title: High throughput deep degradome sequencing reveals microRNAs and their targets in response to drought stress in mulberry (Morus alba).
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.
authors.affiliation: School of Biology and Technology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, P. R. China.|The Sericultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui, P. R. China.
authors.forename: Ruixue
authors.initials: R
authors.lastname: Li
authors.affiliation: School of Biology and Technology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, P. R. China.
authors.forename: Dandan
authors.initials: D
authors.lastname: Chen
authors.affiliation: The Sericultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui, P. R. China.
authors.forename: Taichu
authors.initials: T
authors.lastname: Wang
authors.affiliation: School of Biology and Technology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, P. R. China.
authors.forename: Yizhen
authors.initials: Y
authors.lastname: Wan
authors.affiliation: School of Biology and Technology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, P. R. China.
authors.forename: Rongfang
authors.initials: R
authors.lastname: Li
authors.affiliation: School of Biology and Technology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, P. R. China.
authors.forename: Rongjun
authors.initials: R
authors.lastname: Fang
authors.affiliation: The Sericultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui, P. R. China.
authors.forename: Yuting
authors.initials: Y
authors.lastname: Wang
authors.affiliation: The Plant Protection and Agro-products Safety Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui, P. R. China.
authors.forename: Fei
authors.initials: F
authors.lastname: Hu
authors.affiliation: School of Biology and Technology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, P. R. China.
authors.forename: Hong
authors.initials: H
authors.lastname: Zhou
authors.affiliation: School of Biology and Technology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, P. R. China.
authors.forename: Long
authors.initials: L
authors.lastname: Li
authors.affiliation: School of Biology and Technology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, P. R. China.
authors.forename: Weiguo
authors.initials: W
authors.lastname: Zhao
mesh_terms: D000222:Adaptation, Physiological; D032461:Chromosomes, Plant / Q000235:genetics; D055864:Droughts; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D058977:Molecular Sequence Annotation; D031625:Morus / Q000502:physiology*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D034622:RNA Interference; D020871:RNA Stability; D018749:RNA, Plant / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D013312:Stress, Physiological; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D010940:Plant Proteins; D018749:RNA, Plant