37 replies to this topic

[Tim Caldwell]

Hi Fernando,

One thought that struck me as a result of our conversation concerns the increased risk of genetic damage due to the oxygen that's produced from pumping water. It's actually something we're all warned about: the reactive properties of oxygen pose a risk of genetic damage that can cause cancer in humans, and we're told to eat lots of anti-oxidants to counteract it. I was actually going to joke about how maybe Utricularia should be eating more vegies, and then I remembered that I'd come across an article about Utricularia that discussed the large amount of algae that is found in Utricularia traps, and whether it was an unavoidable and detrimental accident that contributed to Utricularia's absence from some bogs; or whether it was intentional and offered some benefit to the genus. Here's the link:

http://www.springerl...upj68u38m142t6/

Suspecting there might be a connection, I did a google search using the key words "algae anti-oxidant" and got some pretty encouraging results!!  And so - I'm just chucking this out there as a possibility - it might be that Utricularia is able to minimise the genetic damage it sustains as a byproduct of carnivory by consuming highly anti-oxidant algae.

Again, just my own hypothesis, for whatever it's worth.

Cheers,
Tim

Edited by Tim Caldwell, 29 September 2010 - 07:45 AM.

[Fernando Rivadavia]

Hey Tim,

Wow, that is actually an amazing connection!! It could certainly be true... However we know for a fact that Utrics and Genlisea are suffering rapid evolution, so it doesn't seem like a hypothetical algae diet is helping them. :)

And yes, recent studies have suggested that there are commensal algae living within the traps of at least some Utrics and Genlisea. But we don't really know what they are doing there, what they get out of it, nor if some of them (dead ones?) are being digested by the traps. One article detected active secretion of sugars into the traps by the plants, supposedly to feed these algae. If so, this would mean that the algae have a very important symbiotic function...

Either way, as you suggest, it could be that they're digesting at least some of these algae and using the anti-oxidants to help minimize the negative effects of the reactive oxygen, very interesting thought!


Best wishes,
Fernando

[Tim Caldwell]

Hi Fernando

Fernando Rivadavia, on 29th September 2010 - 18:14 PM, said:

Wow, that is actually an amazing connection!! It could certainly be true... However we know for a fact that Utrics and Genlisea are suffering rapid evolution, so it doesn't seem like a hypothetical algae diet is helping them. :)

As you say, the genus is having to deal with some serious genetic challenges, and if algae is indeed there to moderate those problems then it might be making all the difference between success and failure for the genus.

Fernando Rivadavia, on 29th September 2010 - 18:14 PM, said:

And yes, recent studies have suggested that there are commensal algae living within the traps of at least some Utrics and Genlisea. But we don't really know what they are doing there, what they get out of it, nor if some of them (dead ones?) are being digested by the traps. One article detected active secretion of sugars into the traps by the plants, supposedly to feed these algae. If so, this would mean that the algae have a very important symbiotic function...

If Utricularia are intentionally 'farming' algae, then the antiodixant thing certainly offers one possible explanation for why they might be doing it. It might be that the algae are excreting antioxidants or leaving them behind for the plant when they die, which would make farming them a much better strategy than just digesting any that randomly enter the traps.

Cheers,
Tim

[Fernando Rivadavia]

Hey Tim,

Quote

As you say, the genus is having to deal with some serious genetic challenges, and if algae is indeed there to moderate those problems then it might be making all the difference between success and failure for the genus.

Quote

If Utricularia are intentionally 'farming' algae, then the antiodixant thing certainly offers one possible explanation for why they might be doing it. It might be that the algae are excreting antioxidants or leaving them behind for the plant when they die, which would make farming them a much better strategy than just digesting any that randomly enter the traps.

Certainly could be true... We'll just have to wait and see what future studies will find!


Best wishes,
Fernando

[droseraman]

Late to the party, but thanks for posting about this. Also enjoyed all the discussion, by the way!

[James O'Neill]

Wait; when you say

Quote

It's a genus of plants...which has what appear to be leaves and roots which are both actually highly modified stolons

Does that mean that even the very leaflike structures of U. nelumbifolia and reniformis are stolons? weird!

[Tim Caldwell]

James O'Neill, on 8th October 2010 - 17:44 PM, said:

Does that mean that even the very leaflike structures of U. nelumbifolia and reniformis are stolons? weird!

Yep, they are, and it certainly is weird!

The true leaves of Utricularia's distant ancestors evolved into the subterranean traps, somethng which wouldn't even have been possible unless another way could be found of photosynthesising. So the genus modified its stolons to serve that function. And as you pointed out, in some species they have become quite large, elaborate and leaflike.

Utricularia represents a very extreme example of the kinds of secondary adaptions you see in many other kinds of CPs, where the carnivory which evolved to solve one problem actually creates other problems, which in turn need to be solved. For example, the traps of nepenthes are actually modified leaves, and as evolution started pushing them in the direction of becoming carnivorous traps they became less and less efficient at collecting sunlight, which might have curtailed their evolution in that direction if the genus hadn't been able to compensate by enlarging its petioles to serve as leaves. So what we call 'leaves' and 'tendrils' on nepenthes are actually a very modified petiole.

But utricularia took this kind of process to a ridiculous extreme and pretty much completely reorganised itself.

Cheers,
Tim

[James O'Neill]

So as has been said, really only the flowers of the Utricularia are reminders of the plants they once were. And even the flowers are strangely shaped.
I can see that the 'leaves' on aquatics are obviously modified stolons, but with the big ones you wouldn't have thought it.

So Utricularia is a very interesting genus indeed. They have no roots, they have leaves that aren't, the flowers are many different shapes, the trapping mechanism is amazing; and the trap evolved from proper leaves. Wow.

[bishybarnabee]

Hi Fernando,

Really interesting discussion! I saw you mentioned that people are working on sequencing the Utricularia gibba genome, can you tell me who it is and whether they are near to publication? I trawled through Google but couldn't find very much information there.

Thanks!

Karen

[Fernando Rivadavia]

Hey Karen, it was a group at CINVESTAV Irapuato, Mexico. Haven't talked to them in over 2 years though, so don't know how it went.

Fernando

[bishybarnabee]

Hi Fernando,

Thanks very much for your help! I just did a quick Google search with that information and they have just published here...http://www.biomedcentral.com/content/pdf/1471-2229-11-101.pdf".

Looks interesting!

Karen

Edited by bishybarnabee, 14 June 2011 - 15:49 PM.

[Fernando Rivadavia]

Hello Karen,

I am only seeing your reply now (I stopped receiving mail warnings from the forum). Coincidentally, I just spoke to someone from the institute this week and learned that they'd published, but hadn't had time to search for it yet, so this saves me time, thanks!

I see they sequenced the transcriptome and not the genome, interesting... Hopefully I'll be able to read and understand the article! :)


Best wishes,
Fernando Rivadavia

[Dave Evans]

Fernando Rivadavia, on 26 September 2010 - 20:20 PM, said:

We simply don't know and may never know.

Dear Fernando and Tim,

You may be aware, some of the species which still have large genomes may still have ancient DNA that is more or less turned off.

If present, it might still work in the right conditions...

Edited by Dave Evans, 29 November 2011 - 03:34 AM.

[LeeBr]

Dave Evans, on 29 November 2011 - 03:34 AM, said:

Dear Fernando and Tim,

You may be aware, some of the species which still have large genomes may still have ancient DNA that is more or less turned off.

If present, it might still work in the right conditions...

Dave,

non-functional "fossil DNA" can accumulate in the genome and bits of non-functional nuclear DNA can get copied into the chloroplast and mitochondrial DNA (and vice-versa) but in the case of Genlisea and Utricularia the oxidative damage would probably soon degrade it to the point that it would no longer be functional even if it were switched back on.

Perhaps that is why their genomes have shrunk; the DNA repair mechanisms have their hands full just repairing the functional DNA without having to repair non-functional DNA as well, so any mutant plant that loses some of the non-functional DNA from its genome will be strongly selected for as its repair mechanisms will then be better able to repair the remaining functional DNA.

LeeB.

[Zlatokrt]

LeeBr, on 29 November 2011 - 05:29 AM, said:

Dave,

non-functional "fossil DNA" can accumulate in the genome and bits of non-functional nuclear DNA can get copied into the chloroplast and mitochondrial DNA (and vice-versa) but in the case of Genlisea and Utricularia the oxidative damage would probably soon degrade it to the point that it would no longer be functional even if it were switched back on.

Perhaps that is why their genomes have shrunk; the DNA repair mechanisms have their hands full just repairing the functional DNA without having to repair non-functional DNA as well, so any mutant plant that loses some of the non-functional DNA from its genome will be strongly selected for as its repair mechanisms will then be better able to repair the remaining functional DNA.

LeeB.

An interesting point Lee. If I understand well, you say, that Utricularia and Genlisea have so week DNA repair mechanisms, that species with small genomes are favoured against those with larger genome because their DNA repair mechanism are less burdened, thus work better? Do i understand correctly?

I have always took it from the other side: Retrotransposons play key role in the genome size increase/shrinking. They are probably mostly useless for the plants (although they can cause potentionally useful mutations, etc...), moreover the plants have to invest nutrients (which are rare in their habitats) to synthetize the whole genome with all those retrotransposons. The species, which have good DNA repair mechanisms, can eliminate retrotransposons and can let only the most necessary part of genome - and the plant doesnt have to invest so much nutrients in it. Because of this theory, i considered Utricularia and Genlisea to have strong DNA repair mechanisms (at least in present. Who knows, how their genome looked like a few milions years back?).

But your theory is interesting too... Now I do not know what to believe
Best regards
Adam

[Dave Evans]

Dear Lee,

Good points.  If anything is left, its probably like alpine swiss cheese.  Full of holes!  I was thinking about it some more and if this mode of evolution is accurate; then Utricularia have even another way to "speed up" their evolution.

The type of damage they suffer will surely induce mutations which are in cells located at the tips of the plant.  But in most species of Utricularia even these areas can bud and grow into a whole new plant with mutation present in most or all cells.  Their perchance for asexual production is actually helping to speed up their accumulation of mutations as the populations can more quickly conserve "sport type mutations".  In most plants, sports have to be grafted in order to be conserved.  Well stoloniferous Utrics don't need to be grafted for this conservation to take place.  A sport can develop and become a flowering individual in a single season.

I'm not familiar with Genlisea, do they grow similarly to Utricularia on stolons?  If not, then perhaps that is why there are so many more Utric species...

Edited by Dave Evans, 30 November 2011 - 03:51 AM.

[LeeBr]

Zlatokrt, on 29 November 2011 - 12:54 PM, said:

An interesting point Lee. If I understand well, you say, that Utricularia and Genlisea have so week DNA repair mechanisms, that species with small genomes are favoured against those with larger genome because their DNA repair mechanism are less burdened, thus work better? Do i understand correctly?

I have always took it from the other side: Retrotransposons play key role in the genome size increase/shrinking. They are probably mostly useless for the plants (although they can cause potentionally useful mutations, etc...), moreover the plants have to invest nutrients (which are rare in their habitats) to synthetize the whole genome with all those retrotransposons. The species, which have good DNA repair mechanisms, can eliminate retrotransposons and can let only the most necessary part of genome - and the plant doesnt have to invest so much nutrients in it. Because of this theory, i considered Utricularia and Genlisea to have strong DNA repair mechanisms (at least in present. Who knows, how their genome looked like a few milions years back?).

But your theory is interesting too... Now I do not know what to believe
Best regards
Adam

Adam,
I don't think the repair mechanisms are weak, I just think the oxidative damage is so high that they have to operate continually just to keep up, which must have a high metabolic cost.
So by shrinking the genome down to the absolute minimum possible they lower this metabolic cost.

This is like the extremophile that was discovered living in very hot water; it was thought that it's DNA had to be very stable to resist being broken down by the heat, but further study showed it was continually being damaged but the repair mechanisms were fixing it even faster.
Like the red queen in Lewis Caroll's "through the looking glass" the repair mechanisms had to run as fast as they could just to stay in the same spot.


LeeB.

[LeeBr]

Dave Evans, on 30 November 2011 - 03:50 AM, said:

Dear Lee,

Good points.  If anything is left, its probably like alpine swiss cheese.  Full of holes!  I was thinking about it some more and if this mode of evolution is accurate; then Utricularia have even another way to "speed up" their evolution.

The type of damage they suffer will surely induce mutations which are in cells located at the tips of the plant.  But in most species of Utricularia even these areas can bud and grow into a whole new plant with mutation present in most or all cells.  Their perchance for asexual production is actually helping to speed up their accumulation of mutations as the populations can more quickly conserve "sport type mutations".  In most plants, sports have to be grafted in order to be conserved.  Well stoloniferous Utrics don't need to be grafted for this conservation to take place.  A sport can develop and become a flowering individual in a single season.

I'm not familiar with Genlisea, do they grow similarly to Utricularia on stolons?  If not, then perhaps that is why there are so many more Utric species...

Dave,

Apparently Genlisea grow from a small rhizome, so mutations to this growing point could result in a changed plant too.
I don't know if the rhizomes branch or not.

LeeB.