College of Food Science and Pharmacy, Zhejiang Ocean University, Haida Road 1, New Town, Zhoushan, Zhejiang Province, 316000, China; Zhejiang Marine Development Research Institute, Tiyu Road 10, New Town, Zhoushan, Zhejiang Province, 316000, China.
Zhejiang Marine Development Research Institute, Tiyu Road 10, New Town, Zhoushan, Zhejiang Province, 316000, China.
Fish Shellfish Immunol. 2019 Jan;84:825-833. doi: 10.1016/j.fsi.2018.09.057. Epub 2018 Sep 21.
The black seabream (Sparus macrocephlus) is an economically pivotal aquaculture species cultured in China and Southeast Asian countries. To understand the molecular immune mechanisms underlying the response to Vibrio parahaemolyticus, a comparative gene transcription analysis were performed with utilized fresh livers of V. parahaemolyticus-immunized Sparus macrocephlus with a control group through RNA-Seq technology. A total of 256663 contigs were obtained after excluded the low-quality sequences and assembly. The average length of contigs collected from this research is 1066.93 bp. Furthermore, blast analysis indicates 30747 contigs were annotated based on homology with matches in the NT, NR, gene, and string databases. A gene ontology analysis was employed to classify 21598 genes according to three major functional categories: molecular function, cellular component, and biological process. A total of 14470 genes were discovered in 303 KEGG pathways. RSEM and EdgeR were introduced to estimate 3841 genes significantly different expressed (False Discovery Rate<0.001) which includes 4072 up-regulated genes and 3771 down-regulated genes. A significant enrichment analysis of these differentially expressed genes and isogenes were conducted to reveal the major immune-related pathways which refer to the toll-like receptor, complement, coagulation cascades, and chemokine signaling pathways. In addition, 92175 potential simple sequence repeats (SSRs) and 121912 candidate single nucleotide polymorphisms (SNPs) were detected and identified sequencely in the Sparus macrocephlus liver transcriptome. This research characterized a gene expression pattern for normal and the V. parahaemolyticus -immunized Sparus macrocephlus for the first time and not only sheds new light on the molecular mechanisms underlying the host-V. parahaemolyticus interaction but contribute to facilitate future studies on Sparus macrocephlus gene expression and functional genomics.
黑鲷（Sparus macrocephlus）是中国和东南亚国家经济上关键的水产养殖品种。为了了解黑鲷对副溶血弧菌反应的分子免疫机制，利用 RNA-Seq 技术对副溶血弧菌免疫的黑鲷新鲜肝脏与对照组进行了比较基因转录分析。排除低质量序列和组装后，共获得 256663 个拼接体。本研究中收集的拼接体的平均长度为 1066.93bp。此外，基于与 NT、NR、基因和 string 数据库中的匹配同源性的 Blast 分析表明，有 30747 个拼接体被注释。使用 GO 分析将 21598 个基因根据三个主要功能类别进行分类：分子功能、细胞成分和生物过程。共有 14470 个基因在 303 个 KEGG 途径中被发现。RSEM 和 EdgeR 被引入以估计 3841 个显著差异表达的基因（错误发现率<0.001），其中包括 4072 个上调基因和 3771 个下调基因。对这些差异表达基因和等位基因进行了显著富集分析，以揭示主要的免疫相关途径，这些途径涉及 Toll 样受体、补体、凝血级联和趋化因子信号通路。此外，在黑鲷肝脏转录组中检测和鉴定了 92175 个潜在的简单序列重复（SSR）和 121912 个候选单核苷酸多态性（SNP）。本研究首次对正常和副溶血弧菌免疫的黑鲷进行了基因表达谱描述，不仅为宿主-副溶血弧菌相互作用的分子机制提供了新的见解，而且有助于促进黑鲷基因表达和功能基因组学的未来研究。
