One of our favorite sessions at last week’s PAG meeting focused on a major sequencing effort to understand the coffee genome. The presentation, from scientists at Cenicafé (Colombia’s National Coffee Research Center) highlighted a new project designed to characterize elements of the coffee genome that might help breeders create strains better suited to a changing climate.
Coffee production has been hard hit in recent years: a coffee leaf rust epidemic in Latin America, for instance, has cost more than $1 billion. The plant is generally more susceptible to insects and diseases recently as a result of climate change, the scientists noted.
They teamed up with PacBio for long-read sequencing of the Coffea arabica cv. Caturra genome, an allotetraploid organism clocking in at about 1.3 Gb. We were delighted to see that they used our BluePippin automated DNA sizing platform to generate the longest possible PacBio reads. They produced about 60x coverage and built the first assembly of this genome.
The scientists plan to validate the assembly using a high-quality assembly of C. eugenioides, the diploid maternal ancestor of C. arabica. That genome assembly consists of sequence data from Roche 454 platforms as well as Illumina’s Moleculo technology.
The team is hopeful this work will make a difference in plant breeding to yield a hardier, healthier coffee plant. As Alvaro Gaitan and his colleagues wrote in their session abstract, the work “should dramatically improve our understanding of coffee genetics and genomics providing direct applications to breeders for climate change adaptation.”