title: Active transposable elements recover species boundaries and geographic structure in Madagascan coffee species.
abstract: 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.
authors.affiliation: Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John's, A1B 3X9, Canada. jroncal@mun.ca.|UMR DIADE, IRD, B.P. 64501, 34394, Cedex 5 Montpellier, France. jroncal@mun.ca.
authors.forename: Julissa
authors.initials: J
authors.lastname: Roncal
authors.affiliation: UMR IPME, IRD, B.P. 64501, 34394, Cedex 5 Montpellier, France.
authors.forename: Romain
authors.initials: R
authors.lastname: Guyot
authors.affiliation: UMR DIADE, IRD, B.P. 64501, 34394, Cedex 5 Montpellier, France.
authors.forename: Perla
authors.initials: P
authors.lastname: Hamon
authors.affiliation: Nestlé R&D Tours, 101 AV. G. Eiffel, Notre Dame d'Oé, 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'Oé, BP 49716, 37097, Tours, Cedex 2, France.
authors.forename: Michel
authors.initials: M
authors.lastname: Rigoreau
authors.affiliation: Université Jean Lorougnon Guédé, BP 150, Daloa, Côte d'Ivoire.
authors.forename: Olivier N'Guessan
authors.initials: ON
authors.lastname: Konan
authors.affiliation: FOFIFA, Ambatobe, Antananarivo, Madagascar.
authors.forename: Jean-Jacques
authors.initials: JJ
authors.lastname: Rakotomalala
authors.affiliation: Science for Life Laboratory, Stockholm University, Tomtebodavägen 23, 17165, Solna, Sweden.
authors.forename: Michael D
authors.initials: MD
authors.lastname: Nowak
authors.affiliation: Royal Botanic Gardens, Kew, Richmond, TW9 3AB, Surrey, UK.
authors.forename: Aaron P
authors.initials: AP
authors.lastname: Davis
authors.affiliation: UMR DIADE, IRD, B.P. 64501, 34394, Cedex 5 Montpellier, France.
authors.forename: Alexandre
authors.initials: A
authors.lastname: de Kochko
mesh_terms: D040503:Coffea / Q000235:genetics*; D003069:Coffee / Q000235:genetics*; D004251:DNA Transposable Elements / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D018628:Gene Dosage / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D010802:Phylogeny
chemical_list: D003069:Coffee; D004251:DNA Transposable Elements; D018744:DNA, Plant
keywords: Coffea canephora; Diversification; LTR retrotransposons; Madagascar; REMAP