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Methodologies for Discovery and Quantitative Profiling of sRNAs in Potato

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Solanum tuberosum

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2354))

Abstract

Small RNAs (sRNAs) are short noncoding RNAs involved in the regulation of a wide range of biological processes in plants. Advances in high-throughput sequencing and development of new computational tools had facilitated the discovery of different classes of sRNAs, their quantification, and elucidation of their functional role in gene expression regulation by target transcript predictions. The workflow presented here allows identification of different sRNA species: known and novel potato miRNAs, and their sequence variants (isomiRs), as well as identification of phased small interfering RNAs (phasiRNAs). Moreover, it includes steps for differential expression analysis to search for regulated sRNAs across different tested biological conditions. In addition, it describes two different methods for predicting sRNA targets, in silico prediction, and degradome sequencing data analysis. All steps of the workflow are written in a clear and user-friendly way; thus they can be followed also by the users with minimal bioinformatics knowledge. We also included several in-house scripts together with valuable notes to facilitate data (pre)processing steps and to reduce the analysis time.

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Acknowledgments

We thank Henrik Krnec for providing the script sRNA_counts.pl. The work was financed by the Slovenian Research Agency (research core funding No. P4-0165 and projects J4-7636 and J4-1777), and by the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 862858.

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Authors and Affiliations

  1. Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia

    Maja Križnik, Maja Zagorščak & Kristina Gruden

Authors
  1. Maja Križnik
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  2. Maja Zagorščak
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  3. Kristina Gruden
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Corresponding author

Correspondence to Maja Križnik .

Editor information

Editors and Affiliations

  1. Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia

    David Dobnik

  2. Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia

    Kristina Gruden

  3. Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia

    Živa Ramšak

  4. Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia

    Anna Coll

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Križnik, M., Zagorščak, M., Gruden, K. (2021). Methodologies for Discovery and Quantitative Profiling of sRNAs in Potato. In: Dobnik, D., Gruden, K., Ramšak, Ž., Coll, A. (eds) Solanum tuberosum. Methods in Molecular Biology, vol 2354. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1609-3_11

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  • DOI: https://doi.org/10.1007/978-1-0716-1609-3_11

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1608-6

  • Online ISBN: 978-1-0716-1609-3

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