Population-level transcriptomic datasets from two benthic invertebrates exposed to long-term experimental warming and acidification

Ocean warming and acidification are major drivers of change in marine ecosystems, with particularly strong impacts on low-mobility benthic organisms. Despite their ecological importance, genomic and transcriptomic resources for sponges (Phylum: Porifera) and marine gastropods (Phylum Mollusca) that capture responses to long-term, combined climate stressors and population-level variability remain limited. Herein, we present population-level RNA-seq datasets from the sponge Chondrilla nucula and the gastropod Hexaplex trunculus , collected from northern and southern Aegean Sea (Eastern Mediterranean) populations and exposed for three months to elevated temperature and reduced pH in a common garden experiment simulating near-future climate change conditions. The datasets comprise high-quality paired-end Illumina reads, a complete de novo transcriptome assembly for C. nucula , and genome-guided alignments for H. trunculus . These datasets provide a valuable resource for investigating transcriptional plasticity and climate change resilience in benthic marine invertebrates.