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ARS Home » Southeast Area » Stoneville, Mississippi » Genomics and Bioinformatics Research » Research » Publications at this Location » Publication #426742
Research Project: Integrative Applied Agricultural Genomics and Bioinformatics Research

Location: Genomics and Bioinformatics Research

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

Author
item MEDRANO, JUAN - University Of California
item CANTU, DARIO - University Of California
item MINIO, ANDREA - University Of California
item DREISCHER, CHRISTIAN - Computomics Gmbh
item GIBBONS, THEODORE - Computomics Gmbh
item CHIN, JASON - Pacific Biosciences Inc
item CHEN, SHIYU - University Of California
item VAN DEYNZE, ALLEN - University Of California
item Hulse-Kemp, Amanda

Submitted to: G3: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/1/2024
Publication Date: 11/15/2024
Citation: Medrano, J.F., Cantu, D., Minio, A., Dreischer, C., Gibbons, T., Chin, J., Chen, S., Van Deynze, A., Hulse-Kemp, A.M. 2024. De novo whole-genome assembly and annotation of a high-quality coffee variety from the primary origin of coffee, Coffea arabica var. Geisha. G3: Genes, genomics, genetics. https://doi.org/10.1093/g3journal/jkae262.
DOI: https://doi.org/10.1093/g3journal/jkae262

Interpretive Summary: Coffee is an important part of every day life around the world. There are many types of coffee, including Geisha coffee which is recognized for its unique aromas and flavors and accordingly, has achieved the highest prices in the specialty coffee markets. Growers and consumers alike would love to know what in its genetics makes Geisha coffees so unique and valuable. The first step to answering this question is to develop a blueprint of the entire genetic code of Geisha and the genes that this blueprint encodes. In this study we developed the first genetic blueprint for Geisha and were able to identify just over 47,000 unique genes that make Geisha, Geisha. This is an important step to now be able to compare Geisha with other coffee types to see why it is unique.

Technical Abstract: 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.