Sequencing the Genome of the Ocean’s Weirdest Creatures

Octopus bimaculoides, one of the species being studied by the CephSeq Consortium

Octopus bimaculoides, one of the species being studied by the CephSeq Consortium

Cephalopods—ocean-dwelling mollusks such as the octopus, squid, cuttlefish, and Nautilus—are ancient and complex creatures. They evoke our primal fascination with mysterious creatures of the sea, with weird and wonderful features like prehensile arms that can regenerate when amputated, huge, vertebrate-like eyes, jet-propulsion systems to help swim by squirting water, and special organs to change skin color to match their environments. The giant squid is so mysterious and elusive that researchers made big news recently when they captured video of one in its natural habitat off the coast of Japan.

Cephalopods are worth studying for the novelty alone, but they also have highly developed brains and nervous systems that provide excellent models for the study of basic neuroscience. An understanding of the genetics underlying their unique features would have applications across many areas of science, from neurobiology to materials science and bioengineering. A group of scientists from around the world recently formed a consortium to tackle this project and assemble complete genomes of ten different cephalopod species.

In May 2012, researchers from nine countries met at Duke University to discuss the need for genome sequencing of cephalopods. They formed the Cephalopod Sequencing—or CephSeq—Consortium, to develop strategies and identify representative species. The group recently published a whitepaper in Standards in Genomic Sciences outlining their plan. They selected 10 species of squid, octopus, and the Nautilus that were representative of the group or had some kind of unique adaptive features worth studying.

There’s one big hurdle at the beginning, though: Even after an explosion of advanced sequencing technology, no one has assembled a complete reference genome for any cephalopod species. This wouldn’t be such a big deal if they weren’t so weird, but on an evolutionary scale, cephalopods are very far away from any other creatures scientists have studied, even other mollusks such as snails and oysters.

Clifton Ragsdale, PhD, professor of neurobiology, is one of the founders of the CephSeq Consortium and chair of its steering committee. He acknowledged that cephalopod researchers are at square one when it comes to this kind of genetic analysis, but the project will build momentum. “Once there’s a good assembly of one of the genomes, then the others will be much easier,” he said.

Ragsdale and Carrie Albertin, a PhD candidate in his lab, are working specifically on the genome for Octopus bimaculoides, a small, brown octopus found in the Pacific off the coast of California and Mexico. Their contribution to the project will be sequencing and assembling transcriptomes for the octopus, which will yield a complete set of mRNA, or the protein coding genes, expressed in target tissues. Albertin has isolated 19 different tissues from various embryonic stages, brain tissue and glands of the octopus, which will then be sequenced at the University of Chicago Genomics Facility, a shared, high-performance computing center on campus. The University of Chicago Center for Research Informatics will support the bioinformatics computing analysis.

Ragsdale said having this kind of technical horsepower a short walk from the lab is a tremendous advantage to working at the University of Chicago.

“For researchers it’s great. We could probably send our samples off somewhere else, but we wouldn’t be able to have face to face meetings to discuss things,” he said. “Having it on campus means the person having the sequencing done can walk over there and have a talk with the technical director and his staff. That makes a huge difference, and it’s gotten strong enough now that lots of outside groups are sending their sequences here.”

Studying cephalopods at a molecular and genetic level has broad applications for both medical science and technology. For instance, the octopus famously can regenerate its arms if they’re amputated. This is a neat trick, but the tentacles are also very complex. They have large nerves running down them that, if you take all eight of them together, have more neurons than its brain. Regenerating an arm means not just regenerating skin and muscle, but this complicated nervous system as well. Learning more about how they do this could provide insight into regenerative medicine for humans.

Materials scientists who study biology for clues on solving engineering problems are also very interested in how cephalopods use different organs and proteins to change their skin color. And of course, learning more about the animals themselves will help researchers understand how cephalopods are responding to environmental change and overfishing.

Ragsdale said the CephSeq Consortium is a unique opportunity because it can lead to so many unexpected insights.

“You can never quite tell when you do this basic research when it’s going to lead somewhere exciting, but cephalopod research certainly has for neurophysiology, and for materials science,” he said.

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Albertin, C., Bonnaud, L., Brown, C., Crookes-Goodson, W., da Fonseca, R., Di Cristo, C., Dilkes, B., Edsinger-Gonzales, E., Freeman, R., Hanlon, R., Koenig, K., Lindgren, A., Martindale, M., Minx, P., Moroz, L., Nödl, M., Nyholm, S., Ogura, A., Pungor, J., Rosenthal, J., Schwarz, E., Shigeno, S., Strugnell, J., Wollesen, T., Zhang, G., & Ragsdale, C. (2012). Cephalopod genomics: A plan of strategies and organization Standards in Genomic Sciences, 7 (1), 175-188 DOI: 10.4056/sigs.3136559

About Matt Wood (507 Articles)
Matt Wood is a senior science writer at the University of Chicago Medicine and nonfiction editor for Another Chicago Magazine.
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