Abstract
Moso bamboo (Phyllostachy heterocycla cv. pubescens L.) is an economically important fast-growing tree. In order to gain better understanding of gene expression regulation in this important species we used next generation sequencing to profile small RNAs in leaf and roots of young seedlings. Since standard kits to produce cDNA of small RNAs are biased for certain small RNAs, we used High Definition adapters that reduce ligation bias. We identified and experimentally validated five new microRNAs and a few other small non-coding RNAs that were not microRNAs. The biological implication of microRNA expression levels and targets of microRNAs are discussed.
Highlights
Small non-coding RNAs with the size of 20–24 nucleotides that are generated by one of the Dicer-like proteins function in transcriptional or post-transcriptional regulation of gene expression [1]
Small RNA fractions of the leaf and root total RNA samples were further isolated by using mirVanamiRNA Isolation Kit (Ambion) following the protocol provided by the manufacturer. 2 mg of sRNA from each sample was ligated to 39 and 59 HD adapters [13] by using the ScriptMiner Small RNA-seq Library preparation Kit (Epicenter) following its protocol
New miRNAs identified in Moso bamboo In addition to the known miRNAs that have been identified in other species, we looked for new miRNAs that have not been described in any species
Summary
Small non-coding RNAs (sRNAs) with the size of 20–24 nucleotides (nts) that are generated by one of the Dicer-like proteins function in transcriptional or post-transcriptional regulation of gene expression [1]. Plant sRNAs show high diversity and one of the best characterized group of sRNAs is the microRNAs (miRNAs), which are mainly nts some are 20, and 24 mers. SRNAs are involved in diverse biological processes including developments and responses to environmental changes [5] it is important to characterize sRNAs in non-model but economically important plants. Many conserved miRNAs were found and putative new miRNAs were predicted. Their expression levels were not confirmed experimentally. Some miRNAs were found in the leaf tissues of ma bamboo (Dendrocalamus latiflorus L.) [9], but the genomic sequence is not available for this species the analysis could not be completed
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