He and colleagues provide a draft genome of the Robusta coffee plant (Coffea canephora), which is a hardy species that provides 30 per cent of the world's coffee.
Robusta is a parent of the genetically more complex premium Arabica coffee (Coffea arabica), that provides most of the rest of the world's coffee.
The researchers found coffee has a high number of genes for N-methyltransferases, which are enzymes involved in caffeine synthesis.
However, the enzymes and biochemical pathway for producing caffeine in coffee are different to those in tea or cacao plants "The interesting thing is that caffeine synthesis has evolved separately in each of the three plants," says Henry. "It's convergent evolution."
"Clearly caffeine is a particularly well-designed or biologically effective molecule if it has evolved independently at least three times," he adds.
Henry says caffeine is involved in the plant's defenses.
"Its bitterness might serve as a warning against some predators," he says.
The researchers also found genes for disease resistance, and genes for linoleic acid, which play a key role in aroma and flavor of coffee.