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In Silico Identification of Stress-Associated Transposable Elements in Arabidopsis thaliana Using Public Transcriptome Data

Part of the Methods in Molecular Biology book series (MIMB,volume 2250)

Abstract

Transposable elements (TEs) have been associated with stress response in many plants, making them a key target of study. However, the high variability, genomic repeat-heavy nature, and widely noncoding character of TEs have made them difficult to study using non-specialized methods, whether experimental or computational. In this chapter, we introduce two computational workflows to analyze transposable elements using publicly available transcriptome data. In the first of these methods, we identify TEs, which show differential expression under salt stress using sample transcriptome libraries that includes noncoding transcripts. In the second, we identify protein-coding genes with differential expression under the same conditions, and determine which TEs are enriched in the promoter regions of these stress-related genes.

Key words

  • Bioinformatics
  • Transposable elements
  • Stress response
  • Plant genome
  • RNA-seq
  • Transcriptomics
  • Public databases

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  • DOI: 10.1007/978-1-0716-1134-0_2
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Acknowledgments

The authors would like to acknowledge Nazmiye Arslan for her contributions to refining the R scripts used in the above workflow, and Ahmet Bursalı for his contributions to the refinement of the included figure.

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Correspondence to Gökhan Karakülah .

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Eskier, D., Karakülah, G. (2021). In Silico Identification of Stress-Associated Transposable Elements in Arabidopsis thaliana Using Public Transcriptome Data. In: Cho, J. (eds) Plant Transposable Elements. Methods in Molecular Biology, vol 2250. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1134-0_2

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  • DOI: https://doi.org/10.1007/978-1-0716-1134-0_2

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