Plant duplications
By Cat HolmesUniversity of GeorgiaSince Charles Darwin heralded evolution more than 150 years ago,scientists have sought to better understand when and how the vastvariety 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 scientiststo infer what the gene order may have looked like in a commonancestor of higher plants. And it shows one way plants may havedifferentiated from their ancestors and each other.”By studying the completed sequence of the smallest floweringplant, Arabidopsis, we showed that most of its genes wereduplicated about 200 million years ago and duplicated again about80 million years ago,” said Andrew Paterson, a UGA plantgeneticist and director of the study. “The ensuing loss of ‘extragenes’ caused many of the differences among modern plants.”Double genes in a little weedTwo years ago, scientists finished the genetic sequencing ofArabidopsis, a small, weedy plant. It was a major event, the firstplant to be completely sequenced. Arabidopsis had been chosenwith the assumption that it would be fairly easy, since it wassmall.Sometimes small packages aren’t so simple.Seeded throughout its five chromosomes were thousands of genesthat seemed to be “junk.” When UGA scientists compared all of thegenes, they found evidence of duplicated “blocks” of similar setsof genes in two, four or eight different places along thechromosomes.It’s well known that many plants contain two or more copies ofmost genes. But why these copies exist and when they occurred hasbeen unknown. Their surprising abundance in the tiny,well-studied Arabidopsis indicates that genome duplications mayhave played a bigger evolutionary role than was previouslythought.Compare and contrastWhy were these blocks of genes duplicated? When did this happen?Answering these questions involved a lot of computerizedcomparing and contrasting.The scientists repeatedly compared related pairs of Arabidopsisgenes with genes from other plants to figure out which genes hadbeen “hanging out with each other,” said UGA graduate studentBrad Chapman, who coauthored the study, along with John Bowers,Junkang Rong and Paterson.”Genomes with similar blocks of duplication, ‘spelled’ in similarways, had been hanging out together for longer periods of time,”Chapman said.”We tested many, many combinations,” Paterson said. “We testedArabidopsis with cotton, cauliflower, alfalfa, soybeans,tomatoes, rice, pine trees and moss.”BreakpointsAfter more than 22,000 such comparisons, the results were pooled,and the scientists looked for breakpoints. The breakpointsindicate duplication events, Paterson said. And the study showsthat Arabidopsis has duplicated at least twice, and perhaps athird time.Each time a duplication event occurred, the entire geneticsequence of Arabidopsis doubled. The plant lived on with sparecopies of all of its genetic material. And over time, the “extragenes” were shuffled around or lost. It is suspected that thismay be one explanation for how different species emerged.”The duplication event that occurred 200 million years agooccurred in virtually all plants,” Paterson said. “Theduplication event 80 million years ago affected a lot of plants,but not as many.”Significant economicallyThe study is attracting attention in the scientific community,because it combines an evolutionary approach with genomic data tolearn more about the natural world.This information will have a significant economic impact becauseit permits scientists to make better use of the Arabidopsissequence. It will allow them to study and improve other plantswhose 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 cottonmap, compare them with the Arabidopsis sequence and, with thisanalysis, make good, educated guesses about where the other48,000 cotton genes are,” Paterson said.