Squid: Also genetically unique – the genome structure of cephalopods is different from that of all other animals

UNIQUE AND MYSTERIOUS: A study reveals that cuttlefish are not only exceptional because of their intelligence and mimicry skills – their genome is fundamentally different from all other animal groups. Thus, the genome of the octopus, squid, and its mates is partly larger than the genome of humans, but it is very differently segmented and synthesized. This unique mosaic of genes may explain some of the squid’s characteristics.

Although cuttlefish are invertebrates, they are not simple – on the contrary: cephalopods have many characteristics that are in no way inferior to those of highly developed mammals. This includes their large lensed eyes, complex nervous system, ability to perform near-perfect simulation, great ability to learn and intelligence – these intelligent marine creatures can even use tools and numbers.

In addition to the ten-armed pygmy squid, squid, and cuttlefish, squids also include eight octopuses such as the Californian octopus (Octopus bimaculoides) shown here. © Tom Kleindienst/Marine Biological Laboratory

More base pairs than human DNA

But how can these invertebrate mollusks reach such a high level of development? Two research teams have now investigated this using genetic analyzes of three different species of squid: an octopus, a ten-armed squid, and a cuttlefish. Analyzes confirmed that these cephalopods have an unusually large genome.

The squid genome contains much more base pairs than those of other mollusks such as mussels or snails and is by far the largest genome of any invertebrate, reports Carolyn Albertin of the Marine Biological Laboratory at Woods Hole and her team. The octopus genome is up to 90 percent the length of the human genome, and the genome of the coastal squid Doryteuthis pealeii is 1.4 times larger than ours.

The genetic distribution is different from all other animals

But even more surprising is the structure of the squid genome. In fact, the genomes of all living things are divided into chromosomes in a very similar way. This basic structure, called synteny, connects all animals over the course of 600 million years of evolution. But cephalopods shy away from this blanket arrangement. Researchers have discovered that genes are arranged and distributed on their chromosomes quite differently from all other animal groups.

“There is a massive restructuring of the genome – as if the original genes had been mashed up in a blender,” explains co-author Clifton Ragsdal of the University of Chicago. As a result, there are more than 500 genetic blocks on the chromosomes of cuttlefish, which are unique in this form in the animal kingdom.

Promote evolution through restructuring?

But what’s interesting is that these gene clusters – the so-called microsyntenia – contain hardly any new genes, but they do contain new sets of genes. Both protein-coding genes and their controls were recombined. “This leads to an interesting situation in which genes acquire new neighbors and come under the influence of new regulatory elements,” Albertine explains.

As such, this reorganization may have given the squid’s ancestors an evolutionary boost that produced many of the animals’ unique traits. Albertine and her colleagues found evidence for this in a family of genes that are primarily active in the nervous system. Cephalopods increased these protocadherins by repeating them in the course of their genetic rearrangement.

“Thus, cephalopods and vertebrates independently transcribed these protocadherins,” Albertin explains. “This resulted in a rich molecular landscape that may have encouraged the parallel development of the large and complex nervous systems in both groups of animals.”

The third squid among the chain squid is the squid Doryteuthis pealeii.© Eileen Bearer

mRNA editing makes protein production more flexible

The cuttlefish genome also has another unique feature: “The amazing feature of the cuttlefish is the extensive editing of messenger RNA by enzymes that convert adenosine bases into inosines,” the researchers report. Scientists have identified such a genetic code change in more than 500,000 code segments in the genome. Although mRNA modifications also occur in vertebrates, they are many times rare.

Highlight: This subsequent modification of the mRNA creation guide that has already been read from DNA can lead to different proteins that can be produced from a genetic code. This expands the functional possibilities of protein synthesis, for example by producing slightly modified proteins in specific tissues or cells despite the same underlying genome. In fact, as Albertine and her colleagues found, this mRNA editing was particularly abundant in squid’s nervous tissue.

Lots of open questions

“This finding now provides the starting point for some questions about the effects of RNA editing,” Albertine says. This mechanism could have facilitated the development of squid’s complex eyes and nervous system, but it could also help them adapt relatively quickly to new environmental conditions.

“Through our research, it is now clear that in order to understand the biology of cephalopods, we must first understand the genetic building blocks of these animals. However, these building blocks appear to be fundamentally different and in many aspects from what we know from other animals,” she says. Hannah Schmidbauer from the University of Vienna. (Nature Communications, 2022; doi: 10.1038/s41467-022-29748-w; doi: 10.1038/s41467-022-29694-7)

Source: Marine Biology Laboratory, University of Vienna

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