Chromosome-scale genome assembly of the European common cuttlefish Sepia officinalis

Coleoid cephalopods, a subclass of mollusks, exhibit remarkable adaptations, including the largest brains among invertebrates, camera-like eyes, and a distinctive embryonic development. They possess an advanced behavioral repertoire including dynamic camouflage. The common cuttlefish Sepia officinalis has served as a key model organism in various research fields, spanning biophysics, neurobiology, behavior, evolution, ecology and biomechanics. More recently, it has become a model to investigate the neural mechanisms underlying cephalopod camouflage, using quantitative behavioral approaches alongside molecular techniques to characterize the identity, evolution and development of neuronal cell types. Despite significant interest in this animal, a high-quality, annotated genome of its species is still lacking. To address this, we sequenced and assembled a chromosome-scale genome for S. officinalis. The final assembly spans 5.68 billion base pairs and comprises 47 repeat-rich chromosomes. Gene linkage analysis confirms the existence of 47 chromosomes, revealing clear homologies with related species such as Euprymna scolopes and Doryteuthis pealeii. Our work includes a comprehensive gene annotation and full-length transcript predictions that should be helpful for further evolutionary and single-cell expression studies. This genome provides a valuable resource for future research on the evolution, brain organization, information processing, development, and behavior in this important clade.