Where's the Junk?

Could an odd plant with a terrible name show us that “junk DNA” has value after all?

The carnivorous bladderwort plant, Utricularia gibba, is a lightweight in the genome game. It has about 80 million DNA base pairs. By comparison, its relatives the grape and tomato have about 490 and 780 million base pairs, respectively. (You and I have about 3.2 billion base pairs, but hey, we’re humans.)

Despite its small genome, the carnivorous bladderwort is a complicated plant. Disguised as a lovely flowering beauty, it actually traps organisms such as insects and small fish in a bladder-shaped trap on its water-soaked roots—for nourishment, of course. And while that’s exciting, a new study in Nature has scientists even more excited about the carnivorous plant.

“The big story is that only 3 percent of the bladderwort’s genetic material is so-called ‘junk’ DNA,” says study co-author Victor Albert. The human genome, in contrast, includes about 98% junk DNA. But what kind of “junk” are we talking about?

Junk in the Trunk

“When complete genomes were first being sequenced, it became clear that only a small fraction of the DNA could be assigned a specific function,” explains Brian Simison, curator and director of the Academy’s Center for Comparative Genomics. “The functional regions or genes are primarily those that produce proteins or ribosomes. It has been hypothesized that these vast regions of unknown function were the product of duplications followed by loss of function due to the accumulation of random mutations and/or the accumulation of exogenous DNA from viruses. The term ‘Junk DNA’ emerged from these hypotheses.

“However, research on junk DNA is shedding new insights into these regions,” Simison adds. Last fall, he spoke with Science Today correspondent Barbara Tannenbaum about the ENCODE project. Conducting a huge international effort to look more into the junk part of the human genome, researchers determined that 80% of our genome actually had some function.

Since that time, ENCODE has come under some scrutiny. “I think the ‘controversy’ is overblown,” Simison says. “ENCODE scientists presented a testable hypothesis and it should be pursued as such. My bet is that some junk DNA will, in fact, turn out to be useless baggage from historical genomic events while other bits will prove to be required for normal human functions.”

No Junk in the Trunk

If our junk DNA is worth having around, then why doesn’t a meat-eating plant like the bladderwort need it? “Based on the miniscule number of complete genomes sequenced, it is unusual that the genome of the carnivorous bladderwort is only 3% junk DNA,” Simison says. “It may reveal interesting information about the function and organization of genomes. However, the sample size of complete genomes is so incredibly tiny that junkless genomes may not be that uncommon.”

So what happened to the junk? “That is the big question. Did it get deleted or did the carnivorous bladderwort not have it to begin with?” Simison asks. “To answer this we need to understand more about the evolutionary history of genomes and, in particular, we need to know more about the genomes of this plant’s ancestors.”

The bladderwort’s lack of junk DNA only adds to the mystery. Scientists hope to learn more as additional organisms’ complete genomes are sequenced—and as more research is conducted on the function of junk DNA.

Image: Bruce Salmon/Wikipedia