By Cat Holmes
University of Georgia
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.”
Double genes in a little weed
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.
Compare and contrast
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.”
Breakpoints
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.”
Significant economically
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.
