Scientists have sequenced the genome of the coffee plant and uncovered some secrets about the evolution of our favorite chemical: caffeine.
The sequences and positions of genes in coffee show that they evolved independently from genes with similar functions in tea and chocolate, which also make caffeine.
In other words, coffee didn’t inherit caffeine-linked genes from a common ancestor, but instead developed the genes on its own.
With more than 2.25 billion cups consumed daily worldwide, coffee is the principal agricultural product of many tropical countries.
According to estimates by the International Coffee Organization, more than 8.7 million tons of coffee were produced in 2013, revenue from exports amounted to $15.4 billion in 2009-2010, and the sector employed nearly 26 million people in 52 countries during 2010.
“Coffee is as important to everyday early risers as it is to the global economy,” says Philippe Lashermes, a researcher at the French Institute of Research for Development (IRD). “Accordingly, a genome sequence could be a significant step toward improving coffee. By looking at the coffee genome and genes specific to coffee, we were able to draw some conclusions about what makes coffee special.”
Larger gene families
Researchers created a high-quality draft of the genome of Coffea canephora, which accounts for about 30 percent of the world’s coffee production, according to the National Coffee Association.
Next, the scientists looked at how coffee’s genetic make-up is distinct from other species.
Compared to other plant species, including the grape and tomato, coffee harbors larger families of genes that relate to the production of alkaloid and flavonoid compounds, which contribute to qualities like aroma and the bitterness of beans.
Coffee also has an expanded collection of N-methyltransferases, enzymes that are involved in making caffeine.
Coffee’s caffeine enzymes are more closely related to other genes within the coffee plant than to caffeine enzymes in tea and chocolate, suggesting that caffeine production developed independently in coffee.
Story of caffeine
If this trait had been inherited from a common ancestor, the enzymes would have been more similar between species, says Victor Albert, professor of biological sciences at the University at Buffalo.
“The coffee genome helps us understand what’s exciting about coffee—other than that it wakes me up in the morning. 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.”
Why caffeine is so important in nature is another question. Scientists theorize that the chemical may help plants repel insects or stunt competitors’ growth. One recent paper showed that pollinators—like humans—may develop caffeine habits. Insects that visited caffeine-producing plants often returned to get another taste.
Breaks the mold
The new study, published in the journal Science, doesn’t offer new ideas about the evolutionary role of caffeine, but it does reinforce the idea that the compound is a valuable asset. It also provides the opportunity to better understand the evolution of coffee’s genome structure.
“It turns out that, over evolutionary time, the coffee genome wasn’t triplicated as in its relatives: the tomato and chile pepper,” says Patrick Wincker, a genome scientist at the French National Sequencing Center (CEA-Genoscope). “Instead it maintained a structure similar to the grape’s. As such, evolutionary diversification of the coffee genome was likely more driven by duplications in particular gene families as opposed to en masse, when all genes in the genome duplicate.”
This stands in contrast to what’s been suggested for several other large plant families, where other investigators have noted correlations between high species diversity in a group and the presence of whole genome doublings or triplings.
“Coffee lies in the plant family Rubiaceae, which has about 13,000 species and is the world’s fourth largest; thus, with no genome duplication at its root,” says France Denoeud, genome scientist at the French National Sequencing Center (CEA-Genoscope).
“It appears to break the mold of a genome duplication link to high biodiversity.”
The US National Science Foundation, University at Buffalo, French National Research Agency, Australian Research Council, Natural Sciences and Engineering Research Council of Canada, CNR-ENEA Agrifood Project of Italy, Funding Authority for Studies and Projects (FINEP Qualicafe) of Brazil, National Institutes of Science and Technology (INCT Cafe) of Brazil, and in-kind support by scientists at Nestle’s research and development center in Tours, France funded the study.
Source: University at Buffalo