Carnivorous bladderwort genome contradicts notion that vast quantities of noncoding DNA crucial for complex life

May 12, 2013
A scanning electron micrograph shows the bladder of Utricularia gibba, the humped bladderwort plant (color added). The plant is a voracious carnivore, with its tiny, 1-millimeter-long bladders leveraging vacuum pressure to suck in tiny prey at great speed. New research shows that the U. gibba genome contains almost no noncoding DNA, demonstrating that vast quantities of this so-called "junk DNA" may not be necessary for complex life. Credit: Enrique Ibarra-Laclette, Claudia Anahí Pérez-Torres and Paulina Lozano-Sotomayor

Genes make up about 2 percent of the human genome. The rest consists of a genetic material known as noncoding DNA, and scientists have spent years puzzling over why this material exists in such voluminous quantities.

Now, a new study offers an unexpected insight: The large majority of noncoding DNA, which is abundant in many living things, may not actually be needed for complex life, according to research set to appear in the journal Nature.

The clues lie in the genome of the carnivorous bladderwort plant, Utricularia gibba.

The U. gibba genome is the smallest ever to be sequenced from a complex, multicellular plant. The researchers who sequenced it say that 97 percent of the genome consists of genes—bits of DNA that code for proteins—and small pieces of DNA that control those genes.

It appears that the plant has been busy deleting noncoding "junk" DNA from its over many generations, the scientists say. This may explain the difference between bladderworts and junk-heavy species like corn and tobacco—and humans.

The international research team, led by the Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO) in Mexico and the University at Buffalo, will report its findings on May 12 in Advanced Online Publication in Nature.

The study was directed by LANGEBIO Director and Professor Luis Herrera-Estrella and UB Professor of Victor Albert, with contributions from scientists in the United States, Mexico, China, Singapore, Spain and Germany.

"The big story is that only 3 percent of the bladderwort's genetic material is so-called 'junk' DNA," Albert said. "Somehow, this plant has purged most of what makes up . What that says is that you can have a perfectly good multicellular plant with lots of different cells, organs, tissue types and flowers, and you can do it without the junk. Junk is not needed."

This is the light micrograph of the bladder of the carnivorous bladderwort plant, Utricularia gibba. A new study finds that U. gibba has a remarkable genome for a complex organism. Just 3 percent of U. gibba 's tiny genome is made from so-called "junk DNA," compared with about 98 percent of the human genome. The finding contradicts the notion that vast quantities of noncoding junk DNA are crucial for complex life. Credit: Enrique Ibarra-Laclette and Claudia Anahí Pérez-Torres

Noncoding DNA is DNA that doesn't code for any proteins. This includes mobile elements called jumping genes that have the ability to copy (or cut) and paste themselves into new locations of the genome.

Scientists have spent countless hours puzzling over why noncoding DNA exists—and in such copious amounts. A recent series of papers from ENCODE, a highly publicized international research project, began to offer an explanation, saying that the majority of noncoding DNA (about 80 percent) appeared to play a role in biochemical functions such as regulation and promotion of DNA conversion into its relative, RNA, which for genes, feeds into the machinery that makes proteins.

But Herrera-Estrella, Albert and their colleagues argue that organisms may not bulk up on genetic junk for reasons of benefit.

Instead, they say, some species may simply have an inherent, mechanistic bias toward deleting a great deal of noncoding DNA while others have a built-in bias in the opposite direction—toward DNA insertion and duplication. These biases are not due to the fact that one way of behaving is more helpful than the other, but because there are two innate ways to behave and all organisms adhere to them to one degree or the other. The place that organisms occupy on this sliding scale of forces depends in part on the extent to which Darwin's natural selection pressure is able to counter or enhance these intrinsic biases.

The new U. gibba genome shows that having a bunch of noncoding DNA is not crucial for . The bladderwort is an eccentric and complicated plant. It lives in aquatic habitats like freshwater wetlands, and has developed corresponding, highly specialized hunting methods. To capture prey, the plant pumps water from tiny chambers called bladders, turning each into a vacuum that can suck in and trap unsuspecting critters.

The U. gibba genome has about 80 million DNA base pairs—a miniscule number compared to other complex plants—and the deletion of noncoding DNA appears to account for most of that size discrepancy, the researchers say. U. gibba has about 28,500 genes, comparable to relatives like grape and tomato, which have much larger genomes of about 490 and 780 million base pairs, respectively.

The small size of the U. gibba genome is even more surprising given the fact that the species has undergone three complete genome doublings since its evolutionary lineage split from that of tomato.

That is, at three distinct times in the course of its evolution, the bladderwort's genome doubled in size, with offspring receiving two full copies of the species' entire genome. "This surprisingly rich history of duplication, paired with the current small size of the bladderwort , is further evidence that the plant has been prolific at deleting nonessential DNA, but at the same time maintaining a functional set of genes similar to those of other plant species" says Herrera-Estrella.

Explore further: 'Dark genome' is involved in Rett Syndrome

More information: Architecture and evolution of a minute plant genome, DOI: 10.1038/nature12132

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Jeddy_Mctedder
2.1 / 5 (7) May 12, 2013
how are they even still calling this "junk dna" the term has been an anachronism for some time now. and this article proves nothing about the plethora of dna that is studied which is 'non-coding' in fact, the rarity of species that have a high ratio of coding dna to all dna shows you a pattern ---that pattern is that MOST species need extra non-coding dna to flourish for a million different reasons that scientists have yet to discover (some of which they already have discovered!) . "junk dna" is is a JUNK term. let it die.
Itrizia
1 / 5 (1) May 13, 2013
i disagree with the previous poster, in fact junk dna is a great term. yes, organisms will evolve to use it to some degree if it is there, but parasitic, frameshifting self-copying genes and their detritus are junk.

the fact that this little plant has such an abnormally condensed chromosome is super interesting for another reason. here's why: if this type of plant cell requires less dna to function as a percentage of biomass, then an increase in yield of crops could be expected. so, if the corn or tomato genome was cleaned up, the plants could put a few percent more energy into useful stuff. cool research!
antialias_physorg
not rated yet May 13, 2013
if this type of plant cell requires less dna to function as a percentage of biomass,

DNA makes up less than 1 percent of the mass of a cell. Reducing its size will not give you more crop yield (or more useful proteins per plant)
That would only happen if the size of the DNA would significantly impact upon the size of the cell. But since it's mostly curled up in the nucleus that 1 percent translates into a cube root of 1 percent as a size factor (i.e. pretty negligible)

Junk DNA may or may not be all useless. It may be active in certain circumstances (e.g. presence of a certain parasite). So preemptively ripping it out of the DNA sequence of food plants may not be a good long term decision.
nowhere
not rated yet May 13, 2013
I think he means that without the junk dna being necessary, the plant will need to be slightly more specialised, resulting in less process requirements to fulfil the same task, and hence will have more energy available to fulfil its primary task (more crop yield). Though it actually doesn't work that way.
Moebius
1 / 5 (1) May 13, 2013
I'll believe this when they strip all the so-called junk from an animal genome and produce a perfectly normal animal from it.
adam_russell_9615
1 / 5 (1) May 13, 2013
line 3428759 /* yahweh was here lol
GoodUserName
not rated yet May 13, 2013
I think they take a big leap from "not crucial to complex life" to "junk". The deleted DNA may very well still be useful even though it isn't entirely necessary. I think it would be appropriate to say that the function is as yet unknown; or that it is possibly non-functional,rather than declare it dead in the water. Maybe some of the deleted DNA helps the organism adapt to environmental pressures over the long term. I do find the push to reconfirm the junk status of non coding sequences interesting, especially as more and more research seems to indicate function. Reference this article from Phys.org "Brain development is guided by 'junk' DNA that isn't really junk".
Itrizia
not rated yet May 13, 2013
a few thoughts: there is more to living dna than just the code. there's all the support proteins, phosphorus and fats for bigger nuclear envelopes, extra energy expenditure for expressing genes from a more diffuse chromatin etc. so a leaner genome requires less of that stuff, how much less i don't know, but it will be significant percentage.

lastly, like goodusername says, junk dna does have roles to play. but imagine the following breeding program: the mechanism at work in the bladderwort is applied to millions of individual corn cells (standard lab techniques). the few survivors with working and shortened dna are hybridized, and the process is repeated again. eventually the dna will be 'cleaned' and full-sized plants can be grown again. all this cell work is automated of course.

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