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for the genome of Coffea canephora, whose beans produce what's known as robusta coffee, which accounts for 30 percent of the world's coffee supply.

"The coffee genome sequence identifies virtually all of the hereditary blueprint of this important crop, provides insight into its function and evolution, and provides rich molecular tools for assisting in its further improvement," says Andrew Paterson, professor and director of the Plant Genome Mapping Laboratory at the University of Georgia, who was not involved in the sequencing project.

The work was a collaboration among scientists worldwide led by researchers at the French Institute of Research for Development (IRD), French National Sequencing Center (CEA-Genoscope), and State University of New York's University at Buffalo. It appears today in the journal Science.

The Story of Caffeine

The evolution of plants' ability to produce caffeine was an event whose consequences can be felt in the buzzing brains of people around the world. We human java-heads are certainly glad for it, but what's in it for the plant, anyway?

The University at Buffalo's Victor Albert, one of the study's lead authors and a plant evolutionary biologist, says that for one thing, caffeine in coffee leaves is thought to deter plant-eating insects. Also, when the leaves fall, the caffeine and other compounds leach into the soil and prevent the seeds of other plants from germinating, Albert says. There's also some evidence that caffeine in coffee nectar "habituates pollinators, so keeps them coming back for more," he adds.

According to this study, it turns out that this marvelous trait arose independently in at least two kinds of caffeine-producing plants. Thus, the pathways to produce the caffeine in your coffee and your tea evolved separately.

Ripe berries of Coffea canephora. Credit: Wikimedia Commons.

To make this discovery, the researchers sequenced the DNA extracted from coffee leaves using advanced sequencing methods that allow for the simultaneous reading of many pieces of DNA. They then used software to piece the DNA sequences together based on their areas of overlap. The complete sequence assembly covered 80 percent of the coffee plant's 710-megabase genome.

With the raw data in hand, the researchers looked for gene families—groups of genes predicted to produce similar proteins—within the coffee genome, as well in the genomes of some of the coffee plant's relatives: grape, tomato, and Arabidopsis, a flowering plant often used in plant genetics experiments. Compared to these other plants, the coffee genome had much larger families of genes involved in pathogen defense and—surprise—caffeine production.

"Of course, anyone studying the genome of coffee would look for these genes," Albert says. "What we didn't know ahead of time was whether there were some special attributes of these genes in coffee."

Coffee, tea, and cocoa all produce caffeine, and they all use enzymes called N-methyltransferases (NMTs) to do so. The enzymes convert xanthosine, a two-ringed organic molecule, to caffeine by adding three methyl groups. But comparing the NMTs used by these three caffeine-producing plants revealed that the coffee family of NMTs arose separately from those used by cocoa and tea.

Engineering the Perfect Cup

Many factors, from brewing to roasting to growing environment, go into separating a crap cup of coffee from a great one. But before all that comes genetics. Various compounds—including alkaloids, flavinoids, and fatty acids—affect coffee flavor.

"All of these, of course, are metabolites that are produced as part of genetic pathways," Albert says. The knowledge of the genetics of flavor could help coffee breeders to improve taste.

The quest for better coffee will be aided when coffee sequencers take on their next project. The other 70 percent of coffee beans in the world—the ones that aren't Coffea canephora—are from Coffea arabica, the species used more often in specialty coffees. Arabica plants are a hybrid of C. canephora and another species, and they have a larger and more complicated genome than C. canephora, which is one reason why researchers tackled the latter genome project first.

Finally, knowing the coffee genome could also help scientists to protect one of the world's most important crops from disease, such as the coffee leaf rust that has crippled crops of C. arabica in Central America for the last two to three years. C. canephora is resistant to the fungus.

"Our findings on the pathogen-resistance genes will be very important in selective breeding experiments or genetic modification experiments," Albert says. "Having a genome is really a prerequisite to doing any advanced agro biotechnology."

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