Feb. 27, 2001 San Francisco — The highly successful Deep Green project to construct a "tree of life" for the green plants has ended, but it has seeded new projects to strengthen the branches and root the tree more firmly in new genetic and fossil data.
Among these projects is "Deep Gene," headed by University of California, Berkeley, botanist Brent D. Mishler, and "Deep Time," headed by Doug Soltis of the University of Florida. The National Science Foundation (NSF) has agreed to fund both projects with $500,000 each over the next five years.
The success of Deep Green also has emboldened NSF to float the idea of a much larger project — generating the definitive tree of life for everything, from bacteria to bats, fungi to flowering plants. NSF director Rita Colwell calls Deep Green one of the best investments the foundation has made, Mishler said.
Mishler and four colleagues briefed reporters Feb. 16, at 2001 Annual Meeting of the American Association for the Advancement of Science in San Francisco, about the accomplishments of Deep Green and its proposed offshoots. Mishler, a spokesman for Deep Green, is director of UC Berkeley's University and Jepson Herbaria and a professor of integrative biology in the College of Letters & Science.
Deep Green has contributed to more than 100 research papers, Mishler said, the latest of which, in the Feb. 1 issue of Nature, nailed down the sister group of the seed plants. The work, coauthored by Kathleen Pryer and Harald Schneider of Chicago's Field Museum of Natural History and Alan R. Smith and Ray Cranfill of the UC Berkeley Herbarium, provided very strong evidence that ferns and horsetails are one another's closest relatives and the group most closely related to the seed plants.
"It clarifies one big chunk of the tree," Mishler said. "We haven't completed the whole tree, but these papers one at a time have dealt with all aspects of the green part of the tree of life."
The Green Plant Phylogeny Research Coordination Group, initially funded for a five-year period by the U.S. Department of Energy, NSF and the Department of Agriculture, was initiated by plant biologists as a way to make sense of the reams of data on plant relationships.
In a series of meetings over the past five years, more than 200 biologists reached consensus on the most important plants to target in genetic studies and the best genes to focus on. Workshops and a Web site clearinghouse for phylogenetic information helped the community of plant biologists coordinate research and answer important questions about plant relationships.
"It is important to emphasize that this field used to be very independent and lab-oriented, where everyone was working in secrecy within the walls of their lab," he said. "But as a result of Deep Green, people began to cooperate. They started sharing data and techniques, and that's where this progress came from."
Among Deep Green's achievements was completion of a good draft of the tree of life for green plants. It identified a cream-colored flower called Amborella as the earliest-diverging lineage in the flowering plants; concluded that land plants first emerged onto land from fresh water, not the salty oceans; and made clear that, at many critical transitions in evolution, only one lineage of green plant survived.
Such information on plant relationships becomes extremely important as researchers try to engineer new traits —from disease resistance to drought tolerance — in crop plants.
With Deep Gene, funded through a Research Coordination Networks grant from NSF, Mishler hopes to repeat the success of Deep Green. This time, however, he is bringing in scientists working on plant genomics to reach consensus on the most important plants to target for genome sequencing.
The genome sequence of the widely-used research plant Arabidopsis thaliana is nearly complete, and sequencing of the rice and corn genomes is underway. Genomic data is publicly available on some 19 other plants. To make the most of sequencing efforts, Mishler said, scientists should choose more diverse plants that cover the range of economically important land plants.
"You have to pick the landmarks. If you want a good representation of the whole tree of life, you need to pick genomes nicely spaced on the tree," he said. "Then, for example, once you understand the genes involved in flower development in one species, it's not too difficult to probe for the genes involved in flower development in nearby species."
He notes that the long-term goal of plant genomics is to identify, isolate and determine the function of genes associated with various plant traits. This can be facilitated by a quality tree of life. Using sister group comparisons, for example, researchers can locate two closely related plants, one with a particular trait and one without, to help them reduce the number of genes they need to look at to isolate those responsible for the trait.
"Ideally, you could narrow the search down to probably just a few genes from thousands," he said.
Alternatively, ancestor-descendent comparisons allow researchers to study complex systems of interacting genes, such as those controlling the angiosperm flower, at a more primitive evolutionary stage, for example, when they were involved in moss and fern reproduction.
One area where this approach has borne fruit is the study of dessication tolerance, the ability of plants to withstand drought. If the trait, common in algae, ferns and lichens, can be transferred to crop plants, they might subsist on less water or better survive drought.
In a report in last November's Journal of Plant Ecology, Mishler and U.S. Department of Agriculture researcher Melvin J. Oliver used sister group comparisons to help unravel this complex phenotype, which involves more than 80 interacting genes.
"When plants first invaded the land, they were all vegetatively dessication tolerant — they could dry up completely and still be rejuvenated. But as plants evolved more complicated structures, they lost this ability," Mishler said.
"The interesting story is, dessication tolerance re-evolved at least eight times within flowering plants, and again when the seed evolved. It appears, from our initial work, that many of the genes involved in seed dessication tolerance are descendents of the early genes that were involved in vegetative dessication tolerance in the first place."
These findings emphasize the value of studying simpler plants to better understand higher plants, Mishler said.
"We now have real hope that we will be able to understand something about these economically very important events in evolution, the evolution of the seed and of the flower, by looking at mosses and ferns and algae, which are much simpler study systems," he said.
More insights are sure to come from the interaction between systematists like Mishler, who chart the evolutionary relationships among plants, and genomicists identifying the genetic makeup of green plants.
"Deep Gene is an attempt to meld together the plant phylogenetics progress we've made rapidly in the last few years with the rapid progress in plant genomics," Mishler said. "We believe this will be a truly synergistic process, where genomicists and phylogeneticists both benefit."
A full account of the progress of Deep Green can be found at: http://ucjeps.berkeley.edu/bryolab/greenplantpage.html.
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