Secrets revealed as the giant squid gets genetically sequenced

For the first time researchers have fully sequenced the genome of the elusive giant squid. It has given us the first real chance of discovering the mysterious surrounding these deep-sea ‘monsters’.

Sucker rings
The suckers of a giant squid specimen (Photo by Natural History Museum)

In 1857 the Danish naturalist Japetus Steenstrup was the first to link the elaborate tales of ships being dragged to the ocean floor, with the very real existence of the giant squid (Architeuthis dux). Now over 160 years later, researchers based in his homeland at the University of Copenhagen have sequenced the entire genetic make-up of Streenstrup’s squid for the first time. Much like finding an actual giant squid in the wild, sequencing the genome of the elusive creature proved to be incredibly difficult and time consuming. However it was worth the effort, as not only have we discovered some surprising details about these cephalopods as a result, but it will also help answer some of the age-old questions that have surrounded these ocean giants for hundreds of years.

Uncooperative specimens

The big problem with genetically sequencing a giant squid, is finding a giant squid to work from. Samples that we have managed to collect are usually dead when we find them, because live squids stay in the deep dark waters of the open oceans. Therefore most museum and laboratory specimens are partially decomposed, really old or incomplete. As well as this the chemicals used to preserve samples, such as formalin and ethanol, also degrade the quality of DNA samples that can be extracted from them. Lead researcher Dr Rute da Fonseca who works at the University of Copenhagen told Science Daily that they ‘underestimated’ the challenge of sequencing the genome and that “this project reminds us that there are a lot of species out there that require individually optimized laboratory and bioinformatics procedures”.

Putting together the pieces

The solution to the problem came by mixing and matching the genes of different samples and even species. Luckily the researchers were able to get their hands on an entire frozen specimen accidentally caught by fishermen in New Zealand. This gave them a template to work off but was still incomplete. To infer what genes were missing the team used several mRNA samples (single stranded mirror images of DNA) from different species of squid and octopuses to fill in the gaps. By extracting mitochondrial DNA from giant squid samples from museums the researchers also concluded that all known samples are from the same species and so they could conclude that the genome they had created was in fact representative for all giant squid.

Specimen
A giant squid specimen kept and studied at the Natural History Museum in London

Obviously a massive and complex genetic project like this required a considerable collaborative effort in order to pull it off. In total 45 researchers from different institutions across the globe were involved in creating and analysing the genome, which was released in a paper recently published in GigaScience. However Dr Fonesca believes all the hard work was worth it, saying “these new results may unlock several pending evolutionary questions regarding this mantled species”. Regardless of what mysteries surrounding giant squid this genome is able to unveil, it will certainly be a lot easier to find clues in their genetic blueprint than diving thousands of metres into the abyss to find them.

A gigantic genome

As you might suspect the finished genome of the gigantic cephalopod is equally large itslef. In total the sequence consists of around 2.7 billion nucleotide bases arranged into genes, still short of our own 3.2 billion bases, but still a record for an invertebrate species. Researchers involved in the study have already begun pouring through the data to see what secrets are hiding within it. “A genome is a first step for answering a lot of questions about the biology of these very weird animals” says Caroline Albertin from the Woods Hole Marine Biology Laboratory in America, talking to Science Daily. She was one of the team members who starting looking at which recognisable genes could be found in the sequence and which were brand new.

How do they get so big?

One of the big mysteries researchers were hoping to uncover from the newly sequenced genome was how these invertebrates manage to get so big. Despite the name, giant squid are not actually the largest squid species known to us. That title belongs to the even more elusive colossal squid (Mesonychoteuthis hamiltoni), which is believed to weigh in at around half a tonne. However at around 13 metres in length, the giant squid is still a comparative goliath among other invertebrates.

Size comparison
A comparison in sizes between humans and giant squid

One theory as to how it has got so large over time is via something known as whole-genome duplication. This is where developmental genes double up over evolutionary time to allow for larger structures to develop, as seen in most large vertebrates. However the genome revealed giant squid only have single copies and so achieved their size by a completely different and unknown route. One explanation may be the increased number of protein encoding genes they have compared to us. The genome revealed they have an increase of over 50% compared to us, despite having a shorter genome. However further research will need to be done individually to find out.

Massive intelligence

One area where the genome has revealed some answers is in cephalopod intelligence. For a while now we have started to realise that cephalopods, in particular octopuses, are one of the most intelligent animals in the ocean. However we have struggled to figure out why, especially because their anatomy is so alien compared to our own. Sequencing cephalopod genomes is also still a relatively new field having only really begun in 2015. What this new giant squid sequence confirms is that genes responsible may be universal across the entire group of animals. Those genes belong to the protocadherin family, normally absent in other invertebrate groups, and the 100 variations found in the new genome could explain why cephalopods can develop vertebrate-level brains in an invertebrate body.

Octopus intelligence
Octopuses have long been an example of rare invertebrate intelligence, but giant squids may share many similarities in how their brains work

Another group of genes found across the cephalopod group are reflectins. These genes code for the proteins that give the cephalopods their iridescence and camouflage ability, by producing chromophores and other colour changing skin pigments. This is another area of research that the giant squid genome lends itself to. Caroline Albertin believes that “having this giant squid genome is an important node in helping us understand what makes a cephalopod a cephalopod” and that “it also can help us understand how new and novel genes arise in evolution and development”.

Exploring the deep

Until now what we know about giant squid and other deep-sea creatures comes from old sailing stories and the incomplete samples that are accidentally caught or wash up on our shores. Some big and fairly costly expeditions have been launched over the last few decades to try and capture or observe the elusive giants in their natural habitat, but most come back emptyhanded. Last year researchers on board OceanX’s research vessel Alucia in the Gulf of Mexico, did manage to capture some incredible footage of a giant squid using a RUV (see video below), but even then what we could learn from the experience was limited. Whilst sequencing an entire genome isn’t cheap or easy, what it does do is give researchers a blueprint for discovering more things about these hard to find creatures, from the comfort of their desk chairs. Regardless of what we can learn from the new giant squid genome, one thing this study does prove is that the best way to study the deep sea might be through DNA.


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