Carnivorous Plant Ejects Junk DNA

sciencehabit writes "The carnivorous humped bladderwort, found on all continents except Antarctica, is a model of ruthless genetic efficiency. Only 3% of this aquatic plant's DNA is not part of a known gene, new research shows. In contrast, only 2% of human DNA is part of a gene. The bladderwort, named for its water-filled bladders that suck in unsuspecting prey, is a relative of the tomato. The finding overturns the notion that this repetitive, non-coding DNA, popularly called 'junk' DNA, is necessary for life."

Comments

No. Bad Conclusion. Bad.

[eldavojohn]

The finding overturns the notion that this repetitive, non-coding DNA, popularly called 'junk' DNA, is necessary for life.

False. Unsurprisingly, nowhere in the paper was this dubious claim even approached. Instead you can find this even in the summary:

However, extreme genome size reductions have been reported in the angiosperm family tree.

Emphasis mine. And then further into the actual paper:

Relaxed selection pressure for unnecessary functions probably led to gene losses, whereas in other cases, gene family expansions may have been promoted by selection. Evidence for localized selection on the U. gibba gene complement, however, does not provide support for the existence of genome-wide selective forces that might favour reduction of nonessential, non-coding DNA.

There would likely be no bladderwort had there been no junk DNA in its ancestral line and other findings point to such noncoded DNA as necessary for evolution.

I believe a more prudent falsifiable hypothesis would run along the lines of (and I'm sorry, I'm only a software developer): Due to relaxed external selective pressures the bladderwort's RNA polymerase has become adept at writing coding errors to the 3% noncoded DNA during replication and this actually still serves a vital function -- especially if the bladderwort is to survive in a much larger window than a few generations.

Re:No. Bad Conclusion. Bad.

[gandhi_2]

Too bad you passed up the "my junk ejecting DNA" opportunity for a cheap insightful comment.

Yeah, I had a cousin who did that a lot too

[TWiTfan]

Even when we begged him not to in front of people.

junk dna

[bdabautcb]

My understanding is that junk DNA is no longer a useful term because the DNA that isn't translated has been found to have structural and other epigenetic properties. I wonder if the complexity of mamallian vs. plant development plays a role here. Any biologists out there?

Re:junk dna

[Hatta]

Not all untranslated DNA has other properties. Some of it really does just exist because it's good at getting itself replicated. It's an open question how much non-coding DNA exerts regulatory effects and how much is actually junk. This paper indicates that in at least one eukaryote, 3% non-coding DNA is sufficient to regulate all the coding DNA.

If that holds in mammals (unlikely, but not out of the question), the vast majority of our non-coding DNA would still be "junk". Human DNA is 98% non-coding, or 2% coding. 3% of 2% is a rounding error here, so it would still be accurate to say the human genome is 98% "junk". If regulatory sequences outnumbered coding sequences 10:1 you're still looking at >75% of the human genome being "junk".

I don't think the concept of "junk" DNA is ever going to go away. Evolution would predict that sequences that are good at replicating themselves would accumulate in the genome, even if they don't do anything "useful". And random errors that accrue during copying will persist unless there's a mechanism to select against them. If we found that 100% of our DNA had a purpose, that would be a pretty strong argument against the theory of evolution.

The interesting question here is what selective forces drive this plant to excise unnecessary DNA, and what mechanism it uses to do this. Understanding that mechanism might lead to future gene therapies.

That's not junk DNA

[MobyDisk]

That's not junk: Those are comments!

Not really proven

[Animats]

This demonstrates only that organisms with little junk DNA can exist. To really demonstrate that "junk DNA" does nothing, someone needs to take an organism that has lots of junk DNA, sequence it, replace all the junk with the DNA equivalent of nulls, synthesize the new DNA, grow a new organism, and produce a few generations of it. Good project for Craig Venter.

There's a suspicion that "junk DNA", while currently turned off, sometimes gets turned on when mutation flips a bit, and this helps evolution along. An organism with little or no junk DNA may not evolve further, but can exist and reproduce just fine.

Re:No. Bad Conclusion. Bad.

[the biologist]

I believe a more prudent falsifiable hypothesis would run along the lines of (and I'm sorry, I'm only a software developer): Due to relaxed external selective pressures the bladderwort's RNA polymerase has become adept at writing coding errors to the 3% noncoded DNA during replication and this actually still serves a vital function -- especially if the bladderwort is to survive in a much larger window than a few generations.

As a biologist and software developer, I have a hard time understanding what you are trying to say here.

The carnivorous humped bladderwort

[Savage-Rabbit]

The carnivorous humped bladderwort...

Sounds like something from an episose of red Red Dwarf.

Re:No. Bad Conclusion. Bad.

[iluvcapra]

Um, where do you get those numbers? At least 76% of the non-coding human genome is transcribed -- to what end we cannot be certain in all cases, but the RNA transcripts from these often are fed back into gene expression and regulation. It's estimated that well over 50% of non-coding DNA is heavily conserved by evolutionary processes and contributes significantly to fitness.

Re:No. Bad Conclusion. Bad.

[Mitchell314]

Junk for an individual. Not necessarily junk for the evolution of a species. This issue comes up in computer science too with genetic algorithms, pushing pressure to keep the encoding as compact as possible 'may' lead to the side effect of increasing the probability of being stuck on a local optima. There's a lot of math 'n stuff involved that can better be explained by experts, but here's the short version: let's say that a genetic algorithm engine has an individual settled for a local optimum with all the bits just right. But there's a possible mutation that could lead to finding a slope leading to a better optimum. Obviously there's the issue that the mutation is going to compromise something important, and you end up with a mutant with good potential but a weaker fitness score, so the mutation is more likely to be discarded. However, if there's non-functional bits in the individual, there's a higher chance that the mutant can score better by compromising something that wasn't in use to being with, hence non-functional coding genes having some use in the long run. Now this is a huge simplification on a complex matter, but this does come up.

Sorry, but junk DNA is not junk

[WillAffleckUW]

I beg to differ with the "conclusion" that most DNA is "junk" DNA.

As we learn how DNA is used to create RNA, mRNA, siRNA, miRNA, circRNA, microRNA, etc - by folding, spindling, adapting to environmental messages and signals, we find that a lot of what you think is "junk" DNA is in fact ... NOT.

Some is, of course, but the conclusion is ... WRONG. Most of the actual junk is actually viral rewrites (true junk), but a lot of the other stuff is boostrap shifted code designed to handle various conditions that may or may not be present.

For example, if you take a drug that shuts down a primary biochemical pathway, the cells turn on a second biochemical pathway - which may or may not be optimized. If the secondary biochemical pathway is shut down by drugs or damage, a tertiary - conserved, usually evolutionarily conserved fallback from when you were a fish or ratlike creature - kicks in.

You think it's junk. It's just code that turns on when you mess with the program or force certain conditions to occur.