High throughput deep degradome sequencing reveals microRNAs and their targets in response to drought stress in mulberry (Morus alba)

PLoS One. 2017 Feb 24;12(2):e0172883. doi: 10.1371/journal.pone.0172883. eCollection 2017.

Abstract

MicroRNAs (miRNAs) play important regulatory roles by targeting mRNAs for cleavage or translational repression. Identification of miRNA targets is essential to better understanding the roles of miRNAs. miRNA targets have not been well characterized in mulberry (Morus alba). To anatomize miRNA guided gene regulation under drought stress, transcriptome-wide high throughput degradome sequencing was used in this study to directly detect drought stress responsive miRNA targets in mulberry. A drought library (DL) and a contrast library (CL) were constructed to capture the cleaved mRNAs for sequencing. In CL, 409 target genes of 30 conserved miRNA families and 990 target genes of 199 novel miRNAs were identified. In DL, 373 target genes of 30 conserved miRNA families and 950 target genes of 195 novel miRNAs were identified. Of the conserved miRNA families in DL, mno-miR156, mno-miR172, and mno-miR396 had the highest number of targets with 54, 52 and 41 transcripts, respectively, indicating that these three miRNA families and their target genes might play important functions in response to drought stress in mulberry. Additionally, we found that many of the target genes were transcription factors. By analyzing the miRNA-target molecular network, we found that the DL independent networks consisted of 838 miRNA-mRNA pairs (63.34%). The expression patterns of 11 target genes and 12 correspondent miRNAs were detected using qRT-PCR. Six miRNA targets were further verified by RNA ligase-mediated 5' rapid amplification of cDNA ends (RLM-5' RACE). Gene Ontology (GO) annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that these target transcripts were implicated in a broad range of biological processes and various metabolic pathways. This is the first study to comprehensively characterize target genes and their associated miRNAs in response to drought stress by degradome sequencing in mulberry. This study provides a framework for understanding the molecular mechanisms of drought resistance in mulberry.

MeSH terms

  • Adaptation, Physiological
  • Chromosomes, Plant / genetics
  • Droughts
  • Gene Expression Regulation, Plant
  • Gene Ontology
  • High-Throughput Nucleotide Sequencing
  • MicroRNAs / genetics*
  • MicroRNAs / metabolism
  • Molecular Sequence Annotation
  • Morus / physiology*
  • Plant Proteins / genetics
  • Plant Proteins / metabolism
  • RNA Interference
  • RNA Stability
  • RNA, Plant / genetics*
  • RNA, Plant / metabolism
  • Sequence Analysis, RNA
  • Stress, Physiological
  • Transcriptome

Substances

  • MicroRNAs
  • Plant Proteins
  • RNA, Plant

Grants and funding

We thank anonymous reviewers and the editor for critically reviewing the manuscript. This work was support by the Sericulture Industry Technology in China Agriculture Research System (project no. CARS-22-ZJ0308), Research and Innovation Project for Jiangsu University of Science and Technology (project no. YCX16B-03), Talent Development Special Project of Anhui Academy of Agricultural Sciences (project no. 17F0609), Public Industry (Agriculture) Specific Research Program (project no. 201403049).