Accessible research: A tiny bladderwort (that’s a plant with little “bladders”) genome

| 20 Comments

The genome from a species of bladderwort (Utricularia gibba) was recently published. Ed Yong has a wonderful summary about the bladderwort genome paper and its relationship with current debates regarding what is functional (introduction to the ENCODE project). Here’s my accessible research introduction:

The bladderwort is a carnivorous plant with beautiful yellow flowers on top:

Horned Bladderwort (4959623968)
This is a captivating “horned bladderwort” (Utricularia cornuta), by Jacopo Werther

And curious “bladders” on its roots that it uses to trap its prey.


Common Bladderwort
Bladder traps on the roots of the “common bladderwort” (Utricularia vulgaris), by pellaea.


The genome of this plant is so interesting because it is quite small. The authors go so far as to call it a “minimal” genome.

What makes it minimal?
Often, when talking about genetics, we usually talk about the genes. These are the pieces of DNA that code for proteins. These are “coding” regions. There are also pieces of DNA that do not code for proteins. We call these “non-coding”. The genome is the full set of coding and non-coding DNA. Some species have lots of non-coding DNA (like humans, and onions). Other species have very little non-coding DNA, including this bladderwort.

Although the bladderwort has nearly 10,000 more genes than a human, these genes are very compressed and overlapping so that the bladderwort genome and the human genome have about the same amount of coding DNA sites. But, the bladderwort genome has a lot less non-coding DNA, for a total genome size of 87 million bases, while the human genome has bloated amount of non-coding DNA a total genome size of 3,164.7 million bases. That’s over 36 times more total DNA than the bladderwort! (Note: the total DNA content does not indicate complexity - whatever that is. Check out the range in genome size of “flowering plants” at the top of this plot.)

Was the bladderwort genome always so slim?
No. By comparing with other yummy plant genomes (papaya, grape, tomato and Arabidopsis, a flowering mustard weed), and by analyzing the gene content within the bladderwort genome, Ibarra-Laclette et al. concluded that the bladderwort genome, like many plants, experienced duplications of its whole genome. Afterward there were some losses of large regions of DNA, but much of the reduction in DNA content from these duplications occured through what they call “microdeletions”, where small pieces of DNA here and there were deleted.

Are all bladderworts the same?
Just like there are many species in the taxonomic family Hominidae (orangutans, gorillas, bonobos, chimpanzees and humans), there are many species in the the taxonomic family of bladderworts (called Lentibulariaceae). Genome shrinking is not unique to this species of bladderwort, but is also not shared across all species of bladderworts. Curiously, genome size in the whole family of bladderworts varies from 60 million base pairs to 1,500 million base pairs. That is a lot of variation considering that genome sizes across all Hominidae are all within the range of 3,000 million base pairs (plants genomes get no respect).

Although genome size varies quite a bit, the bladderworts look and function in similar ways. So, while some of the noncoding sequence is functional (providing instructions for how and when to turn the genes on and off, in time, in response to the environment, and in particular tissues), it seems highly unlikely that there would be so many more instructions in the bladderwort with 1,500 million base pairs than in the bladderwort with 60 million base pairs. A lot of the non-coding DNA, therefore, is likely also non-functional.

Utricularia vulgaris 003
bladderwort (Utricularia vulgaris) in the water. by H. Zell.


In the closing line of the bladderwort genome paper:

In summary, U. gibba genome architecture demonstrates that angiosperms can evolve diverse gene landscapes while overall genome size contracts, not only during expansions. Furthermore, in contrast to recent publications that highlight a crucial functional role of non-coding DNA in complex organisms such as animals24, the necessary genomic context required to make a flowering plant may not require substantial hidden regulators in the non-coding ‘dark matter’ of the genome.




Enrique Ibarra-Laclette, Eric Lyons, Gustavo Hernández-Guzmán, Claudia Anahí Pérez-Torres, Lorenzo Carretero-Paulet, Tien-Hao Chang, Tianying Lan, Andreanna J. Welch, María Jazmín Abraham Juárez, June Simpson, Araceli Fernández-Cortés, Mario Arteaga-Vázquez, Elsa Góngora-Castillo, Gustavo Acevedo-Hernández, Stephan C. Schuster, Heinz Himmelbauer, André E. Minoche, Sen Xu, Michael Lynch, Araceli Oropeza-Aburto, Sergio Alan Cervantes-Pérez, María de Jesús Ortega-Estrada, Jacob Israel Cervantes-Luevano, Todd P. Michael, Todd Mockler, Douglas Bryant, Alfredo Herrera-Estrella, Victor A. Albert,  & Luis Herrera-Estrella.  
Architecture and evolution of a minute plant genome. 2013. Nature
 http://dx.doi.org/10.1038/nature12132

20 Comments

Does anyone know what selection pressures might operate in order to select for such small genome size? It seems that they would have to vary substantially within the group in order to produce this type of genome size variation.

Of course, some creationist is bound to pop up soon claiming “see there is no junk DNA in that plant” completely missing the point that this means that there is lots of “junk DNA” in many other organisms.

It should be noted that Utricularia is a pet plant of IDcreationists because Wolff-Ekkehart Lonnig described the its traps as irreducible complex.

They try to address which evolutionary pressures might be at work, but basically find that there isn’t a great explanation for what would “drive” this gene loss.

One supposition is that some of the genome reduction may have been related to its embryogenesis, but I think that this would be similar across other bladderworts with larger genomes.

If wide-spread selection were acting to reduce genome size, it might also be expected to reduce diversity, but they find that diversity is not reduced in this bladderwort (small genome) compared to Arabidopsis (large genome).

Also interesting to note that:

“Unlike the contracted nuclear genome, the plastid and mitochondrial genomes of U. gibba are quite similar in structure to those of other angiosperms…Therefore, the evolutionary forces acting to reduce U. gibba genome size seem to have affected only the nucleus.”

Well I can think of a few possibilities, including nucleotypic effects and selection on cell size or overall plant size, or selection for reduced DNA replication and cell cycle time, possibly even generation time. Of course, comparative data would be needed to test these and other hypotheses.

Maybe something changed in the copy and/or repair mechanisms to allow more deletion mutations to occur and/or spread in the gene pool?

https://www.google.com/accounts/o8/[…]vtiF0BBqF10Q said:

It should be noted that Utricularia is a pet plant of IDcreationists because Wolff-Ekkehart Lonnig described the its traps as irreducible complex.

Well their traps are pretty clever. There’s a video here describing how they work, which is quite remarkable. But that’s the usual Creationist tactic of focusing on something really nifty in nature and proclaiming it impossible to evolve. If only IDists would address complexity and genome size to describe how two bladderworts (plants which are not-too-distantly related plants with the same general functions, structures, and survival strategies) need to have genomes that are sized differently by two orders of magnitude. Where is all that extra Design going?

Carnivorious plants usually trap animals for the nitrogen and minerals. DNA contains a lot of nitrogen. Maybe the reducded genome is an adaptation to conserve nitrogen

The curious thing is that genome size varies so much much across the carnivorous plants than any explanation that relates to the biology or function of such plants cannot be used, unless very creatively. It would have to explain both why some carnivorous plants have very small proportions of noncoding DNA and why some have lots of noncoding DNA.

Ed Yong’s article notes that in this case carnivory appears to be an adaptation to low levels of phosphorus – which DNA also uses a lot of.

It seems to be extremely well-established that the amount of non-coding, non-regulatory DNA can vary incredibly widely in eukaryotes, including varying quite widely between quite similar species.

Perhaps the real mystery is not so much why some species have less of it, but how it can build up so much in others without really disrupting gene function all that much.

At this point, the human genome is mainly non-regulatory and non-coding, so it’s tempting to say that if you add more, just by random chance, it’s going to go into an already junk part of the genome.

But what about the “first” junk DNA? If we assume a model of an early proto-eukaryotic genome without “junk”, then the “first junk” would be nearly guaranteed to disrupt a coding or regulatory region. Maybe the junk was there first, and the genes came later? But of course, bacteria have almost no junk. At least not now.

You know an experiment somebody should do?

Pick the bladderwort with the biggest genome– let’s say Genlisea hispidula with 1510 Mbp [about one-half the size of the human genome].

Now do an ENCODE-type experiment with that, totting up all its biochemical “activities” as Ewan Birney would say– find all its low-abundance RNA transcripts, everywhere a protein binds to the DNA, everywhere the DNA is chemically modified.

Who is willing to bet that the fraction of “biochemical activity” in Genlisea hispidula will be close to, or more than, the 80% “activity” reported by ENCODE for human beings?

And since Utricularia gibba with its measly 88 Mbp is so closely related to Genlisea, nature has already done for us the experiment of asking, “Hey, what would happen if you delete all that junk?”

Think the NIH would give me a grant for that?

That is a great experiment. I appreciate the snark, but I think it would actually be pretty awesome to do the same study in both species, to help identify which of the few noncoding regions (with high confidence) actually are integral.

But, you’d have to create a bunch of cell lines first.

This is completely off-topic, but the TalkOrigins.org site seems to be down. Every page I try returns a 404 error. Does anyone know what’s going on?

Same for me. I don’t see any message traffic about it. Sometimes they just go down.

I am saying this from a position of ignorance so those who know feel free to correct me. Plants occasionally speciate by polyploidy. A friend of mine found a new grass species that was a tetraploid version of a known species but could no longer mate back to the parent species because the chromosome number didn’t match. It instead self pollinated. Is it possible that the smaller genome represents the ancestoral form of the species and the higher DNA content species are due to a polyploiding event (does that have a specific name?)and that these later forms reduced their DNA content after the event, but would still have a greater DNA content then U. gibba? Maybe this is obvious from the paper but I didn’t have time to read it.

Mary H said:

I am saying this from a position of ignorance so those who know feel free to correct me. Plants occasionally speciate by polyploidy. A friend of mine found a new grass species that was a tetraploid version of a known species but could no longer mate back to the parent species because the chromosome number didn’t match. It instead self pollinated. Is it possible that the smaller genome represents the ancestoral form of the species and the higher DNA content species are due to a polyploiding event (does that have a specific name?)and that these later forms reduced their DNA content after the event, but would still have a greater DNA content then U. gibba? Maybe this is obvious from the paper but I didn’t have time to read it.

Sure that’s possible, but it would require at least two whole genome duplications in order to get a four fold range. And, after polyploidy occurs, diploidization would occur, with selection driving reduction in genome size, especially in genomes that contained four or more copies of all the “junk DNA”.

DS said:

Mary H said:

I am saying this from a position of ignorance so those who know feel free to correct me. Plants occasionally speciate by polyploidy. A friend of mine found a new grass species that was a tetraploid version of a known species but could no longer mate back to the parent species because the chromosome number didn’t match. It instead self pollinated. Is it possible that the smaller genome represents the ancestoral form of the species and the higher DNA content species are due to a polyploiding event (does that have a specific name?)and that these later forms reduced their DNA content after the event, but would still have a greater DNA content then U. gibba? Maybe this is obvious from the paper but I didn’t have time to read it.

Sure that’s possible, but it would require at least two whole genome duplications in order to get a four fold range. And, after polyploidy occurs, diploidization would occur, with selection driving reduction in genome size, especially in genomes that contained four or more copies of all the “junk DNA”.

Doesn’t self pollination rather refer to an intraindividual process? Wouldn’t getting from 2n to 4n only require a single duplication in the germline which can easily happen during the first meiotic division?

https://www.google.com/accounts/o8/[…]vtiF0BBqF10Q said:

Doesn’t self pollination rather refer to an intraindividual process? Wouldn’t getting from 2n to 4n only require a single duplication in the germline which can easily happen during the first meiotic division?

Sure, that’s one way it can happen. But fertilization with unreduced gametes is another major mechanism by which polyploidy can arise. The problem is that, no matter how it happens, if you are the first on your block to go polyploid, you often cannot mate with anyone else successfully. So, you either have to reproduce clonally, or you can self fertilize, or you just die out.without leaving any offspring.

But the issue is not just getting from 2N to 4N in an individual, it’s getting from 2C to 8C in a single genus. (C referring to DNA content and N referring to number of whole genomes). And of course up to 1000C in other plants, so more than one process may be responsible.

DS said:

https://www.google.com/accounts/o8/[…]vtiF0BBqF10Q said:

Doesn’t self pollination rather refer to an intraindividual process? Wouldn’t getting from 2n to 4n only require a single duplication in the germline which can easily happen during the first meiotic division?

Sure, that’s one way it can happen. But fertilization with unreduced gametes is another major mechanism by which polyploidy can arise. The problem is that, no matter how it happens, if you are the first on your block to go polyploid, you often cannot mate with anyone else successfully. So, you either have to reproduce clonally, or you can self fertilize, or you just die out.without leaving any offspring.

But the issue is not just getting from 2N to 4N in an individual, it’s getting from 2C to 8C in a single genus. (C referring to DNA content and N referring to number of whole genomes). And of course up to 1000C in other plants, so more than one process may be responsible.

Polyploidy is interesting. Humans are extremely sensitive to gene dosage - germ line or somatic mutations that change chromosome number often tend to have severe effects. Many types of plants, less so, although the polyploid ones may have larger flowers or whatever.

Birds can use parthogenesis, and in fact its important in turkey breeding, but humans are often sensitive to gene imprinting based on what parent a chromosome came from.

But anyway, did I misunderstand this article? I thought the plants in question had less non-coding “junk” DNA (somewhat like the healthy trasgenic mice that were bred with a fair amount of it missing, relative to other mice). Which is not quite the same thing as a ploidy issue. A genome could have very little “junk” DNA but be polyploid relative to genes and regulatory elements (*I realize that not every allele would necessarily be expressed but it’s still not the same thing as increasing non-coding “junk” DNA*).

About this Entry

This page contains a single entry by M. Wilson Sayres published on May 14, 2013 10:22 AM.

John Searle’s homunculus announces phased retirement was the previous entry in this blog.

My breasts. My genes. is the next entry in this blog.

Find recent content on the main index or look in the archives to find all content.

Categories

Archives

Author Archives

Powered by Movable Type 4.38

Site Meter