PDF(Pubmed)
Abstract：
The tiger pufferfish (Takifugu rubripes), also known as fugu, has recently suffered from severe C. irritans infections under aquaculture environment, yet the underlying immune mechanisms against the parasite remain poorly understood. In this study, we conducted a comprehensive transcriptome analysis of the gill tissue from infected and uninfected fish using PacBio long-read (one pooled sample each for seriously infected and healthy individuals, respectively) and Illumina short-read (three pools for mildly infected, seriously infected, and healthy individuals, respectively) RNA sequencing technologies. After aligning sequence data to fugu\'s reference genome, 47,307 and 34,413 known full-length transcripts were identified and profiled in healthy and infected fish, respectively. Similarly, we identified and profiled 1126 and 803 novel genes that were obtained from healthy and infected fish, respectively. Interestingly, we found a decrease in the number of alternative splicing (AS) events and long non-coding RNAs (lncRNAs) after infection with C. irritans, suggesting that they may be involved in the regulation of the immune response in fugu. There were 687 and 1535 differentially expressed genes (DEGs) in moderately and heavily infected fish, respectively, compared to uninfected fish. Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that immune-related DEGs in the two comparison groups were mainly enriched in cytokine-cytokine receptor interactions, ECM-receptor interactions, T-cell receptor signaling pathways, Th1 and Th2 cell differentiation, and Th17 cell differentiation pathways. Further analysis revealed that a large number of immune-related genes were downregulated in infected fish relative to uninfected ones, such as CCR7, IL7R, TNFRSF21, CD4, COL2A1, FOXP3B, and ITGA8. Our study suggests that C. irritans is potentially a highly efficient parasite that may disrupt the defense mechanisms of fugu against it. In addition, in combination of short-read RNA sequencing and previous genome-wide association analyses, we identified five key genes (NDUFB6, PRELID1, SMOX, SLC25A4, and DENND1B) that might be closely associated with C. irritans resistance. This study not only provides valuable resources of novel genic transcripts for further research, but also provides new insights into the immune mechanisms underlying C. irritans infection response in farmed fugu.
摘要：
虎河豚（Takifugurublopes），也被称为河豚，最近在水产养殖环境下遭受了严重的梭菌感染，然而，针对寄生虫的潜在免疫机制仍然知之甚少。在这项研究中,我们使用PacBiolong-read对感染和未感染鱼类的ill组织进行了全面的转录组分析（每个样本为严重感染和健康个体，分别）和Illumina短阅读（轻度感染的三个池，严重感染,和健康的个体，分别)RNA测序技术。将序列数据与河豚的参考基因组进行比对后，在健康和受感染的鱼类中鉴定和剖析了47,307和34,413个已知的全长转录本，分别。同样，我们鉴定并分析了从健康和受感染的鱼类中获得的1126和803个新基因，分别。有趣的是,我们发现，感染猪链球菌后，可变剪接（AS）事件和长链非编码RNA（lncRNAs）的数量减少，表明它们可能参与河豚免疫反应的调节。在中度和重度感染的鱼类中有687和1535个差异表达基因（DEGs），分别,与未感染的鱼相比。京都基因和基因组百科全书（KEGG）分析表明，两个比较组中的免疫相关DEGs主要富集在细胞因子-细胞因子受体相互作用中，ECM-受体相互作用，T细胞受体信号通路,Th1和Th2细胞分化，和Th17细胞分化途径。进一步分析发现,相对于未感染的鱼类,大量免疫相关基因在感染鱼类中下调,如CCR7、IL7R、TNFRSF21,CD4,COL2A1,FOXP3B,ITGA8我们的研究表明，C.irritans可能是一种高效的寄生虫，可能会破坏河豚的防御机制。此外,结合短读RNA测序和先前的全基因组关联分析，我们确定了五个关键基因(NDUFB6，PRELID1，SMOX，SLC25A4和DENND1B）可能与梭菌耐药性密切相关。本研究不仅为进一步研究提供了新的基因转录本的宝贵资源,而且还提供了对养殖河豚梭菌感染反应的免疫机制的新见解。
