Abstract
Plant microRNAs (miRNAs) are a class of non-coding RNAs that play important roles in plant development, defense, and symptom development. Here, 547 known miRNAs representing 129 miRNA families, and 282 potential novel miRNAs were identified in Beta macrocarpa using small RNA deep sequencing. A phylogenetic analysis was performed, and 8 Beta lineage-specific miRNAs were identified. Through a differential expression analysis, miRNAs associated with Beet necrotic yellow vein virus (BNYVV) infection were identified and confirmed using a microarray analysis and stem-loop RT-qPCR. In total, 103 known miRNAs representing 38 miRNA families, and 45 potential novel miRNAs were differentially regulated, with at least a two-fold change, in BNYVV-infected plants compared with that of the mock-inoculated control. Targets of these differentially expressed miRNAs were also predicted by degradome sequencing. These differentially expressed miRNAs were involved in hormone biosynthesis and signal transduction pathways, and enhanced axillary bud development and plant defenses. This work is the first to describe miRNAs of the plant genus Beta and may offer a reference for miRNA research in other species in the genus. It provides valuable information on the pathogenicity mechanisms of BNYVV.
Highlights
IntroductionPlant microRNAs (miRNAs) are a class of 20–24 nt endogenous small non-coding RNAs. Plant microRNAs (miRNAs) are a class of 20–24 nt endogenous small non-coding RNAs
Plant microRNAs are a class of 20–24 nt endogenous small non-coding RNAs
To investigate the B. macrocarpa miRNAs involved in Beet necrotic yellow vein virus (BNYVV) infection, two small RNA libraries were constructed from leaves of virus-free (L) and BNYVV-infected (VL) plants
Summary
Plant microRNAs (miRNAs) are a class of 20–24 nt endogenous small non-coding RNAs. Plant microRNAs (miRNAs) are a class of 20–24 nt endogenous small non-coding RNAs Their coding genes possess their own transcriptional units [1] and are mostly located in intergenic regions, introns or inverse repeats of coding sequences [2]. These miRNA genes (MIR) are transcribed into primary miRNAs with a secondary stem-loop structure in the partial sequence by RNA polymerase II [3, 4]. The mature miRNA guide strand enters into the RNA-induced silencing complex and regulates gene expression by target cleavage, translational inhibition and DNA methylation. The miRNA passenger strand (miRNAÃ) is degraded by an unclear mechanism [5, 6], and some miRNAÃ may function in plant defense and development [7, 8]
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