Squid and octopus genome studies reveal how cephalopods' unique traits evolved

Even the scientists who study them are wonderfully weird. The soft-bodied or coleoid cephalopods have a large nervous system and are known for their dexterous suckers.

Scientists are trying to understand how these animals came to be. They discovered that the genomes of the cephalopods are just as weird as the animals'. Scientists from the Marine Biological Laboratory in Woods Hole, the University of Vienna, the University of Chicago, the Okinawa Institute of Science and Technology, and the University of California, Berkeley have reported their findings in two new studies.

The MBL co-lead author said that large and elaborate brains have evolved a couple of times. The soft-bodied cephalopods are an example of how a large and complicated nervous system can be put together. We can gain insight into the genes that are important in setting up the nervous system, as well as into neuronal function, by understanding the cephalopod genome.

The team analyzed and compared the genomes of two squids and an octopus.

The Grass Foundation funded a tour de force effort to sequence the three cephalopod genomes, which took place over several years in labs around the world.

The co-author of the new work said that the greatest advance in this work is providing chromosomal-level assembly of no less than three cephalopod genomes, all of which are available for study at the MBL.

The genome is less fragmented, which allowed us to better refine what genes are there and what their order is.

The scientists concluded that the evolution of novel traits in soft-bodied cephalopods is mediated by three factors.

• massive reorganization of the cephalopod genome early in evolution
• expansion of particular gene families
• large-scale editing of messenger RNA molecules, especially in nervous system tissues.

Albertin said that the cephalopod genome is incredibly churned up.

The team explored how the reorganized genome in Euprymna scolopes affects the expression of genes. New interactions that may be involved in making many of the novel cephalopod tissues, including their large, elaborate nervous systems, were found by the team.

Albertin said that the genes within the genome have been preserved in many animals. New regulatory elements are driving the expression of genes in this situation. That could create opportunities for novel traits to evolve.

What is striking about the genomes of Cephalopods?

The studies give key insights into the genomes of the cephalopods.

They are large. The human genome is less than half the size of the Doryteuthis genome.

Two rounds of whole-genome duplication are one of the key events in the evolution of humans.

With this new information, we can begin to ask how large-scale genome changes might underlie those key unique features that cephalopods and vertebrates share, specifically their capacity for large bodies with disproportionately large brains.

Surprisingly, they found that the three cephalopod genomes are very different from each other.

Albertin said that it makes sense thatOctopus and squid have different evolutionary histories.

They have novel gene families. The team found hundreds of genes that are unique to the cephalopods. The regulation of the genes appears to be different in the new cephalopod gene families than it is in other animals. The squid brain is one of the unique features of the cephalopod.

Albertin said that the Protocadherin genes are an exciting example of that. This duplication has resulted in a rich framework that may be involved in the independent evolution of large and complex nervous systems.

The genes involved in making the squid's beak or suckers were not found in the octopus. Albertin said that these separate groups of animals are coming up with novel gene families.

Another arrow in the quiver is what RNA editing is about.

The MBL has shown that squid and octopus have high rates ofRNA editing, which diversifies the kinds of proteins that the animals can produce. Albertin and his team looked at the editing rates across the different tissues after they found that there were 26 different tissues in Doryteuthis.

Albertin said that they found a strong signal forRNA editing that changes the sequence of aProtein to be restricted to the nervous system.

This catalog of editing across different tissues gives a resource to ask follow-up questions. Is it happening to help the animal adapt to changes in temperature or other environmental factors? Along with the genome sequence, there is a catalog of editing sites and rates.

Why did these creatures make the cut?

Albertin said that the genome provides an important toolkit for any sort of investigations going forward.

They are.

• The Atlantic longfin inshore squid (Doryteuthis pealeii). Nearly a century of research on this squid at the MBL and elsewhere has revealed fundamental principles of neurotransmission (some discoveries garnering a Nobel Prize). Yet this is the first report of the genome sequence of this well-studied squid (in Albertin et al., funded by the Grass Foundation). Two years ago, an MBL team achieved the first gene knockout in a cephalopod using Doryteuthis pealeii, taking advantage of preliminary genomic sequence data and CRISPr-Cas9 genome editing.
• The Hawaiian bobtail squid (Euprymna scolopes). A glowing bacterium lives inside a unique "light organ" in the squid, to the mutual benefit of both. This species has become a model system for studying animal-bacterial symbiosis and other aspects of development. A draft E. scolopes genome assembly was published in 2019.
• The California two-spot octopus (Octopus bimaculoides). A relative newcomer on the block of scientific research, this was the first octopus genome ever sequenced. Albertin co-led the team that published its draft genome in 2015.

More information: Genome and Transcriptome Mechanisms Driving Cephalopod Evolution, Nature Communications (2022). DOI: 10.1038/s41467-022-29748-w

The emergence of novel cephalopod genes through large-scale genome reorganization was reported by Hannah Schmidbaur and her team. There is a DOI of 10.1038/s41467-022-29694-7.

Journal information: Nature Communications Citation: Squid and octopus genome studies reveal how cephalopods' unique traits evolved (2022, May 4) retrieved 4 May 2022 from https://phys.org/news/2022-05-squid-octopus-genome-reveal-cephalopods.html This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no part may be reproduced without the written permission. The content is provided for information purposes only.