Developmental and geographic transcriptomic variation in Anisakis simplex (s. s.) reveals lncRNA-mediated regulation of mRNA expression

Marine nematodes of the genus Anisakis are shaped by complex life cycles and heterogeneous marine environments, yet the molecular basis of their developmental and population differentiation remains poorly understood. Here, we analyzed mRNA and long non-coding RNA expression in third- and fourth-stage larvae of Anisakis simplex (s. s.) collected from the Baltic Sea and the Northeast Atlantic using high-throughput RNA sequencing. Larval development was associated with extensive transcriptional remodeling involving cuticle organization, metabolism, proteolysis, and host-interaction pathways. Comparisons between populations revealed pronounced geographic divergence, including population-specific gene expression and reversal patterns shared across developmental stages. A subset of long non-coding RNAs was linked to the regulation of developmentally and population-biased genes, targeting pathways related to energy metabolism, ion transport, and protein synthesis. These findings demonstrate that developmental progression and geographic origin jointly shape the transcriptomic architecture of Anisakis simplex (s. s.), providing insight into molecular mechanisms underlying parasite adaptation with potential relevance for ecology, evolution, and anisakiasis risk.