Faculty of Mathematics, Physics
and Informatics
Comenius University in Bratislava

Researchers from the faculty helped to decipher the legendary kraken genome

January 17, 2020. The Computational Biology Research Group at the faculty collaborated on sequencing and analysis of the giant squid, a legendary creature measuring over 10 meters. The study was published yesterday by an international team of researchers led by scientists from the University of Copenhagen in GigaScience journal.

17. 01. 2020 15.02 hod.
By: Tomáš Vinař

The Scandinavian legend of kraken describes a huge octopus-like creature living deep in the sea off the coasts of Norway and Greenland, attacking and sinking whaling ships. Several authors attribute this legend to the occasional sightings of giant squids (Architeuthis dux), which live 1200 meters below sea level, grow to 13-15 meters, and weigh up to 900kg. It is very rare to see a live giant squid in its natural environment, so research must be based on a few  washed-out remains of dead animals.

“This project reminds us that there are a lot of species out there that require individually optimized laboratory and bioinformatics procedures. An effort that is sometimes underestimated when designing single-pipeline approaches in large genome-sequencing consortia,” says Dr. Rute da Fonseca of the Center for Macroecology, Evolution and Climate, University of Copenhagen, who led the whole project. From the beginning, the project was confronted with the problems of obtaining high quality DNA from decomposing samples conserved with ethanol, as well as with organism-specific problems, such as increased ammonium and polysaccharide content in giant squid tissues.

The key step in further research of the new organism is to find the occurrence of individual genes in the sequenced genome and characterize their function using bioinformatics methods. “We had very little information available to help us to find genes in this organism. Usually, the annotation is based on information about genes of evolutionarily related species, as well as the sequencing of RNA molecules from a living organism. However, the giant squid’s evolutionary distance to other species with well characterized genomes is too high, and due to the unavailability of live samples, it is not possible to analyze RNA either,” adds Dr. Broňa Brejová from the Computational Biology Research Group at the Faculty of Mathematics, Physics and Informatics at Comenius University in Bratislava. Fortunately, researchers from the Computational Biology Research Group have encountered similar challenges in previous projects and have used their own software developed and adapted for this purpose to annotate the genome.

In spite of all the obstacles, the giant squid genome published yesterday in GigaScience journal is currently one of the best-quality cephalopod genomes available. High-quality genome is an important prerequisite for further study. In the future, it will allow, for example, further research on the adaptation to huge body size, or the mechanisms that result in a unique body plan of giant squid and other cephalopods. “The high contiguity of this genome assembly uncovered a peculiarity regarding the genes responsible for a correct body plan – the Hox genes. In the giant squid these genes span a large  11 million bases long segment of the genome, which is much larger region than in any other animal (in humans, it is about 500,000 bases long). This presents an intriguing avenue of future research.”, says Dr. Agostinho Antunes of the Interdisciplinary Center for Marine and Environmental Research at the University of Porto.

Study “A draft genome sequence of the elusive giant squid, Architeuthis dux” was published on January 16, 2020 in GigaScience journal. The Computational Biology Research Group participated in the study in an international consortium led by the University of Copenhagen.

Article: https://doi.org/10.1093/gigascience/giz152
Computational Biology Research Group: http://compbio.fmph.uniba.sk/