The grand accomplishments of our genomic age—which are reliant to a large extent on unheralded, bleary-eyed graduate students staring at seemingly infinite bytes of data on their screens for hours on end—might never have come to pass were it not for the copious amounts of coffee fueling said students. So it's only fitting that some of them have now analyzed the genome of the coffee plant itself.

An international team of researchers spanning both coffee growing and coffee consuming regions of the globe sequenced Coffea canephora, one of the parent strains of the heavily cultivated C. arabica. They found that the plant has extra copies of genes called N-methyltransferases (NMTs), which encode a class of enzymes that mediates the late steps in caffeine biosynthesis.

Coffee has a total of 23 NMT genes, which arose primarily via a series of gene duplication events. The collection of duplicated genes is distinct from the ones found in tea and cacao, two other caffeine-producing plants that are more closely related to each other. That suggests that these two lineages evolved the ability to give humans a jolt separately.

Coffee's NMTs also exhibited evidence of positive evolutionary selection, indicating that caffeine biosynthesis may serve an adaptive purpose only in coffee. The function of its convergent evolution in the other drinks was not explored.

The coffee plant is also enriched in a class of enzymes that makes linoleic acid, a polyunsaturated fatty acid that contributes to the aroma and flavor retention of coffee beans after roasting. There are also a lot of genes involved in secondary metabolites other than caffeine, like flavonoids, isoflavones, and alkaloids, including quinine. The quinine might explain the unfortunate inspiration for the coffee tonic.

Science, 2014. DOI: 10.1126/science.1255274 (About DOIs).