The first sequence for the species responsible for more than 70% of global coffee production, was released by researchers at the University of California, Davis.
Funding for the sequencing was provided by Suntory group, an international food and beverage company based in Tokyo. Now available for immediate use by scientists and plant breeders around the world, the new genome sequence has been posted to Phytozome.net, the public database for comparative plant genomics coordinated by the US Department of Energy's Joint Genome Institute.
"This new genome sequence for Coffea arabica contains information crucial for developing high-quality, disease-resistant coffee varieties that can adapt to the climate changes that are expected to threaten global coffee production in the next 30 years," said Juan Medrano, a geneticist in the UC Davis College of Agricultural and Environmental Sciences and co-researcher on the sequencing effort. "We hope that the C. arabica sequence will eventually benefit everyone involved with coffee—from coffee farmers, whose livelihoods are threatened by devastating diseases like coffee leaf rust, to coffee processors and consumers around the world," he said.
The sequencing was conducted through a collaboration between Medrano, plant scientists Allen Van Deynze and Dario Cantu, and postdoctoral research scholar Amanda Hulse-Kemp, all from UC Davis. In 2014, researchers elsewhere sequenced the genome of Coffea canephora — commonly known as robusta coffee and used for making coffee blends and instant coffee. There has been, however, no publicly accessible genome sequence for the higher-value and more genetically complex C. arabica.
C. arabica is a hybrid cross derived from two other plant species: C. canephora (robusta coffee), and the closely related C. eugenioides. As a result of that hybrid crossing, C. arabica's complex genome has four sets of chromosomes — unlike many other plants and humans, which have only two chromosome sets.
Using sequencing technology developed by Pacific Biosciences of Menlo Park, California, the UC Davis researchers estimated that UCG-17 Geisha has a genome made up of 1.19 billion base pairs—about one-third that of the human genome. The study used a combination of the latest technologies for genome sequencing and genome assembly from Dovetail Genomics of Santa Cruz, California, revealing an estimated 70,830 predicted genes.
Going forward, the researchers will focus on identifying genes and molecular pathways associated with coffee quality, in hopes that these will provide a better understanding of the flavor profiles of Geisha coffee. They have sequenced samples from 22 other Geisha coffee trees to obtain a glimpse of the genetic variation within that variety and among 13 other C. arabica varieties, which will also be important for developing plants that can resist disease and cope with other environmental stresses.
Funding for the sequencing project was provided by the Suntory group, through its Suntory Global Innovation Center Limited, located in Kyoto, Japan. The C. arabica sequencing was of particular interest for the Suntory group, whose many brands include coffee drinks, marketed in Japan.
"We anticipate that functional analysis of the genes identified by the C. arabica sequencing will lead to development of new, disease-resistant coffee varieties with enhanced flavor and aroma characteristics," said Yoshikazu Tanaka, senior general manager for Suntory Global Innovation Center Limited.