Carnivorous bog plant features smallest genome to date

_{Denyse O'Leary

December 17, 2014

Genomics, News}

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The genus Genlisea (corkscrew plants) belongs to the bladderwort family (Lentubulariaceae), a family of carnivorous plants. Some of the 29 species of Genlisea that have been described possess tiny genome sizes. Indeed, the smallest genome yet discovered among flowering plants belongs to a member of the group.

The LMU researchers also discovered a new record-holder. Genlisea tuberosa, a species that was discovered only recently from Brazil, and was first described by Andreas Fleischmann in collaboration with Brazilian botanists, turns out to have a genome that encompasses only 61 million base pairs (= Mbp; the genome size is expressed as the total number of nucleotide bases found on each of the paired strands of the DNA double helix) Thus G. tuberosa possesses now the smallest plant genome known, beating the previous record by 3 Mbp. Moreover, genome sizes vary widely between different Genlisea species, spanning the range from ~60 to 1700 Mbp.

The reasons for the wide range of genome size found in different species remain largely enigmatic. “Interestingly, the size of an organism’s genome does not correlate with its complexity or evolutionary level. Although unicellular organisms like brewer’s yeast, as well as some plant species, have far less DNA in their cells than humans do, many plants have much larger genomes than ours,” Fleischmann explains. The genus Genlisea, with its broad range of variation in genome size between different species, therefore offers a perfect group of model organisms to study the evolutionary pressures that determine genome size. “Genlisea is an ideal model system for understanding the molecular basis for genome reduction and the mechanisms that drive it, especially since the complete genome of G. aurea has already been sequenced and published,” says Günther Heubl. – “Evolution of genome size and chromosome number in the carnivorous plant genus Genlisea (Lentibulariaceae), with a new estimate of the minimum genome size in angiosperms.” Ann Bot (2014) 114 (8): 1651-1663 first published online October 1, 2014 DOI: 10.1093/aob/mcu189

Photos here. (The one accompanying the press release is not of the actual plant, but of a close relative. )

See also: Crown of Thorns starfish shows “surprising” chordate-like gene organization

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Comments

Nice of Nick to actually quote some ID people. Unfortunately none of them make the argument he attributes to ID'ers. Nick says his argument is a simple one, and I agree. Too simple. Did he answer any of the charges leveled against it? 1. Cherry picking 2. Straw man (see the opening paragraph of this post) 3. non sequitur 4. making unwarranted assumptions/begging the question 5. it's actually a problem for evolutionary theory, not ID That's a lot for such a simple argument, but Nick manages to pull it off somehow. Let's talk about cherry picking. If an ID'er picked out an organism with a very simple genome and it turned out that the genome is mostly or all functional and then used that to argue that junk DNA is a "myth" Nick would no doubt be quick to charge them with cherry picking the data. And rightly so. But that's what Nick has done, but in reverse. But what's worse is his argument seems incoherent at the start. Are we to assume that the species with the smaller genome has a smaller genome because it is mostly not junk or has no junk? Nick can't say. But his argument depends on it. Nick could argue that he is only arguing for a large amount of junk dna in this specific instance based upon the difference in genome size. But then his argument isn't generalizable and it doesn't demonstrate anything.Mung_{December 19, 2014
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Hi Nick, Your right, the use of buying and selling is a poor metaphor. What I meant by spending, is that DNA is disposed of (exported) and DNA is acquired (imported), often times for some benefit, or need. Males (including flowering plants) certainly donate (or spend) their DNA when they mate, LOL. So obviously they are investing in offspring. Microbes import DNA from other microbes or their environment for one reason or another. More commerce? Anyhow, there is certainly an economy in nature, especially in living systems, and DNA appears to be a valuable resource. I think you make my point about our total knowledge- we just don't know as much as we may think?littlejohn_{December 19, 2014
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63 littlejohnDecember 19, 2014 at 4:52 pm Nick, Could it be possible that “Junk” DNA is a valuable resource? After all, it appears to be a commodity among many microbes, is it not? Maybe that’s why certain species retain more (savers), while others streamline (spenders)? At least it does not appear to be a problem for those organisms that have apparently exceeding large DNA savings accounts? Anyhow, how much do we really know about what DNA is doing, and what populations are doing with it? Would you say our total knowledge is 1% complete?, 10%?, ___%? Appreciate your time!
Hi -- I'm not sure to do with questions like these. Is there a nice way to say that they indicate an almost complete unfamiliarity with basic biology? :-) How could an organism "spend" DNA? What would they be "buying"? Usually in these discussions someone raises the idea that maybe junk DNA is kept around because it will be useful in the future -- but this would be an argument for keeping the DNA, not "spending" it and thereby getting rid of it. (The "saved for future use" idea is hopelessly flawed itself, but that's another topic -- at least it is a parse-able idea.) The question also seems not to realize that there is DNA in (almost) every cell of every individual organism, and there may be thousands or billions of individual organisms in a species, living and breeding and dying each generation. What would it even mean for a big collection of animals or plants to "spend" its DNA? As for assigning a percentage to our total knowledge of DNA -- what does that even mean? What's our percentage knowledge of Mars? Of Shakespeare? I think we pretty much know that genes are where most of the action is in terms of building organisms, that and regulation of the genes, and we pretty much know that the amount of non-genic DNA that serves important regulation purposes is not dramatically larger than the amount of genic DNA. It's the latter bit that many people (IDists, and some poorly educated biologists) dispute when they claim that most junk DNA is functional. Their idea is based mostly on naive intuition/"common sense" ("if it's there it must be doing something") and failure to educate themselves about the relevant data which has shown that common sense is unreliable here: basically: (1) diversity of genome sizes, (2) simple genetic load arguments, (3) the composition of junk DNA looks mostly like the product of genomic parasites (viruses, transposons, etc.). We could add (4) conservation arguments but that's a more recent development.NickMatzke_UD_{December 19, 2014
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Nick, Could it be possible that "Junk" DNA is a valuable resource? After all, it appears to be a commodity among many microbes, is it not? Maybe that's why certain species retain more (savers), while others streamline (spenders)? At least it does not appear to be a problem for those organisms that have apparently exceeding large DNA savings accounts? Anyhow, how much do we really know about what DNA is doing, and what populations are doing with it? Would you say our total knowledge is 1% complete?, 10%?, ___%? Appreciate your time!littlejohn_{December 19, 2014
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We have explained it. You’re just being your typical Darwinist, a weaver of lies and deception. Nothing to see here, people. It’s the same old crap. Moving right along.
Your explanation, like Nick's, doesn't have the experimental data to resolve this particular case of a seemingly unnecessarily massive genome. No one knows what the extra information does. It's possible that the extra information only "activates" under unusual and or extreme conditions, it's also possible that it is junk. Until someone starts growing variants with clipped genomes under a host of conditions, all we'll have are guesses and "just-so" stories.rhampton7_{December 19, 2014
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The above review was from 2014. Here's another, Casey Luskin from 2007: http://www.evolutionnews.org/2007/06/wired_magazine_unashamedly_mix003762.html
Intelligent Design has Long Predicted This Day Proponents of intelligent design have long maintained that Neo-Darwinism's widely held assumption that our cells contain much genetic "junk" is both dangerous to the progress of science and wrong. As I explain here, design theorists recognize that "Intelligent agents typically create functional things," and thus Jonathan Wells has suggested, "From an ID perspective, however, it is extremely unlikely that an organism would expend its resources on preserving and transmitting so much 'junk'." [4] Design theorists have thus been predicting the death of the junk-DNA paradigm for many years: [...Luskin goes on to quote Mims 1994, Dembski 1998, Wells, etc.]
NickMatzke_UD_{December 19, 2014
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59 ppolishDecember 19, 2014 at 12:24 pm “big, slow, sluggish, low effective population size = big genome, lots of junk small, fast, active, high effective population size = small genome, less junk” Thank you Nick for that general rule, it makes sense. I don’t understand most of the fuss, and I sure don’t see any incompatibility to ID either. So thanks again. And btw, you’re a dick. Sorry, just kidding:) but had to throw that in. Had to.
Heh, funny :-) But, regarding: "I don’t understand most of the fuss, and I sure don’t see any incompatibility to ID either." Really?!? Is this a joke too? http://www.evolutionnews.org/2014/07/stephen_meyers_4087941.html E.g.:
ID researcher William Dembski in 1998: "On an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function." Meyer affirms that "the discovery in recent years that nonprotein-coding DNA performs a diversity of important biological functions has confirmed this prediction." He goes on to present a list of ten important functions of nonprotein-coding regions of the genome, including regulating DNA replication, regulating transcription, influencing the proper folding and maintenance of chromosomes, controlling RNA processing, editing, and splicing, and others, noting that in some cases, "junk" DNA has even been found to code functional genes. Meyer sums up his argument this way (p. 407):
Indeed, far from being "junk," as materialistic theories of evolution assumed, the nonprotein-coding DNA directs the use of other information in the genome, just as an operating system directs the use of the information contained in various application programs stored in a computer. In any case, contrary to the often heard criticism that the theory makes no predictions, intelligent design not only makes a discriminating prediction about the nature of "junk DNA"; recent discoveries about nonprotein-coding DNA confirm the prediction it makes.
In a footnote on the same page, Meyer references a letter submitted to the journal Science in 1994 by pro-ID scientist Forrest M. Mims III. The letter, which was rejected by the publication, suggests that looks can be deceiving when it comes to nonprotein-coding DNA:
They have always reminded me of strings of NOP (No OPeration) instructions. A do-nothing string of NOPs might appear as "junk code" to the uninitiated, but, when inserted in a program loop, a string of NOPs can be used to achieve a precise time delay. Perhaps the "junk DNA" puzzle would be solved more rapidly if a few more computer scientists would make the switch to molecular biology.
Meyer also reviews the functions of nonprotein-coding regions of the genome in the Epilogue to Signature in the Cell. On page 464, he notes that
the design logic of an information-processing system precludes carrying a preponderance of useless code, especially in biological settings where such excess would impose a burdensome energy cost on the cell."
Rather, Meyer argues, nonprotein-coding DNA "provides services and needed functions to the protein-coding DNA during gene expression. The prediction that "junk" DNA is actually functional is just one expectation of intelligent design. Meyer details a dozen other ID-inspired predictions in Appendix A at the end of the book.
NickMatzke_UD_{December 19, 2014
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"big, slow, sluggish, low effective population size = big genome, lots of junk small, fast, active, high effective population size = small genome, less junk" Thank you Nick for that general rule, it makes sense. I don't understand most of the fuss, and I sure don't see any incompatibility to ID either. So thanks again. And btw, you're a dick. Sorry, just kidding:) but had to throw that in. Had to.ppolish_{December 19, 2014
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Nick Matzke:
Well, this is a hilarious thread. The ID movement has been going on for years about the functionality of junk DNA and the foolishness of the idea that a lot of the DNA in large genomes is junk, yet no one can explain how that position can remain legitimate when one species has 3.5% of the genome of a very similar species.
We have explained it. You're just being your typical Darwinist, a weaver of lies and deception. Nothing to see here, people. It's the same old crap. Moving right along.Mapou_{December 19, 2014
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56 MungDecember 19, 2014 at 11:52 am Nick Matzke: Well, this is a hilarious thread. The ID movement has been going on for years about the functionality of junk DNA and the foolishness of the idea that a lot of the DNA in large genomes is junk, yet no one can explain how that position can remain legitimate when one species has 3.5% of the genome of a very similar species. First, you’re cherry-picking. Second, you’ve created a straw-man. When did the argument from junk DNA become dependent on the size of the genome? And let’s lay out your logic: Species x has a genome consisting of n base pairs. Species y is closely related to species x but has a genome consisting of only m base pairs, a small fraction of teh size of the genome of species x. Therefore most of the genome of species x is junk. a.) that’s a non-sequitur. b.) you’re assuming that species x and species y are closely related. c.) closely related species should have closely related genomes but these don’t, which is actually a problem for evolutionary theory, not for ID.
Mung, It's not a complex argument. 1. The species are very similar. 2. The genes are very similar (which is why we think they are closely related, in addition to the morphological similarity; heck, even the YECs typically admit that the special creation of each individual species is incorrect, and that species within genera share common ancestry). 3. We have lots and lots of evidence that genes are very important for building organisms. The debate (amongst the clueless) is over whether most of that non-genic DNA is also very important. 4. Nature has done the experiment showing what happens to the organism if you keep the genes, but delete most of the non-genic DNA. The answer is: not much. Everything needed for building the organism is in the 3.5% that was kept (which has a lot of genes, and undoubtedly also some non-genic DNA used for regulating the genes). 5. Therefore, most of the non-genic DNA is doing: not much. In other words, it's junk. We've known about this kind of thing for decades (the Genlisea and Utricularia examples are just particularly spectacular examples), but the ID movement systematically ignores it. On the rare occasions that it has come up (e.g. Jonathan Wells's book), they do nothing but flail helplessly.NickMatzke_UD_{December 19, 2014
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Nick Matzke:
Well, this is a hilarious thread. The ID movement has been going on for years about the functionality of junk DNA and the foolishness of the idea that a lot of the DNA in large genomes is junk, yet no one can explain how that position can remain legitimate when one species has 3.5% of the genome of a very similar species.
First, you're cherry-picking. Second, you've created a straw-man. When did the argument from junk DNA become dependent on the size of the genome? And let's lay out your logic: Species x has a genome consisting of n base pairs. Species y is closely related to species x but has a genome consisting of only m base pairs, a small fraction of teh size of the genome of species x. Therefore most of the genome of species x is junk. a.) that's a non-sequitur. b.) you're assuming that species x and species y are closely related. c.) closely related species should have closely related genomes but these don't, which is actually a problem for evolutionary theory, not for ID.Mung_{December 19, 2014
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wd400:
I can explain it. Most of the genome in the species with larger genomes will be junk DNA.
Surely you realize that you have not offered an explanation. Also, here's what you are claiming: The smaller the size of a genome, the more likely it is that the genome is fully functional. There's no reason for that to be the case, not without begging the question. At least none that I can see.Mung_{December 19, 2014
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I don’t think the founders of modern synthesis had anything to say about the evolution of genome size, since genomes were not exactly a focus in those days. But, as I have mentioned several times, much of genome size evolution can be explained by evolutionary genetics: absent a strong fitness costs repeats will copy them selves, so genomes will drift towards larger size, selection is stronger is larger populations so you’d expect creatures with smaller population sizes to be less able to stop the spread of repeats and so have larger genomes (check) and the correlation of genome size to cell size means genome-size will in turn correlate with the energetic needs of the genome’s host — salamanders have huge repeat-riddled genome, hummingbirds little clean ones.
It's never clear what IDists mean by "modern synthesis" -- usually it just means whatever they are opposing at the moment. But, as wd400 is alluding, modern neutral theory (e.g. Michael Lynch) is pretty effective here. The explanation of junk DNA mostly comes down to effective population size and cell size. Effective population size determines the efficiency of selection. For small populations, traits that are mildly deleterious (e.g. the tiny cost of replicating extra DNA) are effectively neutral, and can accumulate without being selected against. Any mutational bias, e.g. transposons self-replicating in the genome, can inflate genome size rapidly. This is slightly more controversial, but there appears to be a physical relationship between genome size and cell size -- the amount of DNA physically determines the size of the nucleus, and cells typically maintain a typical cell volume:nucleus volume relationship. In some cases, smaller cells might be selected for: rapid growth, high metabolism (smaller cells=more surface area), and/or more complexity in morphology (smaller cells can build more complex structures). These factors often correlate, so teasing them apart is not always easy, but it looks like: big, slow, sluggish, low effective population size = big genome, lots of junk small, fast, active, high effective population size = small genome, less junk Carnivorous plants often have high metabolism (for plants) and complex micro-structures, so the selection pressure for deletions of junk may be there, in cases where the population size is big enough. They also have the peculiar situation of usually being in low-nutrient environments, and especially if phosphate is the limiting nutrient in some carnivorous environments, they may have extra selection pressure against junk DNA.NickMatzke_UD_{December 19, 2014
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So an ancient snail should be junky and a roadrunner clean? Interesting.ppolish_{December 19, 2014
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Well, this is a hilarious thread. The ID movement has been going on for years about the functionality of junk DNA and the foolishness of the idea that a lot of the DNA in large genomes is junk, yet no one can explain how that position can remain legitimate when one species has 3.5% of the genome of a very similar species.
ppolishDecember 18, 2014 at 5:39 pm Nick, is the percentage of junk similar between the 60 Mbp and 1700 Mbp?
No. The small-genome species has basically all of the same genes as the large-genome species. Its genome is smaller because it has lost most of the transposons, fossil viruses, internal duplications of noncoding DNA, long introns, etc. and other detritus that accumulate in the genomes of large-genomed species.
37 MungDecember 18, 2014 at 8:34 pm The designers are not opposed to differing sizes of data storage media.
Oh, so you know the designers? Can you give us their contact information, I imagine a lot of people have questions for them. Also, please tell the ID leadership that they were wrong to say that ID theory doesn't include hypotheses about the IDers in ID explanations.NickMatzke_UD_{December 19, 2014
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For closely related species like these, and ignoring the effect of polyploidisation which doesn't appear to be a factor here, that would a pretty good approximation. It wouldn't work as well for species seperated by more evoluionary time. I don't think the founders of modern synthesis had anything to say about the evolution of genome size, since genomes were not exactly a focus in those days. But, as I have mentioned several times, much of genome size evolution can be explained by evolutionary genetics: absent a strong fitness costs repeats will copy them selves, so genomes will drift towards larger size. Some of that drift depend on the particular repeats found in a given clade (as I set earlier, most mammals repeats are dead). Selection is stronger is larger populations so you'd expect creatures with smaller population sizes to be less able to stop the spread of repeats and so have larger genomes (check) and the correlation of genome size to cell size means genome-size will in turn correlate with the energetic needs of the genome's host -- salamanders have huge repeat-riddled genome, hummingbirds little clean ones.wd400_{December 19, 2014
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WD, ranking organisms by size of genome would therefore also give one a junk ranking. That was easy. Are the results predicted by modern synthesis? Explainable?ppolish_{December 19, 2014
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I can explain it. Most of the genome in the species with larger genomes will be junk DNA.wd400_{December 19, 2014
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Can you answer Nicks’ question? How can you maintain that most DNA is functional while these very similar plants have such radically difference genome sizes?
You're asking a non-biologist to explain something that neither of you guys can explain? Again, that says a lot. But you give ID quite a lot of credit every time you do that. "Sure, evolution has a lot of lame arguments, but what does ID have?" You can go on giving ID that kind of credibility and equivalency all day long. If I merely say that your explanation is weak and that we don't know the function (we don't even know how or if any size genome fully causes function) then that makes my "ignorant" post quite worthwhile. I'm not claiming to be a scientist, but the little I know was enough to expose how weak the evolutionary response really is. And this is important - every day on this blog I can benefit from the arguments of evolutionary biologists like yourself. So, if you had knock-down arguments, I would have heard them by now. Instead, I think you can see what I learned in this case. It's a lot of smoke-and-mirrors and very minor claims.Silver Asiatic_{December 19, 2014
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The Junk DNA paradigm is just one of those problems and some are backing away from that terminology, at least.
Maybe this was not the paper to start in on the Junk DNA topic? Can you answer Nicks' question? How can you maintain that most DNA is functional while these very similar plants have such radically difference genome sizes? As to the rest, you have backed a long way for your orginal "grandiose" post, so I guess that's something. Of course each little sub-field within evolutionary biology and aligned subjects doesn't provide a knock-down argument for the fact life evolved. All I wanted to point out here is that, contra your ignorant rant at the top, evolutionary biology is a profitable framework in which to do science (something that can't be said for ID) and one of the things it can help us explain is the variation in genome size you were going on about.wd400_{December 19, 2014
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butifnot @35
From the ID view we are observing FANTASTICALLY engineered systems, of which we are just beginning to scratch the surface of understanding. Evolutionists seem to have the child-like and ignorant position that having recently stumbled into DNA they almost have it wrapped up.
That's it. When we step back and look at what evolutionists are really claiming - as having The Answer for the entire panoply of life on earth. Then we look at the abundance of those fantastically engineered systems - the same evolutionists cannot even explain how those systems work today. Supposedly they can claim knowing their origin? It's laughable. It's an incredibly ignorant position and lacks an obvious appreciation for what is observed. To follow that up and claim that some statistical alignments between the genome size and morphology (let's say nothing about the actual functions of the organism), for example, are evidence supporting the grand claim is, truly, child-like.Silver Asiatic_{December 19, 2014
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And evolutionary biology gives us the framework to explain test and even predict (did you read the pterosaur paper..) those correlations for genome size.
With evolution, it's the quality and relevance of the predictions when compared to the grandiose claims that are offered. I can predict lots of things about the next new species of insect that will be discovered. I think the evolutionary framework also leads to dead-ends, as many scientists are discovering. The Junk DNA paradigm is just one of those problems and some are backing away from that terminology, at least. From a design perspective, there may be something else going on to explain the variation in size and the non-correlation to complexity of function. Yes, I did read the paper. Statistical analysis alone does not offer convincing explanations. The paper revealed quite a lot of territory that remains 'enigmatic' (my word for it). Why a negative correlation in those species and not others? There are lots of reasons one could speculate. Selective pressures are called in as explanations, but that's not much different than saying "the designer wanted it that way". BA77 mentioned just-so-stories, I'd at least call the interpretations of the data to be evolutionary-storytelling at this point.
What does ID have?
From my perspective, ID has a lot going for it because it's true. So it is the correct framework for analysis (as many scientists have affirmed). It can drive us to search beyond what is claimed for mutation, selection and drift. Designed systems may be built with self-organizing principles, or they may use non-physical connections (language) to communicate function. ID opens up a lot of ideas for science. Just the effort to describe complexity, information, design, function, etc. is very worthwhile. When Michael Behe sought to find the Edge of Evolution, he was criticized as being wrong. But did his critics show what 'the real' Edge is? They were content to leave that ambiguous. If evolution, at least, made more modest claims for itself it would be less ridiculous, in my view. If someone wants to go around making statistical analysis of genome size and body size, I can't imagine why anyone would care. But to claim some correlations, with all the variation and margin of error that entails, are the evidence of the evolution of all of the functional DNA in the earth's biosphere is absurd, as I see it. That only shows how weak the evidence really is. The fact that those understandings are controversial, even among evolutionists only makes it worse.Silver Asiatic_{December 19, 2014
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REC:
From you reply, I think it follows, that in other organisms, if experiments were conducted where DNA was deleted to no ill effect, would you admit there is “junk” DNA in that genome.
That doesn't follow and demonstrates ignorance of intelligent designs. Redundant features can be deleted with no ill effects . Future needs can be deleted with no ill effects too.Joe_{December 19, 2014
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There have been no experiments to determine what the “extra” 1600Mbps is or does, so you can’t truthfully say that it is redundant features or anomalies.
Then you don't have any clue and shouldn't say anything. BTW the "anomaly" I was referring to is genome duplications that were kept.Joe_{December 19, 2014
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rhamton @36 From you reply, I think it follows, that in other organisms, if experiments were conducted where DNA was deleted to no ill effect, would you admit there is "junk" DNA in that genome.REC_{December 18, 2014
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"This is a perfectly sensible outcome within ID theory" As the near-hysterical responses to Nick's very reasonable query demonstrate, all things are sensible within "ID "theory"" ....double square quotes intended. Every base is precious. Every base is precious in some (undetermined) circumstance. Every base is precious because the designer loves artisic flourishes. Both parsimonious and massively expanded genomes are evidence of precise and fantastic design.REC_{December 18, 2014
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If you want to reduce the size of your junk, eat bugs. That is the takeaway from this study I think. Hmm, maybe I can sell a junk reducing concoction on the internet? "Tired of being compared to a Marbled Lungfish? Reduce the size of your junk with ppolish's scientifically proven bug juice"ppolish_{December 18, 2014
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IMO, the "extra" or seemingly unused sequences in a genome are probably not expressed for various environmental reasons. It's possible that transplanting the organism to a different environment (e.g., colder, warmer, wetter or drier climates; or different soil compositions) may suddenly reveal new traits. This is a perfectly sensible outcome within ID theory, IMO.Mapou_{December 18, 2014
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Obviously, with such a small genome, this was the earliest plant. I think this is a remarkable discovery.Mung_{December 18, 2014
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The designers are not opposed to differing sizes of data storage media. When someone buys a computer they often get to choose how much hard disk space they want. Different people can even buy the same brand of computer which might have different storage capacities even though the same brand and model. Can't you just imagine what anti-ID theory would make of computer hard drive sizes? Therefore computers aren't designed. right.Mung_{December 18, 2014
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