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.
Publication types
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Research Support, Non-U.S. Gov't
MeSH terms
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Arabidopsis / genetics
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DNA, Circular / chemistry
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DNA, Circular / genetics*
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DNA, Plant / chemistry
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DNA, Plant / genetics
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Endosperm / genetics
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Flowers / genetics
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Gene Expression Regulation, Plant
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Genome, Plant / genetics
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High-Throughput Nucleotide Sequencing
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Interspersed Repetitive Sequences / genetics*
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Models, Genetic
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Mutagenesis, Insertional
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Oryza / genetics
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Phylogeny
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Plant Leaves / genetics
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Plants / genetics*
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Retroelements / genetics*
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Reverse Transcriptase Polymerase Chain Reaction
Substances
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DNA, Circular
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DNA, Plant
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Retroelements
Grants and funding
SL is supported by a French National Agency for Research PhD fellowship (ANR-13-JSV6-0002). This work was funded by IRD, an Agropolis Fondation grant (Labex AGRO, “RetroCrop” 1202-041) and a young investigator grant from the French National Agency for Research (ANR-13-JSV6-0002 “ExtraChrom”) to MM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.