Background Penaeus monodon is the second most widely cultured marine shrimp species in the global shrimp aquaculture industry. However, the growth of P. monodon production has been constantly impaired by disease outbreaks. Recently, there is a lethal bacterial infection, known as acute hepatopancreatic necrosis disease (AHPND) caused by Vibrio parahaemolyticus AHPND strain (Vp AHPND), which led to mass mortalities in P. monodon. Unfortunately, there is still insufficient knowledge about the underlying immune response of P. monodon upon AHPND infection. The present study aims to provide an insight into the antibacterial immune response elicited by P. monodon hepatopancreas towards AHPND infection. Methods We have employed high-throughput RNA-Seq technology to uncover the transcriptome changes of P. monodon hepatopancreas when challenged with Vp AHPND. The shrimps were challenged with Vp AHPND through immersion method with dissected hepatopancreas samples for the control group (APm-CTL) and treatment group at 3 (APm-T3), 6 (APm-T6), and 24 (APm-T24) hours post-AHPND infection sent for RNA-Seq. The transcriptome de novo assembly and Unigene expression determination were conducted using Trinity, Tgicl, Bowtie2, and RSEM software. The differentially expressed transcripts were functionally annotated mainly through COG, GO, and KEGG databases. Results The sequencing reads generated were filtered to obtain 312.77 Mb clean reads and assembled into 48662 Unigenes. Based on the DEGs pattern identified, it is inferred that the PAMPs carried by Vp AHPND or associated toxins are capable of activating PRRs, which leads to subsequent pathway activation, transcriptional modification, and antibacterial responses (Phagocytosis, AMPs, proPO system). DAMPs are released in response to cell stress or damage to further activate the sequential immune responses. The comprehensive interactions between Vp AHPND, chitin, GbpA, mucin, chitinase, and chitin deacetylase were postulated to be involved in bacterial colonization or antibacterial response. Conclusions The outcomes of this research correlate the different stages of P. monodon immune response to different time points of AHPND infection. This finding supports the development of biomarkers for the detection of early stages of Vp AHPND colonization in P. monodon through host immune expression changes. The potential genes to be utilized as biomarkers include but not limited to C-type lectin, HMGB1, IMD, ALF, serine proteinase, and DSCAM.

中文翻译：

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耐病马达加斯加-马来西亚杂交黑虎虾、斑节对虾肝胰腺对急性肝胰腺坏死病（AHPND）感染的差异转录组分析：免疫基因反应和相互作用的推断。

背景斑节对虾是全球对虾养殖业中第二广泛养殖的海虾品种。然而，斑节对虾产量的增长一直受到疾病爆发的影响。最近，有一种致命的细菌感染，即由副溶血性弧菌 AHPND 菌株 (Vp AHPND) 引起的急性肝胰腺坏死病 (AHPND)，导致斑节对虾大量死亡。不幸的是，关于斑节对虾对 AHPND 感染的潜在免疫反应的知识仍然不足。本研究旨在深入了解斑节对虾肝胰腺对 AHPND 感染引起的抗菌免疫反应。方法 我们采用高通量 RNA-Seq 技术来揭示 P. 当用 Vp AHPND 攻击时斑节节肝胰腺。对照组 (APm-CTL) 和治疗组在术后 3 (APm-T3)、6 (APm-T6) 和 24 (APm-T24) 小时通过浸泡法对虾进行 Vp AHPND 攻击-AHPND 感染发送 RNA-Seq。使用 Trinity、Tgicl、Bowtie2 和 RSEM 软件进行转录组从头组装和 Unigene 表达测定。差异表达的转录本主要通过 COG、GO 和 KEGG 数据库进行功能注释。结果 生成的测序读数经过过滤，得到 312.77 Mb 的干净读数，并组装成 48662 个 Unigene。根据鉴定的 DEGs 模式，推断 Vp AHPND 或相关毒素携带的 PAMPs 能够激活 PRRs，从而导致随后的通路激活，转录修饰和抗菌反应（吞噬作用、AMPs、proPO 系统）。DAMP 响应细胞应激或损伤而释放，以进一步激活连续免疫反应。Vp AHPND、几丁质、GbpA、粘蛋白、几丁质酶和几丁质脱乙酰酶之间的综合相互作用被认为与细菌定植或抗菌反应有关。结论 本研究结果将斑节对虾免疫反应的不同阶段与不同时间点的 AHPND 感染相关联。这一发现支持开发用于通过宿主免疫表达变化检测斑节对虾中 Vp AHPND 定植的早期阶段的生物标志物。可用作生物标志物的潜在基因包括但不限于 C 型凝集素、HMGB1、IMD、ALF、丝氨酸蛋白酶和 DSCAM。