Researchers have for the first time decoded the genome of the vampire squid (Vampyroteuthis infernalis), using a Pacific bycatch specimen processed with PacBio sequencing. Published 27 November in iScience, the study finds an 11-billion-base-pair genome—almost four times the size of the human genome—and the largest cephalopod genome sequenced so far. Despite the species sitting within the octopod lineage, its chromosomes retain a squid- and cuttlefish-like arrangement, suggesting a deep ancestral genetic architecture that dates back roughly 300 million years. The result casts the vampire squid as a “living fossil” that preserves genomic features lost or rearranged in other modern octopuses.
- The vampire squid genome is approximately 11 billion base pairs long, nearly four times the human genome and the largest cephalopod genome sequenced to date.
- Sequencing used PacBio long-read technology on a single specimen collected as bycatch in the West Pacific during a research cruise.
- Chromosome structure in Vampyroteuthis mirrors that of squids and cuttlefish, despite its classification within the octopod clade.
- Phylogenetic evidence indicates an ancient split about 300 million years ago between the vampire squid lineage and other modern octopuses and squids.
- Unlike many modern octopuses, which show frequent chromosomal reshuffling, the vampire squid genome preserves a more ancestral chromosome arrangement.
- The species’ rarity and deep-sea habitat mean only one high-quality sample was available, limiting within-species comparative analysis.
Background
Cephalopods (squids, octopuses, cuttlefish and relatives) have long puzzled evolutionary biologists because their body plans and cognitive traits vary widely while the fossil record is sparse. Molecular studies have been central to reconstructing relationships, but gaps remain, especially for deep-sea lineages that are hard to sample. The vampire squid has an unusual mix of traits—eight arms with webbing reminiscent of some octopuses, paired light-producing organs, and a deep-red hue—that confounded early taxonomists who first misclassified it in 1903.
In the mid-20th century scientists established the vampire squid in its own order, Vampyromorphida, distinct from both true octopuses and most squids. That taxonomic isolation, combined with its preference for oxygen-poor mesopelagic and bathypelagic zones, has made it rare in collections and studies. Genomic data have been sparse for deep-sea cephalopods, limiting researchers’ ability to place the vampire squid more precisely on the cephalopod family tree and to infer ancestral genomic states.
Main Event
The research team obtained a tissue sample from a vampire squid recovered as bycatch during a West Pacific research cruise; no additional specimens were available. Using Pacific Biosciences (PacBio) long-read sequencing, they generated a high-contiguity assembly that revealed a genome roughly 11 billion base pairs in length. The assembly and subsequent analyses identified chromosome-scale scaffolds that the authors compared with genomes from other cephalopods including Argonauta hians, Octopus vulgaris and Eledone cirrhosa.
Comparative mapping showed that many chromosomes in the vampire squid align more closely with squid and cuttlefish chromosomes than with those of modern octopuses. Where extant octopuses exhibit frequent intrachromosomal rearrangements and gene shuffling, the vampire squid’s chromosomes appeared to retain an ancestral arrangement. The authors interpret this pattern as evidence that the vampire squid lineage split early from other octopods and has undergone comparatively limited chromosomal reorganization.
The team dates the divergence between the vampire-squid lineage and other cephalopods to roughly 300 million years ago, placing the split in the late Carboniferous to early Permian period. Based on chromosomal synteny and gene content, they suggest the common ancestor of modern squids and octopuses may have had a genome architecture more like the vampire squid’s than like that of present-day octopuses. The paper refers to the species as a ‘living fossil’ in the genomic sense: retaining ancestral features while occupying a modern ecological niche.
Analysis & Implications
The finding that the vampire squid preserves a squid-like chromosomal layout despite its octopod classification has several implications for cephalopod evolution. First, it provides a plausible genomic template for the ancestral condition before the extensive chromosomal reshuffling observed in many modern octopuses. That helps clarify how major genomic reorganizations could underlie the morphological and behavioral novelties in octopus lineages.
Second, the large genome size—11 Gbp—raises questions about the drivers of genome expansion in cephalopods. Repetitive elements, transposable elements, and possible segmental duplications likely contribute to the bulk, but the study’s single-sample design limits inferences about variability in genome size and composition across populations or related species. Understanding whether expansion correlates with life history, deep-sea adaptation, or other ecological factors will require broader sampling.
Third, the preservation of ancestral synteny suggests that certain chromosome arrangements are compatible with extreme deep-sea lifestyles and have been maintained under stabilizing selection or low rates of genomic turnover. Conversely, the genomic dynamism seen in many coastal octopuses may have facilitated the evolution of derived traits such as complex camouflage, neural elaboration, and flexible limb use. This genomic snapshot therefore helps split hypotheses about trait evolution into those driven by structural genome change versus those driven by regulatory or sequence-level modifications.
Comparison & Data
| Species | Genome size (Gbp) | Notes |
|---|---|---|
| Vampyroteuthis infernalis | 11.0 | New assembly; largest cephalopod genome sequenced |
| Homo sapiens | ~3.2 | Human reference genome for scale |
| Octopus vulgaris | ~2.7–3.0* | Modern octopus genomes show chromosomal rearrangement |
The table highlights the striking size of the vampire squid genome relative to humans and to octopus assemblies used in the comparison. The octopus value is an approximate range drawn from published octopus genomes, which tend to be smaller and more rearranged than the vampire squid assembly. Researchers note that genome assembly quality, repeat annotation, and sequencing technology affect reported sizes; long-read methods like PacBio provide improved resolution for repetitive, expanded genomes.
Reactions & Quotes
“It’s a very ancient split; the vampire squid retains a lot of ancestral genome architecture that other octopods have lost,”
Oleg Simakov, lead author, Univ. of Vienna (study correspondence)
Simakov framed the result as evidence that chromosomal conservation in the vampire squid preserves a window into the early cephalopod ancestor. He emphasized the combination of long-read sequencing and comparative chromosomal mapping that made the inference possible.
“The study is nice to have resolved; vamps may be a key to the puzzle because they preserve traits that other lineages have rearranged,”
Bruce Robison, senior scientist, Monterey Bay Aquarium Research Institute (external comment)
Robison, not involved in the study, noted the logistical challenges of studying this species—its solitary habits, rarity, and intolerance of captivity—which make genomic data from any specimen especially valuable.
Unconfirmed
- Whether the single sequenced specimen represents genomic diversity across vampire squid populations remains unconfirmed because no additional high-quality samples were available.
- The functional consequences of the retained chromosome arrangement for physiology or deep-sea adaptation have not been demonstrated and require further experimental work.
- Exact timing and sequence of chromosomal events leading to octopus genomic reshuffling are inferred from comparisons but cannot be pinpointed without more fossil-calibrated molecular data.
Bottom Line
The new vampire squid genome offers a rare genomic snapshot of a deep-sea lineage that appears to have preserved ancestral chromosome structures lost in many modern octopuses. Its 11-billion-base-pair assembly provides a reference point for reconstructing the early genomic architecture of coleoid cephalopods and reframes hypotheses about how chromosomal change contributed to cephalopod innovation.
However, the study rests on a single, hard-won specimen; expanding sampling across individuals and related taxa will be essential to confirm how representative this genome is for the species and its lineage. Still, this work demonstrates the power of long-read sequencing to recover large, complex genomes and underscores the scientific value of rare deep-sea collections.
Sources
- Live Science (news report summarizing iScience study; media)
- University of Vienna (institutional affiliation of study lead author; official)
- Monterey Bay Aquarium Research Institute (MBARI) (independent research institute; external expert comment)
- iScience (peer-reviewed journal where the study was published; publisher)