Scott Edmunds

**Deep (ocean) sequencing. Big-(fish) data.  
![mola_mola](http://gigasciencejournal.com/blog/wp-content/uploads/2016/09/Mola_mola-300x265.jpg){.alignright
.size-medium .wp-image-1838 loading="lazy" decoding="async" width="300"
height="265"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2016/09/Mola_mola-300x265.jpg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2016/09/Mola_mola-768x677.jpg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2016/09/Mola_mola-1024x903.jpg 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2016/09/Mola_mola.jpg 1345w"
sizes="(max-width: 300px) 100vw, 300px"}**The ocean sunfish, must
officially be one of the [world's
weirdest](https://www.youtube.com/watch?v=U60obmWODLQ&feature=youtu.be)
creatures to enter the ["genome
club"](https://twitter.com/sketchscience/status/748231202939748352), and
have its genetic code mapped. Laying the most eggs of any other known
vertebrate (up to 300,000,000 at a time), and starting out as the size
of the head of a pin, sunfish grow to become to largest bony fish in the
sea. Eventually weighing up to 2,300kg and measuring up to 3.3m in
length, the ocean sunfish has been observed to grow at almost one
kilogram per day. To put this in context, other fish grow at 0.02 to 0.5
kilogram per day. The morphology of the ocean sunfish is also very
different from other fish, having lost its caudal fin and hence also
known as a "half-fish". Despite "[Survive! Mola
mola](https://play.google.com/store/apps/details?id=jp.selectbutton.manbotheworld&hl=en)!"
being one of the most popular video games in Japan, how they manage to
survive and grow so rapidly from munching nutritionally poor jellyfish
is an interesting challenge to understand from a scientific perspective
as well.

Wading into this challenge have been a team of scientists including the
[lab of Byrappa Venkatesh and Sydney
Brenner](http://www.imcb.a-star.edu.sg/php/venkatesh.php), who, [in
2002](http://science.sciencemag.org/content/297/5585/1301.long) brought
the genome sequence of the Pufferfish (*Takifugu rubripes*) to light,
making it the second vertebrate genome to be sequenced. *Fugu* was found
(at the time) to have [the smallest genome](http://www.fugu-sg.org/) of
any vertebrate, at 390Mb roughly one eight the size of the human genome,
making it an excellent 'reference' genome for understanding the
structure and evolution of genomes. As one of the closest relatives of
the *Takifugu rubripes*, the group were interested to see how compact
the *Mola mola* genome was, but being 730 Mb this is compact for a
vertebrate genome, but not spectacularly so.

Venkatesh, who led the project from A\*STAR, said: "Pufferfish and ocean
sunfish belong to the same order but differ dramatically in morphology.
At the early stages of development, ocean sunfish larvae look similar to
pufferfish larvae with spines sticking out. We thought ocean sunfish
would be a useful species to identify the genetic basis of morphological
innovations. So we were keen to sequence the ocean sunfish genome and
compare with the pufferfish genome, to identify genetic changes that
have occurred in the sunfish lineage and that might give clues to the
highly derived phenotype."

**The Genome in Sydney Brenner's hand luggage.  
**

::: {#attachment_1835 .wp-caption .alignleft style="width: 310px"}
![Brenner visiting BGI in
2010.](http://gigasciencejournal.com/blog/wp-content/uploads/2016/09/brenner-300x232.jpg){.size-medium
.wp-image-1835 loading="lazy" decoding="async"
aria-describedby="caption-attachment-1835" width="300" height="232"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2016/09/brenner-300x232.jpg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2016/09/brenner-768x594.jpg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2016/09/brenner-1024x792.jpg 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2016/09/brenner.jpg 1961w"
sizes="(max-width: 300px) 100vw, 300px"}

Brenner visiting BGI in 2010.
:::

Nearly two decades on from the initiation of the project, Sydney
Brenner, has given some further background on how it came about: "I
became interested in the *Mola mola* in the 1990's, not long after we
began work on the Pufferfish, Fugu. We chose that genome because it was
the smallest one reported and reading about the evolution of fishes made
me interested in the *Mola mola*. It seemed to be the end of the line
with many features lost. I tried for many years to obtain a sample but
failed. There was one on display at the aquarium in Northern California
but when it died it was their policy to return it to the ocean. When I
visited the Marine sciences laboratory in Florida I mentioned my
interest in it. To my great surprise, Paul Linser who had worked with in
the Scripps telephoned me one day to tell me that a *Mola mola* had swum
up the intercoastal canal and had been found by the private aquarium
close to the Marine Laboratory. It would be exhibited there and when it
died he would arrange for me get some blood. This was our sample which
was brought to me frozen in liquid nitrogen to the Scripps and which I
carried to Singapore and which we used for the sequencing. Fish have
nucleated red blood cells a very useful source of DNA. We still have
many friends in marine institutes to help us in this exotic interest."

Despite the less interesting genome size meant the species was passed
over for much of the genome evolution work, being a bizarre "natural
mutant" meant there was continuing interest in studying the
extraordinary phenotypes. With the launch of the G10K project to
sequenced 10,000 vertebrate species, this was high on the list for BGI
to sequenced as part of their pilot to 100 species for the consortium.
Funded by [China National Genebank
(CNGB)](http://www.cngb.org/en/index.html), Guojie Zhang, Associate
Director of CNGB, and a corresponding author says: "This is one of the
30 fish genomes have been sequenced for the G10K project. The
availability of high throughput DNA sequencing technology makes it
possible to sequence whole genomes of a wide range of 'non-model'
species, allowing us to uncover the genetic basis of their phenotypic
diversity and their adaptation. Our study mainly focused on the genetic
background of the ocean sunfish's fast growth rate and particular body
shape. We found that several genes involved in growth hormone signalling
evolve very fast in the ocean sunfish when compared to other bony
fishes, which may explain its large size and fast growth rate."

Venkatesh added: "We found changes in genes encoding for collagen and
cartilage formation. This may contribute to the development of
predominantly cartilaginous skeleton in this gigantic fish. Vertebrates
exhibit a wide diversity in their morphology, physiology and behaviour.
Understanding the genetic basis of this diversity is a major goal of
evolutionary biology." Further adding "I think we still have a lot to
learn from the sunfish genome assembly. One way to pinpoint more genetic
changes specific to sunfish would be to sequence more closely related
species such as porcupine fish, box fish, triggerfish, and triplespines
(all are tetraodontiformes fishes) and a closest outgroup to this Order.
Our present analysis also suggests that the genetic changes underlying
many of the derived phenotypes could be in the regulatory sequences."

The genomics data is available in the public databases [and
GigaDB](http://dx.doi.org/10.5524/100214) for others to mine and do
these future comparative studies. With us recently publishing a project
announcement for the ["Transcriptomes of 1,000 Fishes"
(Fish-T1K)](http://gigascience.biomedcentral.com/articles/10.1186/s13742-016-0124-7)
project (also featuring Venkatesh) and the genome of the [channel
catfish](http://gigascience.biomedcentral.com/articles/10.1186/s13742-016-0142-5),
fish 'omics research is reaching a high water mark, but few of these
coming genome projects will likely be as bizarre as this new
[paper](http://gigascience.biomedcentral.com/articles/10.1186/s13742-016-0144-3)
looking at these gentle giants of the deep.

### References

Pan H, Yu H, Ravi V, Li C, Lee AP, Lian MM, Tay BH, Brenner S, Wang J,
Yang H, Zhang G, Venkatesh B. The genome of the largest bony fish, ocean
sunfish (Mola mola), provides insights into its fast growth rate.
Gigascience. 2016 Sep 9;5(1):36.
https://doi.org/10.1186/s13742-016-0144-3

The post [Of big fish and small genomes. Ocean sunfish
shines.](http://gigasciencejournal.com/blog/big-fish-small-genomes-ocean-sunfish-shines/){rel="nofollow"}
appeared first on
[GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.


<strong>
 Deep (ocean) sequencing. Big-(fish) data.
</strong>
The ocean sunfish, must officially be one of the world’s weirdest creatures to enter the “genome club”, and have its genetic code mapped. Laying the most eggs of any other known vertebrate (up to 300,000,000 at a time), and starting out as the size of the head of a pin, sunfish grow to become to largest bony fish in the sea.

Publicaciones de Rogue Scholar

Of big fish and small genomes. Ocean sunfish shines.