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

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.

Keywords: Hi-C; Octopus vulgaris; chromosome-scale; coleoid cephalopods.

Fig. 1.

Octopus vulgaris assembly statistics and quality control. a) A specimen of O. vulgaris. b) A cladogram showing the phylogenetic relationship between the compared species and the family Argonautidae as an outgroup (Taite et al. 2023). Chromosome-scale genome assemblies are available for the starred species (*). c) The snail plot generated using Blobtools2 (Challis et al. 2020) shows that the final version of the chromosome-scale O. vulgaris assembly has N50 of 119 Mb, the longest scaffold is 225 Mb long, and a BUSCO score for complete genes of 86.6% against the mollusca_odb10 database. d) The Hi-C heatmap of the final genome assembly shows 30 chromosome-scale scaffolds with very few sequences in unplaced scaffolds. Photography credit: panel a - © Antonio, Valerio Cirillo (BEOM SZN).

Fig. 2.

Comparative analyses of available chromosome-scale Octopodidae genomes. The figure shows the inferred phylogenetic relationship (Amor et al. 2017; Jiang et al. 2022; Taite et al. 2023) and the inferred divergence times (Amor et al. 2019; Jiang et al. 2022) of four octopus species. The diagrams show genome-genome alignments for each species compared to O. vulgaris.