Identification and Characterization of miRNA Transcriptome in Potato by High-Throughput Sequencing

Runxuan Zhang; David Marshall; Glenn J. Bryan; Csaba Hornyik

doi:10.1371/journal.pone.0057233

Identification and Characterization of miRNA Transcriptome in Potato by High-Throughput Sequencing

Runxuan Zhang, David Marshall, Glenn J. Bryan, Csaba Hornyik

Research output: Contribution to journal › Article › peer-review

106 Citations (Scopus)

Abstract

Micro RNAs (miRNAs) represent a class of short, non-coding, endogenous RNAs which play important roles in post-transcriptional regulation of gene expression. While the diverse functions of miRNAs in model plants have been well studied, the impact of miRNAs in crop plant biology is poorly understood. Here we used high-throughput sequencing and bioinformatics analysis to analyze miRNAs in the tuber bearing crop potato (Solanum tuberosum). Small RNAs were analysed from leaf and stolon tissues. 28 conserved miRNA families were found and potato-specific miRNAs were identified and validated by RNA gel blot hybridization. The size, origin and predicted targets of conserved and potato specific miRNAs are described. The large number of miRNAs and complex population of small RNAs in potato suggest important roles for these non-coding RNAs in diverse physiological and metabolic pathways.

Original language	English
Article number	ARTN e57233
Number of pages	9
Journal	PLoS ONE
Volume	8
Issue number	2
DOIs	https://doi.org/10.1371/journal.pone.0057233
Publication status	Published - 2013

Keywords

GENES
ROLES
SIRNA BIOGENESIS
GENOME SEQUENCE
MICRORNAS
EXPRESSION
ARABIDOPSIS
STRESS RESPONSES
EVOLUTION
PLANT SMALL RNAS

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title = "Identification and Characterization of miRNA Transcriptome in Potato by High-Throughput Sequencing",

abstract = "Micro RNAs (miRNAs) represent a class of short, non-coding, endogenous RNAs which play important roles in post-transcriptional regulation of gene expression. While the diverse functions of miRNAs in model plants have been well studied, the impact of miRNAs in crop plant biology is poorly understood. Here we used high-throughput sequencing and bioinformatics analysis to analyze miRNAs in the tuber bearing crop potato (Solanum tuberosum). Small RNAs were analysed from leaf and stolon tissues. 28 conserved miRNA families were found and potato-specific miRNAs were identified and validated by RNA gel blot hybridization. The size, origin and predicted targets of conserved and potato specific miRNAs are described. The large number of miRNAs and complex population of small RNAs in potato suggest important roles for these non-coding RNAs in diverse physiological and metabolic pathways.",

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TY - JOUR

T1 - Identification and Characterization of miRNA Transcriptome in Potato by High-Throughput Sequencing

AU - Zhang, Runxuan

AU - Marshall, David

AU - Bryan, Glenn J.

AU - Hornyik, Csaba

PY - 2013

Y1 - 2013

N2 - Micro RNAs (miRNAs) represent a class of short, non-coding, endogenous RNAs which play important roles in post-transcriptional regulation of gene expression. While the diverse functions of miRNAs in model plants have been well studied, the impact of miRNAs in crop plant biology is poorly understood. Here we used high-throughput sequencing and bioinformatics analysis to analyze miRNAs in the tuber bearing crop potato (Solanum tuberosum). Small RNAs were analysed from leaf and stolon tissues. 28 conserved miRNA families were found and potato-specific miRNAs were identified and validated by RNA gel blot hybridization. The size, origin and predicted targets of conserved and potato specific miRNAs are described. The large number of miRNAs and complex population of small RNAs in potato suggest important roles for these non-coding RNAs in diverse physiological and metabolic pathways.

AB - Micro RNAs (miRNAs) represent a class of short, non-coding, endogenous RNAs which play important roles in post-transcriptional regulation of gene expression. While the diverse functions of miRNAs in model plants have been well studied, the impact of miRNAs in crop plant biology is poorly understood. Here we used high-throughput sequencing and bioinformatics analysis to analyze miRNAs in the tuber bearing crop potato (Solanum tuberosum). Small RNAs were analysed from leaf and stolon tissues. 28 conserved miRNA families were found and potato-specific miRNAs were identified and validated by RNA gel blot hybridization. The size, origin and predicted targets of conserved and potato specific miRNAs are described. The large number of miRNAs and complex population of small RNAs in potato suggest important roles for these non-coding RNAs in diverse physiological and metabolic pathways.

KW - GENES

KW - ROLES

KW - SIRNA BIOGENESIS

KW - GENOME SEQUENCE

KW - MICRORNAS

KW - EXPRESSION

KW - ARABIDOPSIS

KW - STRESS RESPONSES

KW - EVOLUTION

KW - PLANT SMALL RNAS

U2 - 10.1371/journal.pone.0057233

DO - 10.1371/journal.pone.0057233

M3 - Article

C2 - 23437348

SN - 1932-6203

VL - 8

JO - PLoS ONE

JF - PLoS ONE

IS - 2

M1 - ARTN e57233

ER -

Identification and Characterization of miRNA Transcriptome in Potato by High-Throughput Sequencing

Abstract

Keywords

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