Chromosome-scale genome assembly of the European common cuttlefish Sepia officinalis
4 affiliations
- 1Max Planck Institute for Brain Research, Frankfurt am Main, Germany
- 2Radboud University, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, Netherlands
- 3Faculty of Biological Sciences, Goethe University, Frankfurt am Main, German
- 4Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
Abstract
Coleoid cephalopods, a subclass of mollusks that includes octopuses, cuttlefish and squid, exhibit sophisticated biological features such as dynamic and neurally driven camouflage behavior, inter-individual communication, single-lens camera-like eyes, the largest brains among invertebrates and a distinctive embryonic development. The common cuttlefish Sepia officinalis has served as a 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 this species is still lacking. To address this, we sequenced and assembled a chromosome-scale genome for S. officinalis. Our assembly spans 5.68 billion base pairs and comprises 1n=47 repeat-rich chromosome scaffolds. This was unexpected because the haploid karyotypes of other decapods indicate 46 chromosomes. Detailed comparisons of our data to those from published decapod genome assemblies and to another recent genome assembly of S. officinalis (itself suggesting 1n=49 chromosomes) in fact revealed clear homologies between 46 scaffolds across all the datasets. The discrepancies between datasets are explained by highly repetitive regions, impairing proper read alignments. We conclude that the true karyotype of S. officinalis is probably 1n=46 chromosomes, a likely ancestral and if true, conserved decapod karyotype. Our results include a comprehensive gene annotation and full-length transcript prediction, which we used to characterize orthologous gene families across mollusks. We identified several large-scale expansions specific to cephalopods, with many genes specific to neural or non-neural tissues of adult S. officinalis. In summary, this genome should provide a valuable resource for future research on the evolution, brain organization, information processing, development and behavior in this important clade.
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BibTeX
@article{rencken2026chromosomescale,
title = {{Chromosome-scale genome assembly of the European common cuttlefish Sepia officinalis}},
author = {Simone Daniela Rencken and Georgi Tushev and David Hain and Elena Ciirdaeva and Oleg Simakov and Gilles Laurent},
journal = {eLife},
year = {2026},
month = may,
doi = {10.7554/elife.107393.3},
url = {https://doi.org/10.7554/elife.107393.3},
note = {CC BY},
}
RIS
TY - JOUR
TI - Chromosome-scale genome assembly of the European common cuttlefish Sepia officinalis
AU - Simone Daniela Rencken
AU - Georgi Tushev
AU - David Hain
AU - Elena Ciirdaeva
AU - Oleg Simakov
AU - Gilles Laurent
PY - 2026
DA - 2026/05/19
JO - eLife
DO - 10.7554/elife.107393.3
UR - https://doi.org/10.7554/elife.107393.3
AB - Coleoid cephalopods, a subclass of mollusks that includes octopuses, cuttlefish and squid, exhibit sophisticated biological features such as dynamic and neurally driven camouflage behavior, inter-individual communication, single-lens camera-like eyes, the largest brains among invertebrates and a distinctive embryonic development. The common cuttlefish Sepia officinalis has served as a 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 this species is still lacking. To address this, we sequenced and assembled a chromosome-scale genome for S. officinalis. Our assembly spans 5.68 billion base pairs and comprises 1n=47 repeat-rich chromosome scaffolds. This was unexpected because the haploid karyotypes of other decapods indicate 46 chromosomes. Detailed comparisons of our data to those from published decapod genome assemblies and to another recent genome assembly of S. officinalis (itself suggesting 1n=49 chromosomes) in fact revealed clear homologies between 46 scaffolds across all the datasets. The discrepancies between datasets are explained by highly repetitive regions, impairing proper read alignments. We conclude that the true karyotype of S. officinalis is probably 1n=46 chromosomes, a likely ancestral and if true, conserved decapod karyotype. Our results include a comprehensive gene annotation and full-length transcript prediction, which we used to characterize orthologous gene families across mollusks. We identified several large-scale expansions specific to cephalopods, with many genes specific to neural or non-neural tissues of adult S. officinalis. In summary, this genome should provide a valuable resource for future research on the evolution, brain organization, information processing, development and behavior in this important clade.
SN - 2050-084X
ER -