Vampire Squid Genome Unlocks Deep Roots of Octopus and Squid Evolution

The deep-sea "vampire squid" (Vampyroteuthis infernalis) has yielded the largest cephalopod genome sequenced to date: an enormous assembly estimated at 11–14 gigabases. Much of that size — roughly 62% — is made up of repetitive DNA, stretches that expand genome length without a proportional increase in protein-coding genes.

What researchers found

Despite its unique position on the cephalopod family tree, the vampire squid retains a surprisingly squid-like chromosomal architecture that appears to predate the split between modern squids and octopuses. Comparative analyses with other cephalopod genomes — including squids, cuttlefish, multiple octopuses, a nautilus and the unusual argonaut (Argonauta hians) — show that early octopus chromosomes once resembled those of ten-armed relatives. Octopuses later underwent extensive chromosomal rearrangements, a process the authors describe as "fusion-with-mixing."

How the study was done

The sequenced specimen was obtained as accidental bycatch by Tokai University’s research vessel T/V Hokuto in Suruga Bay. Vampire squids inhabit dark, deep waters (deeper than 600 meters / ~2,000 feet), so opportunities for fresh specimens are rare. When researchers decoded the DNA, they found the genome far larger than those of many other cephalopods: for context, the longfin inshore squid (Doryteuthis pealeii) is ~4.4 Gb, the Hawaiian bobtail squid (Euprymna scolopes) ~4.9 Gb, the common cuttlefish (Sepia officinalis) ~5.5 Gb, and octopus genomes are typically ~2.2–2.7 Gb.

Evolutionary implications

Because its chromosomes remain largely unchanged while repetitive elements inflated overall genome size, the vampire squid acts as a genomic reference point — a kind of Rosetta Stone — for reconstructing early cephalopod evolution. "The vampire squid sits right at the interface between octopuses and squids," says genomicist Oleg Simakov (University of Vienna). "Its genome reveals deep evolutionary secrets on how two strikingly different lineages could emerge from a shared ancestor."

"The vampire squid retains a genetic heritage that predates both [squid and octopus] lineages," says genomicist Emese Tóth (University of Vienna). "It gives us a direct look into the earliest stages of cephalopod evolution."

The study suggests that octopuses underwent an early, rapid phase of chromosomal compaction and fusion-with-mixing that likely contributed to their distinctive adaptations, while the vampire squid lineage preserved an ancestral chromosome layout even as its genome expanded through repetitive elements.

Why it matters

Understanding how chromosome structure and repetitive DNA shaped cephalopod genomes helps explain how complex traits evolved independently in different lineages. The vampire squid genome gives scientists a new baseline for investigating gene regulation, developmental programs and the evolutionary innovations that produced the remarkable diversity of squids, cuttlefish and octopuses.

The research has been published in the journal iScience.