Abstract
Transposable elements (TEs) have long been considered junk DNA; however, the availability of genome sequences and the growth of omics databases have accelerated the study of TEs, and they are now considered evolutionary signatures. TEs, essential genetic elements in plant genomes, can move around the genome by either “cut-paste” (DNA transposons) or “copypaste” mechanisms (RNA transposons). TEs often affect host genome size and interact with host genes, resulting in altered gene expression and regulatory networks. Several genes have been identified to be influenced/modified by the action of TEs. TEs have diverse structures and functions. Plants are capable of using TEs as promoters and enhancers to drive epigenetic mechanisms in a tissue-specific manner. However, our knowledge about TEs remains poor despite extensive research in plants. Plant physiological functions associated with TEs have been challenging to analyse due to a lack of focused research. Another limitation is the lack of sufficient genetic information. The different functions displayed by plant genomes are genetically regulated, which opens up opportunities in areas such as genomic evolution and epigenetic modification. Indeed, understanding the contribution of TEs in the plant genome is indispensable to assess the diversity of evolutionary adaptability in plant taxa. In this study, we review the applications of TEs and discuss the value of genetic information in the plant genome. Genomic information about TEs has a significant value in high throughput research, including forward and reverse genetics. We discuss current strategies in using TEs for the genetic dissection of plant genomes. This review covers opportunities to use different TEs databases to increase the productivity of economically important plants for sustainable development
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Acknowledgements
This work was funded by Metasequoia Faculty Research Start-up Funding (grant number 163100028) at the Bamboo Research Institute, Nanjing Forestry University, for first author MR. This work was also supported by grants from the National Key Point Research and Invention Program of the 13th Five-Year (Grant No. 2018YFD0600101), the National Natural Science Foundation of China (grant numbers 31870656, 31470615, 32071848, 31670602, 31960336) and the Zhejiang Provincial Natural Science Foundation of China (grant number LZ19C160001).
Funding
National Natural Science Foundation of China, 31870656, Mingbing Zhou, 31470615, Mingbing Zhou, 32071848, Qiang Wei, 31670602, Qiang Wei, 31960336, Qiang Wei, Natural Science Foundation of Zhejiang Province, LZ19C160001, Mingbing Zhou, Nanjing Forestry University, 163100028, Muthusamy Ramakrishnan, National Key Point Research and Invention Program of the 13th Five-Year, 2018 YFD0600101, Qiang Wei.
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MR, QW and MZ planned, designed and wrote the review together with KKV. MR, LS and AS drew the images and tables. MR, KKV and AE edited and revised the review.
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Ramakrishnan, M., Satish, L., Sharma, A. et al. Transposable elements in plants: Recent advancements, tools and prospects. Plant Mol Biol Rep 40, 628–645 (2022). https://doi.org/10.1007/s11105-022-01342-w
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DOI: https://doi.org/10.1007/s11105-022-01342-w