Long noncoding RNAs: Unexplored players in the drug response of the sea louse Caligus rogercresseyi

Long non-coding RNAs (lncRNAs), endogenous RNAs with restricted or null coding potential, are emerging as key regulators of multiple biological processes in several species. Despite the importance of these transcripts, few studies have characterized marine crustacean lncRNAs or the modulation of these in response to chemical exposure. Therefore, the present study mainly focused on identifying lncRNAs in the sea louse Caligus rogercresseyi, an ectoparasite of primary concern to the Chilean salmon industry. A bioinformatics pipeline for lncRNAs discovery was designed, revealing 1835 putative lncRNA sequences in the C. rogercresseyi transcriptome. Furthermore, C. rogercresseyi lncRNAs evidenced features classical of lncRNAs, such as lower values of GC content, length, transcription activity, and minimum free energy as compared with coding transcripts. Furthermore, since developed resistance against delousing drugs is a major threat to the management and control of sea lice, the transcriptional modulation of C. rogercresseyi lncRNAs during exposure to delousing drugs was also evaluated. Unlike coding transcripts, lncRNAs were mainly downregulated after exposure to either deltamethrin or azamethiphos, showing transcription patterns similar to other, better studied non-coding RNAs in arthropods. Finally, a subset of lncRNAs exhibited a strong transcriptional correlation to genes commonly associated with the drug response, such as ABC transporters, cytochrome p450, and glutathione S-transferase, among others. Our findings provide one of the first comprehensive lncRNA characterizations in a crustacean, contributing towards understandings on the regulatory role of lncRNAs during the drug response in Caligus rogercresseyi.