A Blog by Ed Yong

Flesh-Eating Plant Cleaned Junk From Its Minimalist Genome

How much of your DNA actually does something useful? Of the 3 billion letters that make up your genome, we know that only 1.5 percent consists of genes, which carry the instructions for making proteins. Of the remaining 98.5 percent, some sequences affect how, when and where our genes are used, but the vast majority have no obvious roles. They contain the corpses of dead genes, parasitic strings of selfish DNA that have run amok, and other bits that seem to do nothing. You might call them junk.

So, what would happen if you got rid of it? If you stripped all these “non-coding” sequences from the human genome, would you still get a normal, living person? This experiment will always be a fantasy for us, for reasons of impossibility and ethics, but it’s one that some living things have unwittingly carried out.

Take the floating bladderwort. This flesh-eating water plant is a genetic minimalist, adrift in a world of hoarders. The onion, for example, has around five times more DNA than you do, with a genome that’s around 15 billion DNA letters long. The wheat genome is slightly bigger still. And even these genetic titans look positively svelte next to the record-breaking genome of the Japanese “canopy plant”—a pretty, white flower whose 150-billion-letter genome is the largest of any plant.

The bladderwort, however, has a paltry 82 million letters in its genome—40 times fewer than you, and 2,000 times fewer than the canopy plant. For comparison, the thale cress, a plant that geneticists chose to focus on for its “small” genome, has almost twice as much DNA.

By sequencing the bladderwort genome, Enrique Ibarra-Laclette from the CINESTAV institute in Mexico City has shown that it’s largely junk-free. Its genes are squashed together and around three-quarters of its DNA codes for proteins. The extraneous sequences between them are few and far between. And yet, the plant survives. “Our results suggest that “junk” DNA is not necessary for the function of complex organisms,” says Luis Herrera-Estrella who led the study.

They say that you never know how important something is until it’s gone. The opposite is also true. Losing something can also make you realise just how dispensable it always was.

Credit: Bruce Salmon (Ecosphere publications, 2001)
Credit: Bruce Salmon (Ecosphere publications, 2001)

Getting bigger to get smaller

There are over 200 species of bladderwort that are all united by their twin loves of water and flesh. The floating bladderwort (Utricularia gibba) grows in ponds and lakes, and produces yellow, orchid-like flowers. Below the surface, it captures prey with pressurised bladders that can rapidly open to suck in passing animals, including insects, tadpoles and even small fish.

When Herrera-Estrella first sequenced the bladderwort’s genome, he expected it to represent the “minimal plant genome”. He thought that the bladderwort must have pared back its genes until only the most essential ones were left. Spare copies, or genes that perform overlapping jobs, would have been ruthlessly culled.

He was wrong. The bladderwort actually has around 28,500 genes—slightly more than plants with much bigger genomes, like the grape. Stranger still, this number hides a turbulent history of expansion and contraction. The team noticed that some genes in relatives like the tomato or grape are found eight times over in the bladderwort. This means that the bladderwort duplicated its entire genome at least three times in its evolutionary history, before promptly losing many of the doubled genes. Its genome went through three cycles of getting bigger before getting smaller.

“There are these natural currents that underlie genome dynamics,” explains Victor Albert from University at Buffalo, who was also involved in the study. Expansion versus contraction. Duplication versus deletion. “The key to the evolution of genome size may be the extent to which these opposing forces can be tolerated by natural selection.”

On the one hand, junk or duplicated DNA could provide fuel for evolution, by allowing natural selection to tinker with sequences that aren’t already used for important roles. On the other hand, having lots of DNA is expensive in energy terms – you need to keep a leash on it, and duplicate it all whenever cells divide. If the benefits outweigh the costs, you might get a bloated onion. If it’s the opposite, you get a lean bladderwort.

Certainly, the bladderwort seems to have jettisoned most of its junk. Repetitive stretches of DNA make up just 3 percent of its genome, compared to 10 and 60 percent in most other plants. Retrotransposons—a type of jumping gene that spreads through DNA by copying and pasting itself—dominate the genomes of most flowering plants, but have been relegated to just 2.5 percent of the bladderwort’s DNA. “The non-coding DNA must not have had a particular evolutionary benefit to the plant, or natural selection would have fought against the tendency to delete it,” says Albert.

The path to minimalism

Herrera-Estrella doesn’t know how the bladderwort ended up with its minimalist genome, but he certainly found no evidence that natural selection has specifically weeded out any non-essential DNA. Andrew Leitch, a plant geneticist at Queen Mary, University of London, finds that surprising. He notes that bladderworts live in environments that are poor in the essential element phosphorus. That’s why it eats meat—to harvest phosphorus from the bodies of animals. And since DNA’s backbone is loaded with phosphorus, it’s reasonable to think that the plant would have evolved to have less DNA, so it can make do with less of this element.

But not so. Instead, the team thinks that the answer probably involves recombination—a process where matching DNA strands swap genetic material with each other. Think of it like this: You’re filling out the missing pages of a book by using a pristine copy as a template. If those missing pages are all the same, you might accidentally skip a few while writing them out or start in the wrong place. Either way, you’d end up with a slightly shorter version of the same book. Do this enough times, and the flabby repetitive middle would dwindle away. Perhaps recombination is exceptionally sloppy in the bladderwort, leading to a natural tendency to delete its DNA.

The study puts an interesting spin on the results from the huge international ENCODE project. In a  controversial paper published last year, ENCODE claimed that around 80 percent of the human genome has some “functional activity”. It either controls the activity of genes, sticks to proteins, or gets transcribed into a related molecule called RNA. Rather than a desolate junkyard, ENCODE portrayed the genome as a thriving jungle full of hidden regulators and “things doing stuff”.

But the project’s many critics argued that it had redefined “function” to the point of meaninglessness. To put it simply: just because something happens at/to a stretch of DNA doesn’t mean that stretch is important. A completely random genome would probably show a lot of such “activity”.

The bladderwort teaches this lesson well. “At least for a complex flowering plant, having a bunch of potential, hidden biological regulators in the non-coding part of the genome simply isn’t necessary,” says Albert. “If a plant can get rid of junk DNA, it is possible that the role of this junk, if any, can be achieved by other means,” says Herrera-Estrella. “Our study also generates some doubts as to whether junk DNA is as important for humans, as stated by the ENCODE initiative.”

“The study further challenges simplistic accounts of genome biology that assume functions for most or all DNA sequences, without addressing the enormous variability in genome size among plants and animals,” says T. Ryan Gregory, who studies the evolution of genome sizes at the University of Guelph.

In 2007, Gregory coined the “Onion Test” to challenge anyone who thinks that non-coding DNA isn’t junk. If that DNA is important, why is it that the onion needs so much more of it than a human, or even other closely related plants? “The Onion Test could just as easily have been called the Bladderwort Test,” he says. “If non-coding DNA is vital for gene regulation or some similar function, then how can a plant such as the bladderwort get by with so little of it?”

Reference: Ibarra-Laclette et al. Architecture and evolution of aminute plant genome. 2013. Nature http://dx.doi.org/10.1038/nature12132

More on bladderworts meat-eating plants with ultrafast traps

More on genome size

10 thoughts on “Flesh-Eating Plant Cleaned Junk From Its Minimalist Genome

  1. I’ve wondered recently whether there may be a benefit to having non-coding DNA in any organism that undergoes recombination, in that it would allow for some sloppiness in the process. (If a recombination event happens in the middle of a functional sequence, it has to be lined up perfectly to avoid mutations — by having introns, etc. many recombination events would avoid that problem.) This makes me wonder, although the fact that so far we only find this in P-poor environments helps, I think.

  2. Statements like ‘Junk DNA ‘ and ‘waste DNA’ are absolutely wrong , these statements reflect the poor understanding of the ‘molecular evolution’ on the part of the researchers makes these comments . First those so called ‘switched off’ DNA’s that never code a protein or involved in the regulation of transcription throughout the life of the organism ,other than ‘may be early stages of embryonic differentiation-than ‘switched off’ after short activity for the rest of the organisms life span ARE NOT waste or junk .. They( so called -Junks/waste DNA that has no coding function) are the MOST PRECIOUS preserved remnants of millions of years of evolution of that particular species’ evolutionary route taken( past history so to speak). They are absolutely needed for the future evolutionary ‘FLEXIBILITY’ and ‘DYNAMICITY’ of ‘NEEDED CHANGE’ for the evolutionary adaptation , they are the ammunition(so to speak) for the adaptation , they are the most important DNA treasures of that species for the future evolutionary change –millions of years to come – ..
    So please , who calls himself/herself a ‘molecular evolutionary scientist’ ; first understand the ‘ fundamental concepts ‘ and ‘intent’ of the evolutionary process ..Why should any living organism will waste ‘precious energy – ( fight against the fundamental Entropy principle of Universe of non living matter ) – indeed lots of it- ‘ ? without purpose ? .. Please get wise … Molecular Evolution has been logical all along , only if you can ‘understand’ the purpose …

  3. Making a machine is one thing. Growing a machine! Planning evolution to evolve a machine, in discrete steps! Wow. Symmetry blows me away. Not quite symmetry.

    I’ve tried making a computer talk at a baud rate so high it has errors. I thought I could do error correction. I gave-up going at rates with errors. I have a feeling DNA and life has extrodinary accuracy.

  4. Last paragraph, the Gregory Onion Test is a thought experiment designed to suggest that junk DNA IS junk, not isn’t junk as suggested in your last paragraph :-)…sorry, it is the little things that bug me about writing..

  5. I’d propose that the extra “junk” really serves as a data protection mechanism. As UV, Gamma and other ionizing radiation and chemical mutagens could and do cause aberrations in DNA, having some room in there with “virtual information noise” could allow for lesser damage if the “junk” gets hit. A tighter genome might mean mutations would be higher. Maybe the current level has been optimized over many generations as a workable “survival” pattern (less damage to key information equals longevity to the organism). So it seems as a possibility to think on.

  6. Just posted a similar comment on my blog: http://phylogenomics.blogspot.com/2013/05/twisted-tree-of-life-award-15-nbc-news.html but I thought I would also post here. I confess I do not see this as that big of a finding. I mean, a small plant genome with lots of genes is really cool and figuring out just what that plant lineage did while it reduced its genome size is very interesting. But I do not see how this tells us much of anything about the role of non coding DNA in other organisms. Sure, it shows that one can make a plant without lots of non coding DNA. But that is very different than saying that non coding DNA in other species does not have a function (mind you, I err more on the side of much of it having little function, but that is not the point here). This is akin to me of finding a reptile without legs. It is really interesting to see how snakes move without limbs. And that a reptile can live without legs is interesting. But this tells us nothing about what legs do in the reptiles that have them.

    So – to me – I think the implications of this work are being way overblown.

  7. There are theories that the size of the genome has profound effects on the size of the nucleus and the size of the cell itself. Moreover, this can also affect the diffusion of nutrients and the rates of metabolism. In other words, maybe genomes need to be a certain size for reasons that have nothing to do with the genes they contain; sometimes organisms maintain genomes that best suit their size and energy expenditures.

    It is worth mentioning that the largest genome found to date belongs to one of the largest single-celled organisms.

    I would venture a hypothesis. What if the bladders that bladderworts use to capture their small prey have to utilize a very specific number of cells in a very specific arrangement? What if they need to maintain very tight tolerances of size and metabolism to function properly? If those requirements are for very small cells with high metabolisms, might this be the selective pressure keeping their genomes as compact as possible?

  8. The journalists probably should be careful about the way in wich say the news. Of course that some of the comments here could be right but….
    I’m wondering, they come from people that read the news or the scientific papers. Many many things, incluiding the wrong terms, was not mention in the paper…. so we need be careful with our readings.

    Actually, I think that is a really interesting work

  9. Junk DNA does refer to junk. Many organisms, humans included, have the majority of their DNA likely to be junk. This hasn’t been overturned, and has been worked on since the 1970s, and people really need to get over the aversion to the word junk.

Leave a Reply

Your email address will not be published. Required fields are marked *