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 Abd. Murad, Jaeyres Jani, Zamri Zainal, Ismanizan Ismail

Research output: Contribution to journalArticle

6 Citations (Scopus)

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.

Original languageEnglish
Article number136
Journal3 Biotech
Volume8
Issue number3
DOIs
Publication statusPublished - 1 Mar 2018

Fingerprint

RNA libraries
High-Throughput Nucleotide Sequencing
MicroRNAs
microRNA
Transcriptome
transcriptome
Computer Simulation
RNA
leaves
biological processes
plant stress
gene
plant development
prediction
stress response
quantitative polymerase chain reaction
high-throughput nucleotide sequencing
Persicaria minor
library
analysis

Keywords

  • Deep sequencing
  • In silico
  • Novel miRNA
  • Persicaria minor
  • Transcriptomic library

ASJC Scopus subject areas

  • Biotechnology
  • Environmental Science (miscellaneous)
  • Agricultural and Biological Sciences (miscellaneous)

Cite this

Deep sequencing and in silico analysis of small RNA library reveals novel miRNA from leaf Persicaria minor transcriptome. / Samad, Abdul Fatah A.; Nazaruddin, Nazaruddin; Abd. Murad, Abdul Munir; Jani, Jaeyres; Zainal, Zamri; Ismail, Ismanizan.

In: 3 Biotech, Vol. 8, No. 3, 136, 01.03.2018.

Research output: Contribution to journalArticle

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