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Coffee Genome Sequenced, Caffeine Enzymes Analyzed

Coffee beans

(Harald Hoyer, Wikimedia Commons)

5 September 2014. An international team of researchers sequenced the genome of a major type of coffee that revealed the evolutionary pathway of this popular drink, and more details about caffeine, a main attraction of coffee. The team was led by Institute of Research for Development and National Sequencing Center, both in France, and University at Buffalo in New York. The findings appear in this week’s issue of the journal Science (paid subscription required).

According to International Coffee Organization, coffee is grown in 70 countries, mainly in tropical and sub-tropical regions, producing some 8.7 million metric tons (9.6 million short tons) in 2013. For many of the countries, coffee is an important cash crop and income generator. International Coffee Organization estimates in 2010 coffee production generated $15.4 billion in revenue and employed some 26 million people worldwide.

The research team — from institutions in Europe, Asia, and North and South America — used a whole genome shotgun sequencing strategy that reveals the order of all DNA molecules in an organism. This analysis makes it possible to pinpoint the evolution of the organism and identify similarities or differences in other species. The results offer a better understanding of strengths and weaknesses of the species, which makes possible tweaks in the genome to make coffee, in this case, resist pests or adapt to changing climatic conditions.

The researchers analyzed the genome of Robusta coffee (Coffea canephora) that accounts for about 30 percent of worldwide coffee production, grown in West and Central Africa, as well as Southeast Asia and Brazil. The team compared the sequencing data from Robusta coffee with a similar analysis of tomatoes, grapes, and Arabidopsis, a well-documented reference plant.

The findings show the coffee genome has similarities in evolutionary development to grapes and tomatoes, but coffee evolved separately, creating unique and more stable families of genes, including those that give coffee its recognizable aroma and flavor. These unique gene families also help make Robusta more resistant to disease than Arabica coffee, grown in more regions of the world.

“By looking at which families of genes expanded in the plant,” says Buffalo biologist and senior co-author Victor Albert in a university statement, “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.”

Caffeine not only produces the mild stimulants that attract drinkers, it is also believed to give the plants protection against pests and disease. The analysis revealed that the genes producing enzymes known as N-methyltransferases or NMTs in turn produce the caffeine in coffee. While this process is similar in tea and cacao, which also produce caffeine, the analysis shows the NMT-producing genes in coffee developed separately from tea and cacao.

Albert tells more about the study in the following video.

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