UC Davis

Geisha coffee is recognized for its unique aromas and flavors and, accordingly, has achieved the highest prices in the specialty coffee markets. We report the development of a chromosome-level, well-annotated, genome assembly of Coffea arabica var. Geisha. Geisha is considered an Ethiopian landrace that represents germplasm from the Ethiopian center of origin of coffee. We used a hybrid de novo assembly approach combining 2 long-read single molecule sequencing technologies, Oxford Nanopore and Pacific Biosciences, together with scaffolding with Hi-C libraries. The final assembly is 1.03 Gb in size with BUSCO assessment of the assembly completeness of 97.7% of single-copy orthologs clusters. RNA-Seq and Iso-Seq data were used as transcriptional experimental evidence for annotation and gene prediction revealing the presence of 47,062 gene loci encompassing 53,273 protein-coding transcripts. Comparison of the assembly to the progenitor subgenomes separated the set of chromosome sequences inherited from Coffea canephora from those of Coffea eugenioides. Corresponding orthologs between the 2 Arabica varieties, Geisha and Red Bourbon, had a 99.67% median identity, higher than what we observe with the progenitor assemblies (median 97.28%). Both Geisha and Red Bourbon contain a recombination event on chromosome 10 relative to the 2 progenitors that must have happened before the geographical separation of the 2 varieties, consistent with a single allopolyploidization event giving rise to C. arabica. Broadening the availability of high-quality genome assemblies of C. arabica varieties paves the way for understanding the evolution and domestication of coffee, as well as the genetic basis and environmental interactions of why a variety like Geisha is capable of producing beans with such exceptional and unique high quality.