RNA-Seq of shallow-water mussel Mytilus galloprovincialis under in situ hydrostatic pressure exposure

Recent studies reveal the deep sea as a rich biosphere, populated by species descended from shallow-water ancestors following mass extinctions. Research tracing the evolution of genomic DNA reveals how species adapt to deep-sea extremes through specific genomic modifications. However, the role of evolutionarily conserved genes, which are usually essential for key biological processes, in gradual adaptation remains largely unexplored. In this study, by examining the transcriptomic shifts in shallow-water mussels exposed to deep-sea in situ conditions, we found that the adaptation of shallow-water mussels to the deep-sea environment involves a complex interplay of gene expression adjustments, particularly in stress and immune responses, homeostasis, and energy metabolism pathways. Further analysis showed that after long-term deep-sea exposure, the expression profiles of shallow-water mussels closely resemble those of native deep-sea mussels, demonstrating a phenomenon of gene expression convergence in response to adaptive shifts. Co-expression network analysis among deep-sea-exposed shallow-water mussels, native shallow-water, and deep-sea mussels confirmed the critical role of mitochondrial processes and protein quality control in sustaining life under the extreme conditions of the deep sea. Overall, our analyses provide novel insights into adaptive transcriptional regulation and highlight the role of evolutionarily conserved genes in adaptation to extreme environments.