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

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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

Edité par CCSD ; Nature Publishing Group -

International audience. 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.

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