The elusive ‘vampire squid from hell‘ has just yielded the largest cephalopod genome ever sequenced, a monster clocking in at more than 11 billion base pairs – more than twice as large as the biggest squid genomes.
Hidden in its mix of A, T, G, and C was a deep evolutionary story. Despite not being an actual squid, Vampyroteuthis infernalis has preserved a surprisingly squid-like chromosomal architecture – a layout shared long ago with the ancestor of modern octopuses and squids.
The vampire squid is a fascinating twig tenaciously hanging onto the cephalopod family tree. It’s neither a squid nor an octopus (nor a vampire), but rather the last, lone remnant of an ancient lineage whose other members have long since vanished.
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It’s considered by many to be a living fossil in some respects, dating back 183 million years or so and retaining many of the traits of its forebears, in addition to the adaptations it needed to make to thrive as a deep-sea scavenger in the dark.
Vestigial traces of body structures and traits the vampire squid shares with squids, octopuses, and cuttlefishes led scientists to believe it might also harbor some genetic information about the mysterious origins of these fascinating creatures, before they all diverged some 300 million years ago.
“The vampire squid sits right at the interface between octopuses and squids,” says genomicist Oleg Simakov of the University of Vienna. “Its genome reveals deep evolutionary secrets on how two strikingly different lineages could emerge from a shared ancestor.”
Although the vampire squid is shy and elusive, living in conditions deeply inhospitable to humans at depths greater than 600 meters (2,000 feet), the researchers were fortunate to obtain a specimen accidentally captured as bycatch by the Tokai University research vessel T/V Hokuto during activities in Suruga Bay.
Sequencing its DNA, they were stunned by the genome’s size of 11 to 14 gigabases. For comparison, the genome of the longfin inshore squid (Doryteuthis pealeii) is 4.4 gigabases, the Hawaiian bobtail squid (Euprymna scolopes) is 4.9 gigabases, and the previous record-holder for the largest known cephalopod genome, the common cuttlefish (Sepia officinalis), is 5.5 gigabases.
Meanwhile, octopus genomes are even smaller, with the genome of the California two-spot octopus (Octopus bimaculoides) at 2.2 gigabases, the East Asian common octopus (Octopus sinensis) at 2.6 gigabases, and the common octopus (Octopus vulgaris) at 2.7 gigabases.
That means the genome of the vampire squid is up to several times larger than the genomes of squids and octopuses.
Interestingly, a massive 62 percent of the genome consists of repetitive elements, stretches of DNA that repeat over and over, inflating its size without adding new coding sequences.
The researchers then compared this vampire squid genome against previously sequenced genomes of other cephalopods, including 10-armed squids and cuttlefish (decapodiformes), eight-armed octopuses (octopodiformes), a nautilus, and a few other mollusks.
They also sequenced the genome of the super-weird muddy argonaut (Argonauta hians), an octopus whose females have an external shell.
These comparisons revealed that, while the vampire squid is an eight-armed ‘octopodiform’, it retains parts of the chromosomal structure of its ten-armed relatives, the decapodiforms. Meanwhile, a study of different octopus genomes revealed that, early on in their evolutionary history, octopuses also had a squid-like chromosomal structure.
Over time, this compacted and fused with the octopus-like chromosomal elements, an irreversible process known as fusion-with-mixing, which may have helped drive specialized octopus adaptations.
This suggests that octopuses underwent an early stage of rapid chromosomal mixing, while the chromosomes of vampire squids remained largely unchanged, even as their genomes ballooned.
These findings position the vampire squid as a potential Rosetta Stone for interpreting and understanding cephalopod evolution.
“The vampire squid retains a genetic heritage that predates both [squid and octopus] lineages,” says genomicist Emese Tóth of the University of Vienna. “It gives us a direct look into the earliest stages of cephalopod evolution.”
The research has been published in iScience.