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Leading the Legume Charge


  • Title: Research Geneticist, US Department of Agriculture's Agricultural Research Service and Iowa State University
  • Education: PhD, University of Minnesota, 2003; Postdoctoral Associate, University of Minnesota
  • Recommended by: Bruce Roe

It's not everyone who thinks of legumes as “a group of plants I just have a personal affinity for,” but it's that interest that makes Steven Cannon especially happy to be at his post as a research geneticist at the USDA's Agricultural Research Service. “The main focus in this position will be soybean sequencing and assembly,” he says. Most of the sequence will come from the Joint Genome Institute, “but because it's a big and complex genome it's going to require a lot of additional work” to whip it into a finished assembly.

Legumes represent the only plant family with three completed genomes — Medicago truncatula, Lotus japonicus, and now soybean — and that provides Cannon with an enviable vantage point. “We want to make all-by-all comparisons between those genomes, and out to other dicot genomes [too],” he says. As that work progresses, he adds, “we'd like to be able to correlate the genome structural comparison and evolutionary phylogenetic comparison for all of these gene families.”

Cannon has background that may be unique in this field: before his days as a sequence-comparing fiend, he was an educational software designer working on projects such as the popular children's game Oregon Trail. While admittedly genome analysis can't be helped by knowing when to caulk your wagon and cross a river, Cannon says that his experience with interactive, multi-user games is important in establishing large-scale collaborations requiring biocuration “where each person is contributing a small piece.” The aspects to keep in mind, he says, are things like ontologies as well as “what are appropriate incentives for each person to contribute their piece of the Arabidopsis 2010 project? … Once you have the incentives right, how do you store and organize and provide access to this data?” he says. The traditional means revolve around publication and relying on scientists to keep up with the literature, “and I'm not sure that's the most efficient way,” he says.

Looking ahead

The future holds massive genomic comparisons, says Cannon — and that includes much more than just sequence data. Right now, he thinks about making comparisons between four genomes, maybe five, he says. But as the price of sequencing drops, it'll be open season on generating terabytes upon terabytes of sequence data for organisms that aren't now considered a priority. Within the next couple of years, Cannon hopes to have “whole proteome sets for 10 species within the legumes” — a comparison that he knows dwarfs his current work on the three legume genomes. “It won't just be the gene sequences,” he says. “It'll be expression data” and whatever else biologists can get their hands on.

Publications of note

Cannon is the lead author on his most recent paper, due out soon from PNAS (it was published online in late September) called “Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes.” In this paper, the authors report results of full-genome, sequence-based com-parisons between Medicago and Lotus, including data about synteny, chromosomal relationships, and genome regions that don't seem to map across organisms. The team also reported evidence for a genome duplication that predated speciation between Medicago and Lotus.

And the Nobel goes to…

“I'm interested in theoretical questions just because I enjoy the pattern identification,” Cannon says. “But one reason that I am in USDA ARS is that I think the planet is under severely increasing population and envi-ronmental challenges, so [I'd want to win for] some contribution to agriculture that addresses the problem, such as drought, salinity, energy, or biofuels.”

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