Abstract

In aquaculture, bacterial pathogens like Francisella noatunensis subsp. noatunensis and Piscirickettsia salmonis significantly impact economic sustainability, causing chronic infections in diverse aquatic environments. Noncoding RNAs (ncRNAs) play crucial roles in bacterial gene regulation, influencing metabolic pathways and stress responses, essential for environmental adaptability. Our comprehensive analysis uncovers a broad spectrum of ncRNAs, both shared across and unique to each pathogen, implicated in essential biological functions such as thiamine biosynthesis, temperature adaptation, and manganese homeostasis. Specifically, the examination of RNA-seq data from the P. salmonis LF-89 strain, representing the LF-89 genogroup, led to the identification of 43 novel trans-small RNAs. This discovery significantly enhances our understanding of the ncRNAmediated regulatory framework within this genogroup. These novel ncRNAs are suggested to play roles in regulating critical cellular processes, including mobile genetic element management and chromosome partitioning, highlighting their potential influence on bacterial virulence and host-pathogen dynamics. Our findings advance the genomic insight into Francisella noatunensis subsp. noatunensis and Piscirickettsia salmonis, offering a foundation for developing targeted interventions. By elucidating ncRNA roles in pathogenicity, this research contributes to creating innovative strategies to mitigate bacterial diseases in aquaculture, enhancing industry sustainability and economic flexibility.