Identification and Characterization of microRNAs from Peanut (Arachis hypogaea L.) by High-Throughput Sequencing

Abstract

BackgroundMicroRNAs (miRNAs) are noncoding RNAs of approximately 21 nt that regulate gene expression in plants post-transcriptionally by endonucleolytic cleavage or translational inhibition. miRNAs play essential roles in numerous developmental and physiological processes and many of them are conserved across species. Extensive studies of miRNAs have been done in a few model plants; however, less is known about the diversity of these regulatory RNAs in peanut (Arachis hypogaea L.), one of the most important oilseed crops cultivated worldwide.ResultsA library of small RNA from peanut was constructed for deep sequencing. In addition to 126 known miRNAs from 33 families, 25 novel peanut miRNAs were identified. The miRNA* sequences of four novel miRNAs were discovered, providing additional evidence for the existence of miRNAs. Twenty of the novel miRNAs were considered to be species-specific because no homolog has been found for other plant species. qRT-PCR was used to analyze the expression of seven miRNAs in different tissues and in seed at different developmental stages and some showed tissue- and/or growth stage-specific expression. Furthermore, potential targets of these putative miRNAs were predicted on the basis of the sequence homology search.ConclusionsWe have identified large numbers of miRNAs and their related target genes through deep sequencing of a small RNA library. This study of the identification and characterization of miRNAs in peanut can initiate further study on peanut miRNA regulation mechanisms, and help toward a greater understanding of the important roles of miRNAs in peanut.

Characterization of small RNA populations in non-transgenic and aflatoxin-reducing-transformed peanut

“…In our data, we found two reads mapping the RNAi-5x insert, in very low abundance, yet, we found consistently low levels of aflatoxin in repeated challenging experiments in one or both transformed lines, particularly in line 288-10. Low copy numbers of sRNAs in peanut has been reported previously [36,37]; where, similar to our study, the majority of the peanut miRNAs had only one copy. Low copy numbers for transgene-derived siRNAs has been reported previously as well: Jahan et al [50] found few and low copy numbers of transgene-derived siRNAs in transgenic potato expressing a hairpin RNA construct targeting the G protein ß-subunit (PiGB1) of Phytophthora infestans, which is an essential gene involved in the pathogenicity of this pathogen.…”

“…In this study a large percentage of the sRNAs had read lengths of 20-24 nucleotides, which is typical for DICER-processed sRNA products [24][25][26]. The size distribution of the sRNAs in peanut is also consistent with previous reports [36,37]. Furthermore, the majority of sRNAs had a uracil or adenine as 5 terminal nucleotide, which suggest preferential loading onto AGO1, and AGO2 and AGO4, respectively [27]; these enzymes have a crucial role in the RNAi process.…”

“…The miRNAs not detected were miR394, miR3510, miR3512, miR3515, miR3517, miR3518, miR3519, and miR3520. Furthermore, miR162, miR166, miR168, miR169, miR171, miR172, miR390, miR894, miR1507, miR1511, and miR2118 are not reported in miRBase as peanut miRNAs, but have been reported by Chi et al [36] and Zhao et al [37], and these miRNAs were detected in our libraries as well (Tables A1, A2). The miRNA families miR319, miR2592, miR2673, miR2916, miR5072, miR5083, miR5368, miR5538, miR5652, miR5724, miR6025, miR6108, miR6300, miR64788175, and miR9410 have not been reported in peanut before.…”

Identification of microRNAs and their targets in Finger millet by high throughput sequencing

“…The sequencing resulted in 20,512,196 raw reads, after filtering out adapter contaminants, low-quality reads and Rfam contaminants 7,755,160 unique reads were got and the percentage of putative small RNA reads were 73% (Table 1). The most abundant sRNAs range from 21-24 nt (Chi et al, 2011;Xu et al, 2013), and the 21 nt sRNAs represented the most abundant followed by 24 nt which was in agreement with previous reports (Morin et al, 2008;Ge et al, 2012) (Fig. 1).…”

“…Eco_N1 was found to be homologous with miR2275 and considered as the new member of the existing miR2275 family identified in Finger millet. The low abundance of novel miRNAs in the data supports the earlier notation of the lower expression levels of novel miRNAs compared with those of conserved miRNAs (Chi et al, 2011). The precursor miRNA candidates were evaluated using RNAfold.…”