Time-series transcriptomic analysis of Nile tilapia reveals the crucial roles of long non-coding RNA and transcription factor in response to Aeromonas veronii infection.

Nile tilapia (Oreochromis niloticus) is a vital aquaculture species worldwide, prized for its rapid growth and high productivity. However, the increasing prevalence of Aeromonas veronii infections has led to significant economic losses in the Nile tilapia industry. To elucidate the molecular mechanisms underlying the host immune response, we performed transcriptome sequencing of Nile tilapia spleen tissues at 3, 7, and 10 days post-infection. Furthermore, weighted gene co-expression network analysis was employed to identify key genes and pathways, and a regulatory network was subsequently constructed to elucidate regulatory relationships. Our results revealed that long non-coding RNA (lncRNA) and transcription factor (TF) played crucial roles in responding to A. veronii infection, particularly lncRNA LOC112842004 and TFs TFAP2B and SP2. The differentially expressed targets of these lncRNAs and TFs, along with other differentially expressed mRNAs, were predominantly enriched in immune-related pathways, progressively shifting from upstream genes to downstream genes within pathways as infection advanced. Additionally, specific pathways were activated at each time point, with the MAPK signaling pathway remaining continuously active during infection. These findings enhance our understanding of the molecular mechanisms underlying Nile tilapia's response to A. veronii infection and provide valuable insights for improving disease management strategies in aquaculture.