Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa that are absent from Arabidopsis

MiR319a-targeted PtoTCP20 regulates secondary growth via interactions with PtoWOX4 and PtoWND6 in Populus tomentosa

Secondary growth is a key characteristic of trees, which requires the coordination of multiple regulatory mechanisms including transcriptional regulators and microRNAs (miRNAs). However, the roles of microRNAs in the regulation of secondary growth need to be explored in depth. Here, the role of miR319a and its target, PtoTCP20, in the secondary growth of Populus tomentosa stem was investigated using genetic and molecular analyses. The expression level of miR319a gradually decreased from primary to secondary growth in P. tomentosa, while that of PtoTCP20 gradually increased. MiR319a overexpression in seedlings resulted in delayed secondary growth and decreased xylem production, while miR319a knockdown and PtoTCP20 overexpression promoted secondary growth and increased xylem production. Further analysis showed that PtoTCP20 interacted with PtoWOX4a and activated PtoWND6 transcription in vitro and in vivo. Our data show that PtoTCP20 controls vascular cambium proliferation by binding to PtoWOX4a, and promotes secondary xylem differentiation by activating PtoWND6 transcription, thereby regulating secondary growth in P. tomentosa. Our findings provide insight into the molecular mechanisms underlying secondary growth in trees.

MicroRNA comparison between poplar and larch provides insight into the different mechanism of wood formation

MiRNA transcriptome analysis of different tissues in poplar and larch suggests variant roles of miRNAs in regulating wood formation between two kinds of phyla. Poplar and larch belong to two different phyla. Both are ecological woody species and major resources for wood-related industrial applications. However, wood properties are different between these two species and the molecular basis is largely unknown. In this study, we performed high-throughput sequencing of microRNAs (miRNAs) in the three tissues, xylem, phloem and leaf of Populus alba × Populus glandulosa and Larix kaempferi. Differentially expressed miRNA (DEmiRNA) analysis identified 85 xylem-specific miRNAs in P. alba × P. glandulosa and 158 xylem-specific miRNAs in L. kaempferi. Among 36 common miRNAs, 12 were conserved between the two species. GO and KEGG analyses of the miRNA target genes showed similar metabolism in two species. Through KEGG and BLASTN, we predicted target genes of xylem differentially expressed (DEmiRNA) in the wood formation-related pathways and located DEmiRNAs in these pathways. A network was built for wood formation-related DEmiRNAs, their target genes and orthologous genes in Arabidopsis thaliana. Comparison of DEmiRNA and target gene annotation between P. alba × P. glandulosa and L. kaempferi suggested the different functions of DEmiRNAs and divergent mechanism in wood formation between two species, providing knowledge to understand wood formation mechanism in gymnosperm and angiosperm woody plants.

Identification of microRNAs and their targets in inflorescences of an Ogura-type cytoplasmic male-sterile line and its maintainer fertile line of turnip (Brassica rapa ssp. rapifera) via high-throughput sequencing and degradome analysis

Cytoplasmic male sterility (CMS) is a widely used trait in angiosperms caused by perturbations in nucleus-mitochondrion interactions that suppress the production of functional pollen. MicroRNAs (miRNAs) are small non-coding RNAs that act as regulatory molecules of transcriptional or post-transcriptional gene silencing in plants. The discovery of miRNAs and their possible implications in CMS induction provides clues for the intricacies and complexity of this phenomenon. Previously, we characterized an Ogura-CMS line of turnip (Brassica rapa ssp. rapifera) that displays distinct impaired anther development with defective microspore production and premature tapetum degeneration. In the present study, high-throughput sequencing was employed for a genome-wide investigation of miRNAs. Six small RNA libraries of inflorescences collected from the Ogura-CMS line and its maintainer fertile (MF) line of turnip were constructed. A total of 120 pre-miRNAs corresponding to 89 mature miRNAs were identified, including 87 conversed miRNAs and 33 novel miRNAs. Among these miRNAs, the expression of 10 differentially expressed mature miRNAs originating from 12 pre-miRNAs was shown to have changed by more than two-fold between inflorescences of the Ogura-CMS line and inflorescences of the MF line, including 8 down- and 2 up-regulated miRNAs. The expression profiles of the differentially expressed miRNAs were confirmed by stem-loop quantitative real-time PCR. In addition, to identify the targets of the identified miRNAs, a degradome analysis was performed. A total of 22 targets of 25 miRNAs and 17 targets of 28 miRNAs were identified as being involved in the reproductive development for Ogura-CMS and MF lines of turnip, respectively. Negative correlations of expression patterns between partial miRNAs and their targets were detected. Some of these identified targets, such as squamosa promoter-binding-like transcription factor family proteins, auxin response factors and pentatricopeptide repeat-containing proteins, were previously reported to be involved in reproductive development in plants. Taken together, our results can help improve the understanding of miRNA-mediated regulatory pathways that might be involved in CMS occurrence in turnip.

The interplay between microRNA and alternative splicing of linear and circular RNAs in eleven plant species

MOTIVATION

MicroRNA (miRNA) and alternative splicing (AS)-mediated post-transcriptional regulation has been extensively studied in most eukaryotes. However, the interplay between AS and miRNAs has not been explored in plants. To our knowledge, the overall profile of miRNA target sites in circular RNAs (circRNA) generated by alternative back splicing has never been reported previously. To address the challenge, we identified miRNA target sites located in alternatively spliced regions of the linear and circular splice isoforms using the up-to-date single-molecule real-time (SMRT) isoform sequencing (Iso-Seq) and Illumina sequencing data in eleven plant species.

RESULTS

In total, we identified 399 401 and 114 574 AS events from linear and circular RNAs, respectively. Among them, there were 64 781 and 41 146 miRNA target sites located in linear and circular AS region, respectively. In addition, we found 38 913 circRNAs to be overlapping with 45 648 AS events of its own parent isoforms, suggesting circRNA regulation of AS of linear RNAs by forming R-loop with the genomic locus. Here, we present a comprehensive database of miRNA targets in alternatively spliced linear and circRNAs (ASmiR) and a web server for deposition and identification of miRNA target sites located in the alternatively spliced region of linear and circular RNAs. This database is accompanied by an easy-to-use web query interface for meaningful downstream analysis. Plant research community can submit user-defined datasets to the web service to search AS regions harboring small RNA target sites. In conclusion, this study provides an unprecedented resource to understand regulatory relationships between miRNAs and AS in both gymnosperms and angiosperms.

AVAILABILITY AND IMPLEMENTATION

The readily accessible database and web-based tools are available at http://forestry.fafu.edu.cn/bioinfor/db/ASmiR.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

MicroRNA6443-mediated regulation of FERULATE 5-HYDROXYLASE gene alters lignin composition and enhances saccharification in Populus tomentosa

Ferulate 5-hydroxylase (F5H) is a limiting enzyme involved in biosynthesizing sinapyl (S) monolignol in angiosperms. Genetic regulation of F5H can influence S monolignol synthesis and therefore improve saccharification efficiency and biofuel production. To date, little is known about whether F5H is post-transcriptionally regulated by endogenous microRNAs (miRNAs) in woody plants. Here, we report that a microRNA, miR6443, specifically regulates S lignin biosynthesis during stem development in Populus tomentosa. In situ hybridization showed that miR6443 is preferentially expressed in vascular tissues. We further identified that F5H2 is the direct target of miR6443. Overexpression of miR6443 decreased the transcript level of F5H2 in transgenic plants, resulting in a significant reduction in S lignin content. Conversely, reduced miR6443 expression by short tandem target mimics (STTM) elevated F5H2 transcripts, therefore increasing S lignin composition. Introduction of a miR6443-resistant form of F5H2 into miR6443-overexpression plants restored lignin ectopic composition, supporting that miR6443 specifically regulated S lignin biosynthesis by repressing F5H2 in P. tomentosa. Furthermore, saccharification assays revealed decreased hexose yields by 7.5-24.5% in miR6443-overexpression plants compared with the wild-type control, and increased hexoses yields by 13.2-14.6% in STTM6443-overexpression plants. Collectively, we demonstrate that miR6443 modulates S lignin biosynthesis by specially regulating F5H2 in P. tomentosa.

Genetic dissection of the gene coexpression network underlying photosynthesis in Populus

Photosynthesis is a key reaction that ultimately generates the carbohydrates needed to form woody tissues in trees. However, the genetic regulatory network of protein-encoding genes (PEGs) and regulatory noncoding RNAs (ncRNAs), including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), underlying the photosynthetic pathway is unknown. Here, we integrated data from coexpression analysis, association studies (additive, dominance and epistasis), and expression quantitative trait nucleotide (eQTN) mapping to dissect the causal variants and genetic interaction network underlying photosynthesis in Populus. We initially used 30 PEGs, 6 miRNAs and 12 lncRNAs to construct a coexpression network based on the tissue-specific gene expression profiles of 15 Populus samples. Then, we performed association studies using a natural population of 435 unrelated Populus tomentosa individuals, and identified 72 significant associations (P ≤ 0.001, q ≤ 0.05) with diverse additive and dominance patterns underlying photosynthesis-related traits. Analysis of epistasis and eQTNs revealed that the complex genetic interactions in the coexpression network contribute to phenotypes at various levels. Finally, we demonstrated that heterologously expressing the most highly linked gene (PtoPsbX1) in this network significantly improved photosynthesis in Arabidopsis thaliana, pointing to the functional role of PtoPsbX1 in the photosynthetic pathway. This study provides an integrated strategy for dissecting a complex genetic interaction network, which should accelerate marker-assisted breeding efforts to genetically improve woody plants.

MicroRNA expression patterns unveil differential expression of conserved miRNAs and target genes against abiotic stress in safflower

Environmental stresses influence the growth and development of plants by influencing patterns of gene expression. Different regulators control gene expression, including transcription factors (TFs) and microRNAs. MicroRNAs (miRNAs: ~21 nucleotides long) are encoded by miRNA genes transcribed by RNA polymerase II (RNP-II) and play key roles in plant development and physiology. There is little knowledge currently available on miRNAs and their function in response to environmental stresses in safflower. To obtain more information on safflower miRNAs, we initially used a comparative genomics approach and succeeded in identifying 126 miRNAs belonging to 29 conserved families, along with their target genes. In this study, we investigated the expression profiles of seven conserved miRNAs related to drought, salinity, heat, and Cd stress in the leaf and root organs using qRT-PCR, for the first time. Gene Ontology (GO) analysis found that target genes of miRNAs are often TFs such as AP2/ERF and HD-ZIP as well as NAC domain-containing proteins. Expression analyses confirmed that miRNAs can play a vital role in keeping safflower stress-tolerant. Differential expression of miR156, miR162, miR164, miR166, miR172, miR398, and miR408 regulate the expression of their respective target genes. These genes activate several pathways leading to physiological and biochemical responses to abiotic stresses. Some conserved miRNAs were regulated by abiotic stresses. Our finding provides valuable information to understand miRNAs in relation to different abiotic stresses in safflower.

miR477 targets the phenylalanine ammonia-lyase gene and enhances the susceptibility of the tea plant (Camellia sinensis) to disease during Pseudopestalotiopsis species infection

MAIN CONCLUSION: miR477 acts as a negative regulator in tea plant immunity against Pseudopestalotiopsis infection by repressing the expression of its target gene PAL. MicroRNA (miRNA)-mediated post-transcriptional regulation plays a fundamental role in various plant physiological processes, including responses to pathogens. Our previous research revealed that miR477 might be involved in the tea plant-Pseudopestalotiopsis interaction (data not shown). In the present study, the accumulation of miR477 significantly decreased in tea plants during Pseudopestalotiopsis species infection. Using miRNA and degradome data sets, the targeting of phenylalanine ammonia-lyase (PAL) by miR477 was validated by 5' RLM-RACE. GUS assay showed that the expression of PAL was post-transcriptionally regulated by miR477 and silenced by mRNA cleavage. A negative correlation between the expression of miR477 and PAL was found in tea plants infected by the pathogen. The transgenic lines overexpressing Csn-miR477 exhibited increased susceptibility to Pseudopestalotiopsis species, which was associated with reduced expression of PAL during infection. The degree of severity of the leaf lesions and the results of trypan blue staining showed that the plants overexpressing Csn-miR477 exhibited more severe damage upon pathogen infection than wild-type plants. In addition, more H2O2 and O2-, higher malondialdehyde (MDA) contents and less superoxide dismutase (SOD) and peroxidase (POD) activities were detected in the transgenic plants than in the wild-type plants after inoculation with Pseudopestalotiopsis species. Taken together, our results implied that Csn-miR477 might act as a negative regulator in pathogen-infected tea plants by inhibiting the expression of its target, PAL, and that Csn-miR477 is a candidate miRNA for improving the adaptation of tea plant to disease.

Identification, characterization and expression analysis of passion fruit (Passiflora edulis) microRNAs

microRNAs (miRNAs) are highly conserved, short (~ 21-nucleotide), endogenous, non-coding RNA molecules that play major roles in post-transcriptional silencing by guiding target mRNA cleavage or translational inhibition. In this study, applying high-stringent genome-wide computational-based approaches, a total of 28 putative miRNAs belonging to 17 miRNA families were identified from an antioxidant-rich medicinal plant passion fruit (Passiflora edulis). Inter-tissue (leaves and fruits) and inter-varietal (yellow and purple fruit varieties) quantitative study of six putative passion fruit miRNAs (ped-miR160, ped-miR164, ped-miR166, ped-miR393, ped-miR394, and ped-miR398) showed differential expression. Using psRNATarget tool, a total of 25 potential target proteins of the characterized passion fruit miRNAs were also identified. Most of the target proteins identified in this study, including SQUAMOSA promoter binding, Class III HD-Zip, NAC, Scarecrow, APETALA2, Auxin response factor, MYB, and superoxide dismutase, were found to be involved in development, metabolism, and defense/stress response signaling.

Identification of Appropriate Reference Genes for Normalizing miRNA Expression in Citrus Infected by Xanthomonas citri subsp. citri

MicroRNAs (miRNAs) are short noncoding RNA molecules that regulate gene expression at the posttranscriptional level. Reverse transcription-quantitative PCR (RT-qPCR) is one of the most common methods used for quantification of miRNA expression, and the levels of expression are normalized by comparing with reference genes. Thus, the selection of reference genes is critically important for accurate quantification. The present study was intended to identify appropriate miRNA reference genes for normalizing the level of miRNA expression in Citrus sinensis L. Osbeck and Citrus reticulata Blanco infected by Xanthomonas citri subsp. citri, which caused citrus canker disease. Five algorithms (Delta Ct, geNorm, NormFinder, BestKeeper and RefFinder) were used for screening reference genes, and two quantification approaches, poly(A) extension RT-qPCR and stem-loop RT-qPCR, were used to determine the most appropriate method for detecting expression patterns of miRNA. An overall comprehensive ranking output derived from the multi-algorithms showed that poly(A)-tailed miR162-3p/miR472 were the best reference gene combination for miRNA RT-qPCR normalization in citrus canker research. Candidate reference gene expression profiles determined by poly(A) RT-qPCR were more consistent in the two citrus species. To the best of our knowledge, this is the first systematic comparison of two miRNA quantification methods for evaluating reference genes. These results highlight the importance of rigorously assessing candidate reference genes and clarify some contradictory results in miRNA research on citrus.

Systematic Analysis of Alkaline/Neutral Invertase Genes Reveals the Involvement of Smi-miR399 in Regulation of SmNINV3 and SmNINV4 in Salvia miltiorrhiza

Alkaline/neutral invertases (NINVs), which irreversibly catalyze the hydrolysis of sucrose into fructose and glucose, play crucial roles in carbohydrate metabolism and plant development. Comprehensive insights into NINV genes are lacking in Salvia miltiorrhiza, a well-known traditional Chinese medicinal (TCM) plant with significant medicinal and economic value. Through genome-wide prediction, nine putative SmNINV genes, termed SmNINV1-SmNINV9, were identified. Integrated analysis of gene structures, sequence features, conserved domains, conserved motifs and phylogenetic trees revealed the conservation and divergence of SmNINVs. The identified SmNINVs were differentially expressed in roots, stems, leaves, flowers, and different root tissues. They also responded to drought, salicylic acid, yeast extract, and methyl jasmonate treatments. More importantly, computational prediction and experimental validation showed that SmNINV3 and SmNINV4 were targets of Smi-miR399, a conserved miRNA previously shown to affect Pi uptake and translocation through the cleavage of PHOSPHATE2 (PHO2). Consistently, analysis of 43 NINV genes and 26 miR399 sequences from Arabidopsis thaliana, Populus trichocarpa, Manihot esculenta, and Solanum lycopersicum showed that various AtNINV, PtNINV, MeNINV, and SlNINV genes were regulated by miR399. It indicates that the miR399-NINV module exists widely in plants. Furthermore, Smi-miR399 also cleaved SmPHO2 transcripts in S. miltiorrhiza, suggesting the complexity of NINVs, PHO2, and miR399 networks.

Function of miR825 and miR825* as Negative Regulators in Bacillus cereus AR156-elicited Systemic Resistance to Botrytis cinerea in Arabidopsis thaliana

Small RNAs function to regulate plant defense responses to pathogens. We previously showed that miR825 and miR825* downregulate Bacillus cereus AR156 (AR156)-triggered systemic resistance to Pseudomonassyringae pv. tomato DC3000 in Arabidopsis thaliana (Arabidopsis). Here, Northern blotting revealed that miR825 and miR825* were more strongly downregulated in wild type Arabidopsis Col-0 (Col-0) plants pretreated with AR156 than in nontreated plants upon Botrytis cinerea (B. cinerea) B1301 infection. Furthermore, compared with Col-0, transgenic plants with attenuated miR825 and miR825* expression were more resistant to B. cinerea B1301, yet miR825- and miR825*-overexpressing (OE) plants were more susceptible to the pathogen. With AR156 pretreatment, the transcription of four defense-related genes (PR1, PR2, PR5, and PDF1.2) and cellular defense responses (hydrogen peroxide production and callose deposition) were faster and stronger in miR825 and miR825* knockdown lines but weaker in their OE plants than in Col-0 plants upon pathogen attack. Also, AR156 pretreatment caused stronger phosphorylation of MPK3 and MPK6 and expression of FRK1 and WRKY53 genes upon B. cinerea B1301 inoculation in miR825 and miR825* knockdown plants than in Col-0 plants. Additionally, the assay of agrobacterium-mediated transient co-expression in Nicotiana benthamiana confirmed that AT5G40910, AT5G38850, AT3G04220, and AT5G44940 are target genes of miR825 or miR825*. Compared with Col-0, the target mutant lines showed higher susceptibility to B. cinerea B1301, while still expressing AR156-triggered induced systemic resistance (ISR). The two-way analysis of variance (ANOVA) revealed a significant (P < 0.01) interactive effect of treatment and genotype on the defense responses. Hence, miR825 and miR825*act as negative regulators of AR156-mediated systemic resistance to B. cinerea B1301 in Arabidopsis.

Identification of Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) responsive miRNAs in banana root

The fungus, Fusarium oxysporum f. sp. cubense (Foc), is the causal agent of Fusarium wilt disease, which is the most serious disease affecting the whole banana industry. Although extensive studies have characterized many Foc-responsive genes in banana, the molecular mechanisms on microRNA level underlying both banana defense and Foc pathogenesis are not yet fully understood. In this study, we aimed to reveal the role of miRNA during banana-Foc TR4 interactions. Illumina sequencing was used to reveal the changes in small RNAome profiles in roots of Foc TR4-inoculated ‘Tianbaojiao’ banana (Musa acuminata cv. Tianbaojiao) in the early stages (i.e. 5 h, 10 h and 25 h post Foc TR4 inoculation, respectively). The expression of some differentially expressed (DE) miRNAs and their predicted target genes was studied by using quantitative real time PCR (qRT-PCR). Totally, 254 known miRNAs from 31 miRNA families and 28 novel miRNAs were identified. Differential expression analysis identified 84, 77 and 74 DE miRNAs at the three respective Foc TR4 infection time points compared with control healthy banana (CK). GO and KEGG analysis revealed that most of the predicted target genes of DE miRNAs (DET) were implicated in peroxisome, fatty acid metabolism, auxin-activated signaling pathway, sulfur metabolism, lignin metabolism and so on, and many known stress responsive genes were identified to be DETs. Moreover, expected inverse correlations were confirmed between some miRNA and their corresponding target genes by using qRT-PCR analysis. Our study revealed that miRNA play important regulatory roles during the banana-Foc TR4 interaction by regulating peroxidase, fatty acid metabolism, auxin signaling, sulfur metabolism, lignin metabolism related genes and many known stress responsive genes.

RNAi-Mediated Resistance Against Viruses in Perennial Fruit Plants

Small RNAs (sRNAs) are 20–30-nucleotide-long, regulatory, noncoding RNAs that induce silencing of target genes at the transcriptional and posttranscriptional levels. They are key components for cellular functions during plant development, hormone signaling, and stress responses. Generated from the cleavage of double-stranded RNAs (dsRNAs) or RNAs with hairpin structures by Dicer-like proteins (DCLs), they are loaded onto Argonaute (AGO) protein complexes to induce gene silencing of their complementary targets by promoting messenger RNA (mRNA) cleavage or degradation, translation inhibition, DNA methylation, and/or histone modifications. This mechanism of regulating RNA activity, collectively referred to as RNA interference (RNAi), which is an evolutionarily conserved process in eukaryotes. Plant RNAi pathways play a fundamental role in plant immunity against viruses and have been exploited via genetic engineering to control disease. Plant viruses of RNA origin that contain double-stranded RNA are targeted by the RNA-silencing machinery to produce virus-derived small RNAs (vsRNAs). Some vsRNAs serve as an effector to repress host immunity by capturing host RNAi pathways. High-throughput sequencing (HTS) strategies have been used to identify endogenous sRNA profiles, the “sRNAome”, and analyze expression in various perennial plants. Therefore, the review examines the current knowledge of sRNAs in perennial plants and fruits, describes the development and implementation of RNA interference (RNAi) in providing resistance against economically important viruses, and explores sRNA targets that are important in regulating a variety of biological processes.

Comparative profile analysis reveals differentially expressed microRNAs regulate anther and pollen development in kenaf cytoplasmic male sterility line

Cytoplasmic male sterility (CMS) is advantageous in extensive crop breeding and represents a perfect model for understanding anther and pollen development research. MicroRNAs (miRNAs) play key roles in regulating various biological processes. However, the miRNA-mediated regulatory network in kenaf CMS occurrence remains largely unknown. In the present study, a comparative deep sequencing approach was used to investigate the miRNAs and their roles in regulating anther and pollen development during CMS occurrence. We identified 283 known and 46 new candidate miRNAs in kenaf anther. A total of 67 differentially expressed miRNAs (DEMs) were discovered between CMS and its maintainer line. Among them, 40 and 27 miRNAs were up- and downregulated, respectively. These 67 DEMs were predicted to target 189 genes. Validation of DEMs and putative target genes were confirmed by using real-time quantitative PCR. In addition, a potential miRNA-mediated regulatory network, which mainly involves the auxin signaling pathway, signal transduction, glycolysis and energy metabolism, gene expression, transmembrane transport, protein modification and metabolism, and floral development, that mediates anther development during CMS occurrence was proposed. Taken together, our findings provide a better understanding of the molecular mechanism of miRNA regulation in pollen development and CMS occurrence in kenaf.

Identification and characterization of Populus microRNAs in response to plant growth-promoting endophytic Streptomyces sp. SSD49

Endophytic Streptomyces sp. SSD49 inhibited eight pathogens, including the human opportunistic pathogenic microorganisms, the plant pathogenic fungi and bacteria. The growth of soybeans, tomatoes, peppers and Populus tomentosa seedings inoculated with SSD49 are remarkably promoted. Here, we constructed two P. tomentosa seedling microRNA (miRNA) libraries inoculated with (PS30d) and without SSD49 (PC30d) to explore the molecular regulatory roles in the plant response to the beneficial bacteria. Totals of 314 known and 144 novel miRNAs were identified, among which 27 known and 11 novel miRNA had significantly different expression. The targets of up-regulated miR160, miR156, ptc114 and down-regulated miR319 and other differential expressed miRNAs primarily regulated genes encoding transcription factors (auxin response factor, small auxin-up RNA, and GRAS proteins), disease resistance proteins, phytohormone oxidase, and response regulators, which could promote plant growth, influence disease resistance and miRNA biosynthesis in P. tomentosa. This is the first report on the genome-wide identification of biocontrol endophytic Streptomyces inoculation-responsive miRNAs using small RNA sequencing in P. tomentosa and these findings provide new insight into understanding the biocontrol effects of endophytic Streptomyces.

Transcriptome-wide identification and characterization of microRNAs responsive to phosphate starvation in Populus tomentosa

miRNAs (microRNAs) are ~ 21-nt non-coding small RNAs (sRNAs) that play crucial regulatory roles in plant biotic and abiotic stress responses. Phosphorus (Pi) deficiency constrains plant growth and reduces yields worldwide. To identify tree miRNAs and evaluate their functions in the response to low Pi, we identified 261 known and 31 candidate novel miRNA families from three sRNA libraries constructed from Populus tomentosa subjected to sufficient or Pi deficiency condition or to restoration of a sufficient Pi level after Pi deficiency. Pi deficiency resulted in significant changes in the abundance of TPM (transcript per million) of 65 known and 3 novel miRNAs. Interestingly, four miRNAs responsive to low N-miR167, miR394, miR171, and miR857-were found to be involved in the response to low Pi. Thirty-five known and one novel miRNAs responded dynamically to Pi fluctuations, suggesting their involvement in the response to Pi deficiency. miRNA clusters comprising 36 miRNAs were identified in 10 chromosomes. Intriguingly, nine pairs of sense and antisense miRNAs transcribed from the same loci were detected in P. tomentosa, which is the first such report in woody plants. Moreover, target genes of the known miRNAs and novel miRNA candidates with significantly changed abundance were predicted, and their functions were annotated. Degradome sequencing supported the identified targets of miRNAs in P. tomentosa. These findings will enhance our understanding of universal and specific molecular regulatory mechanisms of trees under nutrition stress and may facilitate improvement of the Pi utilization efficiency of woody plants.

Genome-Wide Analysis of the miRNA-mRNAs Network Involved in Cold Tolerance in Populus simonii × P. nigra

Background: Cold tolerance is important for plants’ geographical distribution and survival in extreme seasonal variations of climate. However, Populus simonii × P. nigra shows wide adaptability and strong cold resistance. Transcriptional and post-transcriptional regulation of cold-responsive genes is crucial for cold tolerance in plants. To understand the roles of regulatory RNAs under cold induction in Populus simonii × P. nigra, we constructed cDNA and small RNA libraries from leaf buds treated or not with −4 °C for 8 h for analysis. Results: Through high-throughput sequencing and differential expression analysis, 61 miRNAs and 1229 DEGs were identified under cold induction condition in Populus simonii × P. nigra. The result showed that miR167a, miR1450, miR319a, miR395b, miR393a-5p, miR408-5p, and miR168a-5p were downregulated, whereas transcription level of miR172a increased under the cold treatment. Thirty-one phased-siRNA were also obtained (reads ≥ 4) and some of them proceeded from TAS3 loci. Analysis of the differentially expressed genes (DEGs) showed that transcription factor genes such as Cluster-15451.2 (putative MYB), Cluster-16493.29872 (putative bZIP), Cluster-16493.29175 (putative SBP), and Cluster-1378.1 (putative ARF) were differentially expressed in cold treated and untreated plantlets of Populus simonii × P. nigra. Integrated analysis of miRNAs and transcriptome showed miR319, miR159, miR167, miR395, miR390, and miR172 and their target genes, including MYB, SBP, bZIP, ARF, LHW, and ATL, were predicted to be involved in ARF pathway, SPL pathway, DnaJ related photosystem II, and LRR receptor kinase, and many of them are known to resist chilling injury. Particularly, a sophisticated regulatory model including miRNAs, phasiRNAs, and targets of them was set up. Conclusions: Integrated analysis of miRNAs and transcriptome uncovered the complicated regulation of the tolerance of cold in Populus simonii × P. nigra. MiRNAs, phasiRNAs, and gene-encoded transcription factors were characterized at a whole genome level and their expression patterns were proved to be complementary. This work lays a foundation for further research of the pathway of sRNAs and regulatory factors involved in cold tolerance.

Vascular Calcification and not Arrhythmia in Idiopathic Atrial Fibrillation Associates with Sex Differences in Diabetic Microvascular Injury miRNA Profiles

BACKGROUND

Atrial Fibrillation (AF) in patients without concomitant cardiovascular pathophysiological disease, is called idiopathic Atrial Fibrillation (iAF). Nonetheless, iAF patients have often times subclinical coronary (micro) vascular dysfunction and, particularly in women, a higher prevalence of subsequent cardiovascular comorbidities. Previously, we identified a plasma miRNA association with diabetes and microvascular injury in Diabetic Nephropathy (DN) patients. Therefore, in this study we assessed whether plasma levels of these diabetic, microvascular injury associated miRNAs reflect microvascular integrity in iAF patients, associated with the presence of paroxysmal arrhythmia or instead are determined by concealed coronary artery disease.

METHODS

Circulating levels of a pre-selected set of diabetic, (micro) vascular injury associated miRNAs, were measured in 59 iAF patients compared to 176 Sinus Rhythm (SR) controls. Furthermore, the presence of coronary artery and aortic calcification in each patient was assessed using Cardiac Computed Tomography Angiography (CCTA).

RESULTS

Paroxysmal arrhythmia in iAF patients did not result in significant miRNA expression profile differences in iAF patients compared to SR controls. Nonetheless, coronary artery calcification (CAC) was associated with higher levels of miRNAs-103, -125a-5p, -221 and -223 in men. In women, CAC was associated with higher plasma levels of miRNA-27a and miRNA-126 and correlated with Agatston scores. Within the total population, ascending Aortic Calcification (AsAC) patients displayed increased plasma levels of miRNA-221, while women, in particular, demonstrated a Descending Aorta Calcification (DAC) associated increase in miRNA-212 levels.

CONCLUSIONS

Diabetic microvascular injury associated miRNAs in iAF are associated with subclinical coronary artery disease in a sex-specific way and confirm the notion that biological sex identifies iAF subgroups that may require dedicated clinical care.

Identification and Characterization of Salt-Responsive MicroRNAs in Vicia faba by High-Throughput Sequencing

Salt stress has detrimental effects on plant growth and development. MicroRNAs (miRNAs) are a class of noncoding RNAs that are involved in post-transcriptional gene expression regulation. In this study, small RNA sequencing was employed to identify the salt stress-responsive miRNAs of the salt-sensitive Hassawi-3 and the salt-tolerant ILB4347 genotypes of faba bean, growing under salt stress. A total of 527 miRNAs in Hassawi-3 plants, and 693 miRNAs in ILB4347 plants, were found to be differentially expressed. Additionally, 284 upregulated and 243 downregulated miRNAs in Hassawi-3, and 298 upregulated and 395 downregulated miRNAs in ILB4347 plants growing in control and stress conditions were recorded. Target prediction and annotation revealed that these miRNAs regulate specific salt-responsive genes, which primarily included genes encoding transcription factors and laccases, superoxide dismutase, plantacyanin, and F-box proteins. The salt-responsive miRNAs and their targets were functionally enriched by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, which showed that the miRNAs were involved in salt stress-related biological pathways, including the ABC transporter pathway, MAPK signaling pathway, plant hormone signal transduction, and the phosphatidylinositol signaling system, among others, suggesting that the miRNAs play an important role in the salt stress tolerance of the ILB4347 genotype. These results offer a novel understanding of the regulatory role of miRNAs in the salt response of the salt-tolerant ILB4347 and the salt-sensitive Hassawi-3 faba bean genotypes.

Transcriptome-wide identification of miRNA targets and a TAS3-homologous gene in Populus by degradome sequencing

BACKGROUND

Degradome sequencing has been applied to identify miRNA-directed mRNA cleavage and understand the biological function of miRNAs and their target genes in plants defense to stress. miRNAs involved in the response to cold stress have been identified in Populus, however, there are few reports about the validated targets of miRNAs in Populus under cold stress.

OBJECTIVES

The primary objective of this investigation was to globally identify and validate the targets of the miRNAs and regulatory components in Populus under cold stress.

METHODS

Populus plantlets grown in vitro were treated with cold (4 °C for 8 h) and total RNA was extracted using Trizol reagent. Approximately 200 µg total RNA was used for the construction of the degradome library, and degradome sequencing was conducted on an Illumina HiSeq 2000. The sequences were mapped to Populus genome using SOAP 2.0 and then were collected for degradome analysis. Additionally, trans-acting siRNA sequences from transacting siRNA gene 3 sequences and mature miRNAs cleaved from precursor miRNAs of Populus were analyzed. 5' RNA ligase-mediated-RACE (5'-RACE) were further conducted.

RESULTS

80 genes were experimentally determined to be the target of 51 unique miRNAs, including three down-regulated miRNAs (pto-miR156k, pto-miR169i-m, and pto-miR394a-5p/b-5p) and two up-regulated miRNAs (pto-miR167a-d and pto-miR167f/g). The specificity and diversity of cleavage sites of miRNA targets were validated through 5'-RACE experiment and the results were similar with that of degradome sequencing, further supporting the empirical cleavage of miRNAs on targets in vivo in Populus. Interestingly, the TAS-homologous gene pto-TAS3 (EF146176.1) was identified and 11 potential ta-siRNAs [D1(+)-D11(+)] and their possible biogenesis sites within the pto-TAS3 transcript sequence were predicted in Populus. In addition, the biosynthesis of miRNA from precursor miRNA (pre-miRNA) was also validated through the detection of a total of 17 pre-miRNAs.

CONCLUSION

Our investigation expands the application of degradome sequencing for evaluating miRNA regulatory elements and evidence of the miRNA synthesis process, and provides empirical evidence of bona fide cleavage of target genes by miRNAs in Populus, which might be used for the research of miRNA-mediated regulation mechanism and molecular improvement of resistance to cold stress.

De novo origination of MIRNAs through generation of short inverted repeats in target genes

MIRNA (MIR) gene origin and early evolutionary processes, such as hairpin precursor sequence origination, promoter activity acquirement and the sequence of these two processes, are fundamental and fascinating subjects. Three models, including inverted gene duplication, spontaneous evolution and transposon transposition, have been proposed for de novo origination of hairpin precursor sequence. However, these models still open to discussion. In addition, de novo origination of MIR gene promoters has not been well investigated. Here, I systematically investigated the origin of evolutionarily young polyphenol oxidase gene (PPO)-targeting MIRs, including MIR1444, MIR058 and MIR12112, and a genomic region termed AasPPO-as-hp, which contained a hairpin-forming sequence. I found that MIR058 precursors and the hairpin-forming sequence of AasPPO-as-hp originated in an ancient PPO gene through forming short inverted repeats. Palindromic-like sequences and imperfect inverted repeats in the ancient PPO gene contributed to initiate the generation of short inverted repeats probably by causing errors during DNA duplication. Analysis of MIR058 and AasPPO-as-hp promoters showed that they originated in the 3'-flanking region of the ancient PPO gene. Promoter activities were gained by insertion of a CAAT-box and multiple-copper-response element (CuRE)-containing miniature inverted-repeat transposable element (MITE) in the upstream of AT-rich TATA-box-like sequence. Gain of promoter activities occurred before hairpin-forming sequence origination. Sequence comparison of MIR1444, MIR058 and MIR12112 promoters showed frequent birth and death of CuREs, indicating copper could be vital for the origination and evolution of PPO-targeting MIRs. Based on the evidence obtained, a novel model for plant MIR origination and evolution is proposed.

Identification of novel miRNAs and their target genes from Populus szechuanica infected with Melampsora larici-populina

Two novel miRNAs were selected from a pre-constructed RNA library of Populus szechuanica infected with the foliar rust fungus Melampsora larici-populina in order to detect the genes regulated as targets of the miRNAs novel_mir_11 and novel_mir_357. The novel miRNAs were identified from P. szechuanica using stem-loop methods and their precursors were able to fold into a complete stem loop structure. The predicted target genes of the novel miRNAs were verified with RNA ligase-mediated 5' rapid amplification of cDNA ends (RLM-5'RACE). The full-length sequences of target genes, RPM1 and RPS2/5, in P. szechuanica were obtained through rapid amplification of cDNA ends (RACE) and officially named PsRPM1 and PsRPS2/5. These genes contain nucleotide binding site-leucine-rich repeats (NBS-LRR) domains typical of resistance genes. The expression levels of miRNAs and their target genes in different periods post infection were analysed with quantitative real-time PCR (qRT-PCR). After infection with the foliar rust fungus, the expression levels of the novel miRNAs and their target genes were dynamic. Both novel_mir_11 and novel_mir_357 negatively regulated the expression of their target genes. In this study, the regulatory effects of two novel miRNAs through their target genes were characterized to provide further mechanistic information regarding the interaction between Populus and a foliar rust fungus. Results of this study improve our understanding of the defence response mechanisms of Populus and will stimulate future work to characterize strategies to prevent and control Populus diseases.

Overexpression of miRNA in Cotton via Agrobacterium-Mediated Transformation

microRNAs (miRNAs) are an extensive class of newly identified endogenous small regulatory molecules. Many studies show that miRNAs play a critical role in almost all biological and metabolic progress through targeting protein-coding genes for mRNA cleavage or translation inhibition. Many miRNAs are also identified from cotton using computational and/or experimental approaches, including the next-generation deep sequencing technology. However, their functions are unclear. In this chapter, we describe a detailed method for overexpressing miRNA, miR156 as an example, in cotton using Agrobacterium-mediated genetic transformation. This provides an approach to investigate the function and regulatory mechanism of miRNAs in cotton.

Analyses of MiRNA Functions in Maize Using a Newly Developed ZMBJ-CMV-2bN81-STTM Vector

Endogenous microRNAs (miRNAs) play pivotal roles in plant development and responses to various biotic or abiotic stresses. Up to now, more than 500 maize miRNAs have been identified. However, functions of these identified miRNAs remained largely unknown due mainly to the lack of rapid and reliable tools. We previously reported a cucumber mosaic virus strain ZMBJ (ZMBJ-CMV)-based gene silencing vector for rapid and efficient gene function studies in maize lines with agronomical importance. Because ZMBJ-CMV induces very mild disease symptoms but strong gene silencing in maize, we decided to further modify this vector to suppress miRNA expressions in maize. The newly developed ZMBJ-CMV-2b_N81-STTM vector expresses a short tandem target mimic (STTM) containing two target-mimic sequences separated by a short spacer sequence. Our results showed that ZMBJ-CMV-2b_N81-STTM can be used to investigate miRNA function in Nicotiana benthamiana and maize seedlings. The ZMBJ-CMV-2b_N81-STTM-based downregulation of Nbe-miR165/166 or Nbe-miR159 induced specific and strong miRNA-sequestering phenotypes, and increased the expressions of their predicted target genes. For maize, the ZMBJ-CMV-2b_N81-STTM based downregulation of zma-miR167 or zma-miR482 caused a decrease of lateral roots growth and a plant stunting phenotypes, respectively. In both cases, the target genes of zma-miR167- or zma-miR482 were increased significantly. Thus, we consider ZMBJ-CMV based VbMS system as a useful tool for high-throughput investigations of miRNA functions in maize.

Identification and expression analysis of a microRNA cluster derived from pre-ribosomal RNA in Papaver somniferum L. and Papaver bracteatum L

Opium poppy (Papaver somniferum L.) is one of the ancient medical crops, which produces several important alkaloids such as morphine, noscapine, sanguinarine and codeine. MicroRNAs are endogenous non-coding RNAs that play important regulatory roles in plant diverse biological processes. Many plant miRNAs are encoded as single transcriptional units, in contrast to animal miRNAs, which are often clustered. Herein, using computational approaches, a total of 22 miRNA precursors were identified, which five of them were located as a clustered in pre-ribosomal RNA. Afterward, the transcript level of the precursor and the mature of clustered miRNAs in two species of the Papaveraceae family, i.e. P. somniferum L. and P. bracteatum L, were quantified by RT-PCR. With respect to obtained results, these clustered miRNAs were expressed differentially in different tissues of these species. Moreover, using target prediction and Gene Ontology (GO)-based on functional classification indicated that these miRNAs might play crucial roles in various biological processes as well as metabolic pathways. In this study, we discovered the clustered miRNA derived from pre-rRNA, which may shed some light on the importance of miRNAs in the plant kingdom.

Systematic analysis of DEMETER-like DNA glycosylase genes shows lineage-specific Smi-miR7972 involved in SmDML1 regulation in Salvia miltiorrhiza

DEMETER-like DNA glycosylases (DMLs) initiate the base excision repair-dependent DNA demethylation to regulate a wide range of biological processes in plants. Six putative SmDML genes, termed SmDML1-SmDML6, were identified from the genome of S. miltiorrhiza, an emerging model plant for Traditional Chinese Medicine (TCM) studies. Integrated analysis of gene structures, sequence features, conserved domains and motifs, phylogenetic analysis and differential expression showed the conservation and divergence of SmDMLs. SmDML1, SmDML2 and SmDML4 were significantly down-regulated by the treatment of 5Aza-dC, a general DNA methylation inhibitor, suggesting involvement of SmDMLs in genome DNA methylation change. SmDML1 was predicted and experimentally validated to be target of Smi-miR7972. Computational analysis of forty whole genome sequences and almost all of RNA-seq data from Lamiids revealed that MIR7972s were only distributed in some plants of the three orders, including Lamiales, Solanales and Boraginales, and the number of MIR7972 genes varied among species. It suggests that MIR7972 genes underwent expansion and loss during the evolution of some Lamiids species. Phylogenetic analysis of MIR7972s showed closer evolutionary relationships between MIR7972s in Boraginales and Solanales in comparison with Lamiales. These results provide a valuable resource for elucidating DNA demethylation mechanism in S. miltiorrhiza.

Overexpression of microRNA408 enhances photosynthesis, growth, and seed yield in diverse plants

The ability of a plant to produce grain, fruit, or forage depends ultimately on photosynthesis. There have been few attempts, however, to study microRNAs, which are a class of endogenous small RNAs post-transcriptionally programming gene expression, in relation to photosynthetic traits. We focused on miR408, one of the most conserved plant miRNAs, and overexpressed it in parallel in Arabidopsis, tobacco, and rice. The transgenic plants all exhibited increased copper content in the chloroplast, elevated abundance of plastocyanin, and an induction of photosynthetic genes. By means of gas exchange and optical spectroscopy analyses, we showed that higher expression of miR408 leads to enhanced photosynthesis through improving efficiency of irradiation utilization and the capacity for carbon dioxide fixation. Consequently, miR408 hyper-accumulating plants exhibited higher rate of vegetative growth. An enlargement of seed size was also observed in all three species overproducing miR408. Moreover, we conducted a 2-year-two-location field trial and observed miR408 overexpression in rice significantly increased yield, which was primarily attributed to an elevation in grain weight. Taken together, these results demonstrate that miR408 is a positive regulator of photosynthesis and that its genetic engineering is a promising route for enhancing photosynthetic performance and yield in diverse plants.

Characterization of Conserved and Novel microRNAs in Lilium lancifolium Thunb. by High-Throughput Sequencing

MicroRNAs (miRNAs) are among the class of noncoding small RNA molecules and play a crucial role in post-transcriptional regulation in plants. Although Lilium is one of the most popular ornamental flowers worldwide, however, there is no report on miRNAs identification. In the present study, therefore, miRNAs and their targets were identified from flower, leaf, bulblet and bulb of Lilium lancifolium Thunb. by high-throughput sequencing and bioinformatics analysis. In this study, a total of 38 conserved miRNAs belonging to 17 miRNA families and 44 novel miRNAs were identified. In total, 366 target genes for conserved miRNAs and 415 target genes for novel miRNAs were predicted. The majority of the target genes for conserved miRNAs were transcriptional factors and novel miRNAs targeted mainly protein coding genes. A total of 53 cleavage sites belonging to 6 conserved miRNAs families and 14 novel miRNAs were identified using degradome sequencing. Twenty-three miRNAs were randomly selected, then, their credibility was confirmed using northern blot or stem-loop qRT-PCR. The results from qRT-PCR analysis showed the expression pattern of 4 LL-miRNAs was opposite to their targets. Therefore, our finding provides an important basis to understand the biological functions of miRNAs in Lilium.

Genome-wide investigation of pentatricopeptide repeat gene family in poplar and their expression analysis in response to biotic and abiotic stresses

Pentatricopeptide repeat (PPR) proteins, which are characterized by tandem 30-40 amino acid sequence motifs, constitute of a large gene family in plants. Some PPR proteins have been identified to play important roles in organellar RNA metabolism and organ development in Arabidopsis and rice. However, functions of PPR genes in woody species remain largely unknown. Here, we identified and characterized a total of 626 PPR genes containing PPR motifs in the Populus trichocarpa genome. A comprehensive genome-wide analysis of the poplar PPR gene family was performed, including chromosomal location, phylogenetic relationships and gene duplication. Genome-wide transcriptomic analysis showed that 154 of the PtrPPR genes were induced by biotic and abiotic treatments, including Marssonina brunnea, salicylic acid (SA), methyl jasmonate (MeJA), mechanical wounding, cold and salinity stress. Quantitative RT-PCR analysis further investigated the expression profiles of 11 PtrPPR genes under different stresses. Our results contribute to a comprehensive understanding the roles of PPR proteins and provided an insight for improving the stress tolerance in poplar.

Antioxidant properties of cumin (Bunium persicum Boiss.) extract and its protective role against abiotic stress tested by microRNA markers

Bunium persicum Boiss. seeds have been used for medicinal and nutritional properties such as antioxidant, antihelmetic and antimicrobial activity. The aim of this study was to to tested protective role of cumin extract against abiotic stress by microRNA markers. Secondary also was to evaluate antioxidant activity as well as total polyphenol, flavonoid and phenolic acid content of cumin extract. We observed that cumin DNA itself has not been damaged by sonication teratment. This protective impact indicates that cumin antioxidant properties can efficiently quench free radicals induced by sonication. On the other side, ultrasound-mediated formation of reactive oxygen species did induce the DNA polymorphism of lettuce samples which was detected by miRNAs-based markers. The range of sonication impact was time-dependent. Markers based of miRNA-DNA sequences has proven to be an effective tool. We have confirmed statistically significant differences (p ≤0.01) in miRNAs markers ability to detect the polymorphism due to sonication treatment.  The antioxidant activity was determined by a method using DPPH radical and phosphomolybdenum method, total polyphenol content with Folin - Ciocalteu reagent, total flavonoid with aluminium-chloride mehod and total phenolic acid with Arnova reagent. Results showed that cumin is rich for biologically active substances and can be used more in different kind of industry as a cheap source of these substances. Antioxidant activity with DPPH method was 1.18 mg TEAC.g-1 (TEAC - Trolox equivalent antioxidant capacity per g of sample) and by phosphomolybdenum method 45.23 mg TEAC.g-1. Total polyphenol content achieved value 4.22 mg GAE.g-1 (GAE - gallic acid equivalent per g of sample), total flavonoid content value 10.91 mg QE.g-1 (QE - quercetin equivalent per g of sample) and total phenolic acid content value 5.07 mg CAE.g-1 (CAE - caffeic acid equivalent per g of sample).

Recent Advances in the Transcriptional Regulation of Secondary Cell Wall Biosynthesis in the Woody Plants

Plant cell walls provide structural support for growth and serve as a barrier for pathogen attack. Plant cell walls are also a source of renewable biomass for conversion to biofuels and bioproducts. Understanding plant cell wall biosynthesis and its regulation is of critical importance for the genetic modification of plant feedstocks for cost-effective biofuels and bioproducts conversion and production. Great progress has been made in identifying enzymes involved in plant cell wall biosynthesis, and in Arabidopsis it is generally recognized that the regulation of genes encoding these enzymes is under a transcriptional regulatory network with coherent feedforward and feedback loops. However, less is known about the transcriptional regulation of plant secondary cell wall (SCW) biosynthesis in woody species despite of its high relevance to biofuels and bioproducts conversion and production. In this article, we synthesize recent progress on the transcriptional regulation of SCW biosynthesis in Arabidopsis and contrast to what is known in woody species. Furthermore, we evaluate progress in related emerging regulatory machineries targeting transcription factors in this complex regulatory network of SCW biosynthesis.

FRG3, a Target of slmiR482e-3p, Provides Resistance against the Fungal Pathogen Fusarium oxysporum in Tomato

The vast majority of plant disease resistance (R) genes encode nucleotide binding site-leucine-rich repeat (NBS-LRR) proteins, which specifically determine the plant immune response and have been demonstrated to be targets of several microRNA (miRNA) families. The fungus Fusarium oxysporum f. sp. lycopersici (FOL) causes vascular wilt disease in tomato worldwide. Here, we explored a possible role for FGR3 in tomato defense against FOL. FRG3 is a predicted NBS-LRR like gene that is targeted by slmiR482e-3p, a member of slmiR482 miRNA family. Northern blot data demonstrated that all seven members of the slmiR482 family were regulated in diverse ways after infection by FOL. The ability of FRG3 to be regulated by slmiR482e-3p was confirmed at the transcript level by co-expression studies in Nicotiana benthamiana. A virus-induced gene silencing (VIGS) approach revealed that FRG3 confers resistance to the Motelle tomato cultivar. Taken together, our study has identified a novel R gene, FRG3, which is targeted by slmiR482e-3p at the transcript level, and is necessary for resistance to tomato wilt disease in planta.

The phenotypic and molecular assessment of the non-conserved Arabidopsis MICRORNA163/S-ADENOSYL-METHYLTRANSFERASE regulatory module during biotic stress

In plants, microRNAs (miRNAs) have evolved in parallel to the protein-coding genes that they target for expression regulation, and miRNA-directed gene expression regulation is central to almost every cellular process. MicroRNA, miR163, is unique to the Arabidopsis genus and is processed into a 24-nucleotide (nt) mature small regulatory RNA (sRNA) from a single precursor transcript transcribed from a single locus, the MIR163 gene. The MIR163 locus is a result of a recent inverted duplication event of one of the five closely related S-ADENOSYL-METHYLTRANSFERASE genes that the mature miR163 sRNA targets for expression regulation. Currently, however, little is known about the role of the miR163/S-ADENOSYL-METHYLTRANSFERASE regulatory module in response to biotic stress. Here, we document the expression domains of MIR163 and the S-ADENOSYL-METHYLTRANSFERASE target genes following fusion of their putative promoter sequences to the β-glucuronidase (GUS) reporter gene and subsequent in planta expression. Further, we report on our phenotypic and molecular assessment of Arabidopsis thaliana plants with altered miR163 accumulation, namely the mir163-1 and mir163-2 insertion knockout mutants and the miR163 overexpression line, the MIR163-OE plant. Finally, we reveal miR163 accumulation and S-ADENOSYL-METHYLTRANSFERASE target gene expression post treatment with the defence elicitors, salicylic acid and jasmonic acid, and following Fusarium oxysporum infection, wounding, and herbivory attack. Together, the work presented here provides a comprehensive new biological insight into the role played by the Arabidopsis genus-specific miR163/S-ADENOSYL-METHYLTRANSFERASE regulatory module in normal A. thaliana development and during the exposure of A. thaliana plants to biotic stress.

Identification and allelic dissection uncover roles of lncRNAs in secondary growth of Populus tomentosa

Long non-coding RNAs (lncRNAs) function in various biological processes. However, their roles in secondary growth of plants remain poorly understood. Here, 15,691 lncRNAs were identified from vascular cambium, developing xylem, and mature xylem of Populus tomentosa with high and low biomass using RNA-seq, including 1,994 lncRNAs that were differentially expressed (DE) among the six libraries. 3,569 cis-regulated and 3,297 trans-regulated protein-coding genes were predicted as potential target genes (PTGs) of the DE lncRNAs to participate in biological regulation. Then, 476 and 28 lncRNAs were identified as putative targets and endogenous target mimics (eTMs) of Populus known microRNAs (miRNAs), respectively. Genome re-sequencing of 435 individuals from a natural population of P. tomentosa found 34,015 single nucleotide polymorphisms (SNPs) within 178 lncRNA loci and 522 PTGs. Single-SNP associations analysis detected 2,993 associations with 10 growth and wood-property traits under additive and dominance model. Epistasis analysis identified 17,656 epistatic SNP pairs, providing evidence for potential regulatory interactions between lncRNAs and their PTGs. Furthermore, a reconstructed epistatic network, representing interactions of 8 lncRNAs and 15 PTGs, might enrich regulation roles of genes in the phenylpropanoid pathway. These findings may enhance our understanding of non-coding genes in plants.

Integrated regulatory network reveals the early salt tolerance mechanism of Populus euphratica

Salinization is one of the major factors that threaten the existence of plants worldwide. Populus euphratica has been deemed to be a promising candidate for stress response research because of its high capacity to tolerate extreme salt stress. We carried out a genome-wide transcriptome analysis to identify the differentially expressed genes (DEGs) response to salt shock and elucidate the early salt tolerance mechanisms in P. euphratica. Both hierarchical clustering and DEG analysis demonstrated a predominant variation from time-course rather than NaCl intensity within 24 hours salt shock. Among the identified 1,678 salt-responsive DEGs, 74.1% (1,244) have not been reported before. We further created an integrated regulatory gene network of the salt response in P. euphratica by combining DEGs, transcription factors (TFs), Helitrons, miRNAs and their targets. The prominent pathways in this network are plant hormone transduction, starch and sucrose metabolism, RNA transport, protein processing in endoplasmic reticulum, etc. In addition, the network indicates calcium-related genes play key roles in P. euphratica response to salt shock. These results illustrated an overview of the systematic molecular response in P. euphratica under different intensities of salt shock and revealed the complex regulatory mechanism.

Advancements in the study of miRNA regulation during the cell cycle in human pituitary adenomas

Pituitary adenomas (PAs), single-clone adenomas arising from pituitary gland cells, comprise one of the most frequent tumors found in the sella region. The prevalence of PAs is approximately 15%, third only after gliomas and meningioma among intracranial tumors. Autopsy and radiological analysis found that the incidence of PAs is approximately 22.5%. Most PAs are benign, although a few are malignant. Just 0.1% of patients with PAs develop pituitary carcinoma. However, owing to mass effects and unregulated secretion of pituitary hormones, PAs also lead to serious morbidity. The low rate of diagnosis at onset and the lack of effective treatments for patients with recurrent disease increase the morbidity rates. Therefore, there is an urgent need to ascertain the pathological mechanism of PAs for improved diagnosis and development of specific therapies. At present, the pathogenesis of PAs is poorly understood; however, disruption of the cell cycle is known to play an important role. MicroRNAs are short noncoding RNAs that regulate gene expression at the post-transcriptional level and play a role in regulating genes involved in carcinogenesis or tumor suppression. Previous studies have demonstrated a strong connection between dysregulation of microRNAs and dysregulation of the cell cycle in PAs. In this review, we summarize the recent progress in the study of microRNA dysregulation resulting in disruption of the cell cycle in PAs.

The role of peu-miR164 and its target PeNAC genes in response to abiotic stress in Populus euphratica

Plant miR164 family is highly conserved and miR164 members regulate conserved targets belonging to NAC transcription factors. Our previous studies have revealed that peu-miR164a-e and its target gene POPTR_0007s08420 participate in abiotic stress response in Populus euphratica according to deep sequencing and degradome sequencing. In this study, miR164 family comprises six members that generate two mature products (miR164a-e and miR164f) and target seven NAC genes in P. euphratica. Co-expression in Nicotiana benthamiana and 5' RACE confirmed that peu-miR164 directs PeNAC070, PeNAC012 and PeNAC028 mRNAs cleavage. Expression profiles of primary peu-miR164 a/b/c/d/e bear similarity to those of peu-miR164a-e, whereas PeNAC070 and PeNAC081 showed inverse expression patterns with peu-miR164a-e under abiotic stresses. Existence of cis-acting elements in PeNAC070 promoter (ABRE,MBs, Box-W1, GC-motif, and W-box) and in peu-MIR164b promoter (HSE) further confirmed different responses of peu-miR164 and PeNAC070 to abiotic stresses. Histochemical β-glucuronidase (GUS) staining revealed that GUS activities increased when ProPeNAC070::GUS transgenic Arabidopsis plants were exposed to NaCl, mannitol and abscisic acid (ABA), whereas GUS activity of Propeu-MIR164b::GUS plants decreased under ABA treatment. Subcellular localization and transactivation assays showed that PeNAC070 protein was localized to the nucleus and exhibited transactivation activity at the C-terminal. Overexpression of PeNAC070 in Arabidopsis promoted lateral root development, delayed stem elongation, and increased sensitivity of transgenic plants to drought and salt stresses. This study aids in understanding the adaptability of P. euphratica to extreme drought and salt environment by analysing tissue-specific expression patterns of miR164-regulated and specific promoter-regulated PeNAC genes.

Differences and commonalities of plant responses to single and combined stresses

In natural or agricultural environments, plants are constantly exposed to a wide range of biotic and abiotic stresses. Given the forecasted global climate changes, plants will cope with heat waves, drought periods and pathogens at the same time or consecutively. Heat and drought cause opposing physiological responses, while pathogens may or may not profit from climate changes depending on their lifestyle. Several studies have been conducted to find stress-specific signatures or stress-independent commonalities. Previously this has been done by comparing different single stress treatments. This approach has been proven difficult since most studies, comparing single and combined stress conditions, have come to the conclusion that each stress treatment results in specific transcriptional changes. Although transcriptional changes at the level of individual genes are highly variable and stress-specific, central metabolic and signaling responses seem to be common, often leading to an overall reduced plant growth. Understanding how specific transcriptional changes are linked to stress adaptations and identifying central hubs controlling this interaction will be the challenge for the coming years. In this review, we will summarize current knowledge on plant responses to different individual and combined stresses and try to find a common thread potentially underlying these responses. We will begin with a brief summary of known physiological, metabolic, transcriptional and hormonal responses to individual stresses, elucidate potential commonalities and conflicts and finally we will describe results obtained during combined stress experiments. Here we will concentrate on simultaneous application of stress conditions but we will also touch consequences of sequential stress treatments.

Genome-wide identification of heat stress-responsive small RNAs in tall fescue (Festuca arundinacea) by high-throughput sequencing

MicroRNAs (miRNAs) play vital roles in the adaptive response of plants to various abiotic and biotic stresses. Tall fescue (Festuca arundinacea Schreb.) is a major cool-season forage and turf grass species which is severely influenced by heat stress. To unravel possible heat stress-responsive miRNAs, high-throughput sequencing was employed for heat-tolerant PI578718 and heat-sensitive PI234881 genotypes growing in presence and absence of heat stress (40°C for 36h). By searching against the miRBase database, among 1421 reference monocotyledon miRNAs, more than 850 were identified in all samples. Among these miRNAs, 1.46% and 2.29% were differentially expressed in PI234881 and PI578718 under heat stress, respectively, and most of them were down-regulated. In addition, a total of 170 novel miRNAs belonging to 145 miRNA families were identified. Furthermore, putative targets of differentially expressed miRNAs were predicted. The regulation of selected miRNAs by heat stress was revalidated through quantitative reverse transcription PCR (qRT-PCR) analysis. Most of these miRNAs shared similar expression patterns; however, some showed distinct expression patterns under heat stress, with their putative targets displaying different transcription levels. This is the first genome-wide miRNA identification in tall fescue. miRNAs specific to PI578718, or those that exhibited differential expression profiles between the two genotypes under high temperature, were probably associated with the variation in thermotolerance of tall fescue. The differentially expressed miRNAs between these two tall fescue genotypes and their putative targeted genes will provide essential information for further study on miRNAs mediating heat response and facilitate to improve turf grass breeding.

Small RNA sequencing reveals a role for sugarcane miRNAs and their targets in response to Sporisorium scitamineum infection

BACKGROUND

Sugarcane smut caused by Sporisorium scitamineum leads to a significant reduction in cane yield and sucrose content. MicroRNAs (miRNAs) play an important role in regulating plant responses to biotic stress. The present study was the first to use two sugarcane genotypes, YA05-179 (smut-resistant) and ROC22 (smut-susceptible), to identify differentially expressed miRNAs in sugarcane challenged with S. scitamineum by using high-throughput sequencing.

RESULTS

The predicted target gene number corresponding to known differentially expressed miRNAs in YA05-179 was less than that in ROC22, however most of them were in common. Expression of differential miRNAs under S. scitamineum challenge was mostly downregulated, with similar trends in the two varieties. Gene ontology (GO) analysis showed that the target gene classification of known miRNAs was similar to that of the newly identified miRNAs. These were mainly associated with cellular processes and metabolic processes in the biological process category, as well as combination and catalytic activity in the molecular function category. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that these predicted target genes involved in a series of physiological and biochemical pathways or disease resistance-related physiological metabolism and signal transduction pathways, suggesting that the molecular interaction mechanism between sugarcane and S. scitamineum was a complex network system. These findings also showed certain predicted target genes of miR5671, miR5054, miR5783, miR5221, and miR6478 play roles in the mitogen-activated protein kinase (MAPK) signaling pathway, plant hormone signal transduction, and plant-pathogen interaction. Quantitative real-time PCR (qRT-PCR) analysis showed that majority of the known miRNAs and its predicted target genes followed a negatively regulated mode. Seven out of eight predicted target genes showed identical expression after 12 h treatment and reached the highest degree of matching at 48 h, indicating that the regulatory role of miRNAs on the target genes in sugarcane was maximized at 48 h after S. scitamineum challenge.

CONCLUSIONS

Taken together, our findings serve as evidence for the association of miRNA expression with the molecular mechanism underlying the pathogenesis of sugarcane smut, particularly on the significance of miRNA levels in relation to the cultivation of smut-resistant sugarcane varieties.

MicroRNA dynamics in a wild and cultivated species of Convolvulaceae exposed to drought stress

Agricultural productivity is severely hampered by drought in many parts of the globe. It is well-known that wild plant species can tolerate drought better when compared with their closely related cultivated plant species. Better drought adaptation of wild species over cultivated ones is accounted for their ability to differentially regulate gene expression. miRNAs, known to regulate gene expression at the post-transcriptional level, are admitted to play an important role in plant adaptation to stresses. This study aims at evaluating miRNA dynamics in a drought-tolerant wild Ipomoea campanulata L. and drought-sensitive cultivated Jacquemontia pentantha (Jacq.) of the family Convolvulaceae under ex situ drought. Sequencing profiles revealed that 34 conserved miRNA families were analogous between the two species. Drought altered expression levels of several of these miRNAs in both the species. Drought-tolerant I. campanulata showed upregulation of miR398, miR168, miR858, miR162 and miR408, while miR394 and miR171 were downregulated. Drought-sensitive J. pentantha showed upregulation of miR394, miR156, miR160, miR164, miR167, miR172, miR319, miR395, miR396, miR403 and downregulation of miR157. Basal miRNA levels and their drought mediated regulation were very different between the two species. Differential drought sensitivities of these two plant species can be attributed to these innate variations in miRNA levels and their expression.

MicroRNA expression profiles during cotton (Gossypium hirsutum L) fiber early development

The role of microRNAs (miRNAs) during cotton fiber development remains unclear. Here, a total of 54 miRNAs belonging to 39 families were selected to characterize miRNA regulatory mechanism in eight different fiber development stages in upland cotton cv BM-1. Among 54 miRNAs, 18 miRNAs were involved in cotton fiber initiation and eight miRNAs were related to fiber elongation and secondary wall biosynthesis. Additionally, 3,576 protein-coding genes were candidate target genes of these miRNAs, which are potentially involved in cotton fiber development. We also investigated the regulatory network of miRNAs and corresponding targets in fiber initiation and elongation, and secondary wall formation. Our Gene Ontology-based term classification and KEGG-based pathway enrichment analyses showed that the miRNA targets covered 220 biological processes, 67 molecular functions, 45 cellular components, and 10 KEGG pathways. Three of ten KEGG pathways were involved in lignan synthesis, cell elongation, and fatty acid biosynthesis, all of which have important roles in fiber development. Overall, our study shows the potential regulatory roles of miRNAs in cotton fiber development and the importance of miRNAs in regulating different cell types. This is helpful to design miRNA-based biotechnology for improving fiber quality and yield.

Characterization of the polyphenol oxidase gene family reveals a novel microRNA involved in posttranscriptional regulation of PPOs in Salvia miltiorrhiza

Salvia miltiorrhiza is a well-known material of traditional Chinese medicine. Understanding the regulatory mechanisms of phenolic acid biosynthesis and metabolism are important for S. miltiorrhiza quality improvement. We report here that S. miltiorrhiza contains 19 polyphenol oxidases (PPOs), forming the largest PPO gene family in plant species to our knowledge. Analysis of gene structures and sequence features revealed the conservation and divergence of SmPPOs. SmPPOs were differentially expressed in plant tissues and eight of them were predominantly expressed in phloem and xylem, indicating that some SmPPOs are functionally redundant, whereas the others are associated with different physiological processes. Expression patterns of eighteen SmPPOs were significantly altered under MeJA treatment, and twelve were yeast extract and Ag⁺-responsive, suggesting the majority of SmPPOs are stress-responsive. Analysis of high-throughput small RNA sequences and degradome data showed that miR1444-mediated regulation of PPOs existing in P. trichocarpa is absent from S. miltiorrhiza. Instead, a subset of SmPPOs was posttranscriptionally regulated by a novel miRNA, termed Smi-miR12112. It indicates the specificity and significance of miRNA-mediated regulation of PPOs. The results shed light on the regulation of SmPPO expression and suggest the complexity of SmPPO-associated phenolic acid biosynthesis and metabolism.

Origin and evolution of MIR1444 genes in Salicaceae

miR1444s are functionally significant miRNAs targeting polyphenol oxidase (PPO) genes for cleavage. MIR1444 genes were reported only in Populus trichocarpa. Through the computational analysis of 215 RNA-seq data, four whole genome sequences of Salicaceae species and deep sequencing of six P. trichocarpa small RNA libraries, we investigated the origin and evolution history of MIR1444s. A total of 23 MIR1444s were identified. Populus and Idesia species contain two MIR1444 genes, while Salix includes only one. Populus and Idesia MIR1444b genes and Salix MIR1444s were phylogenetically separated from Populus and Idesia MIR1444a genes. Ptr-miR1444a and ptr-miR1444b showed sequence divergence. Compared with ptr-miR1444b, ptr-miR1444a started 2 nt upstream of precursor, resulting in differential regulation of PPO targets. Sequence alignments showed that MIR1444 genes exhibited extensive similarity to their PPO targets, the characteristics of MIRs originated from targets through an inverted gene duplication event. Genome sequence comparison showed that MIR1444 genes in Populus and Idesia were expanded through the Salicoid genome duplication event. A copy of MIR1444 gene was lost in Salix through DNA segment deletion during chromosome rearrangements. The results provide significant information for the origin of plant miRNAs and the mechanism of Salicaceae gene evolution and divergence.