 16(1): 443. doi: 10.1186/s12864-015-1563-8
[19]	Ren Hangxing, Wang Gaofu, Jiang Jing, et al. Comparative transcriptome and histological analyses provide insights into the prenatal skin pigmentation in goat (Capra hircus)[J]. Physiological Genomics, 2017, 49(12): 703−711. doi: 10.1152/physiolgenomics.00072.2017
[20]	Cho M, Ryu M, Jeong Y, et al. Cardamonin suppresses melanogenesis by inhibition of Wnt/β-catenin signaling[J]. Biochemical and Biophysical Research Communications, 2009, 390(3): 500−505. doi: 10.1016/j.bbrc.2009.09.124
[21]	Dunn K J, Brady M, Ochsenbauer-Jambor C, et al. WNT1 and WNT3a promote expansion of melanocytes through distinct modes of action[J]. Pigment Cell Research, 2005, 18(3): 167−180. doi: 10.1111/j.1600-0749.2005.00226.x
[22]	Nagao Y, Suzuki T, Shimizu A, et al. Sox5 functions as a fate switch in medaka pigment cell development[J]. PLoS Genetics, 2014, 10(4): 1004246. doi: 10.1371/journal.pgen.1004246
[23]	Tief K, Hahne M, Schmidt A, et al. Tyrosinase, the key enzyme in melanin synthesis, is expressed in murine brain[J]. European Journal of Biochemistry, 1996, 241(1): 12−16. doi: 10.1111/j.1432-1033.1996.0012t.x
[24]	Ghanem G, Fabrice J. Tyrosinase related protein 1 (TYRP1/gp75) in human cutaneous melanoma[J]. Molecular Oncology, 2011, 5(2): 150−155. doi: 10.1016/j.molonc.2011.01.006
[25]	Picardo M, Cardinali G. The genetic determination of skin pigmentation: KITLG and the KITLG/c-Kit pathway as key players in the onset of human familial pigmentary diseases[J]. Journal of Investigative Dermatology, 2011, 131(6): 1182−1185. doi: 10.1038/jid.2011.67
[26]	Fang Dong, Tsuji Y, Setaluri V. Selective down-regulation of tyrosinase family gene TYRP1 by inhibition of the activity of melanocyte transcription factor, MITF[J]. Nucleic Acids Research, 2002, 30(14): 3096−3106. doi: 10.1093/nar/gkf424
[27]	Seo E Y, Jin S P, Sohn K C, et al. UCHL1 regulates melanogenesis through controlling MITF stability in human melanocytes[J]. Journal of Investigative Dermatology, 2017, 137(8): 1757−1765. doi: 10.1016/j.jid.2017.03.024
[28]	George A, Zand D J, Hufnagel R B, et al. Biallelic mutations in MITF cause coloboma, osteopetrosis, microphthalmia, macrocephaly, albinism, and deafness[J]. The American Journal of Human Genetics, 2016, 99(6): 1388−1394. doi: 10.1016/j.ajhg.2016.11.004
[29]	Hornyak T J, Hayes D J, Chiu L Y, et al. Transcription factors in melanocyte development: distinct roles for Pax-3 and Mitf[J]. Mechanisms of Development, 2001, 101(1/2): 47−59.