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

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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.

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Data availability

The raw RNA sequencing data were deposited in NCBI SRA database (BioProject: PRJEB19194). The updated common carp genes were deposited at DDBJ/EMBL/GenBank under the accession of GFWU00000000. The protein sequences, GO terms, and gtf file were available at figshare (https://figshare.com/s/d34e4ad1ba113c9b4b09, https://figshare.com/s/150a49fc5f62522199b7, and https://figshare.com/s/e5faf21db6bfbba16a34).

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Acknowledgements

This study is supported by National Natural Science Foundation of China (31672644) and the Special Scientific Research Funds for Central Non-profit Institutes, Chinese Academy of Fishery Sciences (2020XT0103 and 2020TD24).

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Authors and Affiliations

  1. College of Fisheries and Life, Shanghai Ocean University, Shanghai, 201306, China

    Yu-Jie Zhao, Jun Xiao & Mei-Di Huangyang

  2. 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

    Yu-Jie Zhao, Jun Xiao, Mei-Di Huangyang, Ran Zhao, Qi Wang, Yan Zhang & Jiong-Tang Li

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  1. Yu-Jie Zhao
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Contributions

JLT conceived and designed the study and all the experiments. YJZ and JX performed the experiments and collected all data. YJZ and JX analyzed the data. JLT and YJZ wrote the manuscript. YJZ, MDHY and RZ edited the figures and tables. QW and YZ participated in discussion. All authors read and approved the final manuscript.

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Correspondence to Jiong-Tang Li.

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The authors declare that there are no conflicts of interest.

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Use of all these samples was approved by the Institutional Animal Care and Use Committee of Key Laboratory of Aquatic Genomics, Chinese Academy of Fishery Science (Animal Ethics No. IACUC-201501).

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Zhao, YJ., Xiao, J., Huangyang, MD. et al. Transcriptome sequencing and analysis for the pigmentation of scale and skin in common carp (Cyprinus carpio). Mol Biol Rep 48, 2399–2410 (2021). https://doi.org/10.1007/s11033-021-06273-5

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