[LINK] On the genetics of the octopus

[rfmcdonald]

I liked to the sensationally-titled Metro.co.uk article "Octopuses ‘are aliens’, scientists decide after DNA study" because it was so sensational. A Facebook friend's suggestion, by way of providing inspiration of science fiction writers, that contemporary cephalopods are actually the technology-less descendants of ancient alien visitors, amused me. Another friend linked to Janet Fang's IFL Science article "The California Two-Spot Is The First Octopus To Have Its Genome Sequenced", much more sober and informative.

Cephalopods, which include the octopus, squid, cuttlefish, and nautilus, emerged as predators throughout the ancient seas half a billion years ago. They were likely the first intelligent life-forms on Earth, and these days, the list of octopus innovations is long and impressive: camera-like eyes, the ability to regenerate complex limbs, a propulsion system, and three hearts that keep blood pumping across the gills, to name a few.

Now, to investigate the molecular basis of the cephalopod brain – the largest nervous system among invertebrates – as well as their cool innovations, a team led by University of Chicago’s Caroline Albertin isolated and sequenced genomic DNA from a single male California two-spot octopus, Octopus bimaculoides. These clever problem solvers have a blue eyespot on either side of their heads. A juvenile female is pictured below to the right.

The octopus genome is about 2.7 billion base pairs in size, with long stretches of repeated sequences and more than 33,000 protein-coding genes. This means that their genome is slightly smaller than ours, but they have more genes. Researchers used to think that the large size of the octopus genome was due to whole genome duplication events during their evolution. But while these can result in increased genomic complexity, the team found no evidence of duplications.

Rather, a couple of gene families expanded, novel genes appeared, and the whole genome was shuffled around. "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," Albertin says in a statement. "This leads to genes being placed in new genomic environments with different regulatory elements."

Nature's "Octopus genome holds clues to uncanny intelligence" goes into more detail.

[T]he octopus genome turned out to be almost as large as a human’s and to contain a greater number of protein-coding genes — some 33,000, compared with fewer than 25,000 in Homo sapiens.

This excess results mostly from the expansion of a few specific gene families, Ragsdale says. One of the most remarkable gene groups is the protocadherins, which regulate the development of neurons and the short-range interactions between them. The octopus has 168 of these genes — more than twice as many as mammals. This resonates with the creature’s unusually large brain and the organ’s even-stranger anatomy. Of the octopus's half a billion neurons — six times the number in a mouse — two-thirds spill out from its head through its arms, without the involvement of long-range fibres such as those in vertebrate spinal cords. The independent computing power of the arms, which can execute cognitive tasks even when dismembered, have made octopuses an object of study for neurobiologists such as Hochner and for roboticists who are collaborating on the development of soft, flexible robots.

A gene family that is involved in development, the zinc-finger transcription factors, is also highly expanded in octopuses. At around 1,800 genes, it is the second-largest gene family to be discovered in an animal, after the elephant’s 2,000 olfactory-receptor genes.

The analysis also turned up hundreds of other genes that are specific to the octopus and highly expressed in particular tissues. The suckers, for example, express a curious set of genes that are similar to those that encode receptors for the neurotransmitter acetylcholine. The genes seem to enable the octopus’s remarkable ability to taste with its suckers.