Key points are not available for this paper at this time.
Genetic variation alone does not fully explain how marine organisms adapt locally; epigenetic mechanisms such as long non-coding RNAs (lncRNAs) may also contribute. This study explores expression differences associated with differentially expressed lncRNAs (DE-lncRNAs) in Mytilus chilensis from two environmentally contrasting natural seedbeds in the inner sea of Chiloé, Cochamó (41°S) and Yaldad (43°S), through a 91-day reciprocal transplant experiment. Twelve RNA-seq libraries were analyzed using 43011 sequences from the M. chilensis lncRNA database and the chromosome-level whole-genome sequence as references. Differential expression was assessed under the local vs. foreign (δ LF ) and home vs. away (δ HA ) criteria to evaluate lncRNA expression patterns consistent with local adaptation, using progressive significance thresholds (fold change ≥|3–10|, FDR p-value ≤0.05). Marked environmental differences between the two sites, combined with contrasting lncRNA expression profiles in self- and cross-transplanted mussels, highlight the potential contribution of epigenetic regulation to genomic patterns associated with local adaptation. Mussels from Yaldad exhibited more transcripts with extreme fold changes, consistent with greater sensitivity to translocation. Genome mapping linked 183 DE-lncRNAs with nearby protein-coding genes (NPC-genes), mainly lincRNAs, with predicted subcellular localization in cytoplasmic (50.2%) and nuclear (29.5%) compartments. Only five NPC-genes overlapped with previously identified candidate adaptive differentially expressed genes (caDEGs), two of which were associated with immune function and cellular recognition. These findings suggest that lncRNAs may represent a complementary epigenetic layer associated with adaptive responses of M. chilensis under heterogeneous environments and aquaculture-related translocations. This study provides novel insights into the interplay between genetic and epigenetic variation, laying a foundation for future research on the role of lncRNAs in adaptation, conservation, and sustainable resource management.
Yévenes et al. (Wed,) studied this question.