A wow moment

As you will already know if you read my L’Oreal foundation blog post, invertebrates are what got me interested in biology in the first place and I now work with fruit flies. Whilst I still get a huge amount of enjoyment out of biology it takes a little bit more to make me go wow, but it still happens and I’d like to share a recent wow moment with you.

Some of you may remember these little creatures from school science lessons. They’re water fleas, Daphnia pulex, and their genome has just been sequenced and was published by Colbourne et al. in the journal Science (Image from Tree of life web project)

They are interesting creatures, really quite robust considering how small and apparently vulnerable they are, and they’re also quite important. They play a critical role in freshwater ecosystems as they graze algae and are eaten by fish, playing a key role in maintaining the balance.

It turns out that the Daphnia pulex genome is about 200 megabases (That’s 200 million A’s, T’s, G’s and C’s in total) and contains 30,907 genes. For comparison the fruit fly (Drosophila melanogaster) genome is ~169 megabases and contains 13,781 genes and the human genome is ~3.3 gigabases (a gigabase is a 1000 million bases) and only contains 21,550 genes. Yes, you read that correctly the water flea genome is far smaller but has a lot more genes than us!

This is achieved basically by everything being more compact. Genes are split into sections, called exons, with bits of non-coding DNA in between them, which you can think of as the punctuation for the code. In water fleas these non-coding sections are much shorter so that each gene takes up less space.

Why do water fleas have so many genes? Well of course the answer is because that’s how they evolved, it just happened that way, but the other question is why are so many genes maintained in their genome? Water fleas live in a wide variety of ponds and lakes, environments which can both vary greatly and change rapidly. To survive water fleas have to be quite adaptable, they can reproduce asexually (To make clones of themselves) or sexually. Amongst other things the amount of hemoglobin they produce to capture oxygen can increase quite rapidly and their migration can change, their physical appearance can also change as they can develop different features in response to predators. Because they are an important species and can respond rapidly to changes in their environment, as well as being sensitive to pollution, they are often used to assess the ecological impact of changes in the environment.

This gives scientists an unparalleled opportunity to study the functional outcome of environmental conditions on the genome, to study evolution in a complex ecological context. Although funding bodies are not always keen to support this kind of work a key step in making full use of Daphnia as a model will be understanding the function of more of those genes.

P.S. For anyone with a subscription to Science you can read the whole article here.

Update: I wanted to write a quick update about this because although it’s quite old a surprising number of you still look at it. It came to my attention that I overlooked a whole group of genes in the human genome which would bring the total to 29,933. This is still 974 genes less and in more than ten times the amount of space!

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2 Responses to A wow moment

  1. Heather says:

    Now *that* is a typical blog post. You write about something interesting, and serious, and no one comments on it for nigh on a week.

    Seriously, though, if the water flea has less non-coding DNA, does it have correspondingly less transcriptional regulation and, presumably, alternative splicing than humans? (I haven’t gone to read the article; I’m already terribly procrastinating as it is.)

  2. Thanks Heather, and sorry for taking so long to reply, particularly busy week for me – no way to run a blog I know!

    The UTR is still a reasonable size average is 370bp compared with 340bp for Apis mellifera (Honey bee) and 260bp for C.elegans (type of round worm) so I would think the transcriptional regulation would be/could be similar.

    The splicing is an interesting point though and honestly I have no idea. They don’t really look at it in the paper but given the large number of gene duplications, for instance there are 11 haemoglobin genes, my guess would be that perhaps you’re right and there is less alternative splicing.

    It’ll be interesting to see some more details when people start to publish work using the genome and of course I’m sure more information will be revealed as they refine it for the next draft.

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