Identification and Comparative Analysis of Drought Responsive microRNA Targets in Mulberry (Morus alba L.) by Degradome Sequencing

ABSTRACT: MicroRNAs (miRNAs) are endogenous non-coding small RNAs containing 21-24 nucleotides, and play an important function in the course of stand up to adversity. Identification of miRNA target mRNAs is essential for their functional analysis. In order to anatomize miRNA guided gene regulation under drought stress, we performed a transcriptome-wide experimental method using high throughput degradome sequencing to directly detect drought stress responsive miRNA targets in mulberry. In this study, drought library (DL) and contrast library (CL) which captured the cleaved mRNA were constructed from mulberry for sequencing by Illumina sequencer, and 409, 373 target genes for 30 conserved miRNA families and 990, 950 target genes for 199, 195 novel miRNAs were identified in CL and DL, respectively. Among those conserved miRNA families in DL, mno-miR156, mno-miR172 and mno-miR396 refer to the highest number of targets, indicating that mno-miR156, mno-miR172 and mno-miR396 families and their target genes might play a key important function in corresponding to drought stress in mulberry. By construction and analysis of miRNA-target network, we found that the DL independent networks consist of 838 miRNA-mRNA pairs (63.34%). Besides, the expression patterns of 11 target genes and 12 correspondent miRNAs were compared and analyzed by qRT-PCR. In addition, 5 of 6 miRNA targets were further verified by RNA ligase-mediated 5’ rapid amplification of cDNA ends (RLM-5’ RACE). Gene ontology (GO) annotations and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis showed that these target transcripts were implicated in a broad range of biological processes and various metabolic pathways. The characterization of target genes and the associated miRNAs in response to drought exposure provides a framework for understanding the molecular mechanism of resistance to drought in plants.

ORGANISM(S): Morus alba

PROVIDER: GSE84889 | GEO | 2017/02/14

SECONDARY ACCESSION(S): PRJNA335564

REPOSITORIES: GEO