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Summary: Securing agricultural supplies for the increasing population without negative impacts on environment demands new crop varieties with higher yields, better quality, and stronger stress resilience. But breeding such super crop varieties is restrained by growth–defense (G–D) trade‐off. MicroRNAs (miRNAs) are versatile regulators of plant growth and immune responses, with several being demonstrated to simultaneously regulate crop growth and defense against biotic stresses and to balance G–D trade‐off. Increasing evidence also links miRNAs to the metabolism and signaling of phytohormones, another type of master regulator of plant growth and defense. Here, we synthesize the reported functions of miRNAs in crop growth, development, and responses to bio‐stressors, summarize the regulatory scenarios of miRNAs based on their relationship with target(s), and discuss how miRNAs, particularly those involved in crosstalk with phytohormones, can be applied in balancing G–D trade‐off in crops. We also propose several open questions to be addressed for adopting miRNAs in balancing crop G–D trade‐off. [ABSTRACT FROM AUTHOR]

Summary: Circular RNA (circRNA) is a kind of new regulatory RNA with diverse biological functions. Numerous circRNAs have been identified in many plant species; however, evolution of plant circRNAs remains largely unknown.In this study, we assembled full‐length sequences of 6519 rice (Oryza sativa) circRNAs and analyzed their conservation in another 46 plant species based on comparison of sequences and expression patterns.We found that, at the genomic level, 8.7% of the 6519 circRNAs were conserved in dicotyledonous plants and 49.1% in Oryza genus. Meanwhile, 57.8% of parental protein‐coding genes of the rice circRNAs originated recently after divergence of monocotyledonous plants, implying recent origin of the majority of rice circRNAs, a conclusion further supported by the results based on analysis of 4663 full‐length circRNAs in Arabidopsis thaliana. Accordingly, we proposed three models to address the origination of different types of circRNAs.Taken together, the results obtained in this study provide new insights for the evolutionary dynamics of plant circRNAs and candidate circRNAs for further functional exploration. [ABSTRACT FROM AUTHOR]

A large number of noncoding circular RNAs (circ RNAs) with regulatory potency have been identified in animals, but little attention has been given to plant circ RNAs., We performed genome-wide identification of circ RNAs in Oryza sativa and Arabidopsis thaliana using publically available RNA-Seq data, analyzed and compared features of plant and animal circ RNAs., circ RNAs (12037 and 6012) were identified in Oryza sativa and Arabidopsis thaliana, respectively, with 56% (10/18) of the sampled rice exonic circ RNAs validated experimentally. Parent genes of over 700 exonic circ RNAs were orthologues between rice and Arabidopsis, suggesting conservation of circ RNAs in plants. The introns flanking plant circ RNAs were much longer than introns from linear genes, and possessed less repetitive elements and reverse complementary sequences than the flanking introns of animal circ RNAs. Plant circ RNAs showed diverse expression patterns, and 27 rice exonic circ RNAs were found to be differentially expressed under phosphate-sufficient and -starvation conditions. A significantly positive correlation was observed for the expression profiles of some circ RNAs and their parent genes., Our results demonstrated that circ RNAs are widespread in plants, revealed the common and distinct features of circ RNAs between plants and animals, and suggested that circ RNAs could be a critical class of noncoding regulators in plants. [ABSTRACT FROM AUTHOR]

Short noncoding RNAs have been demonstrated to play important roles in regulation of gene expression and stress responses, but the repertoire and functions of long noncoding RNAs ( lnc RNAs) remain largely unexplored, particularly in plants., To explore the role of lnc RNAs in disease resistance, we used a strand-specific RNA-sequencing approach to identify lnc RNAs responsive to Fusarium oxysporum infection in Arabidopsis thaliana., Antisense transcription was found in c. 20% of the annotated A. thaliana genes. Several noncoding natural antisense transcripts responsive to F. oxysporum infection were found in genes implicated in disease defense. While the majority of the novel transcriptionally active regions ( TARs) were adjacent to annotated genes and could be an extension of the annotated transcripts, 159 novel intergenic TARs, including 20 F. oxysporum-responsive lnc TARs, were identified. Ten F. oxysporum-induced lnc TARs were functionally characterized using T- DNA insertion or RNA-interference knockdown lines, and five were demonstrated to be related to disease development. Promoter analysis suggests that some of the F. oxysporum-induced lnc TARs are direct targets of transcription factor(s) responsive to pathogen attack., Our results demonstrated that strand-specific RNA sequencing is a powerful tool for uncovering hidden levels of transcriptome and that Inc RNAs are important components of the antifungal networks in A. thaliana. [ABSTRACT FROM AUTHOR]

The lack of a MIRNA set and genome sequence of wild rice ( Oryza rufipogon) has prevented us from determining the role of MIRNA genes in rice domestication., In this study, a genome, three small RNA populations and a degradome of O. rufipogon were sequenced by Illumina platform and the expression levels of microRNAs (mi RNAs) were investigated by mi RNA chips., A de novo O. rufipogon genome was assembled using c. 55× coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. rufipogon genome based on c. 5.2 million unique small RNA reads from three different tissues of O. rufipogon. Of these, O. rufipogon MIRNAs, 259 were not found in the cultivated rice, suggesting a loss of these MIRNAs in the cultivated rice. We also found that 48 MIRNAs were novel in the cultivated rice, suggesting that they were potential targets of domestication selection. Some mi RNAs showed significant expression differences between wild and cultivated rice, suggesting that expression of mi RNA could also be a target of domestication, as demonstrated for the miR164 family., Our results illustrated that MIRNA genes, like protein-coding genes, might have been significantly shaped during rice domestication and could be one of the driving forces that contributed to rice domestication. [ABSTRACT FROM AUTHOR]