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May 13, 2013
Another Big Genome Disparity (With Bonus ENCODE Bashing)
I notice that the recent sequencing of the bladderwort plant is being played in the press in an interesting way: as the definitive refutation of the idea that "junk DNA" is functional. That's quite an about-face from the coverage of the ENCODE consortium's take on human DNA, the famous "80% Functional, Death of Junk DNA Idea" headlines. A casual observer, if there are casual observers of this sort of thing, might come away just a bit confused.
Both types of headlines are overblown, but I think that one set is more overblown than the other. The minimalist bladderwort genome (8.2 x 107 base pairs) is only about half the size of Arabidopsis thaliana, which rose to fame as a model organism in plant molecular biology partly because of its tiny genome. By contrast, humans (who make up so much of my readership), have about 3 x 109 base pairs, almost 40 times as many as the bladderwort. (I stole that line from G. K. Chesterton, by the way; it's from the introduction to The Napoleon of Notting Hill)
But pine trees have eight times as many base pairs as we do, so it's not a plant-versus-animal thing. And as Ed Yong points out in this excellent post on the new work, the Japanese canopy plant comes in at 1.5 x 1011 base pairs, fifty times the size of the human genome and two thousand times the size of the bladderwort. This is the same problem as the marbled lungfish versus pufferfish one that I wrote about here, and it's not a new problem at all. People have been wondering about genome sizes ever since they were able to estimate the size of genomes, because it became clear very quickly that they varied hugely and according to patterns that often make little sense to us.
That's why the ENCODE hype met (and continues to meet) with such a savage reception. It did nothing to address this issue, and seemed, in fact, to pretend that it wasn't an issue at all. Function, function, everywhere you look, and if that means that you just have to accept that the Japanese canopy plant needs the most wildly complex functional DNA architecture in the living world, well, isn't Nature just weird that way?
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