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Untangling the Octopus Genome

Scientists sequenced and analyzed the genome of the California two-spot octopus, shown here. Comparing the genomes of different species can help researchers better understand our own genome. Judit Pungor

The octopus seems almost like an alien species. It’s spineless. It has 3 hearts. It has 8 arms lined with suckers. It can change color, texture, and shape to camouflage itself. It can climb walls and open jars. And its nervous system contains nearly half a billion neurons, more than 6 times the number in a mouse brain.

To understand the genetic features of this highly specialized animal, an international team—led by Dr. Clifton W. Ragsdale of the University of Chicago and Dr. Daniel S. Rokhsar of Okinawa Institute of Science and Technology Graduate University in Japan and the University of California, Berkeley—collaborated to sequence and analyze its genome. The research was supported in part by NIH’s Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD). The findings were published on August 13, 2015, in Nature.

The researchers found that the genome of the common California two-spot octopus was almost as large as a human’s genome (2.7 billion base pairs compared to 3 billion base pairs, respectively). But they estimated that it contains over 33,000 protein-coding genes—considerably more than the approximately 20,500 found in humans.

The octopus is a member of the cephalopod class, a group that includes squid and cuttlefish. The scientists found that the octopus has hundreds of genes present in cephalopods that haven’t been detected in other animals. Many of these genes are highly expressed (turned on) in specialized structures, such as the skin, the suckers, and the nervous system. For example, they found 6 genes for reflectins, which play a role in rapid, reversible changes in iridescence.

The team found a greatly expanded number of genes in 2 specific groups, or families, which were previously thought to only be enlarged in vertebrates. They noted 168 protocadherin genes, more than twice as many as humans. These genes regulate nervous system development and organization. The researchers also found nearly 1,800 genes from a group known as zinc-finger transcription factors. This is one of the largest groups of genes discovered to date in any animal. These genes, which code for proteins that regulate the activities of other genes, are mainly expressed in embryonic and nervous tissues, and are thought to play a role in brain development.

Nearly half of the octopus genome is composed of elements known as transposons—small pieces of DNA that can move from one location in the genome to another. They originally were referred to as “jumping genes.” A notable feature of the octopus genome is that it seems to have expanded largely through transposons moving around and reorganizing the genome.

“We have already found several gene types that are dramatically expanded in the octopus relative to other invertebrates, and we think they play a critical role allowing a new level of neuronal complexity to be reached in octopus relative to other invertebrates,” Rokhsar says.

“The octopus genome makes studies of cephalopod traits much more tractable, and now represents an important point on the tree of life for comparative evolutionary studies,” Ragsdale says. “The study of diverse genomes can give new insight into the structure and function of our own genes.”

—by Carol Torgan, Ph.D.