Highly contiguous chromosome-level assembly of the rock goby (Gobius paganellus) genome

The gobies represent the most species-rich family of marine fishes and occupy a remarkable range of ecological niches. Despite their abundance and key role in coastal ecosystems, Mediterranean gobies remain underrepresented in genomic resources. The rock goby (Gobius paganellus), a common inhabitant of rocky intertidal and subtidal habitats throughout the Northeast Atlantic and Mediterranean Sea, exemplifies ecological and physiological resilience to highly variable environments. Here, we present a chromosome-level genome assembly for G. paganellus, generated using a combination of PacBio HiFi and Hi-C sequencing. The final assembly spans 813 Mb, with more than 99.9% of the sequence anchored to 23 pseudochromosomes (Scaffold N50: 36.4 Mb; Contig N50: 20.3 Mb), and shows high completeness, as indicated by a 98.8% BUSCO score. We characterised the genome's repeat landscape and identified 23,493 protein-coding genes, over 96% of which showed homology to known proteins. This high-quality genomic resource provides a foundation for future population genomics-based research into this species and holds the potential to foster comparative genomic analysis across gobies and teleosts more broadly.