Nitrogen is a key component in the growth of crop plant. To increase the yield of crops, an enormous amount of nitrogen fertilizer is currently being used, which increases the total production cost and leads to environmental pollution by the residual nitrogen sources. For these reasons, researchers have tried to improve the crop’s nitrogen use efficiency (NUE) as a solution for reducing the amount of nitrogen fertilizer used. MicroRNAs are a class of small non-coding RNAs regulating the expression of target genes. Recent studies suggested that the expression pool of microRNAs changes in response to a variety of nutrient deficiencies and that such changes play important roles in adapting to or resisting the consequential nutritional stresses. Here, we aim to identify and characterize rice microRNAs whose expression changes upon nitrogen starvation and re-supplementation. By applying RNA-Seq, we observed that the expression of a set of genes involved in nitrogen assimilation was altered in response to nitrogen deprivation. We also found that a considerable number of microRNAs exhibited dynamic expression changes in a nitrogen supply state-dependent manner and that the expression of genes targeted by those differentially regulated microRNAs was altered reciprocally. Our study suggests that microRNAs may have roles in regulating the response of rice to nitrogen supply state and subsequently modulating NUE.

MicroRNAs (miRNAs) are a class of non-coding RNAs approximately 21-nt in length which play important roles in regulating gene expression in plants. Although many miRNA studies have focused on a few model plants, miRNAs and their target genes remain largely unknown in hot pepper (Capsicum annuum), one of the most important crops cultivated worldwide. We here employed high-throughput small-RNA and degradome sequencing to comprehensively identify small-RNAs and their targets in pepper. From these, we identified several novel targets of miRNAs, including the major de novo methylation enzyme involved in RNA-directed DNA methylation in plants. Furthermore, we identified several highly abundant 22-nt miRNA families that target conserved domains in NB-LRRs and trigger the production of phased secondary siRNAs. We showed that transient co-expression of can-miR482 with Rpi-blb1, one of the potato NB-LRRs, resulted in the attenuation of the hypersenstive responses in Nicotiana benthamiana, suggesting that interaction between miR-482 family and disease resistance proteins is likely to serve as a conserved trigger for defense mechanism in Solanaceae. This work provides the first reliable draft of the pepper small RNA transcriptome that offers an expanded picture of miRNAs in relation to NB-LRR regulation, providing a basis for understanding the functional roles of miRNAs in disease resistance pepper.

MicroRNAs (miRNAs) are a class of non-coding RNAs approximately 21-nt in length which play important roles in regulating gene expression in plants. Although many miRNA studies have focused on a few model plants, miRNAs and their target genes remain largely unknown in hot pepper (Capsicum annuum), one of the most important crops cultivated worldwide. We here employed high-throughput sequencing to comprehensively identify small RNAs and their targets in pepper. From these, we identified several novel targets of miRNAs, including the major de novo methylation enzyme involved in RNA-directed DNA methylation in plants. Furthermore, we identified several highly abundant 22-nt miRNA families that target conserved domains in NB-LRRs. We showed that transient co-expression of the miRNA with NB-LRRs, resulted in the attenuation of the hypersenstive responses in Nicotiana benthamiana, suggesting that interaction between miRNA family and disease resistance proteins is likely to serve as a conserved trigger for defense mechanism in Solanaceae. This work provides the first reliable draft of the small RNA transcriptome in pepper that offers an expanded picture of miRNAs in relation to NB-LRR regulation, providing a basis for understanding the functional roles of miRNAs in disease resistance.

MicroRNAs (miRNAs) are a class of non-coding RNAs of approximately 21-nt which play important roles in regulating gene expression in plants. Although many miRNA studies have focused on a few model plants, the miRNAs and their target genes remain largely unknown in pepper, one of the most important crops cultivated worldwide. Here we employed high-throughput small RNA sequencing to extensively identify miRNAs in pepper from 10 different libraries, including leaf, stem, root, flower, and six developmental stage fruits. Based on bioinformatics pipeline, we successfully identified 29 and 35 families of conserved and novel miRNAs, respectively. We noticed that some miRNAs, whose targets were validated experimentally in this study, exhibited prominent changes in expression levels during fruit development stages. From the qRT-PCR analysis of the target mRNAs, including the SBP-transcription factor and F-box protein, we found that expression of these two target mRNAs gradually decreased in general during fruit development and was negatively correlated with the expression of their corresponding miRNAs. The validation of miRNA-directed cleavage of these target mRNAs, combined with the results of qRT-PCR analysis, likely suggests that some miRNAs in pepper may play a role in fruit development. Conclusively, our study first utilizes high-throughput sequencing to identify and characterize conserved and novel miRNAs and their targets in pepper, providing a basis for understanding the functional roles of miRNAs in pepper.