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

Invasive species often worry scientists—how will native species respond to competition in their ecosystem? The Academy’s Brian Simison shares this concern, but he looks a little deeper. He asks: how does invasive species’ DNA affect that of native species?

Studying slider turtles (Trachemys) is a good way to this address this question. Some species, like the abundant red-eared slider, are invasive all over the world. Others are threatened native species. The invasive and native species often mate with each other, creating offspring. This mixing of two species genomes through crossing, that is, hybridization, can have a profound effect on the evolution of these species and on ecosystem health.

Recently Brian and Academy Research Associate James Parham of CSU Fullerton published a paper on slider populations in the Caribbean. The native sliders there “are endangered, largely because of habitat destruction, and being harvested for food,” Brian explains.

In some places, natives are also threatened by invasive species like the Cuban slider on Jamaica or the red-eared slider in Puerto Rico. “It appears that people have been moving turtles around for hundreds of years, and for some islands there may have been different sources of the introductions,” Brian says.

The recent study reveals a lot of hybridization among the invasive and native species. “We used genetic data to show that there are multiple hybridization events, both recent and ancient, both from natural contact and because of human activities,” Brian describes. “This pattern also shows that the past and ongoing movement of turtles by humans is impacting their DNA.”

But Brian suspects that human impacts may not be the only reason for hybridization. “In addition to the genetic pollution caused by people moving turtles into the range of other turtles, different species also contact each other naturally. So hybridization may be an important part of the natural evolution of these turtles. We have to keep this in mind when reconstructing their evolutionary history. We also need to be very careful determining whether evolution is the result of unnatural (human) or natural processes.”

If hybridization is due to unnatural, human causes, conservation efforts are a top priority in protecting the native turtles from the invasive species. Brian and his colleagues are also confronting these hybridization and conservation issues in the US. “The turtle project is a long-term multi-component project that will last for decades. This publication about Caribbean turtles is a small piece of the entire slider puzzle, which we are unraveling piece by piece.”

And the project goes beyond turtles. “Another facet of the current study addresses how we study genomic data in species that are hybridizing. In other words, we demonstrate how the presence of hybridization confounds certain methods that people are using to reconstruct how different species are related.”

These turtles get to the root of Brian’s work. “Asking, testing and answering evolutionary questions is why I became a scientist,” he explains. “Turtles are one of the few vertebrates that hybridize across deep historical divisions, which provides my colleagues and me the opportunity to test some of the most fundamental questions about the processes of speciation, the engine generating biodiversity.”

Image: James Parham

An international consortium of researchers recently announced another milestone in the quest to unravel the genetic makeup of the human species. The project—ENCODE, for Encyclopedia of DNA Elements—is a collaborative effort among 440 researchers in 32 global institutions, coordinated by the National Human Genome Research Institute (NHGRI). The results of this international effort will stand alongside such research breakthroughs as Watson and Crick’s 1953 description of DNA’s double helix structure and the Human Genome Project’s 2003 complete sequencing of humanity’s 3.2 billion nucleotides.

ENCODE mapped more than four million non-coding regions of the genome that regulate and interact with protein-producing DNA. The scientific consortium also confirmed that 80 percent of the genome performs specific biological functions. This upends the previous consensus that long stretches of DNA were no more than “junk DNA.”

“This is one of the most important collections of information the world is trying to decode,” explains Brian Simison, head of the Academy’s Center for Comparative Genomics.

Not only does ENCODE solve a bit more of the human genome puzzle, but it offers the potential to accelerate medical research. “We’ve known for a long time that there is a genetic basis to many diseases,” says Simison. “What we didn’t realize is that the source of many diseases would be found in the vast regions of the genome previously known as junk DNA.”

While others describe the project as having found the on/off switches to our genes, Simison prefers the term ‘regulatory function.’

“We are learning that junk DNA has a regulatory role in dosage, duration, timing and other regulatory functions. Understanding these functions will transform Western medicine,” Simison adds. “ENCODE reveals that Western medicine is in its infancy.”

Simison points out that ENCODE is also altering our vision of the genetic composition of life. “Most people think all genetic material is passed down to us by our direct ancestors. Actually,” Simison explains, “the human species is filled with ‘fossil DNA’ transferred to us from viruses.”

As an example, Simison describes a retrovirus that has inserted its DNA into a person’s genome. These endogenous retroviruses (ERVs) are found throughout the genome and it is now believed that some of these have been repurposed.

Finally, Simison explains that it’s not just what ENCODE found but how they found it that is significant.

“The wow factor is enormous,” Simison laughs. As the National Institute of Health reports, hundreds of international researchers performed more than 1,600 sets of experiments on 147 types of tissue with technologies standardized across the consortium.

“Although technology has improved, no single institution could have analyzed the genome data on its own,” Simison remarks. “You need many people sifting through the many layers of data to decode the human genome.”

“I believe it is a positive development that so many nations are sharing this knowledge,” he said, lauding the consortium for its cooperative methods. “These illustrate how the path towards lofty ambitions is often as fruitful as the objectives themselves. Unlike the U.S. space program, the Human Genome Project and ENCODE were international projects where the benefits that emerge are shared with and benefit the world.”

ENCODE’s results were published last month in a wide range of scientific journals and posted online to ensure transparency and public access. To learn more, review the publications here.

Barbara Tannenbaum is a science writer working with the Academy’s Digital Engagement Studio. Her work has appeared in the New York Times, San Francisco Magazine and many other publications.