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As we have heard in the summaries of the human ENCODE project, 80 per cent of junk DNA appears to have an essential function. Many fish have a genome with only one tenth the size of a usual vertebrate genome. Why can fish have 1/10th of junk DNA and be still fully functional? What has a frog more than a fish has? I'm especially interested if we can see the difference somewhere, complexity of physiology or anatomy, or such.

Jap. puffer fish genome: 390 Megabases, 47,800-49,000 genes (UniProt)

Medaka genome: 690 Megabases, 24,600 genes

Clawed frog: 1,500 Megabases, 23,500 genes

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I think this question, like at least a few others, is based on a misunderstanding of ENCODE’s use of the word “function”. Maybe we should have a kind of FAQ for that. (Disclaimer: I agree with their usage of the word. Others, e.g. Larry Moran, disagree – vehemently.) –  Konrad Rudolph Jan 4 '13 at 19:31
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Genome size is a poor indicator of an organism's complexity (already an ill-defined term). We cannot assume by any means that a larger genome corresponds to a more "complex" organism. There are some plants whose genomes are larger than most mammals, and indeed the largest eukaryotic genome (at least as of 2010) is the plant Paris japonica, weighing in at 1C = 152.23 pg (compared to Homo sapiens at 1C = 3 pg). Anecdotally, in my previous research lab I discussed with a colleague a fungal species whose genome size differed by orders of magnitude between different individuals of that species.

It should never surprise you to see an organism with a larger genome size than what you may consider to be a more complex organism.

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Just saw this on Twitter, and wanted to point it out. twitter.com/DanGraur/status/372712933525946368 –  Daniel Standage Aug 28 '13 at 14:58
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See here for an ENCODE author's reflections on their use of the word "functional". (I don't think anyone is using the word "essential".)

It is clear from this that, for them, one class of functional DNA is intronic DNA: i.e. introns are defined by ENCODE as functional DNA. It is well known that puffer fish have reduced genomes and that this is largely due to the presence of much smaller introns, although the number and positioning of these introns is broadly similar to what is seen in other vertebrates. One classic example of this is the huntingtin gene which is 7.5 times shorter in pufferfish than in humans even though both genes have 67 introns. In fact the average fish genome size is 5-6 times bigger than that for pufferfish (zebrafish is around this average value).

Although ENCODE are defining intronic DNA as functional I don't think that they are claiming a specific function for each and every intron, let alone each base in those introns. So there is still a lot of scope for the observed differences in genome size.

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I think the last paragraph nails it (and, incidentally, the controversy about ENCODE’s 80% figure) – although intronic DNA is just a small part, much more is in repeat elements. –  Konrad Rudolph Jan 4 '13 at 20:01
    
That's a good read! –  Ryan Aug 9 '13 at 21:50
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