3 Biotech

, 8:136 | Cite as

Deep sequencing and in silico analysis of small RNA library reveals novel miRNA from leaf Persicaria minor transcriptome

  • Abdul Fatah A. Samad
  • Nazaruddin Nazaruddin
  • Abdul Munir Abdul Murad
  • Jaeyres Jani
  • Zamri Zainal
  • Ismanizan Ismail
Short Reports
  • 4 Downloads

Abstract

In current era, majority of microRNA (miRNA) are being discovered through computational approaches which are more confined towards model plants. Here, for the first time, we have described the identification and characterization of novel miRNA in a non-model plant, Persicaria minor (P. minor) using computational approach. Unannotated sequences from deep sequencing were analyzed based on previous well-established parameters. Around 24 putative novel miRNAs were identified from 6,417,780 reads of the unannotated sequence which represented 11 unique putative miRNA sequences. PsRobot target prediction tool was deployed to identify the target transcripts of putative novel miRNAs. Most of the predicted target transcripts (mRNAs) were known to be involved in plant development and stress responses. Gene ontology showed that majority of the putative novel miRNA targets involved in cellular component (69.07%), followed by molecular function (30.08%) and biological process (0.85%). Out of 11 unique putative miRNAs, 7 miRNAs were validated through semi-quantitative PCR. These novel miRNAs discoveries in P. minor may develop and update the current public miRNA database.

Keywords

Deep sequencing In silico Novel miRNA Transcriptomic library Persicaria minor 

Notes

Acknowledgements

The author, Abdul Fatah A. Samad is sponsored by MyBrain 15 under MyPhD scholarship from Ministry of Higher Education (Malaysia). This research was supported by Dana Impak Perdana (DIP-2015-018).

Compliance with ethical standards

Conflict of interest

There are no conflicts to declare by authors.

Supplementary material

13205_2018_1164_MOESM1_ESM.pptx (106 kb)
Supplementary material 1 (PPTX 105 kb)
13205_2018_1164_MOESM2_ESM.docx (13 kb)
Supplementary material 2 (DOCX 12 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Abdul Fatah A. Samad
    • 1
  • Nazaruddin Nazaruddin
    • 1
    • 3
  • Abdul Munir Abdul Murad
    • 1
  • Jaeyres Jani
    • 4
  • Zamri Zainal
    • 1
    • 2
  • Ismanizan Ismail
    • 1
    • 2
  1. 1.School of Biosciences and Biotechnology, Faculty of Science and TechnologyUniversiti Kebangsaan MalaysiaBangiMalaysia
  2. 2.Institute of Systems BiologyUniversiti Kebangsaan MalaysiaBangiMalaysia
  3. 3.Department of Chemistry, Faculty of Mathematics and Natural SciencesUniversity of Syiah KualaDarussalam, Banda AcehIndonesia
  4. 4.BioEasy Sdn. Bhd. and ScienceVision Sdn. Bhd., Setia AlamShah AlamMalaysia

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