Cephalopod Genome Studies Reveal How Weird They Really Are

Squid, octopus, and cuttlefish are known as soft-bodied or coleoid cephalopods. They have the largest nervous system of any invertebrate, complex behaviors such as instant camouflage, dexterous sucker-studded arms, and other unique evolutionary traits.

Now, an international team of scientists has dug into the cephalopod genome and discovered that it’s just as weird as the animals themselves. These genomes are large, have been scrambled and rearranged dramatically, and contain hundreds of unique genes and exceptionally large gene families.

Their research has been reported in two new studies published in Nature Communication.

In the first studythe team analyzed and compared the genomes of three species of cephalopods – two squids (Doryteuthis pealeii and Scolopes of Euprymna) and an octopus (bimaculoid octopus). The exploit lasted several years and involved laboratories all over the world.

“Big and elaborate brains have evolved multiple times,” says co-lead author Caroline Albertin, Hibbitt Fellow at the Marine Biology Laboratory (MBL) in the US. “A famous example is that of the vertebrates.

“Another is the soft-bodied cephalopods, which serve as a distinct example of how a large and complicated nervous system can be put together,” she adds. “By understanding the cephalopod genome, we can better understand the genes that are important in the establishment of the nervous system, as well as in neuronal function.”

California two-spotted octopuses (bimaculoid octopus) emerging from their egg envelopes. Credit: Caroline Albertin/ Marine Biology Laboratory

What’s so striking about cephalopod genomes?

For starters, these genomes are really big. the Doryteuthis The genome is 1.5 times larger than the human genome, and the octopus genome is 90% the size of a human.

The team identified hundreds of genes in new gene families that are unique to these organisms, and some of them are highly expressed in unique cephalopod features, including in the squid brain.

Other gene families are exceptionally extended (when there are additional gene copies), such as the genes of protocadherins. These are call-adhesion molecules expressed primarily in the nervous system which appear to be involved in both development and functioning of the nervous system.

“Cephalopods and vertebrates independently duplicated their protocadherins, unlike flies and nematodes, which lost this gene family over time,” Albertin explains. “This duplication resulted in a rich molecular framework that is possibly involved in the independent evolution of large and complex nervous systems in vertebrates and cephalopods.”

They also followed previous research which showed that squid and octopus exhibited an extraordinary high rate of RNA editing – editing of messenger RNAs carrying instructions from DNA to control protein synthesis.

RNA editing diversifies the types of proteins the animal can produce, and they found in Doryteuthis that this phenomenon is limited to the nervous system.

Atlantic coastal squid, Doryteuthis pealeiihas been studied for nearly a century by scientists as a model system for neuroscience research.

But the most striking thing, according to Albertin, is that the cephalopod genome “is incredibly mixed”.

As if the ancestral genomes were put in a blender, the three cephalopod genomes have seen immense genome rearrangements and are highly rearranged relative to each other (as well as relative to other animals).

“In many animals, the order of genes within the genome has been preserved during evolution,” says Albertin. “But in cephalopods, the genome has gone through periods of restructuring.

“This presents an interesting situation: genes are placed in new locations in the genome, with new regulatory elements that drive gene expression. This could create opportunities for new traits to evolve.

In a second studypublished last week, the team explored how the highly rearranged genome in Scolopes of Euprymna affects gene expression. They found that the genome rearrangements lead to new genetic interactions that may be involved in making many new tissues of cephalopods, including their large, elaborate nervous systems.