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

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 from 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.