Hans Zauner

**Today, *GigaScience* published a report on the genome of a truly
unique species: the giant squid *Architeuthis dux*. The elusive animal
is the main character in ancient stories about sea monsters and it is
known as "the kraken" in many legends. For a long time its mere
existence was questionable, until, in 1857, the Danish naturalist
Japetus Steenstrup made the link between those legends and the enormous
cephalopod. Now an international team led by researchers at the
University of Copenhagen has dragged the mysterious monster into the
genomic age. **

As *GigaScience* editors, we regularly see papers about [unusual and
bizarre
animals](http://gigasciencejournal.com/blog/on-the-trail-of-the-elusive-solenodon-genome-qa-with-taras-oleksyk/),
but this one really spurs the imagination:  A ten-armed invertebrate
that is believed to grow up to 13 meters and weigh over 900 kg.  With
the new genome sequence of *A. dux,* which is 2.7 Gb in size, the
researchers can tackle perplexing  questions of cephalopod genome
evolution and explore the genetics of [ the giant squid's size, growth
rate and age.]{style="font-weight: 400;"}

::: {#attachment_3203 .wp-caption .alignleft style="width: 235px"}
![giant squid
genome](http://gigasciencejournal.com/blog/wp-content/uploads/2020/01/Adux-225x300.jpg){.wp-image-3203
.size-medium loading="lazy" decoding="async"
aria-describedby="caption-attachment-3203" width="225" height="300"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2020/01/Adux-225x300.jpg 225w, http://gigasciencejournal.com/blog/wp-content/uploads/2020/01/Adux-768x1024.jpg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2020/01/Adux.jpg 1512w"
sizes="(max-width: 225px) 100vw, 225px"}

Image courtesy of Craig Henderson
:::

The [genome assembly presented in today's
paper](https://doi.org/10.1093/gigascience/giz152) is of high quality,
it is currently the best available cephalopod genome (and beating our
[*Octopus minor* genome](https://doi.org/10.1093/gigascience/giy119)).
This is even more remarkable given the difficulties the authors faced
when trying to get hold of samples for the genome sequencing project.
Giant squids are rarely observed alive and the main source of biological
material are dead pieces of tissue preserved in natural history museums.
The authors describe the obstacles:

::: {#attachment_3205 .wp-caption .alignright style="width: 310px"}
![giant squid
genome](http://gigasciencejournal.com/blog/wp-content/uploads/2020/01/Copy-of-GiantSquid_suckers-small-300x190.jpeg){.wp-image-3205
.size-medium loading="lazy" decoding="async"
aria-describedby="caption-attachment-3205" width="300" height="190"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2020/01/Copy-of-GiantSquid_suckers-small-300x190.jpeg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2020/01/Copy-of-GiantSquid_suckers-small-768x488.jpeg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2020/01/Copy-of-GiantSquid_suckers-small-1024x650.jpeg 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2020/01/Copy-of-GiantSquid_suckers-small.jpeg 1893w"
sizes="(max-width: 300px) 100vw, 300px"}

Giant suckers (species at Museum of New Zealand)
:::

["The challenges in the lab started with the fact that available samples
originate from decomposing animals, usually preserved in formalin or
ethanol at museums around the world. This means that most of them cannot
be used to obtain the high-quality DNA necessary for a good genome
assembly. ]{style="font-weight: 400;"}

[Furthermore, elevated levels of ammonia and polysaccharides in the
tissues were likely behind the repeated failures in producing suitable
libraries for nearly all available sequencing
technologies."]{style="font-weight: 400;"}

> [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]{style="font-weight: 400;"}

[ says Rute da Fonseca, who started leading the project when working as
an Assistant Professor at the Department of Biology at the University of
Copenhagen. ]{style="font-weight: 400;"}

::: {#attachment_3204 .wp-caption .alignleft style="width: 310px"}
![giant squid
genome](http://gigasciencejournal.com/blog/wp-content/uploads/2020/01/me-tom-squidMug-300x216.jpg){.wp-image-3204
.size-medium loading="lazy" decoding="async"
aria-describedby="caption-attachment-3204" width="300" height="216"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2020/01/me-tom-squidMug-300x216.jpg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2020/01/me-tom-squidMug-768x553.jpg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2020/01/me-tom-squidMug-1024x738.jpg 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2020/01/me-tom-squidMug.jpg 1765w"
sizes="(max-width: 300px) 100vw, 300px"}

First author R. da Fonseca and last author M. T. P. Gilbert.
:::

However, the authors [got hold of a freshly frozen tissue sample of a
giant squid, collected by a fishing vessel near New Zealand. "An
incredible stroke of luck", according to da
Fonseca. ]{style="font-weight: 400;"}

To annotate genes, usually an analysis of RNA sequences would come in
handy -- but again, this is easier said than done with such an elusive
animal. To get around the difficulties at the gene annotation front, the
authors brought in proteomic data and also used external evidence from
other cephalopod species.

[In the paper, the research team also take a first look at some of the
genes that will be worthy of in-depth investigation in the
future. ]{style="font-weight: 400;"}

One genome region of special interest to every genomically inclined
zoologist is the Hox cluster, a series of genes that act as master
control switches to coordinate an animal's development. As the authors
explain in the article, "different combinations of Hox gene expression
in the same tissue type can lead to a wide variety of different
structures. This makes the Hox genes a key subject for understanding the
origins of the multitude of forms found in the cephalopods.
\[...\] The *A. dux* Hox cluster is spread across 11 Mb of a 38-Mb
scaffold, and this suggests a far larger size range in the cephalopods
than in other described animals."

However, the exact configuration and function of the Hox region still
needs more fine-grained investigation.

> "Having this giant squid genome is an important node in helping us
> understand what makes a cephalopod a cephalopod. And it also can help
> us understand how new and novel genes arise in evolution and
> development"

adds co-author Caroline Albertin of the Marine Biological Laboratory
(MBL), Woods Hole.

With the genome assembly in hand, the giant squid is on track to loose
its status as enigmatic mystery of the deep and we can look forward to 
learning a lot more about its biology in the near future.

::: {#attachment_3209 .wp-caption .aligncenter style="width: 713px"}
![giant squid
genome](http://gigasciencejournal.com/blog/wp-content/uploads/2020/01/Squid-tissue.jpg){.wp-image-3209
loading="lazy" decoding="async"
aria-describedby="caption-attachment-3209" width="703" height="532"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2020/01/Squid-tissue.jpg 912w, http://gigasciencejournal.com/blog/wp-content/uploads/2020/01/Squid-tissue-300x227.jpg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2020/01/Squid-tissue-768x581.jpg 768w"
sizes="(max-width: 703px) 100vw, 703px"}

Squid tentacles in jars (various species) at Museum of New Zealand.
Photo: Scott Edmunds.
:::

### **References**

da Fonseca RR, Couto A, Machado AM, et al. A draft genome sequence of
the elusive giant squid, Architeuthis dux. *Gigascience*.
2020;**9**(1):giz152 doi:10.1093/gigascience/giz152

**Data in GigaDB:  
**da Fonseca RR et al. (2020): Supporting data for "A draft genome
sequence of the elusive giant squid, Architeuthis dux" GigaScience
Database. http://dx.doi.org/10.5524/100676

**Press release from the University of Copenhagen:  
**<https://news.ku.dk/all_news/2020/01/a-sea-monsters-genome/>

**Press release from Woods Hole Marine Biology Laboratory (via
EurekAltert):  
**<https://www.eurekalert.org/pub_releases/2020-01/mbl-tml011320.php>

**Press coverage:**

["Newly Sequenced Giant Squid Genome Raises as Many Questions as It
Answers." ](https://gizmodo.com/newly-sequenced-giant-squid-genome-raises-as-many-quest-1841026840) 
 GIZMODO

["Scientists Have Sequenced The Genome Of The Elusive Giant
Squid"](https://www.forbes.com/sites/allenelizabeth/2020/01/29/scientists-have-sequenced-the-genome-of-the-elusive-giant-squid/#7ae72037395e)
FORBES

More news stories
[here](https://oxfordjournals.altmetric.com/details/74081198/news).

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**Today,
<em>
 GigaScience
</em>
published a report on the genome of a truly unique species: the giant squid
<em>
 Architeuthis dux
</em>
. The elusive animal is the main character in ancient stories about sea monsters and it is known as “the kraken” in many legends. For a long time its mere existence was questionable, until, in 1857, the Danish naturalist Japetus Steenstrup made the link between those legends and the enormous cephalopod.

Messaggi di Rogue Scholar

The genome of an elusive giant