The cephalopod genomes are as amazing as the animals

The cephalopod genomes are as amazing as the animals ...

Even those who study them are brilliantly weird creatures. These soft-bodied or coleoid cephalopods have the most basic nervous system in any invertebrate, complex behaviors such as instantaneous camouflage, arms studded with dexterous suckers, and other evolutionarily unique traits.

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, have revealed their findings in two new experiments inNature Communications.

According to co-lead authorCaroline Albertin, the MBL''s hibbitt fellow, large and elaborate brains have evolved a couple of times. One famous example is the vertebrates, which use as a separate example for how a large and complex nervous system can be formed. By understanding the cephalopod genome, we can gain insight into the genes that are vital in the formation of the nervous system, as well as into neuronal function.

The group, which was published this week, examined and compared the genomes of three cephalopod species two squids (Doryteuthis pealeiiandEuprymna scolopes) and an octopus (Octopus bimaculoides).

Sequencing these three cephalopod genomes, never mind comparing them, was a tour de force effort created by the Grass Foundation, which took place in labs around the world for over a decade.

According to ProfessorClifton Ragsdale, he has announced that the MBL has provided chromosomal-level assemblies of no less than three cephalopod genomes.

Because the genome is less splintered, Chromosomal-level assemblies helped us better refine what genes are there and what their order is. So now, we may begin to look at the regulatory limitations that might be driving these genes'' expression.

In the end, a genome comparison led the researchers to conclude that the development of novel traits in soft-bodied cephalopods is mediated, in part, 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 the cephalopod genome is quite churned up, most strikingly.

The researchers, according to Schmidbauret al., explored how the highly reorganized genome inEuprymna scolopes affects gene expression. The researchers found that the genome rearrangements entaild new interactions that might be involved in making many of the most novel cephalopod tissues, including their large, intricate nervous systems.

According to Albertin, the genome''s gene order has been preserved over evolutionary time. However, in cephalopods, the genome has experienced a lot of restructuring. This presents an interesting situation: genes are placed in new locations in the genome, with new regulatory elements driving the gene expression. That might provide opportunities for new traits to develop.

Whats so Striking about Cephalopod Genomes?

These research provide key insights into cephalopod genomes, including:

  • Theyre large.TheDoryteuthisgenome is 1.5 times larger than the human genome, and the octopus genome is 90% the size of a humans.
  • Theyre scrambled.Key events in vertebrate evolution, leading to humans, include two rounds of whole-genome duplication, Ragsdale said. With this new work, we now know that the evolution of soft-bodied cephalopods involved similarly massive genome changes, but the changes are not whole-genome duplications but rather immense genome rearrangements, as if the ancestral genomes were put in a blender.

Wecan begin to look into how large-scale genome changes might help define important features that cephalopods and vertebrates share, specifically their ability for large bodies with extremely large brains.

The three cephalopod genomes are quite reorganized compared to each other, although they are quite similar to other animals.

Octopus and squid were divided from one other 300 million years ago, so it makes sense that they appear to have very different evolutionary histories, according to Albertin. This interesting conclusion suggests that the dramatic rearrangements in cephalopod genomes have provided new gene orders that were crucial in squid and octopus evolution.

hundreds of genes in novel gene families that are similar to the cephalopod found in these new gene families have been identified. Although some ancient gene orders common to other animals are preserved in these new gene families, the length of the genes appears to be quite different. Some of these cephalopod-specific genes are often expressed in unique cephalopod features, including in the squid brain.

This is why some gene families are unusually expanded. According to Albertin, the protocadherin genes are a fascinating example of that. In addition, animals and animals have independently replicated their protocadherins, unlike flies and nematodes, who lost this gene family over time. This duplication has resulted in a broad molecular framework that may be involved in the independent evolution of large and complex nervous systems in vertebrates and cephalopods.

Both species were found in the octopus, and neither of these gene families were found. So, these distinct groups of animals are developing novel gene families to fulfill their new biology.

Another Arrow in the Quiver to Generate Novelty is RNA Editing

Prior experiments at the MBL have shown that squid and octopus display an extraordinary rate of RNA editing, which diversifies the kinds of proteins that the animals can produce. In the following experiments, Albertinet al.sequenced RNA from 26 different tissues inDoryteuthisand evaluated RNA editing rates across the different tissues.

Albertin said that we found a very strong signal for RNA editing that allows the sequence of a protein to be restricted to the nervous system, particularly in the brain and in the gigantic fiber lobe.

This selection of transcription services across several tissues provides a space to answer additional questions about the editing''s effects. For example, is it a process of RNA editing to assist the animal adapt to temperature changes or other environmental factors? Along with the genome sequences, a catalog of RNA editing sites and rates will greatly facilitate future work.

Why did these Cephalopods make the cut?Sidebar: Why did these people make the cut?

These three cephalopod species were chosen for research because of their past and future commitment to scientific research. Albertin said the genome is an important toolkit for any kind of investigations.

They are:

  • The Atlantic longfin inshore squid (Doryteuthis pealeii).Nearly a century of researchon 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 Albertinet al.,funded by the Grass Foundation). Two years ago,an MBL team achieved the first gene knockout in a cephalopodusingDoryteuthis 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 draftE. scolopesgenome assembly waspublished 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 thatpublished its draft genomein 2015.

References to the following sections:

et al. Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization. Nat Comms. 2022;13(1):2172. doi: 10.1038/s41467-022-29694-7

et al. Genome and transcriptome factors influencing cephalopod evolution. Nat Comms. 2022;13(1):2427. doi: 10.1038/s41467-022-29748-w.

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