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Active transposable elements recover species boundaries and geographic structure in Madagascan coffee species

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Abstract

The completion of the genome assembly for the economically important coffee plant Coffea canephora (Rubiaceae) has allowed the use of bioinformatic tools to identify and characterize a diverse array of transposable elements (TEs), which can be used in evolutionary studies of the genus. An overview of the copy number and location within the C. canephora genome of four TEs is presented. These are tested for their use as molecular markers to unravel the evolutionary history of the Millotii Complex, a group of six wild coffee (Coffea) species native to Madagascar. Two TEs from the Gypsy superfamily successfully recovered some species boundaries and geographic structure among samples, whereas a TE from the Copia superfamily did not. Notably, species occurring in evergreen moist forests of eastern and southeastern Madagascar were divergent with respect to species in other habitats and regions. Our results suggest that the peak of transpositional activity of the Gypsy and Copia TEs occurred, respectively, before and after the speciation events of the tested Madagascan species. We conclude that the utilization of active TEs has considerable potential to unravel the evolutionary history and delimitation of closely related Coffea species. However, the selection of TE needs to be experimentally tested, since each element has its own evolutionary history. Different TEs with similar copy number in a given species can render different dendrograms; thus copy number is not a good selection criterion to attain phylogenetic resolution.

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Acknowledgments

We are grateful to the Plate-forme de Séquençage LabEx CeMEB of the Université de Montpellier for DNA fragment analysis. Clémence Hatt helped with laboratory work and Emily Fitzgerrald with raw data reading.

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Authors and Affiliations

  1. Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John’s, A1B 3X9, Canada

    Julissa Roncal

  2. UMR DIADE, IRD, B.P. 64501, 34394, Cedex 5 Montpellier, France

    Julissa Roncal, Perla Hamon & Alexandre de Kochko

  3. UMR IPME, IRD, B.P. 64501, 34394, Cedex 5 Montpellier, France

    Romain Guyot

  4. Nestlé R&D Tours, 101 AV. G. Eiffel, Notre Dame d’Oé, BP 49716, 37097, Tours, Cedex 2, France

    Dominique Crouzillat & Michel Rigoreau

  5. Université Jean Lorougnon Guédé, BP 150, Daloa, Côte d’Ivoire

    Olivier N’Guessan Konan

  6. FOFIFA, Ambatobe, Antananarivo, Madagascar

    Jean-Jacques Rakotomalala

  7. Science for Life Laboratory, Stockholm University, Tomtebodavägen 23, 17165, Solna, Sweden

    Michael D. Nowak

  8. Royal Botanic Gardens, Kew, Richmond, TW9 3AB, Surrey, UK

    Aaron P. Davis

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  1. Julissa Roncal
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  2. Romain Guyot
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  7. Jean-Jacques Rakotomalala
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  10. Alexandre de Kochko
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Corresponding author

Correspondence to Julissa Roncal.

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Funding

This study was funded by the Marie Curie Intra-European Fellowship Program (Grant Number PIEF-GA-2009-251702 to JR).

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The authors declare that they have no conflict of interest.

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This article does not contain any studies with human participants or animals performed by any of the authors.

Additional information

Communicated by S. Hohmann.

Data deposition: KM489129, KM489130, KM489131, KM489132, PRJNA242989.

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Roncal, J., Guyot, R., Hamon, P. et al. Active transposable elements recover species boundaries and geographic structure in Madagascan coffee species. Mol Genet Genomics 291, 155–168 (2016). https://doi.org/10.1007/s00438-015-1098-3

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