A chromosome-scale assembly reveals chromosomal aberrations and exchanges generating genetic diversity in Coffea arabica germplasm

Simone Scalabrin, Gabriele Magris, Mario Liva, Nicola Vitulo, Michele Vidotto, Davide Scaglione, Lorenzo Terra, Manuela Rosanna Ruosi, Luciano Navarini, Gloria Pellegrino, Jorge Carlos Berny Mier y Teran, Lucile Toniutti, Furio Suggi Liverani, Mario Cerutti, Gabriele Gaspero () and Michele Morgante ()
Additional contact information
Simone Scalabrin: IGA Technology Services
Gabriele Magris: Istituto di Genomica Applicata
Mario Liva: IGA Technology Services
Nicola Vitulo: University of Verona
Michele Vidotto: IGA Technology Services
Davide Scaglione: IGA Technology Services
Lorenzo Terra: illycaffè SpA
Manuela Rosanna Ruosi: Lavazza Group
Luciano Navarini: illycaffè SpA
Gloria Pellegrino: Lavazza Group
Jorge Carlos Berny Mier y Teran: World Coffee Research
Lucile Toniutti: World Coffee Research
Furio Suggi Liverani: illycaffè SpA
Mario Cerutti: Lavazza Group
Gabriele Gaspero: Istituto di Genomica Applicata
Michele Morgante: Istituto di Genomica Applicata

Nature Communications, 2024, vol. 15, issue 1, 1-15

Abstract: Abstract In order to better understand the mechanisms generating genetic diversity in the recent allotetraploid species Coffea arabica, here we present a chromosome-level assembly obtained with long read technology. Two genomic compartments with different structural and functional properties are identified in the two homoeologous genomes. The resequencing data from a large set of accessions reveals low intraspecific diversity in the center of origin of the species. 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 so-called 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.

Date: 2024
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DOI: 10.1038/s41467-023-44449-8

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