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Cited by 36Cephalopods and Marine BiologyGenomics and Phylogenetic StudiesChromosomal and Genetic Variations

A chromosome-level reference genome for the common octopus, Octopus vulgaris (Cuvier, 1797)

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Destanović, Dalila, Schultz, Darrin T, Styfhals, Ruth, Cruz, Fernando, Gómez-Garrido, Jèssica, Gut, Marta, Gut, Ivo, Fiorito, Graziano +4 more·2023·G3: Genes, Genomes, Genetics
DOI 10.1093/g3journal/jkad220PMC PMC10700109

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Abstract

Cephalopods are emerging animal models and include iconic species for studying the link between genomic innovations and physiological and behavioral complexities. Coleoid cephalopods possess the largest nervous system among invertebrates, both for cell counts and brain-to-body ratio. Octopus vulgaris has been at the center of a long-standing tradition of research into diverse aspects of cephalopod biology, including behavioral and neural plasticity, learning and memory recall, regeneration, and sophisticated cognition. However, no chromosome-scale genome assembly was available for O. vulgaris to aid in functional studies. To fill this gap, we sequenced and assembled a chromosome-scale genome of the common octopus, O. vulgaris. The final assembly spans 2.8 billion basepairs, 99.34% of which are in 30 chromosome-scale scaffolds. Hi-C heatmaps support a karyotype of 1n = 30 chromosomes. Comparisons with other octopus species' genomes show a conserved octopus karyotype and a pattern of local genome rearrangements between species. This new chromosome-scale genome of O. vulgaris will further facilitate research in all aspects of cephalopod biology, including various forms of plasticity and the neural machinery underlying sophisticated cognition, as well as an understanding of cephalopod evolution.

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Crossref · 10.1093/g3journal/jkad220

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  • Overall genome topology, including TAD organization, shows conservation across distant lineages but does degrade over macroevolutionary time.

    “Preliminary studies suggest that overall genome topology, including TAD organization, shows conservation across distant lineages (124–126) but does degrade over macroevolutionary time (121, 132, 133).”

    From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [125]

    This source is cited for the claim that genome organization degrades over evolutionary time, not for the preceding conservation claim. In Results and discussion, “The octopus karyotype” (page unavailable), the paper reports more chromosomal rearrangements and less collinearity between more distantly related octopus species. That supports a loss of chromosome-scale similarity over time, but the paper does not assess TAD organization or establish that overall genome topology degrades. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

  • Chromosomal rearrangements often occur at TAD boundaries, preserving internal topological structures.

    “Notably, chromosomal rearrangements often occur at TAD boundaries, preserving internal topological structures (125).”

    From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [125]

    The Results and discussion section (‘The octopus karyotype’; page unavailable) describes intrachromosomal rearrangements and conservation of individual chromosomes, but does not address where rearrangements occur relative to TAD boundaries or whether they preserve internal topological structures. Searches for ‘TAD boundaries’ and ‘topologically associating domains’ found no passage addressing that claim. (LLM, conf=0.76)

    Experimental — accuracy not yet measured

  • TAD and lamina-associated domain boundaries are often conserved between species and correspond with breaks of synteny between species, implying that chromosomal inversions that break TADs are selected against.

    “For example, TAD and lamina-associated domain (120) boundaries are often conserved between species and correspond with breaks of synteny between species (124–126), implying that chromosomal inversions that break TADs are selected against.”

    From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [125]

    The Results and discussion section on the octopus karyotype reports chromosomal collinearity and inversions among octopus species, but does not discuss TAD or lamina-associated domain boundaries, their correspondence with synteny breaks, or selection against inversions that disrupt TADs. Searches for those domain and selection terms found no passage addressing the attributed claim. (LLM, conf=0.76)

    Experimental — accuracy not yet measured

  • Many higher-order chromosomal features, including TADs, lamina-associated domains, chromatin loops, and nuclear compartments, are conserved across distantly related species.

    “Many such features are conserved across distantly related species.”

    From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [125]

    In Results and discussion, ‘The octopus karyotype’ (page unavailable), the paper reports homologous chromosomes among compared octopus species, not conservation of TADs, lamina-associated domains, chromatin loops, or nuclear compartments across distantly related species. It says a more-distant species’ genome would be needed even to claim karyotype stasis in octopuses. Searches for the named higher-order features found no passage addressing the claim. (LLM, conf=0.76)

    Experimental — accuracy not yet measured

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Cited by

Sorted by citations

Authors
Destanović, D., Schultz, D. T., Styfhals, R., Cruz, F., Gómez-Garrido, J., Gut, M., Gut, I., Fiorito, G., Simakov, O., Alioto, T. S., Ponte, G., & Seuntjens, E.
Affiliations
  • University of Vienna (AT)
  • Stazione Zoologica Anton Dohrn (IT)
  • Centro Nacional de Análisis Genómico (ES)
  • Centro Nacional de Análisis Genómico (CNAG) , Barcelona 08028 , Spain
  • KU Leuven (BE)
Corresponding author
  • Ponte, Giovanna
  • Seuntjens, Eve
ORCID
Venue
G3: Genes, Genomes, Genetics
Publisher
Oxford University Press (OUP)
Published
2023-10-18
Volume
13
Issue
12
ISSN
2160-1836 (ISSN-L)
DOI
10.1093/g3journal/jkad220
PMC
PMC10700109
OpenAlex
W4387729372
Cited by
36
References
1
Citations by year
2026: 16 · 2025: 11 · 2024: 6 · 2023: 3
FWCI
8.48
Type
journal article
Language
en
Open access
Licence
Locations
  • G3 Genes Genomes Genetics (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Lirias (KU Leuven) (submittedVersion, cc-by)
Funders
  • European Union Research and Innovation Programme (824110, 945026, IDN/20/007, C14/21/065)
  • KU Leuven
Topics
  • Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Cephalopods and Marine Biology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
Keywords
Octopus vulgaris, chromosome-level genome assembly, karyotype, genome rearrangement, neuroplasticity, cephalopod evolution, functional genomics
MeSH terms
Animals, Chromosomes, Nervous System, Genome, Genomics, Octopodiformes

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