ArticleG3 (Bethesda, Md.)2016
Inter-genomic DNA Exchanges and Homeologous Gene Silencing Shaped the Nascent Allopolyploid Coffee Genome (Coffea arabica L.).
Article in G3 (Bethesda, Md.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Genome-Wide Analysis of the GRF-GIF Module inInternational journal of molecular sciences · 2026Article
- FFrontiers in plant science · 2026Review
- Rapid formation of stable autotetraploid rice from genome-doubled F1 hybrids of japonica-indica subspecies.Nature plants · 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
- Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles.Systematic biology · 2024Article
- A chromosome-scale assembly reveals chromosomal aberrations and exchanges generating genetic diversity in Coffea arabica germplasm.Nature communications · 2024Article
- Article
- New cup out of old coffee: contribution of parental gene expression legacy to phenotypic novelty in coffee beans of the allopolyploid Coffea arabica L.Annals of botany · 2023Article
- Cross-kingdom transcriptomic trends in the evolution of hybrid gene expression.Journal of evolutionary biology · 2022Article
- A major quantitative trait locus on chromosome A9, BnaPh1, controls homoeologous recombination in Brassica napus.The New phytologist · 2021Article
- 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.Scientific reports · 2020Article
- Homeologous regulation of Frigida-like genes provides insights on reproductive development and somatic embryogenesis in the allotetraploid Coffea arabica.Scientific reports · 2019Article
- The strawberry genome: a complicated past and promising future.Horticulture research · 2019Review
- Divergent Expression Patterns and Function of Two cxcr4 Paralogs in Hermaphroditic Epinephelus coioides.International journal of molecular sciences · 2018Article
- Whole Genome Incorporation and Epigenetic Stability in a Newly Synthetic Allopolyploid of Gynogenetic Gibel Carp.Genome biology and evolution · 2018Article
- Early Selection Enabled by the Implementation of Genomic Selection inFrontiers in plant science · 2018Article
- Genome-wide patterns of homoeologous gene flow in allotetraploid coffee.Applications in plant sciencesArticle
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Allopolyploidization is a biological process that has played a major role in plant speciation and evolution. Genomic changes are common consequences of polyploidization, but their dynamics over time are still poorly understood. Coffea arabica, a recently formed allotetraploid, was chosen to study genetic changes that accompany allopolyploid formation. Both RNA-seq and DNA-seq data were generated from two genetically distant C. arabica accessions. Genomic structural variation was investigated using C. canephora, one of its diploid progenitors, as reference genome. The fate of 9047 duplicate homeologous genes was inferred and compared between the accessions. The pattern of SNP density along the reference genome was consistent with the allopolyploid structure. Large genomic duplications or deletions were not detected. Two homeologous copies were retained and expressed in 96% of the genes analyzed. Nevertheless, duplicated genes were found to be affected by various genomic changes leading to homeolog loss or silencing. Genetic and epigenetic changes were evidenced that could have played a major role in the stabilization of the unique ancestral allotetraploid and its subsequent diversification. While the early evolution of C. arabica mainly involved homeologous crossover exchanges, the later stage appears to have relied on more gradual evolution involving gene conversion and homeolog silencing.
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