Ban Yawen, Cui Ting, Zhao Lifei, Li Xue, Bai Qing, Wu Qingfa
Division of Life Sciences and Medicine, Department of Pharmacy, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China.
Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, University of Science and Technology of China, Hefei, China.
Front Microbiol. 2025 Jul 2;16:1643735. doi: 10.3389/fmicb.2025.1643735. eCollection 2025.
Long non-coding RNAs (lncRNAs) are crucial regulators of development and stress responses in eukaryotes, but their roles in non-model insects, particularly rice planthoppers, remain poorly characterized. Here, we present a comprehensive identification and characterization of full-length lncRNAs in the white-backed planthopper (), a major rice pest and efficient vector of Southern rice black-streaked dwarf virus (SRBSDV). By integrating PacBio single-molecule real-time (SMRT) sequencing with publicly available Iso-Seq datasets, we reconstructed a high-confidence, full-length transcriptome and identified 1,211 lncRNAs spanning 1,174 loci. These lncRNAs displayed canonical features, including lower GC content, shorter transcript length, and fewer exons. Unlike mRNAs, which exhibited extensive alternative splicing, only 21 splicing events were detected among lncRNAs. Stage-specific lncRNAs were predominantly expressed during embryogenesis (e.g., 93 transcripts between 0 and 72 h post-oviposition) and molting (e.g., 16 in pre-ecdysis), while sex-biased expression patterns emerged after 24 h. Functional enrichment analysis linked male-biased lncRNAs to metabolic pathways and molting-associated lncRNAs to tissue remodeling processes, including Wnt signaling. Upon SRBSDV infection, approximately 50% of differentially expressed lncRNAs responded to both virus exposure (feeding on infected plants) and confirmed viral replication, exhibiting distinct sex-dimorphic regulation. K-means clustering defined four major expression modules: female-biased (Cluster 1), male-biased (Cluster 2), and two virus-suppressed clusters (Clusters 3 and 4), which were significantly enriched for immune-related pathways such as PI3K-Akt signaling and phagosome formation. We further experimentally validated five sex-independent virus-responsive lncRNAs, , , , and (upregulated), and (downregulated), with predicted involvement in NF-κB signaling, ubiquitin-mediated proteolysis, and metabolic adaptation through AMPK/PPAR pathways. Altogether, this study provides the first full-length lncRNA reference for and reveals the dynamic regulation of lncRNAs across development and in response to viral infection. The identification of sex-specific and conserved virus-responsive lncRNAs offers promising molecular targets for disrupting vector competence and advancing RNAi-based pest management strategies.
长链非编码RNA（lncRNAs）是真核生物发育和应激反应的关键调节因子，但其在非模式昆虫，特别是稻飞虱中的作用仍鲜为人知。在此，我们对白背飞虱（一种主要的水稻害虫和南方水稻黑条矮缩病毒（SRBSDV）的高效传播媒介）中的全长lncRNAs进行了全面鉴定和表征。通过将PacBio单分子实时（SMRT）测序与公开可用的Iso-Seq数据集相结合，我们重建了一个高可信度的全长转录组，并鉴定出跨越1174个位点的1211个lncRNAs。这些lncRNAs具有典型特征，包括较低的GC含量、较短的转录本长度和较少的外显子。与表现出广泛可变剪接的mRNA不同，lncRNAs中仅检测到21个剪接事件。阶段特异性lncRNAs主要在胚胎发育期间（例如，产卵后0至72小时有93个转录本）和蜕皮期间（例如，蜕皮前有16个）表达，而性别偏向的表达模式在24小时后出现。功能富集分析将雄性偏向的lncRNAs与代谢途径联系起来，将蜕皮相关的lncRNAs与包括Wnt信号在内的组织重塑过程联系起来。在感染SRBSDV后，约50%的差异表达lncRNAs对病毒暴露（取食感染植株）和确认的病毒复制均有反应，表现出明显的性别二态性调节。K均值聚类定义了四个主要表达模块：雌性偏向（聚类1）、雄性偏向（聚类2）以及两个病毒抑制聚类（聚类3和聚类4），这些聚类在免疫相关途径如PI3K-Akt信号传导和吞噬体形成方面显著富集。我们进一步通过实验验证了五个不依赖性别的病毒反应性lncRNAs，即、、、（上调）和（下调），预测它们参与NF-κB信号传导、泛素介导的蛋白水解以及通过AMPK/PPAR途径的代谢适应。总之，本研究为白背飞虱提供了首个全长lncRNA参考，并揭示了lncRNAs在发育过程中和对病毒感染反应中的动态调节。性别特异性和保守的病毒反应性lncRNAs的鉴定为破坏传播媒介能力和推进基于RNA干扰的害虫管理策略提供了有前景的分子靶点。
