Environmental and epigenetic regulation of Rider retrotransposons in tomato

TY - JOUR

T1 - Environmental and epigenetic regulation of Rider retrotransposons in tomato

AU - Benoit, Matthias

AU - Drost, Hajk-Georg

AU - Catoni, Marco

AU - Gouil, Quentin

AU - Lopez-Gomollon, Sara

AU - Baulcombe, David

AU - Paszkowski, Jerzy

N1 - Publisher Copyright: © 2019 Benoit 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.

PY - 2019/9/16

Y1 - 2019/9/16

N2 - Transposable elements in crop plants are the powerful drivers of phenotypic variation that has been selected during domestication and breeding programs. In tomato, transpositions of the LTR (long terminal repeat) retrotransposon family Rider have contributed to various phenotypes of agronomical interest, such as fruit shape and colour. However, the mechanisms regulating Rider activity are largely unknown. We have developed a bioinformatics pipeline for the functional annotation of retrotransposons containing LTRs and defined all full-length Rider elements in the tomato genome. Subsequently, we showed that accumulation of Rider transcripts and transposition intermediates in the form of extrachromosomal DNA is triggered by drought stress and relies on abscisic acid signalling. We provide evidence that residual activity of Rider is controlled by epigenetic mechanisms involving siRNAs and the RNA-dependent DNA methylation pathway. Finally, we demonstrate the broad distribution of Rider-like elements in other plant species, including crops. Our work identifies Rider as an environment-responsive element and a potential source of genetic and epigenetic variation in plants.

AB - Transposable elements in crop plants are the powerful drivers of phenotypic variation that has been selected during domestication and breeding programs. In tomato, transpositions of the LTR (long terminal repeat) retrotransposon family Rider have contributed to various phenotypes of agronomical interest, such as fruit shape and colour. However, the mechanisms regulating Rider activity are largely unknown. We have developed a bioinformatics pipeline for the functional annotation of retrotransposons containing LTRs and defined all full-length Rider elements in the tomato genome. Subsequently, we showed that accumulation of Rider transcripts and transposition intermediates in the form of extrachromosomal DNA is triggered by drought stress and relies on abscisic acid signalling. We provide evidence that residual activity of Rider is controlled by epigenetic mechanisms involving siRNAs and the RNA-dependent DNA methylation pathway. Finally, we demonstrate the broad distribution of Rider-like elements in other plant species, including crops. Our work identifies Rider as an environment-responsive element and a potential source of genetic and epigenetic variation in plants.

UR - https://www.scopus.com/pages/publications/85072717098

U2 - 10.1371/journal.pgen.1008370

DO - 10.1371/journal.pgen.1008370

M3 - Article

C2 - 31525177

AN - SCOPUS:85072717098

SN - 1553-7390

VL - 15

JO - PLoS Genetics

JF - PLoS Genetics

IS - 9

M1 - e1008370

ER -