University of Georgia scientists plot key events in plants’ evolution

Since Charles Darwin heralded evolution more than 150 years ago, scientists have sought to better understand when and how the vast variety of plants today diverged from common ancestors.

A new University of Georgia study, just published in Nature, demonstrates key events in plant evolution. It allows scientists to infer what the gene order may have looked like in a common ancestor of higher plants. And it shows one way plants may have differentiated from their ancestors and each other.

“By studying the completed sequence of the smallest flowering plant, Arabidopsis, we showed that most of its genes were duplicated about 200 million years ago and duplicated again about 80 million years ago,” said Andrew Paterson, a UGA plant geneticist and director of the study. “The ensuing loss of ’extra genes’ caused many of the differences among modern plants.”

Two years ago, scientists finished the genetic sequencing of Arabidopsis, a small, weedy plant. It was a major event, the first plant to be completely sequenced. Arabidopsis had been chosen with the assumption that it would be fairly easy, since it was small. Sometimes small packages aren’t so simple.

Seeded throughout its five chromosomes were thousands of genes that seemed to be “junk.” When UGA scientists compared all of the genes, they found evidence of duplicated “blocks” of similar sets of genes in two, four or eight different places along the chromosomes.

It’s well known that many plants contain two or more copies of most genes. But why these copies exist and when they occurred has been unknown. Their surprising abundance in the tiny, well-studied Arabidopsis indicates that genome duplications may have played a bigger evolutionary role than was previously thought.

Why were these blocks of genes duplicated? When did this happen? Answering these questions involved a lot of computerized comparing and contrasting.

The scientists repeatedly compared related pairs of Arabidopsis genes with genes from other plants to figure out which genes had been “hanging out with each other,” said UGA graduate student Brad Chapman, who coauthored the study, along with John Bowers, Junkang Rong and Paterson. “Genomes with similar blocks of duplication, ’spelled’ in similar ways, had been hanging out together for longer periods of time,” Chapman said.

“We tested many, many combinations,” Paterson said. “We tested Arabidopsis with cotton, cauliflower, alfalfa, soybeans, tomatoes, rice, pine trees and moss.”

After more than 22,000 such comparisons, the results were pooled, and the scientists looked for breakpoints. The breakpoints indicate duplication events, Paterson said. And the study shows that Arabidopsis has duplicated at least twice, and perhaps a third time.

Each time a duplication event occurred, the entire genetic sequence of Arabidopsis doubled. The plant lived on with spare copies of all of its genetic material. And over time, the “extra genes” were shuffled around or lost. It is suspected that this may be one explanation for how different species emerged.

“The duplication event that occurred 200 million years ago occurred in virtually all plants,” Paterson said. “The duplication event 80 million years ago affected a lot of plants, but not as many.”

The study is attracting attention in the scientific community, because it combines an evolutionary approach with genomic data to learn more about the natural world.

This information will have a significant economic impact because it permits scientists to make better use of the Arabidopsis sequence. It will allow them to study and improve other plants whose DNA hasn’t yet been completely sequenced, such as peanuts, cotton or wheat, saving both time and money.

“For example, we can take the 2,000 genes known on the cotton map, compare them with the Arabidopsis sequence and, with this analysis, make good, educated guesses about where the other 48,000 cotton genes are,” Paterson said.