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

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 e...

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Autores principales: Bajus, Marko, Macko-Podgórni, Alicja, Grzebelus, Dariusz, Baránek, Miroslav
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9751208/
https://www.ncbi.nlm.nih.gov/pubmed/36531345
http://dx.doi.org/10.3389/fpls.2022.1080993
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author Bajus, Marko
Macko-Podgórni, Alicja
Grzebelus, Dariusz
Baránek, Miroslav
author_facet Bajus, Marko
Macko-Podgórni, Alicja
Grzebelus, Dariusz
Baránek, Miroslav
author_sort Bajus, Marko
collection PubMed
description 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.
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spelling pubmed-97512082022-12-16 A review of strategies used to identify transposition events in plant genomes Bajus, Marko Macko-Podgórni, Alicja Grzebelus, Dariusz Baránek, Miroslav Front Plant Sci Plant Science 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. Frontiers Media S.A. 2022-12-01 /pmc/articles/PMC9751208/ /pubmed/36531345 http://dx.doi.org/10.3389/fpls.2022.1080993 Text en Copyright © 2022 Bajus, Macko-Podgórni, Grzebelus and Baránek https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Bajus, Marko
Macko-Podgórni, Alicja
Grzebelus, Dariusz
Baránek, Miroslav
A review of strategies used to identify transposition events in plant genomes
title A review of strategies used to identify transposition events in plant genomes
title_full A review of strategies used to identify transposition events in plant genomes
title_fullStr A review of strategies used to identify transposition events in plant genomes
title_full_unstemmed A review of strategies used to identify transposition events in plant genomes
title_short A review of strategies used to identify transposition events in plant genomes
title_sort review of strategies used to identify transposition events in plant genomes
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9751208/
https://www.ncbi.nlm.nih.gov/pubmed/36531345
http://dx.doi.org/10.3389/fpls.2022.1080993
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