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

Abstract

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.

Fig 1. Length distribution (A), first nucleotide bias (B) and composition (C) of the small RNA in CK and TR libraries.

Fig 2. First nucleotide bias of novel miRNA in CK (A) and TR (B) libraries.

Fig 3. Common and specific sequences between CK and TR lirbary.

Fig 4. Scatter-plot graphs represent the conserved miRNA (A) and novel miRNA (B) differential expression patterns between control (CK) and copper stress (TR).

The X axis indicates normalized gene expression levels in control and the Y axis indicates the normalized gene expression levels (per transcript) in copper-stresses tissues. The dots which are located at the upper and lower side of the diagonal line reflects the changes in the expression levels of miRNA genes; above the diagonal line, indicating up-regulation whereas below the diagonal line indicating down-regulation. For miRNA deep-sequencing experiment, the fold change cut-off was set at 1.5.

Fig 5. The differentially expression of significant changed miRNAs between CK and TR libraries.