LOS ANGELES — Wake up and smell the genome.
LOS ANGELES — Wake up and smell the genome.
Researchers have pieced together the genetic atlas of the two most commonly cultivated species of coffee plant and uncovered a rather independent streak in their evolution.
Coffee developed its caffeine-generating capacity independently from its cousin, cacao, according to the first whole genome study of the plant behind the brew quaffed every morning by about 100 million Americans, published online Thursday in the journal Science.
There’s been a lot of genetic sleuthing on coffee, most of it far from the tree. Scientists have a good idea about how caffeine affects animal (particularly human) genes and alters brain chemistry. They know which genes seem to draw humans toward consuming coffee, tea or chocolate, as well. And there’s also been a heady, if somewhat contradictory, brew of studies purporting to demonstrate caffeine’s beneficial and deleterious effects on humans.
But how caffeine production got kick-started has been as hard to see as a spoon in a demitasse of espresso.
The international team that spent years piecing together coffee’s massive genome suggests the caffeine chemical factory developed independently at least twice, in cacao and coffee, in what’s known as convergent evolution. (Koalas and humans, for instance, have fingerprints, and widely divergent animals developed prickly outsides to protect their gooey insides.)
Compared with its close relatives and ancestors, coffee harbors larger families of the genes linked to aroma and bitterness and has a wider array of genes linked to caffeine production, the study found.
How those new genes popped up and proliferated appears to be a series of small, fortuitous accidents, the study suggests. Neighboring genes were duplicated by a process roughly equivalent to erratic coding and processing in a computer. Unlike computers, biological systems are ruthless housekeepers, shucking duplicates such as excess baggage. Sometimes, duplicates develop their own specialty, which appears to be what happened in the case of coffee, the authors suggest.
“A small percentage of them survive, either by splitting functions or evolving new ones,” said study co-author Victor A. Albert, an evolutionary biologist at the University at Buffalo, part of the State University of New York. “In the case of caffeine genes, we have a series of duplications that occurred all next to each other, which gave rise to enzymes that catalyze different steps” in caffeine production.
Evolution favored caffeinated plants because caffeine repels insects that prey on its leaves and halts the germination of seeds from competing plants, giving the plant a niche in which to thrive. Recent research also has suggested caffeine can help orient beneficial pollinators toward the coffee flower, Albert said.
Duplication of an entire genome is thought to be the driving force in the rise of new species and wide diversification of life. But coffee appears to have taken the slower, piecemeal approach of small duplications. That could mean biologists have been underestimating its relative importance, Albert said.
The common ancestor of coffee and such plants as cacao, tomatoes, grapes, papaya, soybeans, strawberries, peaches and poplars experienced no such whole-genome duplication.
“Yet the coffee family is the fourth largest family of flowering plants and it’s very diverse in flower, plant and fruit form,” Albert said. “Here’s a diversification without a whole genome duplication having stimulated it.”
The largely French team used crushed stems, leaves and flower parts from Coffea canephora and its hybrid offspring, Coffea arabica, to assemble the genome, which consists of 710 million building blocks.
The database is expected to boost researchers’ ability to study the highly sensitive plant behind the top revenue-generating export of dozens of nations on three continents. About 39 countries exported 5.3 metric tons coffee of coffee beans last year, according to the International Coffee Organization, a trade group.
Coffee has a relatively narrow temperature and rain tolerance, and its cultivation is threatened by shifting climate patterns and by several pests. Researchers have been eager to find ways to alter the plant’s natural defenses, while others have successfully created strains that are all but caffeine-free. Food corporations such as Nestle have sought to patent genetically modified coffee as well.