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 R Ming, Ramanjulu Sunkar

Research output: Contribution to journalArticle

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

Fingerprint

Ananas
pineapples
small interfering RNA
MicroRNAs
microRNA
Small Interfering RNA
loci
Nucleotides
nucleotides
RNA
Small Untranslated RNA
Crassulacean acid metabolism
Photosynthesis
grain crops
translation (genetics)
Fruit
photosynthesis
Genome
flowers
Messenger RNA

Keywords

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

ASJC Scopus subject areas

  • Genetics
  • Plant Science

Cite this

Zheng, Y., Li, T., Xu, Z., Wai, C. M., Chen, K., Zhang, X., ... Sunkar, R. (2016). Identification of microRNAs, phasiRNAs and Their Targets in Pineapple. Tropical Plant Biology, 9(3), 176-186. https://doi.org/10.1007/s12042-016-9173-4

Identification of microRNAs, phasiRNAs and Their Targets in Pineapple. / Zheng, Yun; Li, Ting; Xu, Zhenning; Wai, Ching Man; Chen, Kun; Zhang, Xiaotuo; Wang, Shengpeng; Ji, Bo; Ming, Ray R; Sunkar, Ramanjulu.

In: Tropical Plant Biology, Vol. 9, No. 3, 01.09.2016, p. 176-186.

Research output: Contribution to journalArticle

Zheng, Y, Li, T, Xu, Z, Wai, CM, Chen, K, Zhang, X, Wang, S, Ji, B, Ming, RR & Sunkar, R 2016, 'Identification of microRNAs, phasiRNAs and Their Targets in Pineapple', Tropical Plant Biology, vol. 9, no. 3, pp. 176-186. https://doi.org/10.1007/s12042-016-9173-4
Zheng, Yun ; Li, Ting ; Xu, Zhenning ; Wai, Ching Man ; Chen, Kun ; Zhang, Xiaotuo ; Wang, Shengpeng ; Ji, Bo ; Ming, Ray R ; Sunkar, Ramanjulu. / Identification of microRNAs, phasiRNAs and Their Targets in Pineapple. In: Tropical Plant Biology. 2016 ; Vol. 9, No. 3. pp. 176-186.
@article{de836bb9bea94ef0a388d86630d0e931,
title = "Identification of microRNAs, phasiRNAs and Their Targets in Pineapple",
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.",
keywords = "MicroRNA, MicroRNA target, PHAS, PhasiRNA, Pineapple, TasiRNA",
author = "Yun Zheng and Ting Li and Zhenning Xu and Wai, {Ching Man} and Kun Chen and Xiaotuo Zhang and Shengpeng Wang and Bo Ji and Ming, {Ray R} and Ramanjulu Sunkar",
year = "2016",
month = "9",
day = "1",
doi = "10.1007/s12042-016-9173-4",
language = "English (US)",
volume = "9",
pages = "176--186",
journal = "Tropical Plant Biology",
issn = "1935-9756",
publisher = "Springer New York",
number = "3",

}

TY - JOUR

T1 - Identification of microRNAs, phasiRNAs and Their Targets in Pineapple

AU - Zheng, Yun

AU - Li, Ting

AU - Xu, Zhenning

AU - Wai, Ching Man

AU - Chen, Kun

AU - Zhang, Xiaotuo

AU - Wang, Shengpeng

AU - Ji, Bo

AU - Ming, Ray R

AU - Sunkar, Ramanjulu

PY - 2016/9/1

Y1 - 2016/9/1

N2 - 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.

AB - 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.

KW - MicroRNA

KW - MicroRNA target

KW - PHAS

KW - PhasiRNA

KW - Pineapple

KW - TasiRNA

UR - http://www.scopus.com/inward/record.url?scp=84975113215&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84975113215&partnerID=8YFLogxK

U2 - 10.1007/s12042-016-9173-4

DO - 10.1007/s12042-016-9173-4

M3 - Article

AN - SCOPUS:84975113215

VL - 9

SP - 176

EP - 186

JO - Tropical Plant Biology

JF - Tropical Plant Biology

SN - 1935-9756

IS - 3

ER -