Transposition ofHOPPLAin siRNA-deficient plants suggests a limited effect of the environment on retrotransposon mobility inBrachypodium distachyon

Abstract

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 roles in evolution is limited. Here, we harness the genetic diversity of 320 sequenced natural accessions of the Mediterranean grassBrachypodium distachyonto 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 inB. distachyonnatural 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 transposition 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 inB. distachyonand reveals that host RNA-directed DNA methylation rather than environmental factors controls their mobility in this wild grass model.

Toward Transgene-Free Transposon-Mediated Biological Mutagenesis for Plant Breeding

“…While transcriptome-based approaches can be useful for the identification of expressed TEs, the direct detection of TE transposition events at the whole-mobilome scale is a prospective approach. The latest high-throughput methods of mobilome analysis, including circular [68][69][70][71][72] and linear ex-trachromosomal DNA [73][74][75] sequencing, provide great opportunities for deciphering conditions that are permissive or provocating for TE activity [76][77][78]. Such large-scale screening performed for different developmental stages, stress conditions, and organs would provide valuable information for the further search of TE activity triggers.…”