Epigenetic variation mediated by lncRNAs accounts for adaptive genomic differentiation of the endemic blue mussel Mytilus chilensis

Epigenetic variation affects gene expression without altering the underlying DNA sequence of genes controlling ecologically relevant phenotypes through different mechanisms, one of which is long non-coding RNAs (lncRNAs). This study identified and evaluated the gene expression of lncRNAs in the gill and mantle tissues of Mytilus chilensis individuals from two ecologically different sites: Cocham ' o (41 degrees S) and Yaldad (43 degrees S), southern Chile, both impacted by climaticrelated conditions and by mussel farming given their use as seedbeds. Sequences identified as lncRNAs exhibited tissue-specific differences, mapping to 3.54 % of the gill transcriptome and 1.96 % of the mantle transcriptome, representing an average of 2.76 % of the whole transcriptome. Using a high fold change value (>=|100|), we identified 43 and 47 differentially expressed lncRNAs (DE-lncRNAs) in the gill and mantle tissue of individuals sampled from Cocham ' o and 21 and 17 in the gill and mantle tissue of individuals sampled from Yaldad. Location-specific DE-lncRNAs were also detected in Cocham ' o (65) and Yaldad (94) samples. Via analysis of the differential expression of neighboring protein-coding genes, we identified enriched GO terms related to metabolic, genetic, and environmental information processing and immune system functions, reflecting how the impact of local ecological conditions may influence the M. chilensis (epi)genome expression. These DE-lncRNAs represent complementary biomarkers to DNA sequence variation for maintaining adaptive differences and phenotypic plasticity to cope with natural and human-driven perturbations.