From wildflower meadows to redwood forests to alpine bogs, the diversity of seed plants rings out as one of evolution's great achievements. An analysis of the genes of more than a dozen plant species has now shown that this variety was jump-started 320 million years ago and received a further kick 120 million years later. These "big bangs" in plant evolution occurred when the genomes of ancient plants duplicated, providing vast numbers of new genes that could take on new functions and lead to new traits.
Geneticists have long known that new traits often require new genes, but the question remains where new genes originate. In plants, they can come from polyploidy, a process in which seeds, through a quirk in cell division, wind up with an extra copy of their DNA. In vertebrates, polyploidy tends to be lethal, but plants can do just fine with all this extra genetic material. Eventually, some of the twinned genes disappear, but others remain, changing over time and potentially taking on new roles.
Claude dePamphilis, an evolutionary biologist at Pennsylvania State University, University Park, and his colleagues wanted to trace the history of genome duplications in plants. So they looked for the same duplicated genes in different parts of the plant family tree. If different branches share a family of duplicated genes, the doubling had to occur before that branch evolved.
He and his colleagues took stock of all the duplicated genes in nine plants whose genomes had been sequenced. Among the species were rice and sorghum, which represent one modern group of flowering plants called the monocots. The researchers also studied papaya, cucumber, and grapes, which represent the much more diverse eudicots, and a moss and a primitive plant called a lycophyte. To look more deeply into the past of plants, they also obtained large numbers of genes from several early-arising flowering plants, including water lilies and the most primitive kind known, Amborella, as well as from nonflowering seed plants such as conifers, cycads, and ginkgoes. The researchers also determined which of those genes were duplicated.
Until now, the oldest genome duplication documented for plants occurred about 135 million years ago. But dePamphilis and his team found very strong evidence of two much earlier duplications. "It's a critical mass of data that comes together that made it possible," says Michael Barker, a plant evolutionary biologist at the University of Arizona in Tucson, who was not involved with the study.
One duplication occurred 200 million years ago, just before monocots and eudicots arose. The other took place about 320 million years ago in the ancestor of seed plants, the researchers report online today in Nature.
"What they have done is identified two new events that were previously undescribed," Barker says. "It highlights that polyploidy clearly has had a long history in shaping the evolution of plants and their genomes."