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G.aurea genome sequenced


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#1 Fernando Rivadavia

 
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Posted 17 February 2010 - 08:36 AM

Hello everyone,

I'm not sure where to post this, but I'm not sure if everyone has heard that the 1st CP to have its genome sequenced is Genlisea aurea! This has been mentioned superficially in a recent article, which actually focuses more on the fast speed of evolution in Utrics & Genlisea as well as the microbial communities living symbiotically within their traps:

Posted Image

In this article, there is a brief passage mentioning the metagenomic analysis of the microbial DNA sequenced with Genlisea traps. This was done with a 2nd-generation DNA sequencing technology called SOLiD. I'm sure future articles by this group will discuss the Genlisea genome in more depth. And I know of another group that is sequencing U.gibba as well.


All the best,
Fernando Rivadavia

#2 kisscool_38

 
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Posted 17 February 2010 - 10:22 AM

I was aware that some groups where sequecing the smallest plant genomes (i.d. Genlisea and Utricularia) but didn't know it was already published. Thank you for update Fernando.
The rise of new sequencing technologies very soon, even faster than solid, will give rise to a lot of new sequencings of many non-model plants. We are at the beggining of a new era of phylogenetics.

#3 patrickn

 
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Posted 19 September 2010 - 17:03 PM

Thanks for sharing this news. I am curious why a Genlisea sp. was sequenced, instead of Drosera sp. Just my opinion, Drosera sp. is more representative in Carnivorous plants.

#4 johns

 
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Posted 19 September 2010 - 19:11 PM

For anybody who is interested the full text can be found here (click one of the Full Text links on the page):
http://jxb.oxfordjou...61/1/5.abstract

#5 Fernando Rivadavia

 
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Posted 20 September 2010 - 07:54 AM

Thanks for sharing this news. I am curious why a Genlisea sp. was sequenced, instead of Drosera sp. Just my opinion, Drosera sp. is more representative in Carnivorous plants.


They chose Genlisea aurea because it was discovered to have the smallest genome known among angiosperms:

http://www.ncbi.nlm....pubmed/17203433

This makes it not only easier to sequence, but scientifically very interesting. Basically, how can an angiosperm survive with so little DNA? What are the essential genes for a minimal genome to work? There has been a huge buzz in the scientific community around Genlisea (and Utricularia) ever since this discovery. Genlisea have the potential to become an important model in understanding angiosperm genomics.


Best wishes,
Fernando

#6 moof

 
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Posted 20 September 2010 - 11:19 AM

Wow, even smaller than Arabidopsis! It may become a scientifically useful plant, very interesting news!

Peter

#7 kisscool_38

 
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Posted 20 September 2010 - 17:27 PM

Has this genome been annoted and published somewhere? I made a quite search this afternoon (as I was curious to find some special genes) but only got genes of Genlisea used for phylogenetics analyses.

Regards

Aymeric

#8 Fernando Rivadavia

 
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Posted 21 September 2010 - 07:44 AM

Has this genome been annoted and published somewhere? I made a quite search this afternoon (as I was curious to find some special genes) but only got genes of Genlisea used for phylogenetics analyses.


Nope, unfortunately the only info published so far is what we have above. As far as I know the 1st sequencing attempt did not get full coverage nor long contigs. So more sequencing would have to be done and may already be under way (or even finished!). We'll have to wait & see...

Best wishes,
Fernando

#9 kisscool_38

 
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Posted 21 September 2010 - 17:12 PM

Hum OK, I see. Quite strange not to get full coverage for a so short genome. I'm waiting for more so.

Regards

Aymeric

#10 patrickn

 
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Posted 21 September 2010 - 17:22 PM

Looking forward to the first complete carnivorous plant genome. :tu:

#11 Fernando Rivadavia

 
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Posted 21 September 2010 - 19:25 PM

Quite strange not to get full coverage for a so short genome. I'm waiting for more so.


It's sort of hard to explain, but the coverage problem has to do with how the genomic DNA is prepared into a library. If too much DNA is lost through the many processing steps, you can have a lot of gaps.

But even if they did get full coverage (which is not certain here), assembly is a completely separate issue, especially because all the sequences obtained were only 25bp in length. They used the 1st version of the SOLiD technology (one of the new 2nd generation sequencing technologies out there) back in 2008. They would now be able to get longer read lengths and better coverage with SOLiD or eitehr one of the other 2nd gen technologies, since they're all evolving so fast.

Last I heard, they were planning complementary runs in the 454 technology, which gives longer reads (<500bp) but much lower total throughput. This should help build a framework onto which align all the short 25bp reads.

Oh, but because there were proportionately A LOT of chloroplasts and also lots of mitochondria, they did get a full sequence for the 1st and almost full assembly for the latter (because the coverage was so much higher than the nuclear DNA).


Best wishes,
Fernando

#12 Zlatokrt

 
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Posted 22 September 2010 - 09:48 AM

They chose Genlisea aurea because it was discovered to have the smallest genome known among angiosperms:



G. margaretae is slightly smaller (if counted whole genome size)... but i am glad that G. aurea was chosen, it is one of my favourite species of this genus :lol:

#13 Fernando Rivadavia

 
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Posted 22 September 2010 - 12:39 PM

G. margaretae is slightly smaller (if counted whole genome size)... but i am glad that G. aurea was chosen, it is one of my favourite species of this genus


Actually, it seems that there may have been a mix-up and the smallest one in that article was also G.aurea, not G.margaretae. :)

Either way, a new article will hopefully be out soon with several new genome sizes for Genlisea, including maybe a new small record... ;)


Best wishes,
Fernando

#14 Tim Caldwell

 
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Posted 25 September 2010 - 06:07 AM

Actually, it seems that there may have been a mix-up and the smallest one in that article was also G.aurea, not G.margaretae. :)


I'm curious as to why it is that the smallest genome should be found in a species of Genlisea, rather than a species of Utricularia which is a genus ultimately derived from an ancient species of Genlisea.

I suppose it would just be that that early "pre-Utricularia" species of Genlisea had a bigger genome than some or all of the surviving species of Genlisea. Does anyone know for sure?

Cheers,
Tim

#15 Fernando Rivadavia

 
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Posted 25 September 2010 - 08:38 AM

Hello Tim,

I'm curious as to why it is that the smallest genome should be found in a species of Genlisea, rather than a species of Utricularia which is a genus ultimately derived from an ancient species of Genlisea.

I suppose it would just be that that early "pre-Utricularia" species of Genlisea had a bigger genome than some or all of the surviving species of Genlisea. Does anyone know for sure?


This is a common misconception about evolution. Utrics are not descended from Genlisea in the same way that we humans are not descended from chimpanzees.

The fact is that Genlisea and Utrics (just like humans and chimps) had a common ancestor, which may have looked more like either one of the modern genera or may have looked like neither one.

Who can say what the last common ancestor between Genlisea & Utrics (or humans and chimps) looked like? Evolution doesn't always move towards higher complexity. It could be that the last common ancestor between Genlisea & Utrics had active traps, but maybe the cost of active traps is very high and the lineage that eventually led to Genlisea lost their active traps as it found a more efficient method of capturing prey without using up so much energy.

Such a thing has happened with the ancestors of Triphyophyllum, which nowadays is carnivorous only during a brief period of its life. And the closely-related Ancistrocladus has apparently shed carnivory altogether.

And who can say what the genome size of the common ancestor of Genlisea & Utrics was like? Was it larger or smaller than either those of Genlisea and Utrics? Or maybe it was intermediate? The truth is, we don't even know why genomes vary so much in size and what the selective pressures are to make them bigger or smaller (nor what it is exactly that makes them bigger or smaller, what they can shed and still get by on in the case of Genlisea mini-genomes)

And to confuse you even further: Only some Genlisea seem to have tiny genomes, whereas others have genomes that are larger than those of Utrics and Pings, reaching up to about half the size of a human genome! That's a difference of >25X in genome size between the smaller and largest Genlisea genomes!!!!

Amazing, isn't it? Well, you will all hear more about Genlisea genome sizes in an upcoming article which I hope will be published in 2011... ;)


Best wishes,
Fernando

#16 Tim Caldwell

 
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Posted 25 September 2010 - 14:12 PM

Hi Fernando,

Who can say what the last common ancestor between Genlisea & Utrics (or humans and chimps) looked like? Evolution doesn't always move towards higher complexity. It could be that the last common ancestor between Genlisea & Utrics had active traps, but maybe the cost of active traps is very high and the lineage that eventually led to Genlisea lost their active traps as it found a more efficient method of capturing prey without using up so much energy.



My understanding (which is very limited BTW) is that the projections found on Utricularia traps have been shown to be vestigial remnants of the spiral tubes of a Genlisea-like ancestor which have 'devolved', but which were retained to serve a different purpose from their original one. If this is correct then the common ancestor of both groups might well have been at least superficially similar to modern Genlisea.

As for what the common ancestor actually looked like there's always the hope of fossils. But as with the common ancestor of chimps and humans, there will be endless debate on whether any particular fossil is ancestral to chimps, or to humans, or whether it belongs to some now-extinct side shoot that branched off at some point.

And to confuse you even further: Only some Genlisea seem to have tiny genomes, whereas others have genomes that are larger than those of Utrics and Pings, reaching up to about half the size of a human genome! That's a difference of >25X in genome size between the smaller and largest Genlisea genomes!!!!


Ah, this at least offers hope that my original suggestion wasn't too far off. I suppose it was based on my assumption that it's easier for a species to lose unnecessary genetic material than it is for it to evolve extra, useful material. But I don't know how true that is.

As you said earlier, it's interesting to ponder how a plant can get away with such a small genome, since most plants clearly need whatever size they have. I think I read a suggestion that Genlisea and Utricularia might have undergone some very rapid evolution in their recent history, and that the intense selective pressure that was driving it also resulted in a barely acceptable loss of extraneous genetic material.

Another question to ponder, assuming the common ancestor was similar to Genlisea, is how and why the transition to Utricularia occurred, and what the intermediate steps were. My own conjecture would be that at some point an 'eel trap' evolved a one-way swinging door at the entrance to the digestive bulb as an extra measure to prevent the escape of prey, which might also have made the inward pointing hairs somewhat redundant and might result in a major overhaul of the trap design that paved the way for the transition to an active suction trap.

Anyway, as far as I know Utricularia is the only genus of CP that has had three completely different types of trapping mechanism in its history: flypaper, eel trap, and now its current unique form.

Cheers,
Tim

Edited by Tim Caldwell, 25 September 2010 - 14:15 PM.


#17 Fernando Rivadavia

 
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Posted 25 September 2010 - 17:26 PM

Hey Tim,

My understanding (which is very limited BTW) is that the projections found on Utricularia traps have been shown to be vestigial remnants of the spiral tubes of a Genlisea-like ancestor which have 'devolved', but which were retained to serve a different purpose from their original one. If this is correct then the common ancestor of both groups might well have been at least superficially similar to modern Genlisea.


I don't know... I think we could only claim this *IF* we had a fossil of the ancestor showing that it had traps similar to Genlisea. Without the fossil, I believe we can only go as far as saying that the spiral traps of Genlisea and the trap appendages are analogous organs (and I don't know that they are).


As for what the common ancestor actually looked like there's always the hope of fossils. But as with the common ancestor of chimps and humans, there will be endless debate on whether any particular fossil is ancestral to chimps, or to humans, or whether it belongs to some now-extinct side shoot that branched off at some point.


Very true!!


Ah, this at least offers hope that my original suggestion wasn't too far off. I suppose it was based on my assumption that it's easier for a species to lose unnecessary genetic material than it is for it to evolve extra, useful material. But I don't know how true that is.


Don't forget that plants are always undergoing polyploidy events, doubling whole sets of chromosomes... And it's very hard to define "useful" DNA, since we don't even know why so much of it is there between the genes!


As you said earlier, it's interesting to ponder how a plant can get away with such a small genome, since most plants clearly need whatever size they have. I think I read a suggestion that Genlisea and Utricularia might have undergone some very rapid evolution in their recent history, and that the intense selective pressure that was driving it also resulted in a barely acceptable loss of extraneous genetic material.


Yes the genomes of Utrics & Genlisea certainly are undergoing extremely rapid evolution as has been shown by recent phylogenies of these groups and the difficulty to align sequences due to all the indels. It seems that even different populations of a single species can have widely different genome sizes and DNA sequences for the same genes!

In the paper that I cite at the top of this topic (http://jxb.oxfordjou...61/1/5.abstract), the authors hypothesize that the loss of DNA is a 2ary result of the trapping mechanism evolved in Genlisea & Utrics. They suggest that the water pumping from within the traps generates reactive oxygen which continuously cleaves the plant's DNA, and that all the new mutations and indels are accidentaly introduced while trying to repair these breaks, See the snippet below from the abstract:

Furthermore, Utricularia and its sister genus Genlisea share anomalous molecular evolutionary features, such as highly increased rates of nucleotide substitution and dynamic evolution of genome size, from approximately 60–1500 megabases depending on the species or even population. A mechanistic hypothesis, based on the mutagenic action of reactive oxygen species (ROS) is proposed to underlie these phenomena, involving error-prone repair at the level of DNA bases and double-strand breaks.


Interesting, huh???

Another question to ponder, assuming the common ancestor was similar to Genlisea, is how and why the transition to Utricularia occurred, and what the intermediate steps were. My own conjecture would be that at some point an 'eel trap' evolved a one-way swinging door at the entrance to the digestive bulb as an extra measure to prevent the escape of prey, which might also have made the inward pointing hairs somewhat redundant and might result in a major overhaul of the trap design that paved the way for the transition to an active suction trap.

Anyway, as far as I know Utricularia is the only genus of CP that has had three completely different types of trapping mechanism in its history: flypaper, eel trap, and now its current unique form.


Without fossils we can only speculate... But how amazing it would be if we could go back in time and study the intermediate forms, huh?? :)

Anyway. we sometimes find tantalizing hints of the past in modern day species. There is an amazing article from 2005, "Trap architecture in carnivorous Utricularia (Lentibulariaceae)" (http://www.sciencedi...f3&searchtype=a) which suggests that the ex-Polypompholyx species of Utricularia do not have an active trapping mechanism, but that it is passive and most similar to that of Genlisea!! See snippet from the abstract:

Some characteristics of the traps of terrestrial Utricularia multifida (subgenus Polypompholyx) differ remarkably from traps of the other species, e.g. trap-door anatomy and trap walls. This might be an indication for a primordial (non-suction) trapping mechanism in the former species, similar to that of the eel-traps of the closely related genus Genlisea.


If true, this article ultimately suggests that maybe Taylor was wrong in lumping Polypompholyx into Utricularia and that (despite recent molecular phylogenies) this genus should be separated once again.


Best wishes,
Fernando Rivadavia

Edited by Fernando Rivadavia, 25 September 2010 - 17:30 PM.


#18 Tim Caldwell

 
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Posted 26 September 2010 - 07:15 AM

Hi Fernando,

In the paper that I cite at the top of this topic (http://jxb.oxfordjou...61/1/5.abstract), the authors hypothesize that the loss of DNA is a 2ary result of the trapping mechanism evolved in Genlisea & Utrics. They suggest that the water pumping from within the traps generates reactive oxygen which continuously cleaves the plant's DNA, and that all the new mutations and indels are accidentaly introduced while trying to repair these breaks, See the snippet below from the abstract:


Yes, if correct it's absolutely amazing! It seems to imply that the evolutionary pressure on these genera to be effective carnivores has been so intense that even a side effect of having a greatly multiplied risk of mutation is actually an acceptable consequence. Of course, being so prone to mutation is probably a prerequisite for very rapid evolution.


the ex-Polypompholyx species of Utricularia do not have an active trapping mechanism, but that it is passive and most similar to that of Genlisea!! See snippet from the abstract:


I'm not sure if I'm understanding the article correctly, but it sounds to me like it's saying that their examination of a species with a basal position within the genus Utricularia shows evidence that the genus formerly had an 'eel trap' trapping mechanism, which is not entirely unexpected given the close relationship between Utricularia and Genlisea, and supports the theory that the common ancestor of the two genera had a similar or analagous structure to modern Genlisea.

But the end result of all this is a pair of genera that are strange by any standard. Carnivory is strange enough, and the trapping mechanism of Utricularia is absolutely extraordinary. It's a genus of plants that has no roots whatsoever, whose true leaves have evolved into strange subterranean carnivorous traps, and which has what appear to be leaves and roots which are both actually highly modified stolons. The only things about the plants that are actually what they seem are the flowers and flower scapes. The plants are doing much the same stuff as any other flowering plant, except that the adaption to carnivory has caused the plants to completely restructure themselves to a pretty much unprecedented degree.

The amount of variation in trap design in Utricularia is also pretty remarkable, and it's a shame that the traps are usually too small for us to appreciate the details, even on our cultivated plants.

Cheers,
Tim

#19 Fernando Rivadavia

 
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Posted 26 September 2010 - 20:20 PM

Hey Tim,


I'm not sure if I'm understanding the article correctly, but it sounds to me like it's saying that their examination of a species with a basal position within the genus Utricularia shows evidence that the genus formerly had an 'eel trap' trapping mechanism, which is not entirely unexpected given the close relationship between Utricularia and Genlisea, and supports the theory that the common ancestor of the two genera had a similar or analagous structure to modern Genlisea.


Speculation, speculation.... mere speculation. :) Without fossils we can't say for sure what the ancestral traps looked like, nor which one of the 2 genera looks more like the last common ancestor. It's very likely that the ancestral traps were passive, but again it could be that Genlisea lost the active part of the trapping mechanism. It could also be that the ancestral traps were small passive vesicles (similar to the ones described in this article for the ex-Polypompholyx species) and that they elongated in the branch that leads to Genlisea. We simply don't know and may never know.



But the end result of all this is a pair of genera that are strange by any standard. Carnivory is strange enough, and the trapping mechanism of Utricularia is absolutely extraordinary.


At least the trapping mechanism of Utrics is more or less understood, whereas Genlisea remains a mystery. Recent studies discussing the passive x active hypotheses have been very interesting, especially the ones showing that there seems to be some sort of mucilage barrier near the entrance to the "stomach"...


It's a genus of plants that has no roots whatsoever, whose true leaves have evolved into strange subterranean carnivorous traps, and which has what appear to be leaves and roots which are both actually highly modified stolons. The only things about the plants that are actually what they seem are the flowers and flower scapes. The plants are doing much the same stuff as any other flowering plant, except that the adaption to carnivory has caused the plants to completely restructure themselves to a pretty much unprecedented degree.


Yeah, this is truly an amazing fact about these plants!

The amount of variation in trap design in Utricularia is also pretty remarkable, and it's a shame that the traps are usually too small for us to appreciate the details, even on our cultivated plants.


I agree! And there's more variation in Genlisea traps than we seem to be aware of too... But right now it's the ex-Polypompholyx group which has captured my imagination and curiosity. I think we have a lot to learn from those species...


Best wishes,
Fernando

#20 Tim Caldwell

 
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Posted 27 September 2010 - 08:06 AM

Hi Fernando,

Speculation, speculation.... mere speculation. :) Without fossils we can't say for sure what the ancestral traps looked like, nor which one of the 2 genera looks more like the last common ancestor. It's very likely that the ancestral traps were passive, but again it could be that Genlisea lost the active part of the trapping mechanism. It could also be that the ancestral traps were small passive vesicles (similar to the ones described in this article for the ex-Polypompholyx species) and that they elongated in the branch that leads to Genlisea. We simply don't know and may never know.


Yep, I'd say it's pretty much speculation. I've only read the short abstract from your link, but I think what's probably going on is that the researchers would have begun their study with certain hypotheses in mind, including the very reasonable one that Utricularia might have evolved from an 'eel trap' similar to its sister genus Genlisea. And when they examined a species of Utricularia with a basal position in the genus, that is likely to retain archaic features, they were looking for features that are consistent with their hypothesis. Apparently they found some, but I agree it doesn't amount to proof.


But right now it's the ex-Polypompholyx group which has captured my imagination and curiosity. I think we have a lot to learn from those species...


I think I'm going to have to visit Langwarrin again soon - haven't been for a while. I think there are about five species of Utricularia there altogether, including U. dichotoma and U. tenella which should both be in flower soon, if they aren't already! OK, I'm a bit jealous of your field trips... but now it's your turn :-)

Cheers,
Tim

Edited by Tim Caldwell, 27 September 2010 - 08:16 AM.