Transcriptome-Wide Identification and Characterization of MicroRNAs from Castor Bean (Ricinus communis L.)

Abstract

BackgroundMicroRNAs (miRNAs) are endogenously encoded small RNAs that post-transcriptionally regulate gene expression and play essential roles in numerous developmental and physiological processes. Currently, little information on the transcriptome and tissue-specific expression of miRNAs is available in the model non-edible oilseed crop castor bean (Ricinus communis L.), one of the most important non-edible oilseed crops cultivated worldwide. Recent advances in sequencing technologies have allowed the identification of conserved and novel miRNAs in many plant species. Here, we used high-throughput sequencing technologies to identify and characterize the miRNAs in castor bean.ResultsFive small RNA libraries were constructed for deep sequencing from root tips, leaves, developing seeds (at the initial stage, seed1; and at the fast oil accumulation stage, seed2) and endosperms in castor bean. High-throughput sequencing generated a large number of sequence reads of small RNAs in this study. In total, 86 conserved miRNAs were identified, including 63 known and 23 newly identified. Sixteen miRNA isoform variants in length were found from the conserved miRNAs of castor bean. MiRNAs displayed diverse organ-specific expression levels among five libraries. Combined with criteria for miRNA annotation and a RT-PCR approach, 72 novel miRNAs and their potential precursors were annotated and 20 miRNAs newly identified were validated. In addition, new target candidates for miRNAs newly identified in this study were proposed.ConclusionsThe current study presents the first high-throughput small RNA sequencing study performed in castor bean to identify its miRNA population. It characterizes and increases the number of miRNAs and their isoforms identified in castor bean. The miRNA expression analysis provides a foundation for understanding castor bean miRNA organ-specific expression patterns. The present study offers an expanded picture of miRNAs for castor bean and other members in the family Euphorbiaceae.

Genomic DNA methylation analyses reveal the distinct profiles in castor bean seeds with persistent endosperms

“…After filtration of raw data (see "Materials and Methods"), we found that the 24-nucleotide class was the most abundant group of small RNAs in castor bean seeds based on their distribution in length (Fig. 7A), consistent with our previous study in castor bean (Xu et al, 2013).…”

“…Small RNA sequencing with three replicates was performed as described in our previous study (Xu et al, 2013) using 35-DAP endosperm and embryo tissues. Briefly, after total RNA isolation and PAGE, the small RNAs (16-30 nucleotides) were isolated and purified using the sRNA Gel Extraction Kit (TaKaRa).…”

Mining NGS transcriptomes for miRNAs and dissecting their role in regulating growth, development, and secondary metabolites production in different organs of a medicinal herb, Picrorhiza kurroa

“…Various tissue-specific miRNA studies have been undertaken in the past in several plant species like Glycine max (Shamimuzzaman and Vodkin 2012), Ricinus communis (Xu et al 2013) and Jatropha curcas .We used qRT-PCR approach to study the expression patterns of 18 conserved miRNAs across six different samples of P. kurroa. It was observed that miRNAs in each organ behave differently under variable conditions of temperature and growth.…”

“…miRNAs are known to show differential expression when investigated in tissue culture ) and organ-specific conditions (Xu et al 2013) in plants. Three organs (root, shoot, and stolon) together with their in vitro culture counterparts were chosen for investigation of miRNA expression specific to each condition.…”

Unravelling the complexity of microRNA-mediated gene regulation in black pepper (Piper nigrum L.) using high-throughput small RNA profiling

“…The downstream computational analyses of small RNA data generated from deep sequencing make use of sequence conservation of mature miRNAs combined with the RNA secondary structure analysis. Recently, several conserved and species-specific miRNAs and their detailed biological functions on gene regulation were discovered from diverse plants such as Ricinus communis (Xu et al 2013), Pinus densata (Wan et al 2012), Stevia rebaudiana (Mandhan et al 2012), Solanum tuberosum (Zhang et al 2013) and Jatropha curcas (Galli et al 2014). The critical role of microRNAs in development, growth as well as various physiological processes has been elucidated in plants.…”