Identification of microRNAs, phasiRNAs and Their Targets in Pineapple

Yun Zheng*, Ting Li, Zhenning Xu, Ching Man Wai, Kun Chen, Xiaotuo Zhang, Shengpeng Wang, Bo Ji, Ray Ming, Ramanjulu Sunkar

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

13 Scopus citations

Abstract

MicroRNAs (miRNAs) are small non-coding RNAs that regulate their target mRNA levels by directing cleavage or repressing its translation. Besides its outstanding nutritional and medicinal significances, pineapple serves as a model for studying genome evolution in cereal crops as well as obligate crassulacean acid metabolism (CAM) photosynthesis. Thus, studying miRNAs in pineapple is critical for better understanding their roles in this plant species. Here we carried out computational and experimental analysis of miRNAs and phased small interfering RNAs (phasiRNAs) in pineapple by analyzing small RNA profiles from flowers, fruits and leaves. The analyses have identified 131 conserved miRNAs that could be grouped into 37 families and 16 novel miRNAs. Three TAS3 loci and forty five 21 nucleotide (nt) PHAS loci, and seventy three 24 nt PHAS loci were also identified. The putative targets of the identified miRNAs and phasiRNAs were predicted. The presented results provide a comprehensive view of small regulatory RNAs and their targets in pineapple.

Original languageEnglish (US)
Pages (from-to)176-186
Number of pages11
JournalTropical Plant Biology
Volume9
Issue number3
DOIs
StatePublished - Sep 1 2016
Externally publishedYes

Keywords

  • MicroRNA
  • MicroRNA target
  • PHAS
  • PhasiRNA
  • Pineapple
  • TasiRNA

ASJC Scopus subject areas

  • Genetics
  • Plant Science

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