ArticleMolecular genetics and genomics : MGG2011
Two novel Ty1-copia retrotransposons isolated from coffee trees can effectively reveal evolutionary relationships in the Coffea genus (Rubiaceae).
Article in Molecular genetics and genomics : MGG, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed.
- Chromosome distribution of four LTR retrotransposons and 18 S rDNA in coffea eugenioides.Scientific reports · 2025Article
- Distribution of Divo in Coffea genomes, a poorly described family of angiosperm LTR-Retrotransposons.Molecular genetics and genomics : MGG · 2017Article
- Ty1-copia elements reveal diverse insertion sites linked to polymorphisms among flax (Linum usitatissimum L.) accessions.BMC genomics · 2016Article
- Active transposable elements recover species boundaries and geographic structure in Madagascan coffee species.Molecular genetics and genomics : MGG · 2016Article
- Large distribution and high sequence identity of a Copia-type retrotransposon in angiosperm families.Plant molecular biology · 2015Article
- Diversity of transposable elements and repeats in a 600 kb region of the fly Calliphora vicina.Mobile DNA · 2013Article
- Genetic structure and diversity of coffee (Coffea) across Africa and the Indian Ocean islands revealed using microsatellites.Annals of botany · 2013Article
- Transcriptional activity, chromosomal distribution and expression effects of transposable elements in Coffea genomes.PloS one · 2013Article
- A survey of mangiferin and hydroxycinnamic acid ester accumulation in coffee (Coffea) leaves: biological implications and uses.Annals of botany · 2012Article
- Development and application of SINE-based markers for genotyping of potato varieties.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2012Article
- Ancestral synteny shared between distantly-related plant species from the asterid (Coffea canephora and Solanum Sp.) and rosid (Vitis vinifera) clades.BMC genomics · 2012Article
- Site-Specific Insertion Polymorphism of the MITE Alex-1 in the Genus Coffea Suggests Interspecific Gene Flow.International journal of evolutionary biology · 2011Article
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11 authors.
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Abstract
In the study, we developed new markers for phylogenetic relationships and intraspecies differentiation in Coffea. Nana and Divo, two novel Ty1-copia LTR-retrotransposon families, were isolated through C. canephora BAC clone sequencing. Nana- and Divo-based markers were used to test their: (1) ability to resolve recent phylogenetic relationships; (2) efficiency in detecting intra-species differentiation. Sequence-specific amplification polymorphism (SSAP), retrotransposon-microsatellite amplified polymorphism (REMAP) and retrotransposon-based insertion polymorphism (RBIP) approaches were applied to 182 accessions (31 Coffea species and one Psilanthus accession). Nana- and Divo-based markers revealed contrasted transpositional histories. At the BAC clone locus, RBIP results on C. canephora demonstrated that Nana insertion took place prior to C. canephora differentiation, while Divo insertion occurred after differentiation. Combined SSAP and REMAP data showed that Nana could resolve Coffea lineages, while Divo was efficient at a lower taxonomic level. The combined results indicated that the retrotransposon-based markers were useful in highlighting Coffea genetic diversity and the chronological pattern of speciation/differentiation events. Ongoing complete sequencing of the C. canephora genome will soon enable exhaustive identification of LTR-RTN families, as well as more precise in-depth analyses on contributions to genome size variation and Coffea evolution.
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