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

Scalabrin Simone, Magris Gabriele, Liva Mario, Vitulo Nicola, Vidotto Michele, Scaglione Davide, Del Terra Lorenzo, Ruosi Manuela Rosanna, Navarini Luciano, Pellegrino Gloria, Berny Mier y Teran Jorge Carlos, Toniutti Lucile, Suggi Liverani Furio, Cerutti Mario, Di Gaspero Gabriele, Morgante Michele. 2024. A chromosome-scale assembly reveals chromosomal aberrations and exchanges generating genetic diversity in Coffea arabica germplasm. Nature Communications, 15:463, 15 p.

https://doi.org/10.1038/s41467-023-44449-8

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Résumé : 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.

Mots-clés Agrovoc : Coffea arabica, génome, Coffea canephora, aberration chromosomique, chromosome, séquence nucléotidique, variation génétique, carte génétique

Agences de financement hors UE : illycaffè SpA, Lavazza Group, Istituto di Genomica Applicata

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