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Plant Genomics Floral Genome Team Finds Old Whole-genome Duplication

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Five years into a project examining the genetic makeup of flowering plants, Claude dePamphilis and his collaborators have found evidence indicating that the earliest of these plants — known today as angiosperms — underwent a drastic whole-genome duplication, which may have been what spurred a swift period of evolution among these species.

DePamphilis, associate biology professor at Penn State, is co-PI for the project, funded by NSF; other collaborators hail from the University of Florida, Cornell, the British Museum of Natural History, and the University of Oslo. Their goal was to study a variety of flowering plants to get a better sense of how angiosperms developed and evolved over time.

To that end, they chose 15 different species that were “carefully selected to represent the major branches of flowering plant diversity,” dePamphilis says. “Most of the species were selected for their phylogenetic position — as close to the base of important diversification events as possible.” These included water lily, magnolia, tomato, and sunflower, among others. The team relied on EST libraries to sample some 6,000 genes thought to be related to flowering function. By examining the sequences as well as using microarray analysis, dePamphilis says, they aimed to “try to piece together a picture of what genes were present in the earliest flowering plant.”

Along the way, they noticed a recurrent blip in the data: what dePamphilis calls “an unexpectedly large number of genes that seem to trace back to the same time in the past” — more than would be expected by chance — giving a strong indication that this line of plants may have gone through a whole-genome duplication event. This duplication, or polyploidy, is thought to be less cataclysmic in plants than in other organisms. “Plants seem to be able to survive this process very frequently,” dePamphilis says, noting that this has historically been a critical process in rapid evolution of species.

The findings, while not precisely what the floral project team was looking for, have shifted priorities a bit for the future direction of the research. “It’s very important to follow up,” dePamphilis says, noting that in particular the team is interested in determining “the function of the duplicated genes that have resulted from the polyploidy events.”

He adds, “It has changed our focus some — we’re pursuing much wider sequencing. … Genome sequence data would actually be the best way to test the hypothesis that there’s been a polyploidy event in the history of angiosperms.” So far, the genomes of three flowering plants have been sequenced; dePamphilis and his collaborators are looking into the best avenues to get more angiosperms sequenced. “We’re making a proposal to NSF to try to generate these tiled BAC libraries and complete our EST sequencing,” dePamphilis says, as a preliminary step toward lobbying for full-genome sequencing. He’s currently in talks with at least three large sequencing providers to get a handle on resources needed to contribute to the floral genome effort.

 — Meredith Salisbury

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