Researchers from the Istituto di Genomica Applicata and elsewhere have released an improved genome assembly for Arabica coffee (Coffea arabica), a hybrid of Coffea eugenioides and Robusta coffee (Coffea canephora) that contributes to approximately 60% of world coffee production.
Coffea arabica. Image credit: Fadhil Asqar.
Coffea arabica is derived from the hybridization between the ancestors of present-day Coffea canephora and another closely related coffee species, Coffea eugenioides.
This hybridization resulted in Coffea arabica’s flavor and its large and complex genome, which poses challenges for breeding and genetic studies.
Several partial genome assemblies of Coffea arabica are currently available, but the mechanisms generating its genetic diversity are unclear.
Istituto di Genomica Applicata researchers Michele Morgante and Gabriele Di Gaspero and their colleagues employed the latest sequencing technologies to generate a more complete genome assembly for Coffea arabica, allowing for a detailed analysis of the structure of its chromosomes.
When analyzing the genome, including previously inaccessible regions, such as those around centromeres, they found differences in the structure, function and evolution of the genomes contributed by its two progenitor species, especially for genes involved in caffeine biosynthesis.
For the study, they also analyzed the genomes of 174 samples collected from different species within the Coffea genus and noticed a very low level of genetic diversity within Coffea arabica.
Diversity was found to increase in some Coffea arabica cultivars at specific genomic regions, due to two different sources of variation: chromosomal abnormalities and genetic segments donated by the so-called Timor hybrid, a Coffea arabica x Coffea canephora hybrid from East Timor.
This hybrid has become the parental line of many modern cultivars that combine the disease resistance trait of Coffea canephora and the unique flavor of Coffea arabica.
The authors suggest that the genetic diversity of Coffea arabica is essential for its commercial success, and the findings may help develop new coffee varieties with desirable traits, such as disease resistance or different flavor profiles.
“The resequencing data from a large set of accessions reveals low intraspecific diversity in the center of origin of Coffea arabica,” the authors wrote in their paper.
“Across a limited number of genomic regions, diversity increases in some cultivated genotypes to levels similar to those observed within one of the progenitor species, Coffea canephora, presumably as a consequence of introgressions deriving from the Timor hybrid.”
“It also reveals that, in addition to few, early-occurring exchanges between homoeologous chromosomes, there are numerous recent chromosomal aberrations including aneuploidies, deletions, duplications and exchanges.”
“These events are still polymorphic in the germplasm and could represent a fundamental source of genetic variation in such a lowly variable species.”
The paper was published this week in the journal Nature Communications.
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S. Scalabrin et al. 2024. A chromosome-scale assembly reveals chromosomal aberrations and exchanges generating genetic diversity in Coffea arabica germplasm. Nat Commun 15, 463; doi: 10.1038/s41467-023-44449-8
