Abstract
MicroRNAs (miRNAs) are non-protein coding RNAs of ~20–24 nucleotides in length that play an important role in many biological and metabolic processes, including the regulation of gene expression, plant growth and developmental processes, as well as responses to stress and pathogens. The aim of this study was to identify and characterize novel and conserved microRNAs expressed in methyl jasmonate-treated Scots pine needles. In addition, potential precursor sequences and target genes of the identified miRNAs were determined by alignment to the Pinus unigene set. Potential precursor sequences were identified using the miRAtool, conserved miRNA precursors were also tested for the ability to form the required stem-loop structure, and the minimal folding free energy indexes were calculated. By comparison with miRBase, 4975 annotated sequences were identified and assigned to 173 miRNA groups, belonging to a total of 60 conserved miRNA families. A total of 1029 potential novel miRNAs, grouped into 34 families were found, and 46 predicted precursor sequences were identified. A total of 136 potential target genes targeted by 28 families were identified. The majority of previously reported highly conserved plant miRNAs were identified in this study, as well as some conserved miRNAs previously reported to be monocot specific. No conserved dicot-specific miRNAs were identified. A number of potential gymnosperm or conifer specific miRNAs were found, shared among a range of conifer species.
Highlights
IntroductionScots pine is a long-lived organism with a wide distribution in the northern hemisphere
Scots pine is a long-lived organism with a wide distribution in the northern hemisphere.This requires an adaption to a broad range of growing and environmental conditions—likely facilitated by substantial phenotypic plasticity and epigenetic variation [1]
The mechanisms by which MeJA regulates paclitaxel biosynthesis were investigated in Taxus × media cells, and this study showed the potential for mRNAs being targeted by miRNAs [40]
Summary
Scots pine is a long-lived organism with a wide distribution in the northern hemisphere. This requires an adaption to a broad range of growing and environmental conditions—likely facilitated by substantial phenotypic plasticity and epigenetic variation [1]. Plants have developed a range of epigenetic mechanisms to deal with biotic and abiotic stress, including DNA methylation, histone modification and expression of various non-coding RNAs (including microRNAs), which influence gene expression and regulation [2]. While miRNAs control essential aspects of plant growth and development, miRNA and sRNA expression are important in the responses to the challenges of stress and pathogens [4,5,6,7]. MiRNA studies have been mainly concentrated in angiosperms and relatively few reports have been made in conifers
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