Octopuses, along with squids, cuttlefish and nautiluses, are cephalopods—a class of predatory molluscs with an evolutionary history spanning more than 500 million years (long before plants moved onto land). Inhabiting every ocean at almost every depth, they possess unique adaptations such as prehensile arms lined with chemosensory suckers, the ability to regenerate complex limbs, vertebrate-like eyes and a sophisticated camouflage system. With large, highly developed brains, cephalopods are the most intelligent invertebrate and have demonstrated elaborate problem-solving and learning behaviors.
To study the genetics of these specialized traits, Ragsdale and his colleagues sequenced the genome of the California two-spot octopus, Octopus bimaculoides, to a high level of coverage—on average, each base pair was sequenced 60 times. To annotate the genome, the team generated transcriptome sequence data—which can be used to measure gene expression based on RNA levels—in 12 different tissues types.
The team estimates the O. bimaculoides genome is 2.7 billion base-pairs in size, with numerous long stretches of repeated sequences. They identified more than 33,000 protein-coding genes, placing the octopus genome at slightly smaller in size, but with more genes, than a human genome.
The large size of the octopus genome was initially attributed to whole genome duplication events during evolution, which can lead to increased genomic diversity and complexity. This phenomenon has occurred twice in ancestral vertebrates, for example. However, Ragsdale and his colleagues found no evidence of duplications.
Instead, the evolution of the octopus genome was likely driven by the expansion of a few specific gene families, widespread genome shuffling and the appearance of novel genes.
The most notable expansion was in the protocadherins, a family of genes that regulate neuronal development and short-range interactions between neurons. The octopus genome contains 168 protocadherin genes—10 times more than other invertebrates and more than twice as many as mammals. It was previously thought that only vertebrates possessed numerous and diverse protocadherin genes. The research team hypothesized that because cephalopod neurons lack myelin and function poorly over long distances, protocadherins were central to the evolution of a nervous system whose complexity depends on short-range interactions.
Other gene families that were dramatically expanded in the octopus include zinc finger transcription factors, which are mainly expressed in embryonic and nervous tissues and are thought to play roles in development. The octopus genome contains around 1,800 C2H2 zinc finger transcription factors, the second largest gene family so far discovered in animals. Olfactory receptor genes in elephants are the largest at around 2,000.
Overall, however, gene family sizes in octopuses are largely similar to those found in other invertebrates.
A ‘Cuisinart’ genome
A unique feature of the octopus genome appears to be widespread genomic rearrangements. In most species, specific cohorts of genes tend to be close together on the chromosome. However, most octopus genes show no such connections. Hox genes, for example, control body plan development and cluster together in almost all animals. Octopus Hox genes are scattered throughout the genome with no apparent linkages.
The octopus genome is enriched in transposons, also known as “jumping genes,” which can rearrange themselves on the genome. While their role in octopuses is unclear, the team found elevated transposon expression in neural tissues. Transposons are known to affect the regulation of gene expression and play major roles in shaping genome structure.
“With a few notable exceptions, the octopus basically has a normal invertebrate genome that’s just been completely rearranged, like it’s been put into a blender and mixed,” said Caroline Albertin, co-lead author and graduate student in Organismal Biology and Anatomy at the University of Chicago. “This leads to genes being placed in new genomic environments with different regulatory elements, and was a completely unexpected finding.”