Comparative analysis of skin transcriptome of two types of monochrome common carp (Cyprinus carpio)
SHI Dongjie, ZHANG Qiang, WU Shihong, GAO Jian, WEI Dong, ZHANG Xin, WANG Saisai, SUN Yansheng, JIANG Jufeng*, LI Wentong*, YANG Haokun
1.Fisheries Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100068, China; 2.Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture and Rural Affairs, Beijing 100097, China; 3.Beijing Tongzhou District Animal Epidemic Disease Prevention and Control Center, Beijing 101101, China; 4.Beijing Boxing Breeding Technology Limited Company, Beijing 102615,China; 5.College of Fisheries, Huazhong Agricultural University, Wuhan 430070,China; 6.College of Fisheries, Tianjin Agricultural University, Tianjin 300380,China; 7.Tianjin Ornamental Fish Technology and Engineering Centre, Tianjin Fisheries Research Institute, Tianjin 300221, China
Abstract: The transcriptomes of skin were sequenced in two types of monochromatic red common carp (Cyprinuscarpio) with body length of (33.42 ±0.24) cm and yellow common carp with body length of (38.75±0.43) cm using Illumina Hi-seq sequencing technology, and differentially expressed genes were identified and selected for analysis in order to investigate the genetic resources of whole red and yellow common carp. The results showed that 129 222 850 clean reads were obtained in whole red and 130 869 572 in whole yellow common carp. Comparison with known genes 58 782 genes were annotated in the Nr, 61 490 in Nt, 11 468 in COG, 31 206 in GO, 31 581 in KEGG, 61 385 in Pfam and 51 805 in Uniprot databases, with 8 378 genes annotated in all seven databases. There were 4 822 differentially expressed genes in skins of whole red and yellow common carp, with 1 929 significantly up-regulated and 2 893 significantly down-regulated. Further clustering analysis of differentially expressed genes revealed similar patterns of high and low expression of differentially expressed genes in both skin samples. The reliability of transcriptome data results was confirmed by qRT-PCR validation of 9 differentially expressed genes, in which some genes found here were involved in body color regulation, such as mitfa, ednrA, wnt7, agouti and mif. KEGG analysis revealed that differential genes were significantly enriched in 43 pathways, including mannose and fructose metabolism, glycolysis/gluconeogenesis, carbon metabolism, pentose phosphate pathway and tyrosine metabolism. The analysis of tyrosine metabolism and melanin synthesis pathways showed that mif, mif4g, agouti, ednrA and ednrB were significantly upregulated and tyr, tyrp1, mitfa and wnt7 were significantly downregulated in genes related to red and yellow pigment synthesis. Analysis of differential genetic variation indicated a total of 388 673 single nucleotide polymorphism (SNP) markers in both whole red and whole yellow common carp. The findings indicated that the differentially expressed genes in the skin tissues of two monochromatic common carp were primarily enriched in energy metabolism, growth, and immunity pathways. The transcriptome data obtained can be used to develop molecular markers as well as cloning, editing, and functional analysis of functional genes in koi.