The Hawaiian bobtail squid (Euprymna scolopes) is a model system for studying animal-bacterial symbiosis. Credit: Tom Kleindinst

WOODS HOLE, Mass. – Squid, octopus, and cuttlefish – even to scientists who study them – are wonderfully weird creatures. Known as the soft-bodied or coleoid cephalopods, they have the largest nervous system of any invertebrate, complex behaviors such as instantaneous camouflage, arms studded with dexterous suckers, and other evolutionarily unique traits.

Now, scientists have dug into the cephalopod genome to understand how these unusual animals came to be. Along the way, they discovered cephalopod genomes are as weird as the animals are. Scientists from the Marine Biological Laboratory (MBL) in Woods Hole, the University of Vienna, the University of Chicago, the Okinawa Institute of Science and Technology and the University of California, Berkeley, reported their findings in two new studies in Nature Communications.  

“Large and elaborate brains have evolved a couple of times,” said co-lead author Caroline Albertin, Hibbitt Fellow at the MBL. “One famous example is the vertebrates. The other is the soft-bodied cephalopods, which serve as a separate example for how a large and complicated nervous system can be put together. By understanding the cephalopod genome, we can gain insight into the genes that are important in setting up the nervous system, as well as into neuronal function.”

In Albertin et al., published this week, the team analyzed and compared the genomes of three cephalopod species – two squids (Doryteuthis pealeii and Euprymna scolopes) and an octopus (Octopus bimaculoides).

Sequencing these three cephalopod genomes, never mind comparing them, was a tour de force funded by the Grass Foundation that took place over several years in labs around the world.

“Probably the greatest advance in this new work is providing chromosomal-level assemblies of no less than three cephalopod genomes, all of which are available for study at the MBL,” said co-author Clifton Ragsdale, professor of Neurobiology and of Biology and Anatomy at the University of Chicago.

“Chromosomal-level assemblies allowed us to better refine what genes are there and what their order is, because the genome is less fragmented,” Albertin said. “So now we can start to study the regulatory elements that may be driving expression of these genes.”

In the end, comparing the genomes led the scientists to conclude that evolution of novel traits in soft-bodied cephalopods is mediated, in part, by three factors:

• Massive reorganization of the cephalopod genome early in evolution. Strikingly, the cephalopod genome "is incredibly churned up," Albertin said.
• Expansion of particular gene families.
• Large-scale editing of messenger RNA molecules, especially in nervous system tissues.

“Comparing the gene content of cephalopod chromosomes allowed us to take the first fundamental steps at deciphering the evolution of cephalopod genomes,” said study co-author Hannah Schmidbaur of the University of Vienna.