Using math to crack the coffee genome for a better brew

Posted on Thursday, September 4, 2014

With more than 2.25 billion cups consumed daily worldwide, coffee is one of the most popular agricultural products of tropical countries. A group of scientists from around the world has just published the first genome sequence of the coffee plant Coffea canephora (Robusta),an important step towards improving your morning brew. Appearing in the journal Science, the study also examines coffee's independent pathway in evolution, showing that enzymes involved in making caffeine — a key ingredient in coffee, tea and cocoa — likely evolved independently for the three plants.

There are 126 coffee species, but only two are cultivated: Coffea arabica and Coffea canephora (Robusta).  These research results will greatly accelerate the sequencing of the more complex Arabica coffee genome, and make many kinds of crop improvements possible, helping improve coffee for consumers, who spend hundreds of billions of dollars on the product.

“In comparing coffee to other sequenced plant genomes, we were surprised at how conservative the genome turned out to be,” says David Sankoff, Canada Research Chair in Mathematical Genomics at the University of Ottawa. Two postdoctoral fellows in Sankoff's bioinformatics lab, Chunfang Zheng and Katharina Jahn, applied new mathematical algorithms to show that the coffee genome reflects the common ancestor of many important eudicot plant families (a group that contains most of the world's non-grain food crops) more closely than any previously studied genome. “This was our first opportunity to test these algorithms, and the results were striking.  The organization of the coffee genome is the most conserved known so far within the asterids (a collection of eudicot families that includes lilac, eggplant, daisy, carrot, ash tree and over 20,000 other species) and very close to that of the ancient eudicot.”

Botanists have previously noted correlations between high species diversity in a group, and the presence of whole genome doublings or triplings. However, Rubiaceae, the asterid family that includes coffee, has considerable species diversity — 13,000 species to be exact — but no genome duplication at its roots.

Compared to several other plant species, coffee also harbours larger families of genes that relate to the production of alkaloid and flavonoid compounds, which account for its most recognized qualities, such as its aroma and the bitterness of its beans.

Characterizing the coffee genome opens up prospects for crop improvement, such as the selection or creation of coffee varieties featuring desirable growth characteristics and improved quality. This could lead to resistance to environmental stresses and pests, such as orange leaf rust, which has devastating impact on the coffee industry and the economy of small producers in Central American countries such as Guatemala, Honduras and Costa Rica.

Professor David Sankoff is a founding member of the coffee genome sequencing consortium, which includes coffee expert Philippe Lashermes of the French Institute of Research for Development (IRD) and Center for Agricultural Research and Development (CIRAD); Patrick Wincker and France Denoeud, genome scientists at the French National Sequencing Centre (Genoscope); biologists Giovanni Giuliano of the Italian National Agency ENEA and Victor Albert of the University at Buffalo, all senior authors of the Science article; as well as ten other teams in France, Italy, the U.S., Brazil, China, India, Spain, Indonesia and Australia.

The research was funded by the French National Research Agency, the Australian Research Council, CNR-ENEA Agrifood Project of Italy, the Funding Authority for Studies and Projects (FINEP) of Brazil, the National Institutes of Science and Technology (INCT) of Brazil, the U.S. National Science Foundation and the College of Arts and Science, University at Buffalo, the Natural Sciences and Engineering Research Council of Canada (NSERC) and the Canada Research Chair in Mathematical Genomics.

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