Over the weekend, Nature released a paper that describes the genome of a fascinating creature with a rather unglamorous name: the bladderwort. These plants live in swampy or liquid environments and find it hard to get sufficient nutrients there, so the plants have turned carnivorous in order to survive. The bladders that give the group of related species its name are actually feeding organs. When an organism brushes up against their triggers, the bladders swell by sucking in the surrounding water, along with any organisms it carries. They then seal off, allowing the plant to digest its prey.

The oddities continue at the molecular level. The genome of this bladderwort, Utricularia gibba, contains more genes than are found in the human genome (something common in plants), but it carries them all in a compact genome that's only a bit over 2 percent of the size of the human version. It does this largely by getting rid of just about everything that could possibly be considered superfluous—which may tell us important things about whether most of the DNA we carry really is superfluous.

First, the details, then some perspective.

A minimalist genome

The bladderwort's 82 million base pair genome contains 28,500 genes, a number only slightly higher than those of its closest relatives. As part of its unusual lifestyle, it no longer produces true roots used for absorbing water and nutrients, so the plant has lost a number of genes involved in root development. Aside from that, there's not a lot in particular about the genes present in the organism that is clearly related to its lifestyle. This suggests that the regulatory DNA—the bits of DNA that don't encode proteins but determine where and when specific proteins get made—plays a significant role in the plant's adaptations.

That's bizarre, because the plant has relatively little regulatory DNA. Many other complex plants and animals distribute regulatory sequences for a single gene over millions of bases, while the bladderwort has contracted that down to a few hundred bases. In some cases a single piece of regulatory DNA controls the genes on either side of it, saving more space that way. At other genes the authors found that the ends of neighboring genes overlapped, essentially eliminating all the DNA between neighboring genes.

In humans, about a quarter of the 3.2 billion base pairs are dedicated to introns, the non-coding sequences that interrupt genes. The bladderwort has fewer introns than closely related plants, and the introns that it has retained are generally smaller; two factors that cut down on the total genome size. Almost half of the human genome is comprised of countless copies of mobile genetic parasites called transposons. The bladderwort has these too, but it only has 569 of them, which account for only three percent of its genome.

Plant genomes normally end up rather large because plants seem to tolerate accidents that duplicate their genomes. Most plant species seem to only get rid of the excess DNA slowly and keep many extra copies of genes around. The bladderwort has also undergone two whole-genome duplications since it last shared a common ancestor with the tomato. The difference is that it ruthlessly purged the extra DNA. It's possible that the extra genes even fostered this process since there were backup copies of genes available when the deletion of DNA took out something important.

Why would deleting DNA be so favorable for these plants but not for most others? The answer might be related to the plant's need to feed on animals in order to get enough nutrients. The authors note that the growth of bladders seems to be triggered by low phosphorus, which is also one of the major components of DNA. It could be that regular phosphorus starvation favors a compact genome.

Active or functional?

This isn't the first organism we've sequenced that has a genome like this. The pufferfish Fugu has a very similarly organized genome with very little space between genes, compact regulatory sequences, and very few copies of transposons. A few of its fishy relatives have some of the largest genomes known in animals. These examples make it clear that you don't need an enormous, sprawling genome to develop as a complex plant or animal. Non-coding sequences remain critical—you can't control genes without them—but the DNA that's actually essential is a lot smaller than the total of what we humans carry around.

This necessarily gets into the arguments about junk DNA, which is DNA that is superfluous for the health and fitness of an organism. In recent years, the ENCODE project has twice published results showing that much of this apparently superfluous DNA is active, with proteins latched on to it and RNA being copied from it. A lot of people took that to mean the DNA was therefore functional, in that it contributed to the organism's fitness. (ENCODE did them no favors by defining "functional" to mean "active" in one of its papers.)

The bladderwort goes a long way toward re-establishing some perspective by showing that most plants and animals probably don't need most of the excess DNA they carry around—that excess fits the definition of junk DNA. We should have already known this because of Fugu, but the response to ENCODE showed that we need another reminder.

Nature, 2013. DOI: 10.1038/nature12132 (About DOIs).