Scientists Have Sequenced the Coffee Genome!

Coffee berries / Caroline Gagné via Flickr
Janet Fang 04 Sep 2014, 22:31

The coffee genome has been sequenced for the first time, brewing up a better understanding of that flavor, aroma, and buzz we love (and need) so much. According to the findings, published in Science this week, the caffeine-producing enzymes in coffee evolved independently from those in tea and chocolate. 

“The coffee genome helps us understand what’s exciting about coffee -- other than that it wakes me up in the morning,” says SUNY Buffalo’s Victor Albert in a news release. “By looking at which families of genes expanded in the plant, and the relationship between the genome structure of coffee and other species, we were able to learn about coffee’s independent pathway in evolution, including -- excitingly -- the story of caffeine.”

Commonly known as robusta coffee, Coffea canephora makes up 30 percent of the coffee produced worldwide -- which totals 8.7 million tons a year or 2.25 billion cups a day. The less acidic-tasting Coffea arabica makes up most of the rest, but this lower caffeine variety has a more complicated genome. 

So, to derive a draft genome of Coffea canephora, a huge consortium led by Albert and researchers from the French Institute of Research for Development and the French National Sequencing Center pieced together DNA sequences and assembled a total length of 568.6 megabases -- that’s 80 percent of the plant’s 710-megabase genome.

After running a comparative genomics software on protein sequences from coffee, grape, tomato, and a flowering plant called Arabidopsis, the team identified 16,000 genes that originated from a single gene in their last common ancestor. They were also able to pinpoint adaptations in genes for disease resistance and caffeine production that were unique to coffee. Overall, the team isolated 25,574 protein-making genes in the Coffea canephora genome and 23 new genes that are only found in coffee.

The robusta coffee genome also revealed that the enzymes involved in coffee’s caffeine production -- called N-methyltransferases -- adapted independently from those in cacao and tea. That is, they didn’t inherit their caffeine-linked genes from a common ancestor: The ability to produce caffeine must have evolved at least twice, and long before we started depending on it.

But what good is caffeine for plants? It may protect the coffee plant from predators like leaf-eating bugs, and when their leaves fall on the ground, the high caffeine concentration stunts the growth of rival plants trying to develop near them. “Caffeine also habituates pollinators and makes them want to come back for more, which is what it does to us, too,” Albert tells Nature. Furthermore, over evolutionary time, the coffee genome wasn't triplicated or duplicated en masse. Instead, the team team thinks that the duplication of individual genes, including the caffeine ones, spurred innovations, Science explains.

The work will not only help scientists improve coffee breeding, but also increase the resistance of the beloved plants to environmental stresses like climate change and pests. Let that percolate. 

Images: Caroline Gagné via Flickr CC BY 2.0 (top), University at Buffalo (middle)

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