De novo whole-genome assembly and annotation of <i>Coffea arabica</i> var. Geisha, a high-quality coffee variety from the primary origin of coffee

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.