title: Two novel Ty1-copia retrotransposons isolated from coffee trees can effectively reveal evolutionary relationships in the Coffea genus (Rubiaceae).
abstract: In the study, we developed new markers for phylogenetic relationships and intraspecies differentiation in Coffea. Nana and Divo, two novel Ty1-copia LTR-retrotransposon families, were isolated through C. canephora BAC clone sequencing. Nana- and Divo-based markers were used to test their: (1) ability to resolve recent phylogenetic relationships; (2) efficiency in detecting intra-species differentiation. Sequence-specific amplification polymorphism (SSAP), retrotransposon-microsatellite amplified polymorphism (REMAP) and retrotransposon-based insertion polymorphism (RBIP) approaches were applied to 182 accessions (31 Coffea species and one Psilanthus accession). Nana- and Divo-based markers revealed contrasted transpositional histories. At the BAC clone locus, RBIP results on C. canephora demonstrated that Nana insertion took place prior to C. canephora differentiation, while Divo insertion occurred after differentiation. Combined SSAP and REMAP data showed that Nana could resolve Coffea lineages, while Divo was efficient at a lower taxonomic level. The combined results indicated that the retrotransposon-based markers were useful in highlighting Coffea genetic diversity and the chronological pattern of speciation/differentiation events. Ongoing complete sequencing of the C. canephora genome will soon enable exhaustive identification of LTR-RTN families, as well as more precise in-depth analyses on contributions to genome size variation and Coffea evolution.
authors.affiliation: IRD, UMR DIADE, BP 64501, Montpellier Cedex 5, France. perla.hamon@ird.fr
authors.forename: Perla
authors.initials: P
authors.lastname: Hamon
authors.forename: Pierre-Olivier
authors.initials: PO
authors.lastname: Duroy
authors.forename: Christine
authors.initials: C
authors.lastname: Dubreuil-Tranchant
authors.forename: Paulo
authors.initials: P
authors.lastname: Mafra D'Almeida Costa
authors.forename: Caroline
authors.initials: C
authors.lastname: Duret
authors.forename: Norosoa J
authors.initials: NJ
authors.lastname: Razafinarivo
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Couturon
authors.forename: Serge
authors.initials: S
authors.lastname: Hamon
authors.forename: Alexandre
authors.initials: A
authors.lastname: de Kochko
authors.forename: Valérie
authors.initials: V
authors.lastname: Poncet
authors.forename: Romain
authors.initials: R
authors.lastname: Guyot
mesh_terms: D040503:Coffea / Q000235:genetics*; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics; D010802:Phylogeny; D018626:Retroelements / Q000235:genetics*
chemical_list: D018626:Retroelements