Degradome Sequencing in Plants

  • Shih-Shun LinEmail author
  • Yihua Chen
  • Mei-Yeh Jade LuEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1932)


Degradome sequencing provides large amounts of data regarding RNA degradation. The degradome library construction described here is modified from the 5′-rapid amplification of cDNA ends (5′-RACE), and each degradome cDNA is sequenced by next-generation sequencing (NGS). Degradome profiles provide information confirming miRNA-mediated cleavage of target genes and allow the identification of novel targets. Furthermore, degradome sequencing provides additional information for the study of RNA processing, such as information regarding RNA-binding proteins. In this chapter, we describe a detailed optimized protocol for constructing a degradome library with high yield and quality, along with NGS and data mining procedures. We hope that the degradome approach will be applied to further studies of non-model organisms.

Key words

Degradome RNA degradation microRNA Target RNA 5′-RACE Next-generation sequencing 



We are grateful to the High Throughput Genomics Core at the Biodiversity Research Center, Academia Sinica, for performing Illumina sequencing. The study described in this chapter was supported by a grant from the Ministry of Science and Technology of Taiwan under contract number MOST 106-2321-B-002-008.


  1. 1.
    Souret FF, Kastenmayer JP, Green PJ (2004) AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets. Mol Cell 15:173–183CrossRefGoogle Scholar
  2. 2.
    Niu QW, Lin SS, Reyes JL, Chen KC, Wu HW, Yeh SD, Chua NH (2006) Expression of artificial microRNAs in transgenic Arabidopsis thaliana confers virus resistance. Nat Biotechnol 24:1420–1428CrossRefGoogle Scholar
  3. 3.
    Zhai J, Arikit S, Simon SA, Kingham BF, Meyers BC (2014) Rapid construction of parallel analysis of RNA end (PARE) libraries for Illumina sequencing. Methods 67:84–90CrossRefGoogle Scholar
  4. 4.
    Lin PC, Lu CW, Shen BN, Lee GZ, Bowman JL, Arteaga-Vazquez MA, Liu LY, Hong SF, Lo CF, Su GM, Kohchi T, Ishizaki K, Zachgo S, Althoff F, Takenaka M, Yamato KT, Lin SS (2016) Identification of miRNAs and their targets in the liverwort Marchantia polymorpha by integrating RNA-Seq and degradome analyses. Plant Cell Physiol 57:339–358CrossRefGoogle Scholar
  5. 5.
    Hou CY, Wu MT, Lu SH, Hsing YI, Chen HM (2014) Beyond cleaved small RNA targets: unraveling the complexity of plant RNA degradome data. BMC Genomics 15:15CrossRefGoogle Scholar
  6. 6.
    Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Institute of BiotechnologyNational Taiwan UniversityTaipeiTaiwan
  2. 2.High Throughput Genomics Core, Biodiversity Research CenterAcademia SinicaTaipeiTaiwan

Personalised recommendations