Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants

• Published in: PLoS genetics Vol. 13; no. 2; p. e1006630
• Main Authors: Lanciano, Sophie, Carpentier, Marie-Christine, Llauro, Christel, Jobet, Edouard, Robakowska-Hyzorek, Dagmara, Lasserre, Eric, Ghesquière, Alain, Panaud, Olivier, Mirouze, Marie
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 17.02.2017; Public Library of Science (PLoS)
• Subjects: Academic libraries; Arabidopsis; Arabidopsis - genetics; Binding sites; Biochemistry, Molecular Biology; Biology and Life Sciences; Colleges & universities; Deoxyribonucleic acid; DNA; DNA, Circular - chemistry; DNA, Circular - genetics; DNA, Plant - chemistry; DNA, Plant - genetics; Endosperm - genetics; Epigenetics; Extrachromosomal DNA; Flowers - genetics; Funding; Gene expression; Gene Expression Regulation, Plant; Genetics; Genome, Plant - genetics; Genomes; Genomics; High-Throughput Nucleotide Sequencing; Interspersed Repetitive Sequences - genetics; Laboratories; Life Sciences; Localization; Models, Genetic; Mutagenesis, Insertional; Oryza - genetics; Phylogeny; Plant genetics; Plant Leaves - genetics; Plants - genetics; Research and Analysis Methods; Retroelements - genetics; Retrotransposons; Reverse Transcriptase Polymerase Chain Reaction; Seeds; France
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1006630

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.