Unprecedented gene study suggests giant squids may be massively intelligent

In the dark depths of the ocean, there is a behemoth that has puzzled humans for centuries. Giant squid inspired lore of the monstrous kraken and tales of its terrifying strength and prowess that captivated humans for centuries. But as fascinating as they are, so too are they elusive — we have never even managed to hold one captive. But now — in a win for science — we have finally cracked at least one mystery surrounding the enigmatic creature, gifting us with our closest encounter yet with the fabled and famed giant squid.

In a study published this week in the journal GigaScience, researchers detail the genome of a giant squid for the very first time. The finding allows “several pending evolutionary questions to be unlocked,” according to the paper.

Knowing what’s inside the genes of a giant squid could help scientists understand its unique traits, the researchers say — like how it came to reach its monstrous size, and how it adapted to life in the ocean’s depths.

“A genome is a first step for answering a lot of questions about the biology of these very weird animals,” Caroline Albertin, Hibbit Fellow at the University of Chicago, said in a statement.

Architeuthis dux was first described by researchers in 1857 in the World Register of Marine Species. The massive cephalopods can reach nearly 60 feet in length, though most are around 30 feet long — that’s a little longer than a double decker bus.

Giant squid have never been caught and kept alive or bred in captivity, so despite the wonder they inspire, there’s much about them that we are yet to discover. But thanks to this new study, we are starting to fill in some of the details of these animals’ biology and lives.

For example, we now know that the giant squid has about 2.7 billion DNA base pairs in its genome, according to the paper. For context, humans have about 3 billion base pairs.

The researchers also found 100 genes that belong to the protocadherin family — typically not found in abundance in invertebrates — in the giant squid genome. These genes are a sign that giant squid have complex and highly-evolved brains.

“Protocadherins are thought to be important in wiring up a complicated brain correctly,” Albertin said. “They were thought they were a vertebrate innovation, so we were really surprised when we found more than 100 of them in the octopus genome (in 2015). That seemed like a smoking gun to how you make a complicated brain. And we have found a similar expansion of protocadherins in the giant squid, as well.”

One question the study doesn’t answer (unfortunately) is how the giant squid got to be so giant. The giant squid genome revealed only single copies of important developmental genes. According to the paper, that finding contradicts a possible reason the squid got to be the size it is — through whole-genome duplication, an evolutionary adaptation to increase size previously seen in vertebrates. For now, the mystery of size remains unsolved.

By creating the annotated genome, the researchers say they “set the stage for future research into the enigmas that enshroud this awe-inspiring creature.” The research also contributes to the genomic knowledge of cephalopods as a whole — a behaviorally advanced group of invertebrates — further adding to researchers’ knowledge of life on Earth and its vast biodiversity.

Abstract:

Background: The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea–dwelling species will allow several pending evolutionary questions to be unlocked.

Findings: We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome.

Conclusions: This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.