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Partial sequencing reveals the transposable element composition of Coffea genomes and provides evidence for distinct evolutionary stories

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Abstract

The Coffea genus, 124 described species, has a natural distribution spreading from inter-tropical Africa, to Western Indian Ocean Islands, India, Asia and up to Australasia. Two cultivated species, C. arabica and C. canephora, are intensively studied while, the breeding potential and the genome composition of all the wild species remained poorly uncharacterized. Here, we report the characterization and comparison of the highly repeated transposable elements content of 11 Coffea species representatives of the natural biogeographic distribution. A total of 994 Mb from 454 reads were produced with a genome coverage ranging between 3.2 and 15.7 %. The analyses showed that highly repeated transposable elements, mainly LTR retrotransposons (LTR-RT), represent between 32 and 53 % of Coffea genomes depending on their biogeographic location and genome size. Species from West and Central Africa (Eucoffea) contained the highest LTR-RT content but with no strong variation relative to their genome size. At the opposite, for the insular species (Mascarocoffea), a strong variation of LTR-RT was observed suggesting differential dynamics of these elements in this group. Two LTR-RT lineages, SIRE and Del were clearly differentially accumulated between African and insular species, suggesting these lineages were associated to the genome divergence of Coffea species in Africa. Altogether, the information obtained in this study improves our knowledge and brings new data on the composition, the evolution and the divergence of wild Coffea genomes.

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Correspondence to Romain Guyot.

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This research was supported Agropolis Fondation through the “Investissement d’avenir” program (ANR-10-LABX-0001-01) under the reference ID 1002-009.

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

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The project has been deposited at DDBJ/EMBL/GenBank BioProject ID PRJNA242989.

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Communicated by S. Hohmann.

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Guyot, R., Darré, T., Dupeyron, M. et al. Partial sequencing reveals the transposable element composition of Coffea genomes and provides evidence for distinct evolutionary stories. Mol Genet Genomics 291, 1979–1990 (2016). https://doi.org/10.1007/s00438-016-1235-7

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