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Molecular biology reports
Mar, 2021;48 (3): 2399-2410.

Transcriptome sequencing and analysis for the pigmentation of scale and skin in common carp (Cyprinus carpio).

Yu-Jie Zhao, Jun Xiao, Mei-Di Huangyang, Ran Zhao, Qi Wang, Yan Zhang, Jiong-Tang Li
Author Information
  1. Yu-Jie Zhao: College of Fisheries and Life, Shanghai Ocean University, Shanghai, 201306, China.
  2. Jun Xiao: College of Fisheries and Life, Shanghai Ocean University, Shanghai, 201306, China.
  3. Mei-Di Huangyang: College of Fisheries and Life, Shanghai Ocean University, Shanghai, 201306, China.
  4. Ran Zhao: Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China.
  5. Qi Wang: Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China.
  6. Yan Zhang: Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China.
  7. Jiong-Tang Li: Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China. lijt@cafs.ac.cn. ORCID
PMID: 33742327 DOI: 10.1007/s11033-021-06273-5

Abstract

BACKGROUND: Teleost scale not only provides a protective layer resisting penetration and pathogens but also participate in coloration. It is interesting to study the mechanism of teleost scale formation. Furthermore, whether there existed consensus genes between scale coloration and skin coloration has not been examined yet.
METHODS AND RESULTS: We analyzed the transcriptome profiles of red scale, white scale, red skin, and white skin of common carp (Cyprinus carpio). Pair-wise comparison identified 3391 differentially expressed genes (DEGs) between scale and skin, respectively. The 1765 up-regulated genes (UEGs) in scale, as the down-regulated genes in skin, preferred mineralization and other scale development-related processes. The 1626 skin UEGs were enriched in the morphogenesis of skin and appendages. We also identified 195 UEGs in white scale and 223 UEGs in red scale. The white scale UEGs primarily participated in regulation of growth and cell migration. The UEGs in red scale preferred pigment cell differentiation and retinoid metabolic process. A total of 22 DEGs had consensus expression patterns in skin and scale of the same coloration. The expression levels of these DEGs clearly grouped skin and scale of the same coloration together with principle component analysis and correlation analysis. Eleven consensus DEGs were homologous to the orthologs of Poropuntius huangchuchieni, 82% of which were under strong purifying selection. Eight processes including lipid storage and lipid catabolism were shared in both scale pigmentation and skin pigmentation.
CONCLUSIONS: We identified consensus DEGs and biological processes in scale and skin pigmentation. Our transcriptome analysis will contribute to further elucidation of mechanisms of teleost scale formation and coloration.

Keywords

Coloration Common carp Scale Skin Transcriptome sequencing

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Grants

  1. 31672644/National Natural Science Foundation of China
  2. 2020XT0103, 2020TD24/Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences

MeSH Term

Animal Scales
Animals
Carps
Conserved Sequence
Gene Expression Profiling
Gene Expression Regulation
Genome
Organ Specificity
Sequence Analysis, RNA
Skin
Skin Pigmentation
Transcriptome
Journal Article
Article has an altmetric score of 1

Word Cloud

Created with Highcharts 10.0.0scaleskincolorationUEGsDEGsconsensusgenesredwhiteanalysispigmentationcarpidentifiedprocessesalsoteleostformationtranscriptomecommonCyprinuscarpiopreferredcellexpressionlipidTranscriptomesequencingBACKGROUND:TeleostprovidesprotectivelayerresistingpenetrationpathogensparticipateinterestingstudymechanismFurthermorewhetherexistedexaminedyetMETHODSANDRESULTS:analyzedprofilesPair-wisecomparison3391differentiallyexpressedrespectively1765up-regulateddown-regulatedmineralizationdevelopment-related1626enrichedmorphogenesisappendages195223primarilyparticipatedregulationgrowthmigrationpigmentdifferentiationretinoidmetabolicprocesstotal22patternslevelsclearlygroupedtogetherprinciplecomponentcorrelationElevenhomologousorthologsPoropuntiushuangchuchieni82%strongpurifyingselectionEightincludingstoragecatabolismsharedCONCLUSIONS:biologicalwillcontributeelucidationmechanismsColorationCommonScaleSkin

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