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Zhao YJ, Xiao J, Huangyang MD, Zhao R, Wang Q, Zhang Y, Li JT. Transcriptome sequencing and analysis for the pigmentation of scale and skin in common carp (Cyprinus carpio). Mol Biol Rep 2021; 48:2399-2410. [PMID: 33742327 DOI: 10.1007/s11033-021-06273-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/09/2021] [Indexed: 11/27/2022]
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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Affiliation(s)
- Yu-Jie Zhao
- College of Fisheries and Life, Shanghai Ocean University, Shanghai, 201306, China
- 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
| | - Jun Xiao
- College of Fisheries and Life, Shanghai Ocean University, Shanghai, 201306, China
- 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
| | - Mei-Di Huangyang
- College of Fisheries and Life, Shanghai Ocean University, Shanghai, 201306, China
- 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
| | - 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
| | - 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
| | - 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
| | - 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.
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Li XM, Song YN, Xiao GB, Zhu BH, Xu GC, Sun MY, Xiao J, Mahboob S, Al-Ghanim KA, Sun XW, Li JT. Gene Expression Variations of Red-White Skin Coloration in Common Carp (Cyprinus carpio). Int J Mol Sci 2015; 16:21310-29. [PMID: 26370964 PMCID: PMC4613254 DOI: 10.3390/ijms160921310] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 08/14/2015] [Accepted: 08/25/2015] [Indexed: 01/12/2023] Open
Abstract
Teleosts have more types of chromatophores than other vertebrates and the genetic basis for pigmentation is highly conserved among vertebrates. Therefore, teleosts are important models to study the mechanism of pigmentation. Although functional genes and genetic variations of pigmentation have been studied, the mechanisms of different skin coloration remains poorly understood. The koi strain of common carp has various colors and patterns, making it a good model for studying the genetic basis of pigmentation. We performed RNA-sequencing for red skin and white skin and identified 62 differentially expressed genes (DEGs). Most of them were validated with RT-qPCR. The up-regulated DEGs in red skin were enriched in Kupffer's vesicle development while the up-regulated DEGs in white skin were involved in cytoskeletal protein binding, sarcomere organization and glycogen phosphorylase activity. The distinct enriched activity might be associated with different structures and functions in erythrophores and iridophores. The DNA methylation levels of two selected DEGs inversely correlated with gene expression, indicating the participation of DNA methylation in the coloration. This expression characterization of red-white skin along with the accompanying transcriptome-wide expression data will be a useful resource for further studies of pigment cell biology.
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Affiliation(s)
- Xiao-Min Li
- CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 10014, China.
| | - Ying-Nan Song
- CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 10014, China.
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China.
| | - Gui-Bao Xiao
- CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 10014, China.
| | - Bai-Han Zhu
- CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 10014, China.
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China.
| | - Gui-Cai Xu
- CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 10014, China.
| | - Ming-Yuan Sun
- CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 10014, China.
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China.
| | - Jun Xiao
- CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 10014, China.
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China.
| | - Shahid Mahboob
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia.
| | - Khalid A Al-Ghanim
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia.
| | - Xiao-Wen Sun
- CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 10014, China.
| | - Jiong-Tang Li
- CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 10014, China.
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