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Distribution of Divo in Coffea genomes, a poorly described family of angiosperm LTR-Retrotransposons

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Abstract

Coffea arabica (the Arabica coffee) is an allotetraploid species originating from a recent hybridization between two diploid species: C. canephora and C. eugenioides. Transposable elements can drive structural and functional variation during the process of hybridization and allopolyploid formation in plants. To learn more about the evolution of the C. arabica genome, we characterized and studied a new Copia LTR-Retrotransposon (LTR-RT) family in diploid and allotetraploid Coffea genomes called Divo. It is a complete and relatively compact LTR-RT element (~5 kb), carrying typical Gag and Pol Copia type domains. Reverse Trancriptase (RT) domain-based phylogeny demonstrated that Divo is a new and well-supported family in the Bianca lineage, but strictly restricted to dicotyledonous species. In C. canephora, Divo is expressed and showed a genomic distribution along gene rich and gene poor regions. The copy number, the molecular estimation of insertion time and the analysis at orthologous locations of insertions in diploid and allotetraploid coffee genomes suggest that Divo underwent a different and recent transposition activity in C. arabica and C. canephora when compared to C. eugenioides. The analysis of this novel LTR-RT family represents an important step toward uncovering the genome structure and evolution of C. arabica allotetraploid genome.

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R.G. was supported by a Special Visiting Scientist grant from the Ciência sem Fronteiras program under the reference ID 84/2013 (Cnpq/CAPES).

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Authors and Affiliations

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

    Mathilde Dupeyron, Perla Hamon, Alexandre de Kochko & Emmanuel Couturon

  2. IRD, CIRAD, Univ. Montpellier, IPME, BP 64501, 34394,, Montpellier Cedex 5, France

    Mathilde Dupeyron & Romain Guyot

  3. Departamento de Biologia Geral, CCB, Universidade Estadual de Londrina,UEL, Londrina, Brazil

    Rogerio Fernandes de Souza

  4. Nestlé R&D Tours, Notre-Dame d’Oé, Tours, France

    Dominique Crouzillat

  5. Department of Botany, Instituto de Biociências, Universidade Estadual Paulista, UNESP, Rio Claro, Brazil

    Douglas Silva Domingues

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  1. Mathilde Dupeyron
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  2. Rogerio Fernandes de Souza
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Correspondence to Romain Guyot.

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Dupeyron, M., de Souza, R.F., Hamon, P. et al. Distribution of Divo in Coffea genomes, a poorly described family of angiosperm LTR-Retrotransposons. Mol Genet Genomics 292, 741–754 (2017). https://doi.org/10.1007/s00438-017-1308-2

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