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Large distribution and high sequence identity of a Copia-type retrotransposon in angiosperm families

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Abstract

Retrotransposons are the main component of plant genomes. Recent studies have revealed the complexity of their evolutionary dynamics. Here, we have identified Copia25 in Coffea canephora, a new plant retrotransposon belonging to the Ty1-Copia superfamily. In the Coffea genomes analyzed, Copia25 is present in relatively low copy numbers and transcribed. Similarity sequence searches and PCR analyses show that this retrotransposon with LTRs (Long Terminal Repeats) is widely distributed among the Rubiaceae family and that it is also present in other distantly related species belonging to Asterids, Rosids and monocots. A particular situation is the high sequence identity found between the Copia25 sequences of Musa, a monocot, and Ixora, a dicot species (Rubiaceae). Our results reveal the complexity of the evolutionary dynamics of the ancient element Copia25 in angiosperm, involving several processes including sequence conservation, rapid turnover, stochastic losses and horizontal transfer.

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Acknowledgments

This research was supported Agropolis Fondation through the “Investissement d’avenir” program (ANR-10-LABX-0001-01) under the reference ID 1002-009 and 1102-006, CAPES (Grants 01/2010 to CMAC and fellowship 9127-11-9 to ESD), Brazilian agencies FAPESP (Fundação de Amparo à Pesquisa do Estado de São Paulo—Grant 2013/15070-4 to CMAC and fellowship 2011/18226-0 to ESD) and CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico—Grant 306493/2013-6 to CMAC) and French agency ANR (Agence Nationale de la Recherche; Genoplante ANR-08-GENM-022-001). Acknowledgments to Dr. A. D’Hont for providing Musa spp. DNA samples; Herman E. Taedoumg for providing Craterispermum samples; Dr. P. De Block for providing Rubiaceae samples; Dr. J-J. Rakotomalala for providing Mascarocoffea samples. Acknowledgements to Philippe Lashermes and the Coffee Genome Consortium for the availability of the C. canephora BAC-end sequences and draft genome.

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Authors and Affiliations

  1. IRD UMR DIADE, EVODYN, BP 64501, 34394, Montpellier Cedex 5, France

    Elaine Silva Dias, Clémence Hatt, Serge Hamon, Perla Hamon & Alexandre de Kochko

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

    Michel Rigoreau & Dominique Crouzillat

  3. Department of Biology, UNESP–Univ. Estadual Paulista, São José do Rio Preto, Araraquara, SP, Brazil

    Elaine Silva Dias & Claudia Marcia Aparecida Carareto

  4. Institut de Recherche pour le Développement (IRD), UMR IPME, BP 64501, 34394, Montpellier Cedex 5, France

    Romain Guyot

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  1. Elaine Silva Dias
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Correspondence to Romain Guyot.

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Data deposition: KM439056 to KM439101.

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Dias, E.S., Hatt, C., Hamon, S. et al. Large distribution and high sequence identity of a Copia-type retrotransposon in angiosperm families. Plant Mol Biol 89, 83–97 (2015). https://doi.org/10.1007/s11103-015-0352-8

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