Great white shark genome decoded

In a major scientific step to understand the biology of this iconic apex predator and sharks in general, the entire genome of the white shark has now been decoded in detail.

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I loved sharks as a kid. Do you guys remember Shark Week?

This is an interesting article too:

Can anyone find the actual paper? It doesn’t seem to have been published online by PNAS just yet.

Can we agree that “decoded” is a terrible word to use for genomic sequencing?


It used to be so good and a huge part of my childhood. I still watch it but the quality has gone way down. Like the discovery channel in general

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Can you or any of the other biologists give me a quick summary of why “decoded” is a terrible word to use? Also, is there “a” genome for a species or is this a genome for one or a few samples from the species? For instance, is my genome unique to me or am I representative of the human genome. Does the “human genome” just mean “genome averaged over the samples we’ve taken?”

It’s kinda hard to keep all this straight, I feel like an idiot :slight_smile: . There are so many discussions about changes (mutations, speciation, etc.) that I’ve gotten this view of DNA and genes as being very fluid and kinda chaotic, but I suspect that’s not right.

another interesting finding is that sharks shares more then 100 genes with human but not with other fishes:

Because the majority of the genome doesn’t code for protein, yet there’s still many important functional sequences in the non-coding part, not to mention much junk DNA is noncoding but can still have implications for diseases, and is phylogenetically informative. That’d be my take on why “decoding” is a bad word. It might also suggest that we have “decoded” how the entire shark genome functions, which is of course incorrect. All we have now is a references sequence that is supposed to be representative of some shark population. What or how any particular piece of that shark genome functions has not been “decoded”.

The sequence has been recorded (and presumably put into some database), and then some comparisons to other genomes have been made, that’s it.


This is super helpful, thanks! So the idea is, then, that this shark genome could be improved with time (as more samples are sequenced?) but it provides an important set of data for further study of sharks from a molecular perspective?


another interesting finding is that sharks shares more then 100 genes with human but not with other fishes:
Humans have a bit of shark in them › News in Science (ABC Science)

Note that they only did this gene set comparison with one other fish (the pufferfish) and that the genes shared between shark and human (but not the puffer fish) were also shared with mice and dogs.

At least, that’s what is stated in the news article. Unfortunately, the link to the original publication is dead. Why these articles don’t provide the full citation is a mystery to me.

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This is the actual paper (presumably):

Some genes were lost in different lineages. Interesting, but not for the reason @scd is probably thinking of.


To quote from a more recent paper by the same author(s):

Protein domains
Comparisons of Pfam domains (Supplementary Note IXa) identified 17 C. milii domains that are missing in bony vertebrates (Supplementary Table IX.2). Sixteen of these are present in amphioxus or other eukaryotes, and are thus ancient protein domains that are still retained in C. milii but have been lost from bony vertebrates. We note that 13 domains shared between C. milii and tetrapods are absent in teleosts (Supplementary Table IX.4), indicating that they have been secondarily lost from the teleost lineage.

Lineage-specific gene losses
Orthologues of more C. milii genes were found to be lost from the teleost lineage (271 genes; Supplementary Note IXb and Supplementary Table IX.6) relative to the tetrapod lineage (34 genes; Supplementary Table IX.7). Human orthologues of many genes lost from teleosts are associated with genetic diseases (104 genes, 38%; Supplementary Table IX.6), indicating their importance for human physiology. The loss of these genes from teleosts supports the idea that teleosts represent a more derived group than do other gnathostomes. The functional annotation of zebrafish orthologues of the 34 genes lost from tetrapods highlighted several genes that are specific to the aquatic lifestyle, such as those regulating fin and lateral-line development and those encoding receptors for water-soluble odorants (Supplementary Table IX.7).

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Because it makes no sense. There is no decoding going on, just sequencing. I presume decoding would be figuring out what the genome means. As already mentioned, most of it doesn’t mean shit, and as for the protein-coding, functional-RNA-coding, and regulatory bits, it would take a whole lot more than sequencing to figure out what they mean, which I interpret as what functions they perform, and how.

Synecdoche. Every person has a genome, and a species has an average genome from which individuals don’t depart all that much. Obviously you can’t sequence the average genome; all you can do is sequence individuals and see how they’re the same or different.


You mean not with fugu. The obvious explanation is that fugu (or their ancient ancestors) have lost some genes that other species have retained.

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not according to the paper:

" Our analysis identified 154 human genes that have orthologs in mouse, dog, and the elephant shark, but not in the teleost fish genomes". they also checked the zebrafish genome and got the same result.

but there is more:

“Interestingly, the human and elephant shark genomes exhibit a higher degree of synteny and sequence conservation than human and teleost fish (zebrafish and fugu) genomes, even though humans are more closely related to teleost fishes than to the elephant shark”

indeed interesting.

The actual paper says that they made comparisons with fugu, tetraodon, and zebrafish, so it seems fair to say that the genes were lost early in the teleost lineage.

The next sentence is informative:

Elephant shark contains putative four Hox clusters indicating that, unlike teleost fish genomes, the elephant shark genome has not experienced an additional whole-genome duplication.

Like everyone else that works with teleost fish, I know that teleosts are a highly derived lineage of fish, one major reason being that teleosts experienced a round of genome duplication that other vertebrate lineages did not. To some extent I’d expect that a shark genome is more syntenic with the human genome than the zebrafish genome.

The paper also explains this in more detail:

Loss of some syntenic blocks in teleost fish could be explained by the differential loss of duplicate genes that arose due to a “fish-specific” whole-genome duplication event in the ray-finned fish lineage [9,10]. For instance, conserved synteny of genes X-Y between the elephant shark and human genomes could be lost in teleost fishes if alternative copies of duplicate genes on paralogous chromosome segments containing duplicate Xa-Ya and Xb-Yb genes are lost resulting in Xa-† and †-Yb genes († represents the lost gene).

So you mean not with fugu or zebra fish.

Simple explanation for that one: teleosts had a round of whole-genome duplication followed by rapid evolution and/or loss of a randomly picked copy of many genes.

actually there is more:

“Out of the 154 genes, 85 have no homologs in C. intestinalis, fruit fly, or the nematode worm.”

so we are also talking about Invertebrates. but there is more:

" Our analysis identified 107 teleost fish genes that have orthologs in the elephant shark assembly, but not in the human, mouse, and dog genomes. Twenty of these genes have no homologs in invertebrate genomes and are likely to be vertebrate-specific"

isnt it interesting if common descent is true?