New analysis reveals octopus and squid genomes are incredibly strange

(ORDO NEWS) — Cephalopods never cease to amaze with their smart abilities, including brain-powered arms, color-changing camouflage, the art of escape, and puzzle-solving skills.

A new analysis of the genetics of squid, octopuses and cuttlefish (colleoids) has shown that their genomes are as unusual as they are.

The cephalopod genome is “incredibly confusing,” says developmental biologist Caroline Albertine, who led one of two new studies that have revealed strange twists in the cephalopod’s genetic history.

In the course of large-scale work, Albertin and colleagues sequenced the genomes of three soft-bodied cephalopods: the California two-spotted octopus (Octopus bimaculoides) – the first octopus whose genome was sequenced back in 2005; the Atlantic long-finned coastal squid (Doryteuthis pealeii), which has been studied for almost a hundred years as a model system for neurology, and the Hawaiian squid (Euprymna scolopes), a reference animal for studying the symbiosis of bacteria and animals.

New analysis reveals octopus and squid genomes are incredibly strange 1
The Hawaiian bobtail squid uses clusters of its colored genes

The researchers discovered many new families of genes, many of which are expressed in the squid brain, as well as extensions of genes already familiar to us, such as gene clusters involved in changing the color of cephalopods, their suckers and beaks.

Other unique gene extensions include protocadherin genes, which may be involved in the creation of complex nervous systems in both humans and cephalopods. However, in cephalopods, diversity in this gene is created by whole copies (in humans, this variation occurs as a result of different ways of expressing genes).

These copies helped cephalopod genomes get big: the Doryteuthis genome is about 1.5 times larger than ours, and the California two-spotted octopus genome is 90% larger than ours.

Unlike us, our genomes have expanded through whole genome duplication, reflecting our increased complexity and ability to create new evolutionary features. The cephalopods seem to have undergone the same massive change, but like so many other things, they have added their own unique style.

“Now we know that the evolution of soft-bodied cephalopods involved similarly large-scale genome changes, but these changes are not duplication of the entire genome, but rather huge rearrangements of the genome, as if the ancestral genomes were put into a blender,” explains neuroscientist Clifton Ragsdale of University of Chicago.

New analysis reveals octopus and squid genomes are incredibly strange 2
Atlantic longfin coastal squid

Perhaps this genetic shuffling gave these unique marine animals their impressive cognitive abilities, endowing them with the largest nervous system of any invertebrate. Between the arms and the head, octopuses have about 500 million neurons, which is comparable to the number that dogs have.

“We compared the squid genome with the scallop genome and found that many of the genes that were scattered throughout the scallop genome came together at certain regions of the squid chromosomes. These new gene clusters form regulatory units.

This means that they can interact with each other and change animal physiology,” says molecular pathologist Akane Kawaguchi, co-author of a second study that examined the bobtail squid genome in more detail.

“One of the gene clusters in the squid genome contains five major genes involved in the development of the nervous system.”

The clustering of related genes made it possible to streamline and create unique forms of genetic regulation.

New analysis reveals octopus and squid genomes are incredibly strange 3
California two-spotted octopus

And finally, the famous ability of cephalopods to edit their own brain genes. This ability to edit messenger RNA is found in only a few important proteins of the human nervous system, less than 1 percent, but it is much more prevalent in cephalopods.

Usually changes in the structure of an animal occur with mutations in its DNA. But in this case, the changes occur in messenger RNA, which builds proteins.

There is speculation that this ability allows cephalopods to adapt more flexibly and quickly to their environment when a builder can improvise to fit new conditions, but this has not yet been fully established.

Albertin and her team found that RNA editing in animals falls into two distinct categories: neural and non-neuronal editing.

Not only do they occur in different tissues, but the frequency with which editing occurs varies dramatically, with nervous system-related editing occurring much more frequently, suggesting that it is extremely important for the functioning of these animals.

All of these unusual mechanisms have contributed to the creation of the alien intelligence that we all now admire in the 300 million years since the squid and octopus had a common ancestor. We can’t wait to see what else their strange genomes will reveal.

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