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Integrated analysis of RNA-seq and microRNA-seq depicts miRNA–mRNA networks involved in stripe patterns of Botia superciliaris skin

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Abstract

Botia superciliaris, an endemic cobitid fish in China, is widely accepted by Chinese consumers because its edibility. Recently, the black and yellow stripes of B. superciliaris skin have made this species increasingly popular as a novel ornamental fish. However, the genetic basis of the stripe patterns in B. superciliaris skin has not been extensively studied. In this study, Illumina sequencing was employed to identify the mRNAs and miRNAs involved in stripe pattern formation in B. superciliaris skin. A total of 147.25 and 155.15 million (M) high-quality transcriptome reads were generated from three black and yellow skin libraries respectively, which resulted in 159,327 unigenes that were used as reference sequences. A total of 3169 genes exhibited significantly differential expression patterns (fold-change ≥ 2 or ≤ 0.5 and q ≤ 0.05), including 1891 upregulated genes (59.67%) and 1278 downregulated genes (40.33%) in black vs yellow skin. These genes were enriched in 50 GO terms and 10 KEGG pathways (q ≤ 0.05), including melanogenesis, with 21 upregulated genes and 5 downregulated genes in black vs yellow skin. Based on the zebrafish genome, miRNA-seq identified a total of 355 miRNAs, which included 38 novel miRNAs. Furthermore, 87 differentially expressed miRNAs including 50 upregulated and 37 downregulated miRNAs were identified in different color skin (fold-change ≥ 2 or ≤ 0.5 and q ≤ 0.05). Then, target prediction revealed a variety of putative target genes; differentially expressed mRNAs and miRNAs patterns of high-throughput sequencing were validated in 5 mRNAs and miR-217-5p by qRT-PCR. In vivo tests and dual-luciferase reporter assay revealed that overexpression of miR-217-5p can inhibit pheomelanin formation by targeting Zgc. In this study, a comparative analysis was conducted to profile the transcriptome of black and yellow skin for B. superciliaris, and we detected key genes and important miRNAs involved in the B. superciliaris skin pigmentation process. These results will enhance understanding of molecular mechanisms underlying skin pigmentation and facilitate molecular-assisted selection of highly valued skin colors.

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Abbreviations

DE genes:

differentially expressed genes

DE miRNA:

differentially expressed miRNA

Nr:

non-redundant protein database

COG:

Cluster of Orthologous Groups of proteins

GO:

Gene Ontology

KEGG:

Kyoto Encyclopedia of Genes and Genomes

qPCR:

quantitative polymerase chain reaction

References

  • Altschmied J, Delfgaauw J, Wilde B, Duschl J, Bouneau L, Volff JN, Schartl M (2002) Subfunctionalization of duplicate mitf genes associated with differential degeneration of alternative exons in fish. Genetics 161:259–267

    CAS  PubMed  PubMed Central  Google Scholar 

  • Berson JF, Harper DC, Tenza D, Raposo G, Marks MS (2001) Pmel17 initiates premelanosome morphogenesis within multivesicular bodies. Mol Biol Cell 12:3451–3464

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bin HE, Chen XJ, Wen T, Long ZH, Meng-Jun LI (2014) Embryonic development of Botia superciliaris Southwest China. J Agric Sci 27:1332–1336

    Google Scholar 

  • Braasch I, Liedtke D, Volff JN, Schartl M (2009) Pigmentary function and evolution of tyrp1 gene duplicates in fish. Pigment Cell Melanoma Res 22:839–850

    Article  CAS  PubMed  Google Scholar 

  • Braasch I, Schartl M, Volff JN (2007) Evolution of pigment synthesis pathways by gene and genome duplication in fish. BMC Evol Biol 7:74

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Budi EH (2011) The role of ErbB3 in adult pigment cell development dissertations & theses - gradworks

  • Chun-Tao LI, Zhu CK, Wang ZJ (2011) The primary studies on the structure of digestive duct in Botia superciliaris. J Southwest China Normal Univ 36:144–149

    Google Scholar 

  • Chung SY, Seo YK, Park JM, Seo MJ, Park JK, Kim JW, Park CS (2009) Fermented rice bran downregulates MITF expression and leads to inhibition of alpha-MSH-induced melanogenesis in B16F1 melanoma. Biosci Biotechnol Biochem 73:1704–1710

    Article  CAS  PubMed  Google Scholar 

  • Citri A, Skaria KB, Yarden Y (2003) The deaf and the dumb: the biology of ErbB-2 and ErbB-3. Exp Cell Res 284:54–65

    Article  CAS  Google Scholar 

  • Ginger R et al (2008) SLC24A5 encodes a trans-Golgi network protein with potassium-dependent sodium-calcium exchange activity that regulates human epidermal melanogenesis. J Biol Chem 283:5486–5495

    Article  CAS  PubMed  Google Scholar 

  • Guarneri F, Asmundo A, Sapienza D, Cannavò SP (2011) Glutathione S-transferase M1/T1 gene polymorphisms and vitiligo in a Mediterranean population. Pigment Cell Melanoma Res 24:731–733

    Article  CAS  PubMed  Google Scholar 

  • Guo J, Zhang JF, Wang WM, Cheung FWK, Lu YF, Ng CF, Kung HF, Liu WK (2014) MicroRNA-218 inhibits melanogenesis by directly suppressing microphthalmia-associated transcription factor expression. RNA Biol 11:732–741

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Henning F, Jones JC, Franchini P, Meyer A (2013) Transcriptomics of morphological color change in polychromatic Midas cichlids. BMC Genomics 14:171–171

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hubbard JK, Uy JA, Hauber ME, Hoekstra HE, Safran RJ (2010) Vertebrate pigmentation: from underlying genes to adaptive function. Trends Genet 26:231–239

    Article  CAS  PubMed  Google Scholar 

  • Jiang Y, Zhang S, Xu J, Feng J, Mahboob S, al-Ghanim KA, Sun X, Xu P (2014) Comparative transcriptome analysis reveals the genetic basis of skin color variation in common carp. PLoS One 9:e108200

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kedam TR, Chittoor P, Kurumala D (2017) Glutathione- S -Transferases

  • Kelsh RN et al (1996) Zebrafish pigmentation mutations and the processes of neural crest development. Development 123:369

    CAS  PubMed  Google Scholar 

  • Kelsh RN, Inoue C, Momoi A, Kondoh H, Furutani-Seiki M, Ozato K, Wakamatsu Y (2004) The Tomita collection of medaka pigmentation mutants as a resource for understanding neural crest cell development. Mech Dev 121:841–859

    Article  CAS  PubMed  Google Scholar 

  • Kennell JA, Cadigan KM, Shakhmantsir I, Waldron EJ (2012) The microRNA miR-8 is a positive regulator of pigmentation and eclosion in Drosophila. Dev Dyn 241:161–168

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kondo S, Iwashita M, Yamaguchi M (2009) How animals get their skin patterns: fish pigment pattern as a live Turing wave. Int J Dev Biol 53:851–856

    Article  PubMed  Google Scholar 

  • Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li S, Wang C, Yu W, Zhao S, Gong Y (2012) Identification of genes related to White and black plumage formation by RNA-Seq from white and black feather bulbs in ducks. PLoS One 7:e36592

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lu L, Wu W, Tu Y, Yang Z, He L, Guo M (2014) Association of glutathione S-transferase M1/T1 polymorphisms with susceptibility to vitiligo. Gene 535:12–16

    Article  CAS  PubMed  Google Scholar 

  • Ng’Oma E, Groth M, Ripa R, Platzer M, Cellerino A (2014) Transcriptome profiling of natural dichromatism in the annual fishes Nothobranchius furzeri and Nothobranchius kadleci. BMC Genomics 15:754

    Article  PubMed  PubMed Central  Google Scholar 

  • Noguchi S, Kumazaki M, Yasui Y, Mori T, Yamada N, Akao Y (2014) MicroRNA-203 regulates melanosome transport and Tyrosinase expression in melanoma cells by targeting kinesin superfamily protein 5b. J Investig Dermatol 134:461–469

    Article  CAS  PubMed  Google Scholar 

  • Pabst MJ, Habig WH, Jakoby WB (1974) Glutathione S-transferase a. a novel kinetic mechanism in which the major reaction pathway depends on substrate concentration. J Biol Chem 249:7140

    CAS  PubMed  Google Scholar 

  • Parichy DM (2006) Evolution of danio pigment pattern development. Heredity 97:200–210

    Article  CAS  PubMed  Google Scholar 

  • Pasello M, Manara MC, Michelacci F, Fanelli M, Hattinger CM, Nicoletti G, Landuzzi L, Lollini PL, Caccuri A, Picci P, Scotlandi K, Serra M (2011) Targeting glutathione-S transferase enzymes in musculoskeletal sarcomas: a promising therapeutic strategy. Anal Cell Pathol 34:131–145

    Article  CAS  Google Scholar 

  • Protas ME, Patel NH (2008) Evolution of coloration patterns. Annu Rev Cell Dev Biol 24:425–446

    Article  CAS  PubMed  Google Scholar 

  • Qiang LI, Yao MY, Zhou B, Chen XJ, Long ZH, Zhou CJ, Meng-Jun LI (2011) Technique of artificial reproduction of Botia superciliaris Günther freshwater fisheries.

  • Robinson MD, Mccarthy DJ, Smyth GK (2009) edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rodgers GM, Kelley JL, Morrell LJ (2010) Colour change and assortment in the western rainbowfish. Anim Behav 79:1025–1030

    Article  Google Scholar 

  • Senjo M, Ishibashi T (2017) Specific localization of glutathione S-transferases in astrocytes and ependymal cells of rat brain: immunocytochemical demonstration. Biomed Res 6:433–436

    Article  Google Scholar 

  • Suzuki I, Tada A, Ollmann MM, Barsh GS, Im S, Lynn Lamoreux M, Hearing VJ, Nordlund JJ, Abdel-Malek ZA (1997) Agouti signaling protein inhibits melanogenesis and the response of human melanocytes to alpha-melanotropin. J Investig Dermatol 108:838–842

    Article  CAS  PubMed  Google Scholar 

  • Vlachos IS et al (2015) DIANA-miRPath v3.0: deciphering microRNA function with experimental support. Nucleic Acids Res 43:460–466

    Article  CAS  Google Scholar 

  • Yan B, Liu B, Zhu CD, Li KL, Yue LJ, Zhao JL, Gong XL, Wang CH (2013) microRNA regulation of skin pigmentation in fish. J Cell Sci 126:3401–3408

    Article  CAS  PubMed  Google Scholar 

  • Yang ZY, Liang HW, Li Z, Wang XY, Zou GW (2013) Mitochondrial genome sequence of the Botia superciliaris (Teleostei, Cypriniformes). Mitochondrial DNA 24:347–349

    Article  CAS  PubMed  Google Scholar 

  • Yuwen L, Jie Z, White KP (2014) RNA-seq differential expression studies: more sequence or more replication? Bioinformatics 30:301

    Article  CAS  Google Scholar 

  • Zamore PD, Tuschl T, Sharp PA, Bartel DP (2000) RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101:25–33

    Article  CAS  Google Scholar 

  • Zhu W, Wang L, Dong Z, Chen X, Song F, Liu N, Yang H, Fu J (2016) Comparative transcriptome analysis identifies candidate genes related to skin color differentiation in red tilapia. Sci Rep 6:31347

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhu Z, He J, Jia X, Jiang J, Bai R, Yu X, Lv L, Fan R, He X, Geng J, You R, Dong Y, Qiao D, Lee KB, Smith GW, Dong C (2010) MicroRNA-25 functions in regulation of pigmentation by targeting the transcription factor MITF in alpaca (Lama pacos) skin melanocytes. Domest Anim Endocrinol 38:200–209

    Article  CAS  PubMed  Google Scholar 

Download references

Funding

This work was financially supported by Breeding Technology and Large- scale Farming Technology for Research and Demonstration of Botia superciliaris (2016ZYPZ027). This research was also supported by the “Double Support Project” fund of Sichuan Agricultural University (SICAU, No. 03573018; No. 03572013).

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Author notes

  1. Jian Zhou and Han Zhao contributed equally to this work.

Authors and Affiliations

  1. Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 611731, Sichuan, China

    Jian Zhou, Lu Zhang, Qiang Li, Hongyu Ke, Xinyu Wang, Chao Liu & Xutao Su

  2. College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China

    Han Zhao, Can Liu, Siyuan Feng, Jideng Ma, Lingyan Liu, Yingkai Liu & Song Yang

Authors
  1. Jian Zhou
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  2. Han Zhao
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  3. Lu Zhang
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  4. Can Liu
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  5. Siyuan Feng
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  11. Chao Liu
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  13. Yingkai Liu
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Contributions

Jian Zhou, Jideng Ma, Han Zhao, and Song Yang designed the experiment and wrote the manuscript. Lu Zhang, Can Liu, Siyuan Feng, and Yingkai Liu carried out the experiments data organization and statistical analyses. Qiang Li, Hongyu Ke, Xinyu Wang, and Lingyan Liu provided the experimental samples. Chao Liu and Xutao Su participated in the study design and discussed the manuscript. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Yingkai Liu or Song Yang.

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Zhou, J., Zhao, H., Zhang, L. et al. Integrated analysis of RNA-seq and microRNA-seq depicts miRNA–mRNA networks involved in stripe patterns of Botia superciliaris skin. Funct Integr Genomics 19, 827–838 (2019). https://doi.org/10.1007/s10142-019-00683-2

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