A High-quality Reference Genome and Tissue Expression Atlas for the European Lobster ( Homarus gammarus )

Abstract Homarid lobsters are notable for their remarkable immunity and longevity, with lifespans reaching up to 80 years in the wild. A reference genome is available for the American lobster (Homarus americanus), but not for the European lobster (H. gammarus), despite its ecological significance and importance to fisheries and aquaculture. Here, we present a high-quality genome assembly and annotation for the European lobster. The assembly spans 1.76 Gb, with a scaffold N50 of 1.82 Mb and a BUSCO completeness of 97.6% (96.8% single-copy, 0.8% duplicated). As observed in the American lobster, the total assembly span is substantially smaller than genome size estimates derived from flow cytometry (3.18 to 3.42 Gb). This discrepancy may reflect the highly repetitive nature of decapod genomes, with 51.8% of the European lobster assembly consisting of repetitive elements. Leveraging a comprehensive multi-tissue RNA-seq dataset, we annotated 23,223 protein-coding genes and characterized gene expression across ten tissues to generate a tissue gene expression atlas, available at www.LobsterGeneX.com. Using single-copy orthologues, we estimated a divergence time of 26 Mya between H. gammarus and H. americanus, corresponding to the Oligocene–Miocene boundary. We also identified lobster-specific gene duplications with roles in immunity and longevity, including telomere maintenance. These genomic resources will facilitate future research into lobster biology, supporting sustainable fisheries and aquaculture, while enabling investigations of homarid evolutionary adaptations.