Comparative genomics of Idotea balthica populations: Evolutionary divergence between Mediterranean and Baltic...

Marine isopods play key ecological roles in coastal ecosystems, yet genomic resources for this group remain scarce, limiting our understanding of their evolutionary history and adaptive potential. Here, we present the first de novo whole-genome assembly of the Mediterranean lineage Idotea balthica basteri (Audouin, 1826), generated using Oxford Nanopore long-read sequencing. The final assembly spans ∼477 Mb, with a contig N50 of 19 kb and a BUSCO completeness of 64.4%, representing the first genomic blueprint for a Mediterranean Idotea population. Structural annotation identified approximately 44,000 predicted genes, revealing a complex architecture characterized by distinctive distributions of mono-exonic and multi-exonic genes. Functional annotation based on COG categories highlighted a metabolically active and highly regulated genome, with strong representation of genes involved in amino acid and carbohydrate metabolism, signal transduction, transcriptional regulation, and genome maintenance. The presence of expanded gene families associated with cellulose degradation, detoxification, stress response, and chemosensory perception reflects adaptation to seagrass-dominated habitats and a detritivorous/herbivorous lifestyle. Comparative analyses with the available Baltic I. balthica genome revealed significant differences in genome size, gene content, and functional capacity, consistent with long-term evolutionary divergence between Mediterranean and Northern European populations. Notably, divergent gene architecture and exon-intron organization provide independent genomic support for the existence of a cryptic Mediterranean lineage, reinforcing previous phylogenetic and biogeographic hypotheses. Together, these results indicate that I. balthica basteri represents a distinct evolutionary unit and offer a valuable genomic resource for future studies on isopod evolution, coastal ecosystem functioning, and the impacts of environmental change on marine biodiversity.