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大连海洋大学学报  2023, Vol. 38 Issue (1): 22-31    DOI: 10.16535/j.cnki.dlhyxb.2022-110
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两种单色鲤皮肤转录组特征分析
史东杰, 张强, 伍仕弘, 高坚, 魏东, 张欣, 王赛赛, 孙砚胜, 姜巨峰*, 李文通*, 杨昊坤
1.北京市农林科学院水产科学研究所,北京 100068; 2.农业农村部华北都市农业重点实验室,北京 100097; 3.北京市通州区动物疫病预防控制中心,北京 101101; 4.北京博兴养殖技术有限公司,北京 102615; 5.华中农业大学 水产学院,湖北 武汉 430070; 6.天津农学院 水产学院,天津 300380; 7.天津市水产研究所暨天津市观赏鱼技术工程中心,天津 300221
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
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摘要 为了探究全红鲤(Cyprinus carpio)和全黄鲤的基因资源,采用Illumina Hi-seq测序技术对两种单色鲤的皮肤进行转录组测序,并对差异表达基因进行注释和富集分析。结果表明:对体长为(33.42±0.24)cm的全红鲤和体长为(38.75±0.43)cm的全黄鲤皮肤测序,分别获得干净数据(clean reads)为129 222 850和130 869 572个;与Nr、Nt、COG、GO、KEGG、Pfam和Uniprot数据库中已知基因进行比对,分别有58 782、61 490、11 468、31 206、31 581、61 385和51 805个基因获得注释,7个数据库中均有注释的基因数为8 378个;在全红鲤和全黄鲤皮肤中存在4 822个差异表达基因,其中,显著上调1 929个,显著下调2 893个;取其中9个差异表达基因进行qRT-PCR验证,证实了转录组数据结果的可靠性;在差异表达基因中,筛选获得了部分参与体色调控的基因,包括mitfaednrAwnt7、agoutimif等;KEGG分析发现,差异表达基因极显著富集在甘露糖与果糖代谢、糖酵解/糖原异生途径、碳代谢、磷酸戊糖途径和酪氨酸代谢等43条通路;对酪氨酸代谢和黑色素合成通路分析发现,与红色素和黄色素合成相关的基因mifmif4gagoutiednrAednrB等显著上调,与黑色素合成相关的基因tyrtyrp1、mitfawnt7等显著下调;差异基因变异分析发现,全红鲤和全黄鲤中均存在的单核苷酸多态性标记(SNP)共388 673个。研究表明,两种单色鲤皮肤组织中差异表达基因主要富集在能量代谢、生长和免疫等通路中,获得的转录组信息可为今后锦鲤分子标记的开发及功能基因的克隆、编辑和功能分析等提供基础数据。
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史东杰
张强
伍仕弘
高坚
魏东
张欣
王赛赛
孙砚胜
姜巨峰
李文通
杨昊坤
关键词:    皮肤  转录组  差异表达基因  代谢通路    
Abstract: The transcriptomes of skin were sequenced in two types of monochromatic red common carp (Cyprinus carpio) 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 mitfaednrAwnt7, 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 mifmif4gagoutiednrA and ednrB were significantly upregulated and tyrtyrp1, 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.
Key words:  Cyprinus carpio    skin    transcriptome    differential expressed gene    metabolic pathway
               出版日期:  2023-03-02      发布日期:  2023-03-02      期的出版日期:  2023-03-02
中图分类号:  S 917.4  
基金资助: 北京市农业农村局、北京市财政局、北京市园林绿化局北京市观赏鱼种质创制及品种选育联合攻关项目(G20220628009);北京市财政局北京淡水鱼种质资源保存;北京市财政局、北京市农业农村局“观赏鱼产业技术体系北京市创新团队-育种与繁殖岗位专家”专项资金(BAIC03);天津市财政局、天津市农业农村委天津市海水养殖产业技术体系海水观赏水族岗位项目(ITTMRS2021004);天津市水产研究所观赏鱼创新团队项目(SCYJI201902)
引用本文:    
史东杰, 张强, 伍仕弘, 高坚, 魏东, 张欣, 王赛赛, 孙砚胜, 姜巨峰, 李文通, 杨昊坤. 两种单色鲤皮肤转录组特征分析[J]. 大连海洋大学学报, 2023, 38(1): 22-31.
SHI Dongjie, ZHANG Qiang, WU Shihong, GAO Jian, WEI Dong, ZHANG Xin, WANG Saisai, SUN Yansheng, JIANG Jufeng, LI Wentong, YANG Haokun. Comparative analysis of skin transcriptome of two types of monochrome common carp (Cyprinus carpio). Journal of Dalian Ocean University, 2023, 38(1): 22-31.
链接本文:  
https://xuebao.dlou.edu.cn/CN/10.16535/j.cnki.dlhyxb.2022-110  或          https://xuebao.dlou.edu.cn/CN/Y2023/V38/I1/22
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