Researchers Sequence Genome of Arabica Coffee

An international team of researchers led by University of California, Davis, geneticists has publicly released the first public genome sequence of Arabica coffee (Coffea arabica).

Roasted beans of Arabica coffee (Coffea arabica). Image credit: University of California, Davis.

Roasted beans of Arabica coffee (Coffea arabica). Image credit: University of California, Davis.

In 2014, researchers led by Dr Philippe Lashermes of the French Institute of Research for Development generated a high-quality draft genome of Robusta coffee, scientifically known as Coffea canephora (syn. Coffea robusta).

There has been, however, no publicly accessible genome sequence for the higher-value and more genetically complex Coffea arabica.

“The 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 three decades,” explained co-author Dr. Juan Medrano, from the University of California, Davis.

“We hope that the Coffea 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.”

Specifically, the genome was sequenced from a remarkable variety called Geisha.

“The variety Geisha originates from the mountains of the western Ethiopian provinces of Maji and Goldija, near the town of Geisha, and is a selection known for its unique aromatic qualities,” the researchers explained.

“Coffee traditionally is grown worldwide at equatorial latitudes below 25 degrees under very specific growing conditions of acid soils, warm temperatures and high humidity,” they said.

“Over the last 6 years, Geisha has been successfully grown near Santa Barbara, California, 19 degrees latitude north of any other plantation.”

Dr. Medrano and his colleagues collected genetic material — DNA and RNA samples — from different tissues and developmental stages of 23 Geisha coffee trees.

“We have sampled and sequenced DNA and transcriptomes from this variety,” they said.

“RNA samples from different tissues and developmental stages were collected and sequenced to enhance gene model prediction in combination with ab initio methods.”

The team estimated that 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, revealing an estimated 70,830 predicted genes.

Going forward, the authors 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.

Details of the sequence were presented Jan. 15, 2017 at the PAG (Plant and Animal Genome) XXV Conference in San Diego, California.

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Allen Van Deynze et al. 2017. Update on the Sequencing of the Coffea arabica Variety, Geisha. PAG XXV, abstract # W176

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