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Thursday, May 30, 2013

What Does the Bladderwort Genome Tell Us about Junk DNA?

The so-called "C-Value Paradox" was described over thirty years ago. Here's how Benjamin Lewin explained it in Genes II (1983).
The C value paradox takes its name from our inability to account for the content of the genome in terms of known function. One puzzling feature is the existence of huge variations in C values between species whose apparent complexity does not vary correspondingly. An extraordinary range of C values is found in amphibians where the smallest genomes are just below 109bp while the largest are almost 1011. It is hard to believe that this could reflect a 100-fold variation in the number of genes needed to specify different amphibians.
Since then we have dozens and dozens of examples of very similar looking species with vastly different genome sizes. These observations require an explanation and the best explanation by far is that most of the genomes of multicellular species is junk. In fact, it's the data on genome sizes that provide the best evidence for junk DNA.

This is the basis of Ryan Gregory's Onion Test. It's supposed to act as a reality check on those speculations suggesting a function for most DNA in the genome.
The onion test is a simple reality check for anyone who thinks they have come up with a universal function for non-coding DNA. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?
Ibarra-Laclette et al. (2013) have just published the genome sequence of the bladderwort plant Utricularia gibba. It turns out to have a very small genome of only 82 × 106 base pairs (82 Mb). This is much smaller that the human genome (3,200 Mb) and smaller than the genome of most plants, which tend to be larger than the human genome.

The bladderwort has about 28,000 genes and this is typical of most plants.1 What's missing in this plant genome is a lot of the DNA that appears to be junk DNA in other genome. For example, only 3% of the genome consists of active and defective transposons whereas these can account for the majority of DNA in other plant genomes. The bladderwort seems like a perfectly normal plant in spite of the fact that it has shed most of its junk DNA.

This is not a surprise. It's perfectly in line with everything we've known about other genomes for several decades. For example, we've been discussing the small pufferfish (Tetraodon nigroviridis) genome (350 Mb) for many years. It's only one-tenth the size of the human genome yet seems to be perfectly adequate for a complex vertebrate. It looks like 90% of our genome is junk.


& Junk DNA
Nevertheless, the publication of the bladderwort genome made a bit of a splash because it was promoted as evidence for junk DNA. You can read an excellent summary by Ed Yong at: Flesh-Eating Plant Cleaned Junk From Its Minimalist Genome.

Jonathan Eisen doesn't think much of the evidence from genome size comparisons. He thinks that other plants might need that extra DNA. It could have a function in those plants but those functions are not needed in the bladderwort. He suggests that it could be like the loss of legs in snakes. Just because snakes don't have legs doesn't mean that legs have no function in other species [Twisted tree of life award #15: NBC News on "Junk DNA mystery"]. It's a silly argument but Jonathan Eisen thought that it was important enough to give a "Twisted Tree of Life Award" to press reports that touted the small bladderwort genome as evidence for junk DNA.

Ryan Gregory set him straight by explaining why these genome size comparisons really do provide evidence that most of the genome is junk [Genome reduction in bladderworts vs. leg loss in snakes].

1. Plants tend to have more genes than animals because their genes families are larger and not because they have an abundance of totally new kinds of genes. They do have plant-specific genes but they're also missing all animal-specific genes.

Ibarra-Laclette, E., Lyons, E., Hernández-Guzmán, G., Pérez-Torres, C. A., Carretero-Paulet, L., Chang, T. H., ... & Herrera-Estrella, L. (2013) Architecture and evolution of a minute plant genome. Nature published online May 12, 2013. [doi: 10.1038/nature12132]


Randy said...

Can we now, or perhaps soon, simply eliminate junk DNA and see what happens? I think of defragmenting the free space on a hard drive. The files are all preserved, but it's a lot neater.

I don't know anything about the subject, but maybe by filling up the space with more junk, perhaps it protects the important DNA by providing a larger target for harmful radiation or whatnot to hit. If it harms the junk DNA, perhaps that's not bad. Is this a reasonable guess?

John Harshman said...

Probably not. A bigger target just means more hits and doesn't change the probability that any particular spot gets hit. If there were some quota for number of mutations per genome, you would have a point.

But be careful. You might attract the attention of Claudiu Bandea.

steve oberski said...

Randy, I believe some work has been done with mice were some of the junk DNA was removed with no observed deleterious effects.

steve oberski said...

Larry has also addressed your comments about the cost of junk DNA to the organism (negligible from what I recall) and the protection it might provide against radiation induced mutations (none as John Harshman indicates) in previous posts.

Steve said...

An easy and very plausible answer is that genomes record and store information for reference purposes when the need arise. It explains why nothing happens when its so-called junk DNA is deleted.

Any effects would not be seen in terms of the survivability of the genome after deletion...but certainly would have an effect if/when that information was needed to adapt to new environmental conditions.

IN principle, this explanation could be tested by exposing a plant to a wide variety of conditions and record the results....then knock out a sizable portion of the genome (several times; each time knocking out a different area) and run it through the same conditions as before the knock-out and compare the difference in performance.

This would be a big undertaking like the Lenski experiments but could conceivably provide evidence that in fact the so-called junk DNA is useful if not essential to a genome.

That would answer the reason why genome sizes are not proportional to their complexity.

Pedro A B Pereira said...

"An easy and very plausible answer is that genomes record and store information for reference purposes when the need arise. It explains why nothing happens when its so-called junk DNA is deleted.

Any effects would not be seen in terms of the survivability of the genome after deletion...but certainly would have an effect if/when that information was needed to adapt to new environmental conditions."

Yes, that has been proposed before and does make sense as an hypothesis. But that doesn't make it any less "junk" by the definition. Junkyards are full of junk, but the reason why they are profitable is because sometimes people find them useful later on. That's why we keep "junk" around at home but not "trash".

Functional DNA means that the DNA is either regulatory or gets transcribed/translated into useful RNA/proteins. Gene duplication generates many pseudogenes that are free to change, eventually maybe turning into something useful under certain conditions. But while they are not useful they are "junk" with no function that can be deleted. This is perfectly accepted in molecular evolution. If you delete them nothing happens, but they may turn into something useful on the long haul. But all these pseudogenes and other forms of nonfunctional DNA are still "junk" as per the definition of the term. What ENCODE proposes is something far different (for which they really have no evidence at all).

Larry Moran said...

You are not the first person to offer such a speculative explanation for junk DNA. Since you can be certain that ideas like yours have been around for at least four decades, ask yourself why they haven't been accepted by the experts. There must be a reason. Do your homework.

Does it pass the Onion Test?