Ixodes ricinus ticks are distributed across Europe and are a vector of tick-borne diseases. Although I. ricinus transcriptome studies have focused exclusively on protein coding genes, the last decade witnessed a strong increase in long non-coding RNA (lncRNA) research and characterization. Here, we report for the first time an exhaustive analysis of these non-coding molecules in I. ricinus based on 131 RNA-seq datasets from three different BioProjects. Using this data, we obtained a consensus set of lncRNAs and showed that lncRNA expression is stable among different studies. While the length distribution of lncRNAs from the individual data sets is biased toward short length values, implying the existence of technical artefacts, the consensus lncRNAs show a more homogeneous distribution emphasizing the importance to incorporate data from different sources to generate a solid reference set of lncRNAs. KEGG enrichment analysis of host miRNAs putatively targeting lncRNAs upregulated upon feeding showed that these miRNAs are involved in several relevant functions for the tick-host interaction. The possibility that at least some tick lncRNAs act as host miRNA sponges was further explored by identifying lncRNAs with many target regions for a given host miRNA or sets of host miRNAs that consistently target lncRNAs together. Overall, our findings suggest that lncRNAs that may act as sponges have diverse biological roles related to the tick–host interaction in different tissues.

Ticks are ectoparasites that modulate host responses to sustain prolonged blood feeding, and in Ixodes ricinus , salivary microRNAs (miRNAs) represent promising candidates for manipulating host gene expression. Using phylogenetic footprinting combined with cooperative targeting analysis, we predicted deeply conserved miRNA–mRNA interactions that appear to contribute to tick lifecycle completion and tick’s ability to parasitize diverse vertebrate hosts. Our analysis suggests that conserved tick miRNAs may mimic host miRNAs by exploiting shared target sites on host transcripts, potentially influencing regulatory circuits active during tick feeding and cross-kingdom communication. We identified 12 core tick salivary miRNAs—highly expressed and enriched in conserved target sites—predicted to cooperatively target 22 human genes, several of which are associated with processes relevant to parasitism establishment. These predicted cooperative interactions involve hub genes such as PDGFRA and NRG1, which are components of MAPK and PI3K–AKT pathways that regulate immune defense, tissue repair, and sensory responses. Our results suggest that I. ricinus miRNAs could potentially influence host homeostasis through cooperative targeting mechanisms, and they introduce a broadly applicable framework that leverages evolutionary conservation to detect meaningful cross-species miRNA–mRNA interactions.