Two novel Ty1-copia retrotransposons isolated from coffee trees can effectively reveal evolutionary relationships in the Coffea genus (Rubiaceae)

Hamon Perla, Duroy Pierre-Olivier, Dubreuil-Tranchant Christine, Mafra d'Almeida Costa Paulo, Duret Caroline, Razafinarivo Norosa J., Couturon Emmanuel, Hamon Serge, De Kochko Alexandre, Poncet Valérie, Guyot Romain. 2011. Two novel Ty1-copia retrotransposons isolated from coffee trees can effectively reveal evolutionary relationships in the Coffea genus (Rubiaceae). Molecular Genetics and Genomics, 287 (1) : 447-460.

https://doi.org/10.1007/s00438-011-0617-0

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Résumé : 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 intraspecies differentiation. Sequence-specific amplification polymorphism (SSAP), retrotransposon-microsatellite amplified polymorphism (REMAP) and retrotransposonbased 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.

Mots-clés Agrovoc : Coffea, Coffea canephora, marqueur génétique, évolution, phylogénie

Mots-clés géographiques Agrovoc : Afrique orientale, Comores, Madagascar, Afrique occidentale, Afrique centrale

Mots-clés complémentaires : Psilanthus

Classification Agris : F30 - Génétique et amélioration des plantes
F70 - Taxonomie végétale et phytogéographie

Champ stratégique Cirad : Axe 1 (2005-2013) - Intensification écologique

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