High‐throughput deep sequencing shows that microRNAs play important roles in switchgrass responses to drought and salinity stress

• Published in: Plant biotechnology journal Vol. 12; no. 3; pp. 354 - 366
• Main Authors: Xie, Fuliang, Stewart, Charles Neal Jr, Taki, Faten A, He, Qiuling, Liu, Huawei, Zhang, Baohong
• Format: Journal Article
• Language: English
• Published: England John Wiley & Sons, Inc 01.04.2014
• Subjects: Acids; Base Sequence; Biodiesel fuels; biofuel; Biofuels; Bioinformatics; Biological activity; Biomass; Biosynthesis; carbon; Cellulose; data collection; Down-Regulation; Drought; Droughts; Energy crops; fatty acids; Fuels; Gene Expression Regulation, Plant; Gene Library; Gene Regulatory Networks; Gene sequencing; Genes; Genomes; Genomics; glucose; High-Throughput Nucleotide Sequencing; high‐throughput sequencing; microRNA; MicroRNAs; MicroRNAs - chemistry; MicroRNAs - genetics; miRNA; Molecular Sequence Data; Nucleic Acid Conformation; Panicum - genetics; Panicum virgatum; Pathways; Proteins; Ribonucleic acid; Ribonucleic acids; RNA; RNA libraries; RNA, Plant - chemistry; RNA, Plant - genetics; Salinity; Salinity effects; salt; salt stress; Salts; Sequence Analysis, RNA; Signal transduction; starch; Stress, Physiological; switchgrass; Transcription factors; Transcriptomes; Up-Regulation; water stress; Xylem; United States > US; microRNA; switchgrass; salt; biofuel; drought; high-throughput sequencing
• ISSN: 1467-7644; 1467-7652
• DOI: 10.1111/pbi.12142

MicroRNAs (miRNAs) are an important class of small regulatory RNAs. The goal of this study was to analyse stress‐responsive miRNAs in switchgrass (Panicum virgatum), the emerging biofuel crop, to facilitate choosing gene targets for improving biomass and biofuel yield. After sequencing three small RNA libraries constructed from control, salt‐ and drought‐treated switchgrass using Illumina sequencing technology, we identified 670 known miRNA families from a total of more than 50 million short reads. A total of 273 miRNAs were identified with precursors: 126 conserved miRNAs and 147 novel miRNAs. Of them, 265 miRNAs were found to have their opposite sequences (miRNA*) with 2‐nt overhang on the 3′ end. Of them, 194 were detected in switchgrass transcriptome sequences generated from 31 high‐throughput RNA sequencing (RNA‐Seq) data sets in NCBI. Many miRNAs were differentially or uniquely expressed during salinity or drought stress treatment. We also discovered 11 miRNA clusters containing 29 miRNAs. These identified miRNAs potentially targeted 28 549 genes with a various function, including transcription factors, stress‐response proteins and cellulose biosynthesis‐related proteins. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the identified miRNAs and their targets were classified to 3779 GO terms including 1534 molecular functions, 1851 biological processes and 394 cellular components and were enriched to 147 KEGG pathways. Interestingly, 195 miRNA families and 450 targets were involved in the biosynthesis pathways of carbon, glucose, starch, fatty acid and lignin and in xylem formation, which could aid in designing next‐generation switchgrass for biomass and biofuel.