Identification and characterization of microRNAs from tree peony (Paeonia ostii) and their response to copper stress

MicroRNAs (miRNAs) are a class of non-coding, small RNAs recognized as important regulators of gene expression. Although plant miRNAs have been extensively studied in model systems, less is known in other plants with limited genome sequence data, including Paeonia ostii. In this work, we used high-t...

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Bibliographic Details
Published in:PloS one 2015-02, Vol.10 (2), p.e0117584-e0117584
Main Authors: Jin, Qijiang, Xue, Zeyun, Dong, Chunlan, Wang, Yanjie, Chu, Lingling, Xu, Yingchun
Format: Article
Language:English
Subjects:
Analysis
Arabidopsis thaliana
Cell cycle
Chemical properties
Conserved sequence
Copper
Copper - pharmacology
DNA methylation
Gene expression
Gene Expression Regulation, Plant - drug effects
Genomes
Genomics
Homeostasis
Homology
Horticulture
Identification
Metals
MicroRNA
MicroRNAs
MicroRNAs - biosynthesis
MicroRNAs - genetics
miRNA
Next-generation sequencing
Nucleotide sequence
Paeonia
Paeonia - genetics
Paeonia - metabolism
Physiology
Plant genetics
Proteins
Regulators
Ribonucleic acid
RNA
RNA, Plant - biosynthesis
RNA, Plant - genetics
Solanum melongena
Stress
Stress response
Stress, Physiological - drug effects
Stresses
Target recognition
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Summary:MicroRNAs (miRNAs) are a class of non-coding, small RNAs recognized as important regulators of gene expression. Although plant miRNAs have been extensively studied in model systems, less is known in other plants with limited genome sequence data, including Paeonia ostii. In this work, we used high-throughput sequencing to identify conserved and nonconserved miRNAs and other short RNAs in Paeonia ostii under control and copper stressed condition. 102 previously known plant miRNAs were identified and classified into 89 families according to their gene sequence identity. Some miRNAs were highly conserved in the plant kingdom suggesting that these miRNA play important and conserved roles. Combined our transcriptome sequencing data of Paeonia ostii under same conditions, 34 novel potential miRNAs were identified. The potential targets of the identified known and novel miRNAs were also predicted based on sequence homology search. Comparing the two libraries, it was observed that 12 conserved miRNAs and 18 novel miRNAs showed significantly changes in response to copper stress. Some of the new identified potential miRNAs might be involved in Paeonia ostii-specific regulating mechanisms under copper stress. These results provide a framework for further analysis of miRNAs and their role in regulating Paeonia ostii response to copper stress.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0117584