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What’s so Striking about Cephalopod Genomes?

Key insights into cephalopod genomes that the studies provide include:

They’re large. The Doryteuthis genome is 1.5 times larger than the human genome, and the octopus genome is 90% the size of a human’s.

They’re 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.”

“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,” Ragsdale said.

Surprisingly, they found the three cephalopod genomes are highly rearranged relative to each other – as well as compared to other animals.

“Octopus and squid diverged from each other around 300 million years ago, so it makes sense that they seem they have very separate evolutionary histories,” Albertin said. “This exciting result suggests that the dramatic rearrangements in cephalopod genomes have produced new gene orders that were important in squid and octopus evolution.”

They contain novel gene families. The team identified hundreds of genes in novel gene families that are unique to cephalopods. While some ancient gene orders common to other animals are preserved in these new cephalopod gene families, the regulation of the genes appears to be very different. Some of these cephalopod-specific gene families are highly expressed in unique cephalopod features, including in the squid brain.

Certain gene families are unusually expanded. “An exciting example of that is the protocadherin genes,” Albertin said. “Cephalopods and vertebrates independently have duplicated their protocadherins, unlike flies and nematodes, which lost this gene family over time. This duplication has resulted in a rich molecular framework that perhaps is involved in the independent evolution of large and complex nervous systems in vertebrates and cephalopods.”

They also found species-specific gene family expansions, such as the genes involved in making the squid’s beak or suckers. “Neither of these gene families were found in the octopus. So, these separate groups of animals are coming up with novel gene families to accomplish their novel biology,” Albertin said.

RNA Editing: Another Arrow in the Quiver to Generate Novelty

Prior research at the ǧ����Ƶ has shown that squid and octopus display an extraordinarily high rate of RNA editing, which diversifies the kinds of proteins that the animals can produce. To follow up on that finding, Albertin et al. sequenced RNA from 26 different tissues in Doryteuthis and looked RNA editing rates across the different tissues.

“We found a very strong signal for RNA editing that changes the sequence of a protein to be restricted to the nervous system, particularly in the brain and in the giant fiber lobe,” Albertin said.

“This catalog of editing across different tissues provides a resource to ask follow-up questions about the effects of the editing. For example, is RNA editing occurring to help the animal adapt to changes in temperature or other environmental factors? Along with the genome sequences, having a catalog of RNA editing sites and rates will greatly facilitate future work.”

Citations

Caroline B. Albertin, Sofia Medina-Ruiz, Therese Mitros, Hannah Schmidbaur et al (2022). Genome and Transcriptome Mechanisms Driving Cephalopod Evolution. Nature Communications, DOI:

Co-authors are from the Marine Biological Laboratory (Caroline Albertin and Joshua Rosenthal), University of California-Berkeley, University of Vienna, Hiroshima University, University of Chicago, Hudson Alpha Institute of Biotechnology, Okinawa Institute for Science and Technology, and Chan-Zuckerberg Biohub.

Hannah Schmidbaur et al. (2022) . Nature Communications, DOI:

Co-authors are from University of Vienna; Research Institute for Molecular Pathology, Vienna; The Frances Crick Institute; The Vienna Zoo; University of Florida; Marine Biological Laboratory; and University of Connecticut.

The Marine Biological Laboratory (MBL) is dedicated to scientific discovery – exploring fundamental biology, understanding marine biodiversity and the environment, and informing the human condition through research and education. Founded in Woods Hole, Massachusetts in 1888, the ǧ����Ƶ is a private, nonprofit institution and an affiliate of the .