ArticleScientific reports2020
A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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48 citing papers in PubMed.
- Contrasting regulation of protein-coding genes and lncRNA homeologs in allotetraploid Coffea arabica.Planta · 2026Article
- Genome-Wide Analysis of the GRF-GIF Module inInternational journal of molecular sciences · 2026Article
- Genome-wide subgenome-resolved analysis validates chromosome 4 differentiation and prioritizes introgressedFrontiers in plant science · 2026Article
- What you plant may not be what you bought: morphological and genetic discordance in specialtyFrontiers in plant science · 2026Article
- FFrontiers in plant science · 2026Review
- Genetic diversity and population structure ofFrontiers in plant science · 2026Article
- Prospects for improvement of coffee quality and stress resilience using genomic and genetic resources.Frontiers in plant science · 2026Review
- Impact of tetraploidization on morphophysiological leaf traits in the drought tolerant 'de Ramellet' tomato landrace.Photosynthetica · 2026Article
- Analysis of changes and biosynthesis mechanism of flavonoids in Peel of Coffea Arabica L. during ripening based on metabolome and transcriptome.BMC genomics · 2025Article
- Genome-Wide Analysis Reveals Chitinases as Putative Defense-Related Proteins Against Fungi in the Genomes ofPlants (Basel, Switzerland) · 2025Article
- Article
- Deciphering octoploid strawberry evolution with serial LTR similarity matrices for subgenome partition.Horticulture research · 2025Article
- Genome-wide characterization of invertases in Arabica coffee and its progenitors reveals putative genes involved in fruit development.Functional & integrative genomics · 2025Article
- Comparative genome-wide characterization and evolutionary insights into the AP2/ERF gene family in three Coffea species (C. canephora, C. eugenioides, and C. arabica).BMC genomics · 2025Article
- Development of a flavour wheel for Coffea canephora using rate-all-that-apply.Scientific reports · 2025Article
- Exploring the Genetic Potential for Multi-Resistance to Rust and Other Coffee Phytopathogens in Breeding Programs.Plants (Basel, Switzerland) · 2025Article
- De novo whole-genome assembly and annotation of Coffea arabica var. Geisha, a high-quality coffee variety from the primary origin of coffee.G3 (Bethesda, Md.) · 2025Article
- Genetic basis of phenotypic diversity inFrontiers in genetics · 2025Article
- Population structure and genetic diversity of a coffee germplasm collection in China revealed by RAD-seq.Frontiers in plant science · 2025Article
- Three new species ofMycoKeys · 2025Article
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29 authors.
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Abstract
The genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently the two component subgenomes (putatively deriving from C. canephora and C. eugenioides) and to perform a genome-wide analysis of the genetic diversity in cultivated coffee germplasm and in wild populations growing in the center of origin of the species. We assembled a total length of 1.536 Gbp, 444 Mb and 527 Mb of which were assigned to the canephora and eugenioides subgenomes, respectively, and predicted 46,562 gene models, 21,254 and 22,888 of which were assigned to the canephora and to the eugeniodes subgenome, respectively. Through a genome-wide SNP genotyping of 736 C. arabica accessions, we analyzed the genetic diversity in the species and its relationship with geographic distribution and historical records. We observed a weak population structure due to low-frequency derived alleles and highly negative values of Taijma's D, suggesting a recent and severe bottleneck, most likely resulting from a single event of polyploidization, not only for the cultivated germplasm but also for the entire species. This conclusion is strongly supported by forward simulations of mutation accumulation. However, PCA revealed a cline of genetic diversity reflecting a west-to-east geographical distribution from the center of origin in East Africa to the Arabian Peninsula. The extremely low levels of variation observed in the species, as a consequence of the polyploidization event, make the exploitation of diversity within the species for breeding purposes less interesting than in most crop species and stress the need for introgression of new variability from the diploid progenitors.
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