Overview
Juan F Medrano, Dario Cantu, Andrea Minio, Christian Dreischer, Theodore Gibbons, Jason Chin, Shiyu Chen, Allen Van Deynze, Amanda M Hulse-Kemp
The journal article: https://academic.oup.com/g3journal/article/15/1/jkae262/7900928
Medrano, J. F. et al. (2025). De novo whole-genome assembly and annotation of Coffea arabica var. Geisha, a high-quality coffee variety from the primary origin of coffee. G3: Genes, Genomes, Genetics, 15(1), jkae262.
Challenge and Solution
Coffee breeders and researchers have long wanted a detailed genetic blueprint of Geisha to understand better what makes it so unique. Until now, no high-quality, complete genome has been available. To solve this, scientists built a full genome assembly of Geisha using advanced DNA sequencing techniques. This approach allowed them to carefully piece together the entire set of Geisha’s chromosomes and identify its genes.
Highlights
Which Methods Were Used?
Researchers collected young leaf and tissue samples from Geisha plants and extracted their DNA and RNA. They combined two cutting-edge long-read sequencing methods, Oxford Nanopore and Pacific Biosciences, to read very long stretches of DNA. They then used a Hi-C technique to correctly arrange these DNA pieces into chromosomes. To ensure accurate gene discovery, the team also added RNA data, which shows which genes are active in the plant.
What Did the Study Find?
The final genome assembly spans about 1.03 billion base pairs, representing nearly 98% of the entire genome. Researchers identified 47,062 gene regions and more than 53,000 predicted protein-coding sequences within it. When they compared Geisha’s genome to that of Red Bourbon, they found a remarkable 99.7 % similarity, confirming that both varieties came from the same ancient hybridization of two wild coffee species. They also discovered a shared genetic swap on chromosome 10, a change that likely occurred before these two varieties separated.
Fig. Timeline of C. arabica origins and migrations, showing its hybridization from C. eugenioides and C. canephora, the early spread through Yemen that produced Bourbon and later Caturra, and the more recent direct journey of the Geisha landrace from Ethiopia to California. Species and varieties with available genome assemblies are marked in red. Right: Dot plot comparing Geisha chromosomes with its two progenitor species, highlighting the chromosome 10 region. (Modified Medrano, J. F. et al. (2025))
Computomics' contribution
Computomics supported this research with its expertise in plant genomics, contributing extensive experience in chromosome-scale genome reconstruction as well as high-quality gene prediction and annotation.
Why Does This Matter? Guidance for Breeders and Agriculture
Having a complete Geisha genome provides breeders with a powerful tool to improve coffee quality and resilience. It can guide the selection of traits linked to flavor, disease resistance, and climate adaptability. With this knowledge, breeders can identify which genes influence unique aromas, bean structure, and plant health, helping them develop new coffee plants that keep these prized qualities even as growing conditions change. The genome also offers insights into how Geisha interacts with its environment—factors like altitude, temperature, and soil quality—that affect bean taste and yield. Farmers and researchers can use this information to select the best locations for planting or to adjust cultivation practices for maximum quality and sustainability. By making the genetic blueprint of Geisha publicly available, the study supports global breeding programs, encourages the development of climate-ready coffee varieties, and helps secure the future supply of high-quality coffee for growers and consumers alike.
Photo by Michael Burrows
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