A review of strategies used to identify transposition events in plant genomes

Abstract

Transposable elements (TEs) were initially considered redundant and dubbed ‘junk DNA’. However, more recently they were recognized as an essential element of genome plasticity. In nature, they frequently become active upon exposition of the host to stress conditions. Even though most transposition events are neutral or even deleterious, occasionally they may happen to be beneficial, resulting in genetic novelty providing better fitness to the host. Hence, TE mobilization may promote adaptability and, in the long run, act as a significant evolutionary force. There are many examples of TE insertions resulting in increased tolerance to stresses or in novel features of crops which are appealing to the consumer. Possibly, TE-driven de novo variability could be utilized for crop improvement. However, in order to systematically study the mechanisms of TE/host interactions, it is necessary to have suitable tools to globally monitor any ongoing TE mobilization. With the development of novel potent technologies, new high-throughput strategies for studying TE dynamics are emerging. Here, we present currently available methods applied to monitor the activity of TEs in plants. We divide them on the basis of their operational principles, the position of target molecules in the process of transposition and their ability to capture real cases of actively transposing elements. Their possible theoretical and practical drawbacks are also discussed. Finally, conceivable strategies and combinations of methods resulting in an improved performance are proposed.

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

“…As the loss of main players of the RdDM silencing pathway leads to increased TE activity (Ito et al ., 2011; Benoit et al ., 2019; Xu et al ., 2020; Baduel et al ., 2021), the two B. distachyon Pol IV (NRPD1) mutants provided an ideal functional tool to experimentally validate our in silico analysis. Since transcriptionally active LTR-RTs are not necessarily able to transpose (Bajus et al ., 2022), we used a mobilome-seq approach to detect TE- derived eccDNAs and transpositionally active LTR-RT families. We deliberately followed a very stringent approach for analysing the data and by doing so, identified HOPPLA as the only highly active LTR-RT family in B. distachyon.…”

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

“…As the loss of main players of the RdDM silencing pathway leads to increased TE activity [18,27,33,63], the two B. distachyon Pol IV (NRPD1) mutants provided an ideal functional tool to experimentally validate our in silico analysis. Since transcriptionally active LTR-RTs are not necessarily able to transpose [76], we used a mobilome-seq approach to detect TE-derived eccDNAs and transpositionally active LTR-RT families. We deliberately followed a very stringent approach for analysing the data and by doing so, identified HOPPLA as the only highly active LTR-RT family in B. distachyon.…”

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.…”