Michael Barker will never look at a Christmas tree the same way again. By thoroughly analyzing the genomes of spruces, pines, firs, and their relatives, he has uncovered that these trees underwent a genomic hiccup in their deep past. The result: They once had a complete second set of genes, the genomicist at the University of Arizona in Tucson and colleagues report today. Such a genome-wide duplication likely helped shape these species into the tallest, hardiest plants in the world and are causing biologists to rewrite the history of gymnosperms, the group of plants that includes conifers and other nonflowering, seed-producing plants.
“This is really exciting work,” says Douglas Soltis, a botanist at the University of Florida in Gainesville. “It has long been known that [genome duplication] was important in flowering plants and ferns,” he says. “This work shows that genome doubling has played an important role in conifers as well.”
As more and more plant and animal genomes have been deciphered and compared, researchers have developed a growing appreciation that the distant ancestors of various groups underwent genome duplications. But when the first pass of the genome of the Norway spruce, a common Christmas tree, came out in 2013, Stefan Jansson, a geneticist from Umeå University in Sweden and his colleagues concluded that although some genes had been copied elsewhere in the genome, the genome itself had not duplicated.
Barker wasn’t so sure. So many other plants had undergone such duplications that “it didn’t make sense that [gymnosperms] didn’t have any,” he says. He and his colleagues therefore sequenced just the genes—which are just a small fraction of the total DNA—for 24 gymnosperms and three other plants. They also developed a sophisticated computer program that could ferret out possible genome duplications by analyzing similarities among genes within and between those plant species.
Two duplications occurred in conifers, they report online in Science Advances. One happened at the base of the spruce, pine, and fir trees. The genome of the ancestor of box shrubs, junipers, and cedars, another group of conifers, also underwent a doubling. But no duplications have taken place in the third branch of conifers, which includes the monkey puzzle tree, they note. As more tree genomes are deciphered, other rounds of duplication may become evident, Barker says. But what is clear is “the mechanisms in which the genomes have evolved in gymnosperms and [flowering plants] are not as different as previously portrayed.”
There's growing evidence an extra copy of a genome provides fodder for the evolution of new traits, and new species. Duplicated genes provide freedom for one copy to change what it does without affecting the organism's survival. Some of those changes may underlie the redwood's height, or the ponderosa pine's longevity.
Claude dePamphilis, a plant genomicist at Pennsylvania State University, University Park, is pleased with the new analysis. His studies had indicated there had been a whole genome duplication in the seed plant that was the common ancestor of gymnosperms and flowering plants, and he was disappointed no one had found remnants of the doubling in the spruce genome. “This work helps to resolve apparent controversies in the literature,” he says.
"I think they probably are right,” Jansson adds. The conifers’ extremely large genomes made their sequencing quite challenging, and from the fragments obtained so far, it’s difficult to line chromosomes up to look for these duplications. “This group has simply generated a better data set for answering this question than we had,” he says.
Next, Jansson hopes researchers will take a close look at different genes that have survived long after the duplication event, as they likely played important roles in plant evolution. James Leebens-Mack, a plant geneticist at the University of Georgia in Athens, agrees: “We now need to determine whether certain types of genes tended to be retained in duplicate and investigate how functional evolution of these genes contributed to major innovations such as the origin of the seed.”