MicroRNA transcriptome analysis reveals the immune regulatory mechanism of Crassostrea hongkongesis against Vibrio harveyi infection

MicroRNAs (miRNAs) are small non-coding RNA molecules that modulate target-genes expression and play crucial roles in post-transcriptional regulation and immune system regulation. The Hong Kong oyster (Crassostrea hongkongesis), as the main marine aquaculture shellfish in the South China Sea, not only has high economic and ecological value, but also is an ideal model for conducting research on pathogen host interaction. Vibrio harveyi, a Gram negative luminescent marine bacterium, is widely distributed in coastal water environments and can cause large-scale death of C. hongkongesis. However, little in formation is available on the immune regulatory mechanisms of C. hongkongesis infected with V. harveyi. Therefore, we performed microRNA transcriptome analysis for elucidating the immunoregulation mechanism of C. hongkongesis infected with V. harveyi. The results show that a total of 308468208 clean reads and 288371159 clean tags were obtained. 222 differentially expressed miRNAs were identified, of which 121 were up-regulated and 173 were down-regulated. A total of 388 target genes that were differentially expressed and negatively correlated with miRNA expression were predicted by 222 DEmiRs. GO enrichment analysis of 388 DETGs showed that they were mainly enriched in the immune-related term of membrane-bounded vesicle, endocytic vesicle lumen, antigen processing and presentation of exogenous peptide antigen via MHC class I, antigen processing and presentation of peptide antigen via MHC class I, and other immune-related term. KEGG enrichment analysis showed that DETGs were mainly enriched in the Complement and coagulation cascades, Herpes simplex virus 1 infection, Bacterial invasion of epithelial cells, Antigen processing and presentation and NOD-like receptor signaling pathway. The 16 key DEmiRs and their target genes form a regulatory network for seven immune-related pathways. These results suggest that V. harveyi infection induces a complex miRNA response with wide-ranging effects on immune gene expression in the C. hongkongesis. This study explored the immune response of C. hongkongesis to V. harveyi infection at the level of miRNAs, which provides new ideas for the healthy culture and selective breeding of C. hongkongesis.

微小RNA（MicroRNAs，miRNAs）是一类小型非编码RNA分子，可调控靶基因表达，在转录后调控与免疫系统调控中发挥关键作用。香港牡蛎（Crassostrea hongkongesis）是我国南海主要的海水养殖贝类，不仅具有极高的经济与生态价值，同时也是研究病原宿主互作的理想模型。哈维氏弧菌（Vibrio harveyi）是一种革兰氏阴性发光海洋细菌，广泛分布于近海水域环境中，可引发香港牡蛎大规模死亡。然而，目前关于香港牡蛎感染哈维氏弧菌后的免疫调控机制相关研究尚少。为此，本研究开展了微小RNA转录组分析，以解析香港牡蛎感染哈维氏弧菌后的免疫调控机制。研究共获得308468208条清洁读段（clean reads）与288371159条清洁标签（clean tags）；共鉴定得到222个差异表达miRNAs（DEmiRs），其中121个上调表达、173个下调表达。通过这222个差异表达miRNAs，共预测得到388个与miRNA表达呈负相关的差异表达靶基因（DETGs）。对388个差异表达靶基因进行GO富集分析结果显示，其主要富集于膜结合囊泡、内吞囊泡腔、经主要组织相容性复合体（Major Histocompatibility Complex，MHC）I类分子对外源肽抗原的抗原加工与呈递、经MHC I类分子的肽抗原加工与呈递等免疫相关条目。KEGG富集分析结果表明，差异表达靶基因主要富集于补体与凝血级联反应、单纯疱疹病毒1型感染、细菌侵袭上皮细胞、抗原加工与呈递以及NOD样受体信号通路。16个关键差异表达miRNAs与其靶基因共同构成了7条免疫相关通路的调控网络。上述结果表明，哈维氏弧菌感染可引发香港牡蛎复杂的miRNA应答，对其免疫基因表达产生广泛影响。本研究从miRNA层面解析了香港牡蛎对哈维氏弧菌感染的免疫应答，为香港牡蛎的健康养殖与选择性育种提供了新的思路。