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

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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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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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Correspondence to Julissa Roncal.

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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.

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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).

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