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

作者：Simone Scalabrin, Gabriele Magris, Mario Liva, Nicola Vitulo, Michele Vidotto, Davide Scaglione, Lorenzo Del Terra, Manuela R. Ruosi, Luciano Navarini, Gloria Pellegrino, Jorge C. Berny Mier y Terán, Lucile Toniutti, Furio Suggi Liverani, Mario Cerutti, Gabriele Di Gaspero, Michele Morgante · 发表于：Nature Communications · 年份：2024 · DOI：10.1038/s41467-023-44449-8 · 被引用次数：51 · 研究领域：Plant Virus Research Studies、Herpesvirus Infections and Treatments、Chromosomal and Genetic Variations

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.