title: Gene Expression Variations of Red-White Skin Coloration in Common Carp (Cyprinus carpio).
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.
authors.affiliation: 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. lxm661t@163.com.
authors.forename: Xiao-Min
authors.initials: XM
authors.lastname: Li
authors.affiliation: 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. songyingnan0602@163.com.|College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China. songyingnan0602@163.com.
authors.forename: Ying-Nan
authors.initials: YN
authors.lastname: Song
authors.affiliation: 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. 13269664238@163.com.
authors.forename: Gui-Bao
authors.initials: GB
authors.lastname: Xiao
authors.affiliation: 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. bhzhu@foxmail.com.|College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China. bhzhu@foxmail.com.
authors.forename: Bai-Han
authors.initials: BH
authors.lastname: Zhu
authors.affiliation: 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. iguicai@163.com.
authors.forename: Gui-Cai
authors.initials: GC
authors.lastname: Xu
authors.affiliation: 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. 18853930061@163.com.|College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China. 18853930061@163.com.
authors.forename: Ming-Yuan
authors.initials: MY
authors.lastname: Sun
authors.affiliation: 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. xiaoj_2015@sina.com.|College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China. xiaoj_2015@sina.com.
authors.forename: Jun
authors.initials: J
authors.lastname: Xiao
authors.affiliation: Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia. mushahid@ksu.edu.sa.
authors.forename: Shahid
authors.initials: S
authors.lastname: Mahboob
authors.affiliation: Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia. kghanim@ksu.edu.sa.
authors.forename: Khalid A
authors.initials: KA
authors.lastname: Al-Ghanim
authors.affiliation: 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. sunxw2002@163.com.
authors.forename: Xiao-Wen
authors.initials: XW
authors.lastname: Sun
authors.affiliation: 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. lijt@cafs.ac.cn.
authors.forename: Jiong-Tang
authors.initials: JT
authors.lastname: Li
mesh_terms: D000818:Animals; D002347:Carps / Q000235:genetics*; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D018899:CpG Islands; D019175:DNA Methylation; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D040641:Quantitative Trait Loci; D012880:Skin Pigmentation / Q000235:genetics*; D059467:Transcriptome
keywords: DNA methylation; pigmentation; teleost; transcriptome sequencing