Characterization of ceRNA framework in the spleen of Chinese soft-shelled turtle (Pelodiscus sinensis) responding to Aeromonas hydrophila infection.

Non-coding RNAs (ncRNAs) have emerged as critical regulators of host immune responses against pathogen infection in aquatic animals, yet their roles in reptiles remain largely unexplored. Herein, we investigated the splenic ncRNA expression profiles of Chinese soft-shelled turtles (Pelodiscus sinensis) following Aeromonas hydrophila infection. Histopathological analysis at 24 h post infection revealed severe splenic lesions, including the obscure red-white pulp demarcation, lymphocyte infiltration, necrosis, and increased melano-macrophages. Transcriptome sequencing identified 843 differentially expressed (DE) mRNAs (DEmRNAs), 108 DE microRNA, 87 DE lncRNAs, and 341 DE circRNAs. Competing endogenous RNA (ceRNA) networks were constructed with these DE RNAs, yielding 253 lncRNA-miRNA-mRNA and 436 circRNA-miRNA-mRNA triplets. Hub nodes showed mRNA LOC102455872 (degree = 10), lncRNAs MSTRG.3526.7 and MSTRG.8091.1 (degree = 10), circRNA novel-circ-026391 (degree = 12), and miRNA novel-m0923-3p (degree = 7) had the large connectivity of network. Functional enrichment revealed four pathways commonly involved in both networks, including MAPK signaling, cell adhesion molecules, notch signaling, and tryptophan metabolism. Notably, tryptophan metabolism and MAPK signaling contained the large hub RNAs, suggesting they served as critical bridges of ceRNA networks. This study described the first comprehensive ceRNA networks in a reptile following bacterial infection and identified novel ncRNAs serving as critical regulators in turtles defending against A. hydrophila.