Big reveals for genome of tiny animal

Tunicates’ scrambled gene order suggests arrangement may not matter for vertebrate body plan and hints at origins of mysterious bits of DNA

As any devotee of Antiques Roadshow can tell you, just because something has been saved doesn’t mean it’s valuable.

UNSTRUCTURED The study of tunicates, the second most abundant type of zooplankton in the oceans, is helping to reveal where mysterious chunks of DNA called introns come from. The tiny, transparent organisms are made visible here by adding milk to seawater. Jean-Marie Bouquet and Jiri Slama, © Science/AAAS

Now, a study of plankton shows that a well-preserved genome isn’t necessarily responsible for how vertebrate animals, including humans, are put together. Researchers in Norway and France have deciphered the genetic blueprints of a tunicate called Oikopleura dioica, a tiny member of one of the most abundant plankton types in the oceans. The animal’s compact genome contains roughly 18,000 genes — nearly as many as the human genome’s 22,000 or so, but with genes in a completely different order and less DNA stuffed in between them, the researchers report online November 18 in Science.

The finding came as something of a surprise to researchers since it’s been thought that the arrangement of genes on chromosomes helps determine how an organism’s body plan will be laid out. Humans and other vertebrates tend to have genes arranged in similar order. So do organisms such as sponges. Many researchers thought that this genomic structure was important since it was preserved over millions of years of evolution. But the tunicate genome’s scrambled gene order could indicate that other organisms’ genomes got and stayed that way without any pressure from natural selection to maintain the structure.

“Intuitively, you wouldn’t believe that just by chance things would be conserved for 500 million years,” says Daniel Chourrout, a developmental and genome biologist at the Sars International Centre for Marine Molecular Biology at the University of Bergen in Norway and a coauthor of the new study. But the new evidence indicates that the common genome structure found in most animals may have been maintained simply due to inertia, or genetic drift, he says.

The tunicate genome contains a few other golden nuggets of information as well, including clues about how introns form. Introns are chunks of DNA that interrupt the protein-building instructions in genes and have been called “junk DNA,” although scientists have discovered that many introns also help regulate activity of the genes they interrupt. Others have no known function.

Most introns are so old that scientists have been unable to infer the introns’ origins. But of the 5,589 introns identified in the tunicate genome, 76 percent have not been seen before in studies of other organisms. Closer examination of the tunicate introns indicates that many are copied from other introns and then inserted into the genome in new places, much like other highly mobile bits of DNA known as jumping genes or transposable elements.

Other scientists have postulated that that’s how introns come about, but the new report is the first direct evidence, says Michael Lynch, an evolutionary biologist at Indiana University in Bloomington. “Still one of the big mysteries in evolutionary biology is where introns come from,” he says, “so any insight into that is welcome.”

Tina Hesman Saey is the senior staff writer and reports on molecular biology. She has a Ph.D. in molecular genetics from Washington University in St. Louis and a master’s degree in science journalism from Boston University.

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