中国水产科学2018，Vol.25Issue(3)：475-484,10.DOI:10.3724/SP.J.1118.2018.17253
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
摘要
Abstract
In recent years, diseases caused by bacteria, viruses, and protozoa have severely limited the develop-ment 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 iden-tification and analysis of key genes associated with "skin ulceration" and corresponding signal pathways are im-portant for establishing the molecular mechanism of SUS. We previously analyzed the gene expression and tran-scriptome 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, respec-tively. Only 28 DEGs were co-expressed in all three stages. KEGG enrichment analysis indicated that the "Com-plement 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 (r) was 0.7714, which con-firmed 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 extracellu-lar matrix glycoproteins which can regulate cell adhesion, migration, proliferation and differentiation. The expres-sion 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 dif-ferent 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.关键词
仿刺参/化皮/差异表达基因/调控网络Key words
Apostichopus japonicus/skin ulceration/differentially expressed gene/regulatory network分类
农业科技引用本文复制引用
杨爱馥,周遵春,高杉,孙红娟,潘泳嘉,陈仲,董颖..基于转录组测序挖掘仿刺参"化皮病"相关基因[J].中国水产科学,2018,25(3):475-484,10.基金项目
国家自然科学基金项目(31672688) （31672688）
辽宁省科技计划项目(2015103044) （2015103044）
辽宁省自然科学基金项目(2015020786) （2015020786）
辽宁省海洋与渔业厅科研项目(201503). （201503）
