- An international research team has sequenced the genome of the
coffee plant Coffea canephora.
- By comparing genes in the coffee, tea and chocolate plants, the
scientists show that enzymes involved in making caffeine likely
evolved independently in these three organisms.
- More than 8.7 million tons of coffee was produced in 2013; it
is the principal agricultural product of many tropical
- The study was led by the French Institute of Research for
Development, the French National Sequencing Center (CEA-Genoscope)
and the University at Buffalo. The findings appear in the journal
BUFFALO, N.Y. — The newly sequenced genome of the coffee
plant reveals secrets about the evolution of man’s best
chemical friend: caffeine.
The scientists who completed the project say the sequences and
positions of genes in the coffee plant show that they evolved
independently from genes with similar functions in tea and
chocolate, which also make caffeine.
In other words, coffee did not inherit caffeine-linked genes
from a common ancestor, but instead developed the genes on its
appears in the journal Science on Sept. 5. A video explaining the
findings is here:
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
“Coffee is as important to everyday early risers as it is
to the global economy. Accordingly, a genome sequence could be a
significant step toward improving coffee,” said Philippe
Lashermes, a researcher at the French Institute of Research for
Development (IRD). “By looking at the coffee genome and genes
specific to coffee, we were able to draw some conclusions about
what makes coffee special.”
Lashermes, along with Patrick Wincker and France Denoeud, genome
scientists at the French National Sequencing Center
(CEA-Genoscope), and Victor
Albert, professor of biological sciences at the University at
Buffalo, are the principal authors of the study.
Scientists from other organizations, particularly the
Agricultural Research Center for International Development in
France, also contributed, along with researchers from public and
private organizations in the U.S., France, Italy, Canada, Germany,
China, Spain, Indonesia, Brazil, Australia and India.
The team 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 Manhattan-based
National Coffee Association.
Next, the scientists looked at how coffee’s genetic
make-up is distinct from other species.
Compared to several 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 such as coffee aroma and the bitterness of beans.
Coffee also has an expanded collection of N-methyltransferases,
enzymes that are involved in making caffeine.
Upon taking a closer look, the researchers found that
coffee’s caffeine enzymes are more closely related to other
genes within the coffee plant than to caffeine enzymes in
tea and chocolate.
This finding suggests that caffeine production developed
independently in coffee. If this trait had been inherited from a
common ancestor, the enzymes would have been more similar between
“The coffee genome helps us understand what’s
exciting about coffee — other than that it wakes me up in the
morning,” Albert said. “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.
The new Science study 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
“It turns out that, over evolutionary time, the coffee
genome wasn’t triplicated as in its relatives: the tomato and
chile pepper,” Wincker said. “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, it appears to break the
mold of a genome duplication link to high biodiversity,”
The research was funded by the 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; the U.S. National Science Foundation; the College of
Arts and Sciences, University at Buffalo; and in-kind support by
scientists at Nestle’s research and development center in