U. gibba tosses out non-coding DNA

[Apoplast]

A new study of Utricularia gibba flies in the face of the view that the high proportion of non-coding DNA found in most species is necessary for multicellular life. As it tuns out, U. gibba only have 3% of their genome that is non-coding, compared with 98% in humans!

Here is the link to the original article:
www.nature.com/nature/journal/vaop/ncurrent/full/nature12132.html

And for those of you who are less scientifically literate, here is a link to a summary:
www.sciencedaily.com/releases/2013/05/130512140559.htm

[Apoplast]

No takers? I guess I'm a little surprised. This is an example of a carnivorous plant forcing us to rethink how we view the genomics of being a multicellular organism. This could be a big deal! Not only are the non-coding regions of DNA, due to their typically high levels of occurrence in most multicellular species, thought to be important for the functioning of the genome (the thinking goes something like this - "How could we humans have 98% of our genome do nothing?! It must be important!").

But on top of that in angiosperms the γ triplication, which is a tripling of the entire genome that occurred at the time of or just prior to the radiation of the core eudicots (which contain ~75% of angiosperm species), is thought to have been important for the impressive speciation within that lineage. The same lineage to which Utricularia, as a member of the Lamiales, belongs!

This means, that the adaptationist stories we have built around the need and utility of the non-coding regions of DNA may not be absolute. And it is one of the most diverse lineages of carnivorous plants (here I am guessing all Utricularia will have similarly small genomes for identical reasons, which I base off the known small genome of some of the Genlisea), which possess some of the most intricate structures know in plants, their bladder traps, that is challenging this dogma.

Okay sure, I'm a nerd. But this is exciting stuff. Carnivorous plants may become model systems for genomic research. And that is big CP news!

[adamcross]

The results are certainly interesting, but I'm surprised it warranted publication in Nature. In phosphorous impoverished habitats, species utilise any mechanisms available to reduce P usage, and DNA production and replication are relatively P intensive. Compressed genomes therefore make sense for P-limited organisms, and this certainly isn't the first reported case of a compressed genome (see Western Australian Cyperaceae). Similarly, even widespread aquatic plants have evolved persistent and specific genotypes which exploit particular and often restricted niches in which success is enhanced, and a compressed genome is favourable under these circumstances also. So, really, the presence of a compressed genome in a clonally reproductive widespread aquatic plant with specific adaptation for persistence in P-limited habitats is not entirely unsurprising.

Also, people often seem to mistake 'non-coding' for 'non-functional'; simply because parts of the genome don't appear to code for anything specific doesn't mean we should assume that those parts have no biological function.

[coline]

Well, I have read about how many plants indeed have needed the DNA duplication at some point of their history for the evolution, as the fact now many of today's crops have a big genome made by that multiplication, it is a really important part of plant evolution as in many cases plants have defficient cross-pollination mechanisms to ensure variability in their habitats, or are widespread so long they may never get different DNA to combine with, and their only big changes could occur by an extremely rare cross-pollination event or the doubling of the genome, or even a part of it.
Indeed, as Adamcross says, a big genome implies the need of extra phosphorus to the cell production and multiplication, and many ecosystems may have a moderate or big lack of the element, same situation as the development of the carnivory to supply some of the necesary elements to the plant, a reduced consumption system is a good adaptation to the plant. Don't really know how exactly would a plant as this would be selected speciffically among others but it has to be for some reason.
And reffering to Non coding DNA, well, it does not make proteins, but it is really an esential part in expression regulation, all the binding sites for different proteins, membrane activated chains, repressors and many other factors that normally are in the upstream region of a sequence that make possible that an organism regulate their system. Or also, the fact of having extra copies of a gene sequence letting the organism live even when having a mutation in other DNA strands are some of the many uses and importante to the non codins sequence.
But some others are bad functions, the Inteins for example, that use the DNA as their reproduction medium, this, by mediating their own expression and multiplication, they many times act as homming endonucleases, that by expressing themselves, they use their machinery to introduce their sequence in a intein free DNA strand, in some cases involving a big additional DNA use, causing the cell to need more energy to multiply both its ADN and the extra intein material. This has no benefits for the organism as they are also called the sellfish proteins; they only use the energy and resources to preserve and multiply their sequences.

[Apoplast]

Excellent! This is the type of discussion I was hoping to stimulate by posting this article. Thanks Adam and Coline!!!

Adam - You are absolutely correct, there is an important stoichiometric counter balance that needs to be considered. In fact, there is a body of literature that predicts exactly the results found in the recent Nature paper, perhaps best typified by the 2009 paper by Hessen et. al. Now, I fully admit that I am not familiar with the examples from the West Australian Cyperaceae (though this reminds me that on so many levels you live in one of the botanically, coolest places in the world). However in my estimation, if what is found in U. gibba (and probably other utrics and Genlisea) is being driven primarily by P limitation, it is potentially ancestral in the lineage and therefore they are diversifying well without this 'genetic fuel' of large quantities of 'surplus' DNA. And that I still think is really cool (though perhaps not unique if the WA Cyperaceae are doing something similar - Do you have some references you'd recommend for those examples?). Plus, utrics may now be a good lineage to test how this process works on a mechanistic/genetic level as well as examining the broad scale evolutionary consequences such streamlined genomes. All that said, was this pub worthy of being in Nature? Maybe. Maybe not. But, that's part of the game high impact journals play. If this results in utrics becoming a genome size selection model organism, then we'll look back and say yes. If it goes nowhere, we'll look back and say no. (Side note: I fully understand "non-coding" is not synonymous with "non-functional".)

Coline - I agree that the non-coding regions are not necessarily useless pieces of DNA. My assertion is that the herculean efforts we have put into finding utility for this largest chunk of our genome have been, at least partly, motivated by our desire to not see the bulk of our genome as "useless". I'm not arguing these endeavors have been in vain, nor that they have been unsuccessful. Simply, that we as a species seem a little uneasy that our genome seems so permissive of containing DNA 'without purpose'. It will be interesting moving forward comparing species at different ends of the continuum for the degree of coding DNA. Is non-coding DNA really just permitted wasted space and resources? Is it stored genetic potential? And, how is the balance between coding and non-coding regions struck through evolutionary time to the potential success of detriment of a lineage? Fun stuff!

And in case anyone out there is interested, despite my interest in this article, I have no connection to the paper or research it contains. I don't even know any of the authors.

[adamcross]

With 29 authors on the paper, that's almost surprising Apoplast!

I don't have the publications to hand, but will try to dig them out if I get the chance. As an aside, having a compressed genome shouldn't necessarily influence diversification rate- the genes themselves are still present, and are readily able to mutate/cross over/other genetic jargon in response to environmental factors and selection pressures.

[Apoplast]

May 14, 2013 14:29:18 GMT adamcross said:

With 29 authors on the paper, that's almost surprising Apoplast!

Hi Adam - Too true. Everyone wants in a on a Nature or Science paper. I've watched authorship requests (read: demands) explode once there was a hint of it going to either of the two biggies.

Though your aside may be correct, the opposing viewpoint has been asserted consistently in a wide range of literature; not only the γ triplication in angiosperms, but the utility of polyploidy in plants in general, as well as a host of other claims. It seems the prevalent belief out there is that this apparently "superfluous" genetic information is useful material to select upon. True enough the genes themselves can and will be selected upon, but that doesn't argue that having extra copies of genes or other regions which are under reduced selection, won't allow for increased variation, being larger targets for mutation for example. I'm not suggesting I agree entirely with this assessment, only that is it relied upon for numerous adaptive arguments in all range of organisms. So regardless of the cause, I think, utrics not fitting into this mold is pretty interesting.

And if you happen to come across some good genome reduction papers for the WA Cyperaceae, please do send the references along. I'd be interested to reading them.

[coline]

Yes, exactly as you mention, those big regions that initially were published as weird junk DNA are only just started to be analized to comprehend their full functionality, as I say they are important regions in the regulation of gene expresssion; but who knows if they have other unknown functions that may be even better. Also as a thought I just had, I think that they still use some P to be build and even some N, but they are built only 1 time in each new cell made, in difference to the proteins, they need to be made and re-made lots of times in a cell's life period, in the process using up some RNA which is recycled, and then occupying more N than the used by a mere DNA sequence, and even more, lots of energy to synthesize those molecules, so I say and wonder; would'nt it be more efficient to regulate DNA expression using the very DNA or proteins made by its translation working in some sort of way?

[leeb]

Hi all, here's some thoughts; if P limitation leads to selection for reduced genomes it would be interesting to see if Utricularia and Genlisea have reduced the size of their mitochondrial and chloroplast DNA as well.
Or as a wild speculation, as some chloroplast and mitochondrial genes have been inserted in the nuclear genome and lost from the organelles DNA, perhaps something like this can work in reverse; perhaps the non coding DNA has been lost from the nucleus because it's function has been transferred to the mitochondrial DNA, after all angiosperms have mitochondria with relatively large amounts of DNA.

LeeB.

[Apoplast]

Hi Leeb - First off welcome to the forum! And thanks for adding such an interesting comment too. What a great start! You raise an interesting point. I must admit my familiarity of mitochondrial DNA is mostly from metazoans. Because metazoan mitochondrial DNA is fairly 'lean', I'd be interested to learn a little about the "relatively large amounts of DNA" in angiosperm mitochondria. I guess the liklihood of your prediction would depend on how much 'play' there is in the mitochondrial DNA. Can you recommend any papers on the topic? Thanks!

[leeb]

Hi apoplast.
Angiosperm mitochondrial DNA is interesting.
Whereas animals have 14-20 kilobases in their mtDNA and fungi have 18-78 kilobases the mtDNA of plants ranges from 200kb up to 11.3 megabases.
It also contains segments of DNA that were originally in nuclear or chloplast DNA.
Also some of the tRNA's in mitochondria appear to be of chloroplast origin.

Apparently there are not that many genes in the mtDNA but lots of repeated DNA sequences between the genes.
So there might be quite a bit of 'play' available.

A couple of recent open access papers are Kitazaki and Kubo; Journal of Botany 2010: "cost of having the largest mitochondrial genome:evolutionary mechanism of plant mitochondrial genome" and Sloan et. al. 2012 in Plos Biology January 17 2012: "rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates".
Incidentally only a few angiosperm mtDNA's have been fully sequenced, so larger ones will probably be found.
So if P limitation is important maybe Utricularia and Genlisea will either have shrunk their mtDNA or else have limited the number of mitochondria per cell.
On the other hand if they have shifted the non coding functions from the nuclear DNA to the mtDNA they may have to retain large mtDNA irrespective of any P limitation.

LeeB.

[ICPS-bob]

Just for ease of reference, here are links to the papers that leeb referenced

Kitazaki and Kubo; Journal of Botany 2010
downloads.hindawi.com/journals/jb/2010/620137.pdf

Sloan et. al. 2012 in Plos Biology January 17 2012
www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001241

[Apoplast]

Hi Leeb - Sorry I didn't reply earlier. I haven't had much time to sit down recently. It's a very interesting point you raise about the cost of repeated DNA sequences outside of the nuclear genome and the relationship to P limitation. If discovered, a slim chloroplast or mitochondrial genome may have the same driving cause which results in a lean nuclear genome. But whether it is P limitation that is the predominant driving force or not, may not be discernible from the pattern any more so than what we know from the nuclear genome alone. However, the reverse is not true. In that case, where the nuclear genome is largely coding and there is a fairly bulky mitochondrial genome, it could argue P limitation is not as important as suggested. Sounds good. Let's do it. Who's funding it?

Hi Bob - Thanks for the links! I actually haven't read the papers yet, but I have no excuse now.