title: The chloroplast genome of the hexaploid Spartina maritima (Poaceae, Chloridoideae): Comparative analyses and molecular dating.
abstract: The history of many plant lineages is complicated by reticulate evolution with cases of hybridization often followed by genome duplication (allopolyploidy). In such a context, the inference of phylogenetic relationships and biogeographic scenarios based on molecular data is easier using haploid markers like chloroplast genome sequences. Hybridization and polyploidization occurred recurrently in the genus Spartina (Poaceae, Chloridoideae), as illustrated by the recent formation of the invasive allododecaploid S. anglica during the 19th century in Europe. Until now, only a few plastid markers were available to explore the history of this genus and their low variability limited the resolution of species relationships. We sequenced the complete chloroplast genome (plastome) of S. maritima, the native European parent of S. anglica, and compared it to the plastomes of other Poaceae. Our analysis revealed the presence of fast-evolving regions of potential taxonomic, phylogeographic and phylogenetic utility at various levels within the Poaceae family. Using secondary calibrations, we show that the tetraploid and hexaploid lineages of Spartina diverged 6-10 my ago, and that the two parents of the invasive allopolyploid S. anglica separated 2-4 my ago via long distance dispersal of the ancestor of S. maritima over the Atlantic Ocean. Finally, we discuss the meaning of divergence times between chloroplast genomes in the context of reticulate evolution.
authors.affiliation: UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1/Université Européenne de Bretagne, 35042 Rennes, France.
authors.forename: M
authors.initials: M
authors.lastname: Rousseau-Gueutin
authors.affiliation: UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1/Université Européenne de Bretagne, 35042 Rennes, France.
authors.forename: S
authors.initials: S
authors.lastname: Bellot
authors.affiliation: UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1/Université Européenne de Bretagne, 35042 Rennes, France.
authors.forename: G E
authors.initials: GE
authors.lastname: Martin
authors.affiliation: UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1/Université Européenne de Bretagne, 35042 Rennes, France.
authors.forename: J
authors.initials: J
authors.lastname: Boutte
authors.affiliation: UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1/Université Européenne de Bretagne, 35042 Rennes, France.
authors.forename: H
authors.initials: H
authors.lastname: Chelaifa
authors.affiliation: UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1/Université Européenne de Bretagne, 35042 Rennes, France.
authors.forename: O
authors.initials: O
authors.lastname: Lima
authors.affiliation: Plate-forme Génomique Environnementale et Fonctionnelle, OSUR-CNRS, Université de Rennes 1, 35042 Rennes, France.
authors.forename: S
authors.initials: S
authors.lastname: Michon-Coudouel
authors.affiliation: Plate-Forme de Bioinformatique, Genouest INRIA/IRISA, Université de Rennes-1, 35042 Rennes, France.
authors.forename: D
authors.initials: D
authors.lastname: Naquin
authors.affiliation: UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1/Université Européenne de Bretagne, 35042 Rennes, France.
authors.forename: A
authors.initials: A
authors.lastname: Salmon
authors.affiliation: UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1/Université Européenne de Bretagne, 35042 Rennes, France.
authors.forename: K
authors.initials: K
authors.lastname: Ainouche
authors.affiliation: UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1/Université Européenne de Bretagne, 35042 Rennes, France. Electronic address: malika.ainouche@univ-rennes1.fr.
authors.forename: M
authors.initials: M
authors.lastname: Ainouche
mesh_terms: D001483:Base Sequence; D017343:Genes, Plant; D054628:Genome, Chloroplast; D018745:Genome, Plant; D054643:INDEL Mutation / Q000235:genetics; D010802:Phylogeny; D006109:Poaceae / Q000235:genetics*; D011123:Polyploidy; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D017422:Sequence Analysis, DNA; D013997:Time Factors
keywords: Chloridoideae; Chloroplast genome; Molecular dating; Molecular phylogeny; Polyploidy; Spartina maritima