title: Large distribution and high sequence identity of a Copia-type retrotransposon in angiosperm families.
abstract: Retrotransposons are the main component of plant genomes. Recent studies have revealed the complexity of their evolutionary dynamics. Here, we have identified Copia25 in Coffea canephora, a new plant retrotransposon belonging to the Ty1-Copia superfamily. In the Coffea genomes analyzed, Copia25 is present in relatively low copy numbers and transcribed. Similarity sequence searches and PCR analyses show that this retrotransposon with LTRs (Long Terminal Repeats) is widely distributed among the Rubiaceae family and that it is also present in other distantly related species belonging to Asterids, Rosids and monocots. A particular situation is the high sequence identity found between the Copia25 sequences of Musa, a monocot, and Ixora, a dicot species (Rubiaceae). Our results reveal the complexity of the evolutionary dynamics of the ancient element Copia25 in angiosperm, involving several processes including sequence conservation, rapid turnover, stochastic losses and horizontal transfer.
authors.affiliation: IRD UMR DIADE, EVODYN, BP 64501, 34394, Montpellier Cedex 5, France. elainedias_bio@yahoo.com.br.|Department of Biology, UNESP-Univ. Estadual Paulista, São José do Rio Preto, Araraquara, SP, Brazil. elainedias_bio@yahoo.com.br.
authors.forename: Elaine Silva
authors.initials: ES
authors.lastname: Dias
authors.affiliation: IRD UMR DIADE, EVODYN, BP 64501, 34394, Montpellier Cedex 5, France. clemhatt@gmail.com.
authors.forename: Clémence
authors.initials: C
authors.lastname: Hatt
authors.affiliation: IRD UMR DIADE, EVODYN, BP 64501, 34394, Montpellier Cedex 5, France. serge.hamon@ird.fr.
authors.forename: Serge
authors.initials: S
authors.lastname: Hamon
authors.affiliation: IRD UMR DIADE, EVODYN, BP 64501, 34394, Montpellier Cedex 5, France. perla.hamon@ird.fr.
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. michel.rigoreau@rdto.nestle.com.
authors.forename: Michel
authors.initials: M
authors.lastname: Rigoreau
authors.affiliation: Nestlé R&D Tours, 101 AV. G. Eiffel, Notre Dame d'Oé, BP 49716, 37097, Tours, Cedex 2, France. dominique.crouzillat@rdto.nestle.com.
authors.forename: Dominique
authors.initials: D
authors.lastname: Crouzillat
authors.affiliation: Department of Biology, UNESP-Univ. Estadual Paulista, São José do Rio Preto, Araraquara, SP, Brazil. carareto@ibilce.unesp.br.
authors.forename: Claudia Marcia Aparecida
authors.initials: CM
authors.lastname: Carareto
authors.affiliation: IRD UMR DIADE, EVODYN, BP 64501, 34394, Montpellier Cedex 5, France. alexandre.dekochko@ird.fr.
authors.forename: Alexandre
authors.initials: A
authors.lastname: de Kochko
authors.affiliation: Institut de Recherche pour le Développement (IRD), UMR IPME, 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
mesh_terms: D040503:Coffea / Q000235:genetics; D019143:Evolution, Molecular; D018628:Gene Dosage / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics; D019684:Magnoliopsida / Q000235:genetics*; D008969:Molecular Sequence Data; D028521:Musa / Q000235:genetics; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D018626:Retroelements / Q000235:genetics*; D019666:Rubiaceae / Q000235:genetics; D017422:Sequence Analysis, DNA; D020079:Terminal Repeat Sequences / Q000235:genetics
chemical_list: D018626:Retroelements
keywords: Copia25; Genome dynamics; Horizontal transfer; Rubiaceae; Sequence conservation; Transposable element