基于转录组测序挖掘仿刺参“化皮病”相关基因  

Identification of genes associated with skin ulceration syndrome in Apostichopus japonicus based on RNA Sequencing

作　　者：杨爱馥[1,2] 周遵春 高杉[1] 孙红娟[1] 潘泳嘉[1] 陈仲 董颖[1] YANG Aifu;ZHOU Zunchun;GAO Shan;SUN Hongjuan;PAN Yongjia;CHEN Zhong;DONG Ying(Key Laboratory of Marine Fishery Molecular Biology of Liaoning Province,Liaoning Ocean and Fisheries Science Research Institute,Dalian 116023,China;Dalian Entry-Exit Inspection and Quarantine Bureau,National Aquatic Product Safety Testing Key Laboratory,Dalian 116600,China)

机构地区：[1]辽宁省海洋水产科学研究院辽宁省海洋水产分子生物学重点实验室,辽宁大连116023 [2]大连出入境检验检疫局国家水产品检测重点实验室,辽宁大连116600

出　　处：《中国水产科学》2018年第3期475-484,共10页Journal of Fishery Sciences of China

基　　金：国家自然科学基金项目(31672688);辽宁省科技计划项目(2015103044);辽宁省自然科学基金项目(2015020786);辽宁省海洋与渔业厅科研项目(201503)

摘　　要：为了寻找仿刺参(Apostichopus japonicus)养殖期间的"化皮病"关键调控基因,并分析这些基因所参与的信号通路,对本课题组前期已获得的仿刺参"化皮"I期(早期)、II期(中期)和III期(后期)3个阶段的病变及其同一个体正常体壁组织之间的差异表达基因(differentially expressed genes,DEGs)进行进一步分析。主成分分析(principal component analysis,PCA)结果显示,"化皮"II期病变组织与正常组织之间的差异最小,"化皮"I期与III期表达关系比较接近,"化皮"II期是一个"转折期"。KEGG富集分析结果显示,补体与凝血级联(Complement and coagulation cascades)通路和细胞外基质受体(ECM-receptor interaction)通路在"化皮"3个阶段都显著改变。通过构建"化皮"过程关键差异表达基因调控网络,发现Ig GFc-binding protein(Fc GBP)基因和Tenascin(TN)蛋白家族基因在"化皮"不同阶段参与到发生显著变化的信号通路。q RT-PCR验证结果显示,5个DEGs在仿刺参"化皮"不同阶段表达趋势与RNA-Seq结果一致,皮尔逊相关系数r值为0.7714。"化皮"过程关键调控基因的筛选将为抗逆品种选育以及"化皮病"的防控提供科学依据。In recent years,diseases caused by bacteria,viruses,and protozoa have severely limited the development of the sea cucumber（Apostichopus japonicus）aquaculture industry.Among such diseases,skin ulceration syndrome（SUS）has become the most universal and serious,owing to its high mortality rates.Therefore,the identification and analysis of key genes associated with＂skin ulceration＂and corresponding signal pathways are important for establishing the molecular mechanism of SUS.We previously analyzed the gene expression and transcriptome of three-stage SUS progression（SUS-I,SUS-II,SUS-III）in A.japonicus that had been challenged by Vibrio splendidus.Here,we further investigated the occurrence of differentially expressed genes（DEGs）among ulcerative and normal body wall（BW）samples from the same individuals at three stages of SUS progression.The R-Bioconductor package（R-2.15.3）was used to perform principal component analysis and Venn diagrams of these DEGs.KEGG enrichment analysis was carried out based on an algorithm（refer to materials and methods 1.2）,using the entire transcriptome set as the background and a cutoff value of Q≤0.05.The regulatory network for SUS progression in A.japonicus was constructed using Cytoscape 3.2.1. PCA analysis indicated that the number of DEGs among the ulcerative and normal BW samples was smallest at SUS stage II and that the gene expression profiles at SUS stages I and III were similar.Venn diagram analysis indicated that the 497,59,and 433 unique DEGs were expressed at stage I,II and III of SUS progression,respectively.Only 28 DEGs were co-expressed in all three stages.KEGG enrichment analysis indicated that the＂Complement and coagulation cascades＂and＂ECM-receptor interaction＂pathways were significantly enriched throughout all three stages of SUS progression.The important SUS-related DEGs,including the Fc GBP and TN family genes,were identified by constructing a regulatory network.Using q RT-PCR,five representative DEGs were selected to validate the

关 键 词：仿刺参 化皮 差异表达基因 调控网络 

分 类 号：S917[农业科学—水产科学]