Enzymes that help produce caffeine evolved independently in coffee, tea and chocolate, according to scientists who have newly sequenced the coffee plant genome.

Shedding light on the evolution of caffeine, man's best chemical friend, researchers at the French Institute of Research for Development say coffee did not 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 tonnes of coffee were produced in 2013.

"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 researcher Philippe Lashermes. "By looking at the coffee genome and genes specific to coffee, we were able to draw some conclusions about what makes coffee special."

For the research, the team created a high-quality draft of the genome of Coffea canephora, ( a species of coffee originating from central and western Africa), which accounts for about 30% of the world's coffee production, according to the Manhattan-based National Coffee Association.

They then 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 contains larger families of genes that relate to the production of alkaloid and flavonoid compounds, which contribute to the 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 species.

"The coffee genome helps us understand what's exciting about coffee — other than that it wakes me up in the morning," said Victor Albert, professor of biological sciences at the University at Buffalo, which was involved in the study.

The importance of caffeine in nature is disputed by scientists. Some suggest that pollinators, like humans, may develop caffeine habits.

"It turns out that, over evolutionary time, the coffee genome wasn't triplicated as in its relatives: the tomato and chile pepper. Instead it maintained a structure similar to the grape's," said researcher Patrick Wincker, of the French National Sequencing Center.

"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," Wincker's colleague France Denoeud added.

The research is published in the journal Science.