title: Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants.
abstract: Retrotransposons are mobile genetic elements abundant in plant and animal genomes. While efficiently silenced by the epigenetic machinery, they can be reactivated upon stress or during development. Their level of transcription not reflecting their transposition ability, it is thus difficult to evaluate their contribution to the active mobilome. Here we applied a simple methodology based on the high throughput sequencing of extrachromosomal circular DNA (eccDNA) forms of active retrotransposons to characterize the repertoire of mobile retrotransposons in plants. This method successfully identified known active retrotransposons in both Arabidopsis and rice material where the epigenome is destabilized. When applying mobilome-seq to developmental stages in wild type rice, we identified PopRice as a highly active retrotransposon producing eccDNA forms in the wild type endosperm. The mobilome-seq strategy opens new routes for the characterization of a yet unexplored fraction of plant genomes.
authors.affiliation: Institut de Recherche pour le Développement (IRD), UMR232 DIADE, 911 Avenue Agropolis, Montpellier, France.|University of Perpignan, Laboratory of Plant Genome and Development, 58 Avenue Paul Alduy, Perpignan, France.
authors.forename: Sophie
authors.identifier: 0000-0002-2958-8405
authors.initials: S
authors.lastname: Lanciano
authors.affiliation: University of Perpignan, Laboratory of Plant Genome and Development, 58 Avenue Paul Alduy, Perpignan, France.|Centre National de la Recherche Scientifique (CNRS), Laboratory of Plant Genome and Development, 58 Avenue Paul Alduy, Perpignan, France.
authors.forename: Marie-Christine
authors.identifier: 0000-0002-4795-9054
authors.initials: MC
authors.lastname: Carpentier
authors.affiliation: University of Perpignan, Laboratory of Plant Genome and Development, 58 Avenue Paul Alduy, Perpignan, France.|Centre National de la Recherche Scientifique (CNRS), Laboratory of Plant Genome and Development, 58 Avenue Paul Alduy, Perpignan, France.
authors.forename: Christel
authors.initials: C
authors.lastname: Llauro
authors.affiliation: University of Perpignan, Laboratory of Plant Genome and Development, 58 Avenue Paul Alduy, Perpignan, France.|Centre National de la Recherche Scientifique (CNRS), Laboratory of Plant Genome and Development, 58 Avenue Paul Alduy, Perpignan, France.
authors.forename: Edouard
authors.initials: E
authors.lastname: Jobet
authors.affiliation: Institut de Recherche pour le Développement (IRD), UMR232 DIADE, 911 Avenue Agropolis, Montpellier, France.
authors.forename: Dagmara
authors.initials: D
authors.lastname: Robakowska-Hyzorek
authors.affiliation: University of Perpignan, Laboratory of Plant Genome and Development, 58 Avenue Paul Alduy, Perpignan, France.|Centre National de la Recherche Scientifique (CNRS), Laboratory of Plant Genome and Development, 58 Avenue Paul Alduy, Perpignan, France.
authors.forename: Eric
authors.initials: E
authors.lastname: Lasserre
authors.affiliation: Institut de Recherche pour le Développement (IRD), UMR232 DIADE, 911 Avenue Agropolis, Montpellier, France.
authors.forename: Alain
authors.initials: A
authors.lastname: Ghesquière
authors.affiliation: University of Perpignan, Laboratory of Plant Genome and Development, 58 Avenue Paul Alduy, Perpignan, France.|Centre National de la Recherche Scientifique (CNRS), Laboratory of Plant Genome and Development, 58 Avenue Paul Alduy, Perpignan, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Panaud
authors.affiliation: Institut de Recherche pour le Développement (IRD), UMR232 DIADE, 911 Avenue Agropolis, Montpellier, France.|University of Perpignan, Laboratory of Plant Genome and Development, 58 Avenue Paul Alduy, Perpignan, France.
authors.forename: Marie
authors.identifier: 0000-0002-0514-1270
authors.initials: M
authors.lastname: Mirouze
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D004270:DNA, Circular / Q000737:chemistry / Q000235:genetics*; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D056625:Endosperm / Q000235:genetics; D035264:Flowers / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D020071:Interspersed Repetitive Sequences / Q000235:genetics*; D008957:Models, Genetic; D016254:Mutagenesis, Insertional; D012275:Oryza / Q000235:genetics; D010802:Phylogeny; D018515:Plant Leaves / Q000235:genetics; D010944:Plants / Q000235:genetics*; D018626:Retroelements / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D004270:DNA, Circular; D018744:DNA, Plant; D018626:Retroelements