Transposition of HOPPLA in siRNA-deficient plants suggests a limited effect of the environment on retrotransposon mobility in Brachypodium distachyon

Thieme, Michael; Minadakis, Nikolaos; Himber, Christophe; Keller, Bettina; Xu, Wenbo; Rutowicz, Kinga; Matteoli, Calvin; Böhrer, Marcel; Rymen, Bart; Laudencia-Chingcuanco, Debbie; Vogel, John P.; Sibout, Richard; Stritt, Christoph; Blevins, Todd; Roulin, Anne C.

doi:10.1371/journal.pgen.1011200

Title: Transposition of HOPPLA in siRNA-deficient plants suggests a limited effect of the environment on retrotransposon mobility in Brachypodium distachyon

Journal Article · 12 March 2024 · PLoS Genetics

DOI: https://doi.org/10.1371/journal.pgen.1011200 · OSTI ID:2370486

^[1];

^[1]; Himber, Christophe ^[2]; Keller, Bettina ^[1]; Xu, Wenbo ^[1]; Rutowicz, Kinga ^[1]; Matteoli, Calvin ^[2]; Böhrer, Marcel ^[2];

^[2]; Laudencia-Chingcuanco, Debbie ^[3]; Vogel, John P. ^[4];

^[5];

^[6];

^[2];

^[1]

Univ. of Zurich (Switzerland)
Univ. de Strasbourg (France)
USDA‐ARS, Albany, CA (United States). Western Regional Research Center
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
Institut National de la Recherche Agronomique Unité BIA-1268 Biopolymères Interactions Assemblages Equipe Paroi Végétale et Polymères Pariétaux (PVPP), Nantes (France)
Swiss Tropical and Public Health Institute (Swiss TPH), Allschwil (Switzerland)

Long terminal repeat retrotransposons (LTR-RTs) are powerful mutagens regarded as a major source of genetic novelty and important drivers of evolution. Yet, the uncontrolled and potentially selfish proliferation of LTR-RTs can lead to deleterious mutations and genome instability, with large fitness costs for their host. While population genomics data suggest that an ongoing LTR-RT mobility is common in many species, the understanding of their dual role in evolution is limited. Here, we harness the genetic diversity of 320 sequenced natural accessions of the Mediterranean grass Brachypodium distachyon to characterize how genetic and environmental factors influence plant LTR-RT dynamics in the wild. When combining a coverage-based approach to estimate global LTR-RT copy number variations with mobilome-sequencing of nine accessions exposed to eight different stresses, we find little evidence for a major role of environmental factors in LTR-RT accumulations in B. distachyon natural accessions. Instead, we show that loss of RNA polymerase IV (Pol IV), which mediates RNA-directed DNA methylation in plants, results in high transcriptional and transpositional activities of RLC_BdisC024 (HOPPLA) LTR-RT family elements, and that these effects are not stress-specific. This work supports findings indicating an ongoing mobility in B. distachyon and reveals that host RNA-directed DNA methylation rather than environmental factors controls their mobility in this wild grass model.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); Swiss National Science Foundation (SNSF)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2370486

Journal Information:: PLoS Genetics, Journal Name: PLoS Genetics Journal Issue: 3 Vol. 20; ISSN 1553-7404

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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Title: Transposition of HOPPLA in siRNA-deficient plants suggests a limited effect of the environment on retrotransposon mobility in Brachypodium distachyon

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