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 DNANevertheless, 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]