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

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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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Acknowledgments

The authors thank Mr. Francis Richard for maintaining the plants in the IRD greenhouses in Montpellier (France), and Dr. Pascal Musoli (NARO/COREC, Uganda) and Dr. Thierry Leroy (CIRAD, France) for kindly providing the Ugandan C. canephora DNAs.

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Author notes

  1. Pierre-Olivier Duroy

    Present address: CIRAD, UMR BGPI, Campus International de Baillarguet, 34398, Montpellier Cedex 5, France

  2. Caroline Duret

    Present address: INRA, UMR ECOFOG, BP 709, 97387, Kourou Cedex, France

  3. Emmanuel Couturon

    Present address: IRD, UMR DIADE, BP 50172, 97492, Sainte Clotilde Cedex, La Réunion, France

Authors and Affiliations

  1. IRD, UMR DIADE, BP 64501, Montpellier Cedex 5, France

    Perla Hamon, Pierre-Olivier Duroy, Christine Dubreuil-Tranchant, Paulo Mafra D’Almeida Costa, Caroline Duret, Norosoa J. Razafinarivo, Emmanuel Couturon, Serge Hamon, Alexandre de Kochko, Valérie Poncet & Romain Guyot

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  1. Perla Hamon
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Correspondence to Perla Hamon.

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Communicated by M.-A. Grandbastien.

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Hamon, P., Duroy, PO., Dubreuil-Tranchant, C. et al. Two novel Ty1-copia retrotransposons isolated from coffee trees can effectively reveal evolutionary relationships in the Coffea genus (Rubiaceae). Mol Genet Genomics 285, 447–460 (2011). https://doi.org/10.1007/s00438-011-0617-0

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