Natural GMOs Part 288. Natural circular mobile plant mini-chromosomes

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.

Author summary

Long time considered as « junk DNA », the evolutive force of transposable elements (TEs) is now well established and TEs contribute strongly to eukaryote genome plasticity. However, it is difficult to fully characterize the mobile part of a genome, or active mobilome, and tracking TE activity remains challenging. We therefore propose to use the detection of extrachromosomal circular DNA as a diagnostic for plant TE activity. Our mobilome-seq technique allowed to identify a new active retrotransposon in wild type rice seeds, and will represent a powerful strategy in characterizing the somatic activity of TEs to evaluate their impact on genome stability and to better understand their adaptive capacity in multicellular eukaryotes.

Citation: Lanciano S, Carpentier M-C, Llauro C, Jobet E, Robakowska-Hyzorek D, Lasserre E, et al. (2017) Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants. PLoS Genet 13(2): e1006630. https://doi.org/10.1371/journal.pgen.1006630

Copyright: © 2017 Lanciano et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.