Recent advancement of NGS technologies to detect active transposable elements in plants

Abstract

Background

Unlike peoples’ belief that transposable elements (TEs) are “junk DNAs” or “genomic parasites”, TEs are essential genomic elements that bring about genetic diversity and enable evolution of a species. In fact, transposons are major constituent of chromosome in crop genomes, particularly in major cereal crops, the primary type of which is long terminal repeat (LTR) retrotransposon. Since TE mobilization can be controlled by specific environmental stimulation and as the result can generate novel genetic variations, it has been suggested that controlled mobilization of TEs can be a plausible method for crop breeding. To achieve this goal, series of sequencing techniques have been recently established to identify TEs that are active in mobility. These methods target and detect extrachromosomal DNAs (ecDNAs), which are final products of integration. The newly identified TEs by these methods exhibit strong transpositional activity which can generate novel genetic diversity and provide useful breeding resources.

Conclusions

In this mini review, we summarize and introduce ALE-seq, mobilome-seq, and VLP DNA-seq techniques employed to detect active TEs in plants.

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Acknowledgements

This work was supported by grants from the National Natural Science Foundation of China (31970518) and Strategic Priority Research Program of the Chinese Academy of Sciences (XDB27030209).

Funding

This work was supported by grants from the National Natural Science Foundation of China (31970518) and Strategic Priority Research Program of the Chinese Academy of Sciences (XDB27030209).

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Conceptualization: JC; Literature search: VS, WF, JC, JC; Writing—figure composition: VS, WF, JC; Writing—original draft: VS, WF; Writing—review and editing: JC; Funding acquisition: JC; Supervision: JC.

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Correspondence to Jungnam Cho.

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Satheesh, V., Fan, W., Chu, J. et al. Recent advancement of NGS technologies to detect active transposable elements in plants. Genes Genom 43, 289–294 (2021). https://doi.org/10.1007/s13258-021-01040-z

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Keywords

  • Transposon
  • Mobilome‐seq
  • ALE-seq
  • Long‐read sequencing