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

Abstract

PDF HTML阅读 XML下载 导出引用 引用提醒 基于转录组测序挖掘仿刺参“化皮病”相关基因 DOI: 作者: 作者单位: 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 作者简介: 杨爱馥(1978-),女,副研究员,博士,研究方向为海洋生物技术.E-mail:yangaifu@sohu.com 通讯作者: 中图分类号: S917 基金项目: 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）. Identification of genes associated with skin ulceration syndrome in Apostichopus japonicus based on RNA Sequencing Author: Affiliation: 1. Key Laboratory of Marine Fishery Molecular Biology of Liaoning Province, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China;2. Dalian Entry-Exit Inspection and Quarantine Bureau, National Aquatic Product Safety Testing Key Laboratory, Dalian 116600, China Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:为了寻找仿刺参（）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IgGFc-binding protein （FcGBP）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。qRT-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。 Abstract:In recent years, diseases caused by bacteria, viruses, and protozoa have severely limited the development of the sea cucumber () 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 . 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 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 FcGBP and TN family genes, were identified by constructing a regulatory network. Using qRT-PCR, five representative DEGs were selected to validate the sequencing results. The Pearson's correlation coefficient () was 0.7714, which confirmed the consistency and accuracy of the two approaches.In sea cucumbers, SUS is characterized by apparent white skin ulcers, as well as by complicated molecular regulation. The significantly affected signal pathways detected among the ulcerative and normal BW in the same individuals at three stages of SUS progression, such as the "Focal adhesion" and "ECM-receptor interaction" pathways, have also been observed in the ulcerative BW of SUS-affected individuals (including SUS stages I, Ⅱ, and Ⅲ), when compared to healthy individuals in our previous studies. The FcGBP gene involved in these two pathways was worthy of further exploration. FcGBP is an Fc fragment of the IgG binding protein in fluids secreted by cells of the stomach and intestinal mucosa layer and might play a role in cell protection and anti-inflammation. FcGBP was up-regulated in crypts of early stage ulcerative colitis in human. In addition, Tenascins are extracellular matrix glycoproteins which can regulate cell adhesion, migration, proliferation and differentiation. The expression of the Aj-TN gene changed significantly during the process of extracellular matrix remodeling during sea cucumber regeneration. In human disease studies, TN proteins are associated with tumor metastasis, skin wound healing, and ulcer healing. The expression of TN-family genes in ulcerative and normal BW was significantly different during SUS progression, which suggests that these genes play important roles in the onset and development of SUS in sea cucumber. These results will be useful in developing strategies for preventing bacterial SUS in sea cucumber. 参考文献 相似文献 引证文献