title: Partial sequencing reveals the transposable element composition of Coffea genomes and provides evidence for distinct evolutionary stories.
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.
authors.affiliation: IRD UMR IPME, CoffeeAdapt, BP 64501, 34394, Montpellier Cedex 5, France. romain.guyot@ird.fr.
authors.forename: Romain
authors.identifier: http://orcid.org/0000-0002-7016-7485
authors.initials: R
authors.lastname: Guyot
authors.affiliation: IRD UMR DIADE, EvoGeC, BP 64501, 34394, Montpellier Cedex 5, France.
authors.forename: Thibaud
authors.initials: T
authors.lastname: Darré
authors.affiliation: IRD UMR DIADE, EvoGeC, BP 64501, 34394, Montpellier Cedex 5, France.
authors.forename: Mathilde
authors.initials: M
authors.lastname: Dupeyron
authors.affiliation: IRD UMR DIADE, EvoGeC, BP 64501, 34394, Montpellier Cedex 5, France.
authors.forename: Alexandre
authors.initials: A
authors.lastname: de Kochko
authors.affiliation: IRD UMR DIADE, EvoGeC, BP 64501, 34394, Montpellier Cedex 5, France.
authors.forename: Serge
authors.initials: S
authors.lastname: Hamon
authors.affiliation: IRD UMR DIADE, EvoGeC, BP 64501, 34394, Montpellier Cedex 5, France.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Couturon
authors.affiliation: Nestlé R&D Tours, 101 AV. G. Eiffel, Notre Dame d'Oe ́, BP 49716, 37097, Tours Cedex 2, France.
authors.forename: Dominique
authors.initials: D
authors.lastname: Crouzillat
authors.affiliation: Nestlé R&D Tours, 101 AV. G. Eiffel, Notre Dame d'Oe ́, BP 49716, 37097, Tours Cedex 2, France.
authors.forename: Michel
authors.initials: M
authors.lastname: Rigoreau
authors.affiliation: FOFIFA, Ambatobe, Madagascar.
authors.forename: Jean-Jacques
authors.initials: JJ
authors.lastname: Rakotomalala
authors.affiliation: FOFIFA, Ambatobe, Madagascar.
authors.forename: Nathalie E
authors.initials: NE
authors.lastname: Raharimalala
authors.affiliation: University Jean Lorougnon Guédé, Daloa, Ivory Coast.
authors.forename: Sélastique Doffou
authors.initials: SD
authors.lastname: Akaffou
authors.affiliation: IRD UMR DIADE, EvoGeC, BP 64501, 34394, Montpellier Cedex 5, France.
authors.forename: Perla
authors.initials: P
authors.lastname: Hamon
mesh_terms: D040503:Coffea / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D014644:Genetic Variation; D059646:Genome Size; D018745:Genome, Plant; D058974:Phylogeography; D018626:Retroelements; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D018626:Retroelements
keywords: Coffea; Genome size; Geographic divergence; LTR retrotransposons; Partial genome sequencing