ArticlePlant molecular biology2012
Genome evolution in diploid and tetraploid Coffea species as revealed by comparative analysis of orthologous genome segments.
Article in Plant molecular biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 82 citations in OpenAlex.
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- Population structure and genetic diversity of a coffee germplasm collection in China revealed by RAD-seq.Frontiers in plant science · 2025Article
- The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars.Nature genetics · 2024Article
- Small RNAs: Promising Molecules to Tackle Climate Change Impacts in Coffee Production.Plants (Basel, Switzerland) · 2023Review
- 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
- Review
- The Rhizosphere Microbiomes of Five Species of Coffee Trees.Microbiology spectrum · 2022Article
- Global Patterns of Subgenome Evolution in Organelle-Targeted Genes of Six Allotetraploid Angiosperms.Molecular biology and evolution · 2022Article
- Metabolomics Combined with Sensory Analysis Reveals the Impact of Different Extraction Methods on Coffee Beverages fromFoods (Basel, Switzerland) · 2022Article
- Genome-Wide Identification, Characterization, and Comparative Analysis ofFrontiers in plant science · 2022Article
- The 3D Genome: From Structure to Function.International journal of molecular sciences · 2021Review
- Transcriptomic Leaf Profiling Reveals Differential Responses of the Two Most Traded Coffee Species to Elevated [COInternational journal of molecular sciences · 2020Article
- 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
- Seed comparative genomics in three coffee species identify desiccation tolerance mechanisms in intermediate seeds.Journal of experimental botany · 2020Article
- Breaking Free: The Genomics of Allopolyploidy-Facilitated Niche Expansion in White Clover.The Plant cell · 2019Article
- Homeologous regulation of Frigida-like genes provides insights on reproductive development and somatic embryogenesis in the allotetraploid Coffea arabica.Scientific reports · 2019Article
- Population genomic footprints of host adaptation, introgression and recombination in coffee leaf rust.Molecular plant pathology · 2018Article
- Genome-wide association study reveals candidate genes influencing lipids and diterpenes contents in Coffea arabica L.Scientific reports · 2018Article
- Early Selection Enabled by the Implementation of Genomic Selection inFrontiers in plant science · 2018Article
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sequence comparison of orthologous regions enables estimation of the divergence between genomes, analysis of their evolution and detection of particular features of the genomes, such as sequence rearrangements and transposable elements. Despite the economic importance of Coffea species, little genomic information is currently available. Coffea is a relatively young genus that includes more than one hundred diploid species and a single tetraploid species. Three Coffea orthologous regions of 470-900 kb were analyzed and compared: both subgenomes of allotetraploid Coffea arabica (contributed by the diploid species Coffea eugenioides and Coffea canephora) and the genome of diploid C. canephora. Sequence divergence was calculated on global alignments or on coding and non-coding sequences separately. A search for transposable elements detected 43 retrotransposons and 198 transposons in the sequences analyzed. Comparative insertion analysis made it possible to locate 165 TE insertions in the phylogenetic tree of the three genomes/subgenomes. In the tetraploid C. arabica, a homoeologous non-reciprocal transposition (HNRT) was detected and characterized: a 50 kb region of the C. eugenioides derived subgenome replaced the C. canephora derived counterpart. Comparative sequence analysis on three Coffea genomes/subgenomes revealed almost perfect gene synteny, low sequence divergence and a high number of shared transposable elements. Compared to the results of similar analysis in other genera (Aegilops/Triticum and Oryza), Coffea genomes/subgenomes appeared to be dramatically less diverged, which is consistent with the relatively recent radiation of the Coffea genus. Based on nucleotide substitution frequency, the HNRT was dated at 10,000-50,000 years BP, which is also the most recent estimation of the origin of C. arabica.
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