Rute da Fonseca

The genome of the Kraken has been unraveled

 

The giant squid is an elusive giant, but its secrets are about to be revealed. A new study led by the University of Copenhagen has sequenced the creature’s entire genome, offering an opportunity to throw some light on its life in the depths of the sea.  

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Sailors’ yarns about the Kraken, a giant sea-monster lurking in the abyss, may have an element of truth. In 1857, the Danish naturalist Japetus Steenstrup linked the tell tales of ships being dragged to the ocean to the existence of the giant squid: A ten-armed invertebrate, that is credibly believed to grow up to 13 meters and weigh over 900 kg.

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Now, more than 160 years later, an international team of scientists have sequenced and annotated the genome of a giant squid. ‘These new results may unlock several pending evolutionary questions regarding this mantled species’, says the research leader, Associate Professor Rute da Fonseca from the Center for Macroecology, Evolution and Climate (CMEC) at the GLOBE Institute of the University of Copenhagen.

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More data, more questions

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Throughout the years only relatively few remains of giant squids – or, Architeuthis dux – have been collected around the world. Using mitochondrial DNA sequences from such samples, researchers at the University of Copenhagen have previously confirmed that all the giant squids belong to a single species.

‘However, our initial genetic analysis generated more questions than it answered,’ says Professor Tom Gilbert of the GLOBE Institute, who was part of the previous work on the giant creature.

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Producing a high-quality genome assembly for the giant squid proved as challenging as spotting one of these animals in their natural environment. This was, however, an important effort as Jonathan Ablett, Senior Curator of Mollusca at the Natural History Museum, London, points out since ‘most of what we know about giant squids comes from museum specimens, therefore data on its genome is essential to discover even more about this iconic species”. A genome is the ultimate toolkit available to an organism.

 

Uncooperative samples

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The challenges in the lab started with the fact nearly available samples originate from decomposing animals, usually preserved in formalin or ethanol at museums around the world, so most cannot be used to obtain the high-quality DNA necessary for a good genome assembly. Furthermore, elevated levels of ammonia and polysaccharides in the tissues were likely the behind the repeated failures in producing suitable libraries for nearly all available sequencing technologies.

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‘This project reminds us that there are a lot of species out there that require individually optimized laboratory and bioinformatics procedures. , an effort sometimes underestimated when designing single-pipeline approaches in large genome-sequencing consortia,’ says Rute da Fonseca, who started leading the project when working as an Assistant Professor at the Department of Biology in the University of Copenhagen.

 

A first step towards getting to know the giant

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Despite the many challenges, ‘the quality of the newly sequenced genome is one of the best among available cephalopds’ highlights another co-author, Oleg Simakov, a group Leader from Department of Molecular Evolution and Development, University of Vienna.

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Henk-Jan Hoving, one of the co-authors who is a group leader in GEOMAR, Helmholtz Centre for Ocean Research in Kiel, said that ‘the draft genome of Architeuthis is the first step towards unravelling the evolution of this species’ and Associate Professor Jan Strugnell from James Cook University adds that ‘Using this genome in a future comparative genomics framework will hopefully allow us to explore the genetic underpinnings of the giant squid’s size, growth rate and age’.

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Ángel Guerra (CSIC, Spain), world’s expert in giant squids, and Álvaro Roura, a marine ecologist  engaged in cephalopod aquaculture, who were not involved in this work, remarked how ‘the huge flexibility of cephalopod genomes shown by the observed diversity in transposable elements and protein-coding gene families confirms once again the fascinating peculiarities of their instruction manuals’.

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Caroline Albertin, a co-author and researcher at the Marine Biological Laboratory in Woods Hole, notes that ‘We could confirm that most of the genes in the giant squid, like the octopus, are shared with other animals, like snails, worms, flies, and humans.’

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Another co-author, Agostinho Antunes, a group leader from CIIMAR, University of Porto, emphasized how ‘the high contiguity in this genome assembly uncovered a peculiarity regarding the usually conserved cluster of homeotic genes responsible for a correct body plan – the Hox genes – that in the giant squid spanned a far larger cluster size range of 11 Mb when compared to any other animal (around 100 kb length in vertebrates and 500 to 10,000 kb in invertebrates), presenting an intriguing avenue of future research.’

 

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The study “A draft genome sequence of the elusive giant squid, Architeuthis dux” has been published in the scientific journal GigaScience.

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Aside from the University of Copenhagen (Denmark), the collaborating scientists come from several universities around the world.

The Villum Fonden, Marie Curie Actions, and the Portuguese Science Foundation (FCT) have supported the research project, among others.

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