The genome of the vampire squid (Vampyroteuthis sp.) is one of the largest animal genomes, exceeding 10 billion base pairs.
The vampire squid (Vampyroteuthis sp.) is one of the most enigmatic animals of the deep sea. Image credit: Steven Haddock / MBARI.
A ‘living fossil,’ the vampire squid inhabits the deep waters of all the world’s ocean basins at depths from 500 to 3,000 m.
The species is a soft-bodied, passive creature, about the size, shape, and color of a football.
It has a dark red body, huge blue eyes, and a cloak-like web that stretches between its eight arms.
When threatened, the squid turns inside out, exposing rows of wicked-looking ‘cirri.’
While other squid reproduce all at once late in their lives, the vampire squid shows evidence of multiple reproductive cycles.
“Modern cephalopods (coleoids) — including squids, octopuses, and cuttlefish — split more than 300 million years ago into two major lineages: the ten-armed Decapodiformes (squids and cuttlefish) and the eight-armed Octopodiformes (octopuses and the vampire squid),” said Shimane University biologist Masa-aki Yoshida and colleagues.
“Despite its name, the vampire squid has eight arms like an octopus but shares key genomic features with squids and cuttlefish.”
“It occupies an intermediate position between these two lineages — a connection that its genome reveals for the first time at the chromosomal level.”
“Although it belongs to the octopus lineage, it retains elements of a more ancestral, squid-like chromosomal organization, providing new insight into early cephalopod evolution.”
In new research, the authors sequenced the genome of the vampire squid from an individual collected in the West Pacific Ocean.
“At over 11 billion base pairs, the vampire squid genome is roughly four times larger than the human genome, making it the largest cephalopod genome ever analyzed,” they said.
“Despite this size, its chromosomes show a surprisingly conserved structure.”
“Because of this, Vampyroteuthis is considered a ‘genomic living fossil’ — a modern representative of an ancient lineage that preserves key features of its evolutionary past.”
The researchers found that it has preserved parts of a decapodiform-like karyotype while modern octopuses underwent extensive chromosomal fusions and rearrangements during evolution.
This conserved genomic architecture provides new clues to how cephalopod lineages diverged.
“The vampire squid sits right at the interface between octopuses and squids,” said Dr. Oleg Simakov, a researcher at the University of Vienna.
“Its genome reveals deep evolutionary secrets on how two strikingly different lineages could emerge from a shared ancestor.”
By comparing the vampire squid with other sequenced species, including the pelagic octopus Argonauta hians, the scientists were able to trace the direction of chromosomal changes over evolutionary time.
“The genome sequence of Argonauta hians (paper nautilus), a ‘weird’ pelagic octopus whose females secondarily obtained a shell-like calcified structure, was also presented for the first time in our study,” they said.
“The analysis suggests that early coleoids had a squid-like chromosomal organization, which later fused and compacted into the modern octopus genome — a process known as fusion-with-mixing.”
“These irreversible rearrangements likely drove key morphological innovations such as the specialization of arms and the loss of external shells.”
“Although it is classified as an octopus, the vampire squid retains a genetic heritage that predates both lineages,” added Dr. Emese Tóth, a researcher at the University of Vienna.
“It gives us a direct look into the earliest stages of cephalopod evolution.”
“Our study provides the clearest genetic evidence yet that the common ancestor of octopuses and squids was more squid-like than previously thought.”
“It highlights that large-scale chromosomal reorganization, rather than the emergence of new genes, was the main driver behind the remarkable diversity of modern cephalopods.”
The results were published on November 21, 2025 in the journal iScience.
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Masa-aki Yoshida et al. 2025. Giant genome of the vampire squid reveals the derived state of modern octopod karyotypes. iScience 28 (11): 113832; doi: 10.1016/j.isci.2025.113832
