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Is Noncoding DNA Required for Complex Life?

Kayt Sukel

Noncoding DNA makes up only 3% of the carnivorous bladderwort plant genome. So does that prove that noncoding DNA is unnecessary for complex life? Find out...

Since scientists first discovered that more than 95% of the human genome was made up of non-coding elements—DNA that does not code for any particular proteins—they’ve struggled to understand the purpose of this so-called junk DNA. In the past few years, the researchers behind the Encyclopedia of DNA Elements (ENCODE) project have supported the idea that most non-coding DNA is not junk at all—but, rather, critical regulatory elements that help coding DNA do its job to support the form and function of complex life.

A scanning electron micrograph shows the bladder of Utricularia gibba, the humped bladderwort plant (color added). Source: Enrique Ibarra-Laclette, Claudia Anahí Pérez-Torres and Paulina Lozano-Sotomayor.

Yet now, a new study led by researchers at the Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO) in Mexico and the University at Buffalo is challenging that notion. Published online this week in Nature, these researchers show that the carnivorous bladderwort plant Ultricularia gibba thrives even though only 3% of its genome consists of non-coding elements.

Victor Albert, a molecular evolutionary biologist at the University of Buffalo and one of the lead authors of the study, believes that U. gibba is a fantastic story for evolutionary genomics. “Why does one plant have a genome of 1 or 2 billion base pairs while this plant has only about 82 million base pairs? Both plants basically have the same number of genes and both are, I would argue, perfectly good, perfectly complex plants. So what is the difference?”

The difference appears to be in the so-called junk DNA elements. U. gibba evolved in such a way that non-coding elements were deleted from its genome over successive generations. And in doing so, this organism demonstrates that large quantities of non-coding DNA, as seen in other related plant species as well as human beings, are unnecessary for complex life forms.

Of course, why and how the bladderwort evolved to shed these elements remains unclear. Albert says that U. gibba belongs to a genus that is very genetically dynamic, and it is difficult to identify some sort of natural selection that would cause a genome to get smaller over time.

“That kind of force would have to be pretty strong for natural selection to act at the level of the genome like this. We haven’t been able to demonstrate it. It doesn’t mean it isn’t there. But we can’t demonstrate it,” said Albert.

Instead, U. gibba may have an inherent bias toward deletion, in contrast to similar plants that have a bias toward copy-and-paste insertion. “That doesn’t mean there’s not a natural selection reason for it. It just means some underlying tendency is pushing things in one direction or the other,” he argues.

In the end, Albert said that biological activity does not equal biological function. “DNA is a chemical. By nature, it’s going to have some sort of chemical biological activity. It might be transcribed to RNA, but whether that actually has some function or not, is open to question,” he said.

“Since we now have a case where 97% of the genome is genes and the regulatory elements associated with them, it’s clear that a complex organism does not require this so-called ‘junk’ DNA to be complex,” said Albert. “That doesn’t mean that junk DNA means nothing for humans. But what that might be, we don’t know for certain.”

1. Ibarra-Laclette, E., E. Lyons, G. Hernandez-Guzman, C. A. Perez-Torres, L. Carretero-Paulet, T.-H. Chang, T. Lan, A. J. Welch, M. J. Juarez, J. Simpson, et al. 2013. Architecture and evolution of a minute plant genome. Nature advance online publication(May).

Keywords:  genomics