Conserved miRNA Families Research Articles

Control of Plant Height and Lateral Root Development via Stu-miR156 Regulation of SPL9 Transcription Factor in Potato.

MicroRNAs (miRNAs) are a class of endogenous, non-coding small-molecule RNAs that usually regulate the expression of target genes at the post-transcriptional level. miR156 is one of a class of evolutionarily highly conserved miRNA families. SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factor is one of the target genes that is regulated by miR156. SPL transcription factors are involved in regulating plant growth and development, hormone response, stress response, and photosynthesis. In the present study, transgenic potato plants with overexpressed miR156 were obtained via the Agrobacterium-mediated transformation method. The results showed that the expression levels of the target gene, StSPL9, were all downregulated in the transgenic plants with overexpressed Stu-miR156. Compared with those of the control plants, the plant height and root length of the transgenic plants were significantly decreased, while the number of lateral roots was significantly increased. These results revealed that the miR156/SPLs module was involved in regulating potato plant height and root growth.

Transcriptional regulatory mechanisms of flavonoid metabolism from flower bud to flower in Hemerocallis citrina

The flower buds of Hemerocallis citrina are well-known functional foods in East Asian countries for their promoting intelligence and forgetting worries, in which their nutrients, especially flavonoids, play an important role. However, they will be discarded when the buds develop into flowers, part of the reason is the type and content of flavonoids change considerably. At present, the developmental mechanism responsible for these differences is still unclear. Based on "multi-omics" technologies, the results of this study revealed that 18 flavonoids were significantly differential, including five flavonoids, eight flavonols and three flavanones, one isoflavone and one anthocyanin, and their biosynthesis involved 50 differential genes and 25 differential enzyme proteins. Among them, nine genes encoding four key enzymes (chalcone isomerase, isoflavone 2′-hydroxylase, flavonol-3-O-l-rhamnoside-7-O-glucosyltransferase and phlorizin synthase) were targeted by seven conserved miRNA (microRNA) families, covering miR394, miR477, miR396, miR528, miR164, miR395 and miR447. Furthermore, 10 genes encoding five transcription factor families (bZIP (basic leucine zipper), NAC (NAM, ATAF1/2 and CUC2), GRAS (GAI, RGA and SCR), TCP (TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR) and MADS (MCM1/AGAMOUS/DEFICIENS/SRF)) were targeted by seven conserved miRNA families, including miR393, miR166, miR171, miR477, miR164, miR528 and miR447. They are jointly involved in the metabolic regulation of flavone and flavonol biosynthesis, isoflavonoid biosynthesis, and flavonoid biosynthesis from flower buds to flowering development of H. citrina.

A microRNA profile of the saliva in the argasid ticks Ornithodoros erraticus and Ornithodoros moubata and prediction of specific target genes

Ornithodoros erraticus and Ornithodoros moubata ticks are the main vectors of the agents of human relapsing fever (TBRF) and African swine fever (ASF) in the Mediterranean Basin and Africa, respectively. Tick ​​saliva is crucial for complete tick feeding and pathogen transmission, as it contains numerous molecules such as proteins, lipids, and non-coding RNAs (ncRNA) including microRNAs (miRNA). MiRNAs are small ncRNAs capable of regulating the expression of their target messenger RNA (mRNA) leading to degradation or inhibition of its translation into protein. Research on miRNAs from ixodid ticks has revealed that miRNAs are involved in the regulation of different physiological processes of ticks, as well as in the modulation of host gene expression, immune response to tick bite and pathogen transmission. Regarding argasid ticks, there is not information about their miRNAs or their potential involvement in tick physiology and/or in the regulation of the tick-host-pathogen interactions. The aim of this work was to profile the miRNAs expressed in the saliva of O. erraticus and O. moubata, and the in silico prediction and functional analysis of their target genes in the swine host. As a whole, up to 72 conserved miRNAs families were identified in both species: 35 of them were shared and 23 and 14 families were unique to O. erraticus and O. moubata, respectively. The most abundant miRNAs families were mir-1, mir-10 and let-7 in O. erraticus and let-7, mir-252, mir-10 in O. moubata. Four miRNAs sequences of each species were validated by RT-qPCR confirming their presence in the saliva. Target gene prediction in the host (Sus scrofa) and functional analysis showed that the selected miRNAs are mainly involved in processes related to signal transduction, regulation of mRNA transcription and gene expression, synapse regulation, immune response, angiogenesis and vascular development. These results suggest that miRNAs could play an important role at the tick-host interface, providing new insights into this complex relationship that may contribute to a more precise selection of tick molecules for the development of therapeutic and immune strategies to control tick infestations and tick-borne pathogens.

Genome‑wide identification and characterization of miR396 family members and their target genes GRF in sorghum (Sorghum bicolor (L.) moench).

MicroRNAs (miRNAs) widely participate in plant growth and development. The miR396 family, one of the most conserved miRNA families, remains poorly understood in sorghum. To reveal the evolution and expression pattern of Sbi-miR396 gene family in sorghum, bioinformatics analysis and target gene prediction were performed on the sequences of the Sbi-miR396 gene family members. The results showed that five Sbi-miR396 members, located on chromosomes 4, 6, and 10, were identified at the whole-genome level. The secondary structure analysis showed that the precursor sequences of all five Sbi-miR396 potentially form a stable secondary stem-loop structure, and the mature miRNA sequences were generated on the 5' arm of the precursors. Sequence analysis identified the mature sequences of the five sbi-miR396 genes were high identity, with differences only at the 1st, 9th and 21st bases at the 5' end. Phylogenetic analysis revealed that Sbi-miR396a, Sbi-miR396b, and Sbi-miR396c were clustered into Group I, and Sbi-miR396d and Sbi-miR396e were clustered into Group II, and all five sbi-miR396 genes were closely related to those of maize and foxtail millet. Expression analysis of different tissue found that Sbi-miR396d/e and Sbi-miR396a/b/c were preferentially and barely expressed, respectively, in leaves, flowers, and panicles. Target gene prediction indicates that the growth-regulating factor family members (SbiGRF1/2/3/4/5/6/7/8/10) were target genes of Sbi-miR396d/e. Thus, Sbi-miR396d/e may affect the growth and development of sorghum by targeting SbiGRFs. In addition, expression analysis of different tissues and developmental stages found that all Sbi-miR396 target genes, SbiGRFs, were barely expressed in leaves, root and shoot, but were predominantly expressed in inflorescence and seed development stage, especially SbiGRF1/5/8. Therefore, inhibition the expression of sbi-miR396d/e may increase the expression of SbiGRF1/5/8, thereby affecting floral organ and seed development in sorghum. These findings provide the basis for studying the expression of the Sbi-mir396 family members and the function of their target genes.

Leaf rust responsive miRNA and their target genes in wheat.

Small RNA sequencing (sRNA-seq) and degradome analysis were used for the identification of miRNAs and their target host genes in a pair of near-isogenic lines (NILs), which differed for the presence of leaf rust resistance gene Lr28. The study led to identification of (i) 506 known and 346 novel miRNAs; and (ii) 5054 target genes including 4557 in silico predicted and 497 degradome-based genes using 105 differentially expressed (DE) miRNAs. A subset of 128 targets (67 in silico + 61 degradome-based) was differentially expressed in RNA-seq data that was generated by us earlier using the same pair of NILs; among these 128 targets, 58 target genes exhibited an inverse relationship with the DE miRNAs (expression of miRNAs and activation/suppression of target genes). Eight miRNAs which belonged to the conserved miRNA families and were known to be induced in response to fungal diseases in plants included the following: miR156, miR158, miR159, miR168, miR169, miR172, miR319, miR396. The target genes belonged to the following classes of genes known to be involved in downstream disease resistance pathways; peroxidases, sugar transporters, auxin response signaling, oxidation-reduction, etc. It was also noticed that although a majority of miRNAs and target genes followed the above classical inverse relationship, there were also examples, where no such relationship was observed. Among the target genes, there were also 51 genes that were not only regulated by miRNAs, but were also differentially methylated at sequences including the following segments: promotors, introns, TSS, exons. The results of the present study suggest a complex interplay among miRNA genes, target genes, and various epigenetic controls, which regulate the expression of genes involved in downstream pathways for disease resistance.

Analysis of Homologous Regions of Small RNAs MIR397 and MIR408 Reveals the Conservation of Microsynteny among Rice Crop-Wild Relatives.

MIRNAs are small non-coding RNAs that play important roles in a wide range of biological processes in plant growth and development. MIR397 (involved in drought, low temperature, and nitrogen and copper (Cu) starvation) and MIR408 (differentially expressed in response to environmental stresses such as copper, light, mechanical stress, dehydration, cold, reactive oxygen species, and drought) belong to conserved MIRNA families that either negatively or positively regulate their target genes. In the present study, we identified the homologs of MIR397 and MIR408 in Oryza sativa and its six wild progenitors, three non-Oryza species, and one dicot species. We analyzed the 100 kb segments harboring MIRNA homologs from 11 genomes to obtain a comprehensive view of their community evolution around these loci in the farthest (distant) relatives of rice. Our study showed that mature MIR397 and MIR408 were highly conserved among all Oryza species. Comparative genomics analyses also revealed that the microsynteny of the 100 kb region surrounding MIRNAs was only conserved in Oryza spp.; disrupted in Sorghum, maize, and wheat; and completely lost in Arabidopsis. There were deletions, rearrangements, and translocations within the 100 kb segments in Oryza spp., but the overall microsynteny of the region was maintained. The phylogenetic analyses of the precursor regions of all MIRNAs under study revealed a bimodal clade of common origin. This comparative analysis of miRNA involved in abiotic stress tolerance in plants provides a powerful tool for future Oryza research. Crop wild relatives (CWRs) offer multiple traits with potential to decrease the amount of yield loss owing to biotic and abiotic stresses. Using a comparative genomics approach, the exploration of CWRs as a source of tolerance to these stresses by understanding their evolution can be further used to leverage their yield potential.

Metabolic and transcriptional regulatory mechanisms of differential carbohydrates formation from flower buds to flowers of Hemerocallis citrina

The flower buds of Hemerocallis citrina that are about to open are an edible vegetable with health care functions of "forgetting worries". However, the flower buds that open into flowers will be discarded due to changes in nutritional composition such as carbohydrates which is still unclear on their difference and formation mechanism from flower buds. In this study, the combined analysis of transcriptome, metabolome and degradome was used to investigate the above problems. The results found that there were 32 differential carbohydrates, 370 differential genes, 23 differential miRNAs and their 49 target genes in flowers compared to flower buds, among which at least nine conserved miRNA families such as miR393, miR394, miR395 and miR156 targeted to act on eleven key enzyme genes, such as INV (beta-fructofuranosidase), BAM (beta-amylase), malZ (alpha-glucosidase) and pgm (phosphoglucomutase), and then involved together in the regulation of differential carbohydrates metabolism including starch and sucrose, amino sugar and nucleotide sugar, fructose and mannose, and galactose metabolism in flower opening development of H. citrina.

Identification and characterization of miRNAs and PHAS loci related to the early development of the embryo and endosperm in Fragaria × ananassa

BackgroundThe strawberry fleshy fruit is actually enlarged receptacle tissue, and the successful development of the embryo and endosperm is essential for receptacle fruit set. MicroRNAs (miRNAs) and phased small interfering RNAs (phasiRNAs) play indispensable regulatory roles in plant growth and development. However, miRNAs and phasiRNAs participating in the regulation of strawberry embryo and endosperm development have yet to be explored.ResultsHere, we performed genome-wide identification of miRNA and phasiRNA-producing loci (PHAS) in strawberry seeds with a focus on those involved in the development of the early embryo and endosperm. We found that embryos and endosperm have different levels of small RNAs. After bioinformatics analysis, the results showed that a total of 404 miRNAs (352 known and 52 novel) and 156 PHAS genes (81 21-nt and 75 24-nt genes) could be found in strawberry seed-related tissues, of which four and nine conserved miRNA families displayed conserved expression in the endosperm and embryo, respectively. Based on refined putative annotation of PHAS loci, some auxin signal-related genes, such as CM3, TAR2, AFB2, ASA1, NAC and TAS3, were found, which demonstrates that IAA biosynthesis is important for endosperm and embryo development during early fruit growth. Additionally, some auxin signal-related conserved (miR390-TAS3) and novel (miR156-ASA1) trigger-PHAS pairs were identified.ConclusionsTaken together, these results expand our understanding of sRNAs in strawberry embryo and endosperm development and provide a genomic resource for early-stage fruit development.

The miR393-Target Module Regulates Plant Development and Responses to Biotic and Abiotic Stresses.

MicroRNAs (miRNAs), a class of endogenous small RNAs, are broadly involved in plant development, morphogenesis and responses to various environmental stresses, through manipulating the cleavage, translational expression, or DNA methylation of target mRNAs. miR393 is a conserved miRNA family present in many plants, which mainly targets genes encoding the transport inhibitor response1 (TIR1)/auxin signaling F-box (AFB) auxin receptors, and thus greatly affects the auxin signal perception, Aux/IAA degradation, and related gene expression. This review introduces the advances made on the miR393/target module regulating plant development and the plant’s responses to biotic and abiotic stresses. This module is valuable for genetic manipulation of optimized conditions for crop growth and development and would also be helpful in improving crop yield through molecular breeding.

Regulatory Role of miRNAs and lncRNAs in Gout.

Objective To explore the regulatory functions of ceRNA networks in the nosogenesis of gout and search for potential therapeutic targets. Methods We searched the GEO database and downloaded the lncRNA microarray chipset GSE160170. This matrix series was analyzed to yield differentially expressed lncRNAs and mRNAs. Then, the correlations between lncRNAs and miRNAs were obtained by comparing the highly conserved miRNA families. The predicted miRNA-regulating mRNAs were matched to the differentially expressed mRNAs from the chipset analyses to obtain miRNA–mRNA interactions. Next, we used the Cytoscape software to model ceRNA networks and the STRING database to determine their protein–protein interactions. The R software was used to algorithmically screen the functional pathways of key PPI modules in the ceRNA networks. Results A total of 354 lncRNAs (140 downregulated and 214 upregulated) and 693 mRNAs (399 downregulated and 294 upregulated) were differentially expressed between the gout group and the healthy group. The ceRNA network of differentially expressed lncRNAs contained 86 lncRNAs (35 downregulated and 51 upregulated), 29 miRNAs, and 57 mRNAs. The processes identified in the GO enrichment analysis included gene transcription, RNA polymerase II transcription, and the regulation of cell growth and apoptosis. The pathways identified in the KEGG enrichment analysis included IL-17, TNF, and MAPK signaling. Nine lncRNAs (AC104024, AC084082, AC083843, FAM182A, AC022819, FAM215B, AP000525, TTTY10, and ZNF346-IT1), eleven miRNAs (hsa-miR-1297, hsa-miR-17-5p, hsa-miR-429, hsa-miR-139-5p, hsa-miR-449c-5p, hsa-miR-125a-5p, hsa-miR-125b-5p, hsa-miR-23b-3p, hsa-miR-217, hsa-miR-363-3p, and hsa-miR-20b-5p), and nine mRNAs (JUN, CASP2, PMAIP1, FOS, TNFAIP3, MAP3K8, BTG2, NR4A2, and DUSP2) were identified in the exploration of the key modules. Conclusion Characterization of ceRNA networks could be a promising approach for better understanding the pathogenesis of gout, with the TTTY10/hsa-miR-139-5p/AP-1 axis likely to be of clinical significance.

Sequencing and de novo transcriptome assembly for discovering regulators of gene expression in Jack (Artocarpus heterophyllus)

Jack (Artocarpus heterophyllus) is a multipurpose fruit-tree species with minimal genomic resources. The study reports developing comprehensive transcriptome data containing 80,411 unigenes with an N50 value of 1265 bp. We predicted 64,215 CDSs from the unigenes and annotated and functionally categorized them into the biological process (23,230), molecular function (27,149), and cellular components (17,284). From 80,411 unigenes, we discovered 16,853 perfect SSRs with 192 distinct repeat motif types reiterating 4 to 22 times. Besides, we identified 2741 TFs from 69 TF families, 53 miRNAs from 19 conserved miRNA families, 25,953 potential lncRNAs, and placed three functional eTMs in different lncRNA-miRNA pairs. The regulatory networks involving genes, TFs, and miRNAs identified several regulatory and regulated nodes providing insight into miRNAs' gene associations and transcription factor-mediated regulation. The comparison of expression patterns of some selected miRNAs vis-à-vis their corresponding target genes showed an inverse relationship indicating the possible miRNA-mediated regulation of the genes.

MiR390-tasiRNA3-ARF4 pathway is involved in regulating flowering time in woodland strawberry.

miR390-tasiRNA3-ARF4 pathway was identified in woodland strawberry. FvemiR390 was involved in the regulation of flowering time, and miR390-tasiRNA3-ARF4 regulated flowering time through FveAP1/FveFUL in woodland strawberry. miRNA is an important type of regulator, and widely involved in plant growth, development and stress response. As a conserved miRNA family, the function of miR390 has been studied in many species, but poorly understood in woodland strawberry. In this study, we found that the members of miR390 family were highly conservative, and FvemiR390a and FvemiR390b have the same mature sequence. Therefore, we chose FveMIR390a to generate FvemiR390 mature sequence for functional studies. Subsequently, the result of transient gene expression assay proved that FvemiR390 negatively regulates FveARF4 through miR390-tasiRNA3-ARF4 pathway. Using transgenic plants, we discovered that the overexpression of FveMIR390a delayed flowering in woodland strawberry. Further studies revealed that the expressions of FveAP1 and FveFUL were lower in transgenic plants, which indicates miR390-tasiRNA3-ARF4 pathway delays flowering time through the FveAP1/FveFUL in woodland strawberry. Moreover, the expression of FvemiR390 responded to exogenous hormones, which also provides a reference for the application of exogenous hormones in regulating the flowering time of woodland strawberry.

Characterization and regulatory mechanism analysis of VvmiR156a-VvAGL80 pair during grapevine flowering and parthenocarpy process induced by gibberellin.

MicroRNA156 (miR156) is an important conserved miRNA family in plants. Recently, we revealed VvmiR156a could involve in the modulation of gibberellin (GA)-mediated flower and berry development process of grapevine (Vitis vinifera L.). However, how to manipulate this process is unclear. For this, we used the GA-induced grapevine parthenocarpy system to investigate the regulatory roles of VvmiR156a during this process. Here, we cloned the mature and precursor sequences of VvmiR156a in Wink grape and identified its potential target gene VvAGL80, which belongs to the MADS-box gene family. Moreover, using RNA ligase-mediated 5' rapid amplification of cDNA ends (RLM-RACE) and poly(A)polymerase-mediated 3' rapid amplification of cDNA (PPM-RACE) technologies, it confirmed that VvAGL80 was the true target gene of VvmiR159a. Analysis of promoter cis-elements and β-glucuronidase (GUS) staining showed that both VvmiR156a and VvAGL80 contained GA-responsive elements and could respond to GA treatments. Quantitative real-time-polymerase chain reaction (qRT-PCR) analysis exhibited the VvmiR156a and VvAGL80 showed opposite expression trends during grapevine flower and berry development, indicating that VvmiR156a negatively regulated the expression of VvAGL80 during this process. After GA treatment, the expression of miR156 in flowers was downregulated significantly, while that of VvAGL80 was upregulated, thereby accelerating grapevine flowering. Furthermore, GA treatment enhanced the negative regulation of VvmiR156a on VvAGL80 in seed, especially at the seed-coat hardening stage, which was the key period of seed growth and development. Our findings enriched the knowledge of the regulatory mechanism of the miRNA-mediated grapevine parthenocarpy process.

Identification and profiling of conserved microRNAs in different developmental stages of crown imperial (Fritillaria imperialis L.) using high-throughput sequencing.

Novel strategies for improvement of ornamental plants and their properties relay on miRNA control of differential plant gene expression modulation. Still, in response to the same abiotic stresses, some conserved miRNA families show different expression patterns in different plant species. In parallel, the use of deep sequencing technologies reveals new levels of complexity of regulatory networks in plants through identification of new miRNAs. Fritillaria imperialis plants were collected from their natural habitats in Koohrang, Chaharmahalva Bakhtiari, Iran. Several tissues including stamen, pistil, petal, sepal, leaf, stem, bulb and fruit were collected during three developmental stages (stem elongation, flower development and seed head stages). Using RNAseq and qRT-PCR approach, this research revealed 21 conserved miRNAs, matching 15 miRNA families, in Fritilaria imperialis. The expression of seven conserved miRNAs (Fim-miR156b, Fim-miR159, Fim-miR166a-5p, Fim-miR169d-5p, Fim-miR171c, Fim-miR393 and Fim-miR396e-3p) was further investigated in different tissues and three developmental stages, suggesting different roles for these miRNAs during growth and development of crown imperial. Gained knowledge from this research can open the door to find efficient ways to secure crown imperial survival, preservation and utilization and if proven useful may be applied in other plant species as well.

MicroRNA 166: an evolutionarily conserved stress biomarker in land plants targeting HD-ZIP family.

MicroRNAs (miRNAs) are significant class of noncoding RNAs having analytical investigating and modulatory roles in various signaling mechanisms in plants related to growth, development and environmental stress. Conserved miRNAs are an affirmation of land plants evolution and adaptation. They are a proof of indispensable roles of endogenous gene modulators that mediate plant survival on land. Out of such conserved miRNA families, is one core miRNA known as miR166 that is highly conserved among land plants. This particular miRNA is known to primarily target HD ZIP-III transcription factors. miR166 has roles in various developmental processes, as well as regulatory roles against biotic and abiotic stresses in major crop plants. Major developmental roles indirectly modulated by miR166 include shoot apical meristem and vascular differentiation, leaf and root development. In terms of abiotic stress, it has decisive regulatory roles under drought, salinity, and temperature along with biotic stress management. miR166 and its target genes are also known for their beneficial synergy with microorganisms in leguminous crops in relation to lateral roots and nodule development. Hence it is important to study the roles of miR166 in different crop plants to understand its defensive roles against environmental stresses and improve plant productivity by reprogramming several gene functions at molecular levels. This review is hence a summary of different regulatory roles of miR166 with its target HD-ZIP III and its modulatory and fine tuning against different environmental stresses in various plants.

PmiREN2.0: from data annotation to functional exploration of plant microRNAs.

Nearly 200 plant genomes have been sequenced over the last two years, and new functions of plant microRNAs (miRNAs) have been revealed. Therefore, timely update of the plant miRNA databases by incorporating miRNAs from the newly sequenced species and functional information is required to provide useful resources for advancing plant miRNA research. Here we report the update of PmiREN2.0 (https://pmiren.com/) with an addition of 19 363 miRNA entries from 91 plants, doubling the amount of data in the original version. Meanwhile, abundant regulatory information centred on miRNAs was added, including predicted upstream transcription factors through binding motifs scanning and elaborate annotation of miRNA targets. As an example, a genome-wide regulatory network centred on miRNAs was constructed for Arabidopsis. Furthermore, phylogenetic trees of conserved miRNA families were built to expand the understanding of miRNA evolution across the plant lineages. These data are helpful to deduce the regulatory relationships concerning miRNA functions in diverse plants. Beside the new data, a suite of design tools was incorporated to facilitate experimental practice. Finally, a forum named ‘PmiREN Community’ was added for discussion and resource and new discovery sharing. With these upgrades, PmiREN2.0 should serve the community better and accelerate miRNA research in plants.

Potential Genetic Target Changes in Height and Branches -A Short Review on Osmir535

OsmiR535 is a member of the miR156/529/535 superfamily, which is one of the most conserved miRNA families in plants. OsmiR535 regulates the cold-stress response, modulates plant growth, and controls panicle design and grain length. However, the significance of OsmiR535 in plant drought and salinity responses is unknown. The miR535s identified in terrestrial plants were less conserved than miR156s during evolution, according to this study. Similar to OsmiR529 in rice, miR535 is expressed a very low level during vegetative growth but is significantly accumulated in early panicles. Overexpression of OsmiR535 in rice decreased plant height by reducing the length of the 1st and 2nd internodes. There was also a significant impact on panicle architecture due to the overexpression of OsmiR535. In addition, OsmiR535 overexpression inhibited the expression of OsSPL7/12/16, as well as OsDEP1, OsLOG, and OsSLR1. OsmiR535 regulates plant height, panicle architecture and grain form in rice in several ways, according to our findings

Identification of Brassica napus small RNAs responsive to infection by a necrotrophic pathogen

BackgroundSmall RNAs are short non-coding RNAs that are key gene regulators controlling various biological processes in eukaryotes. Plants may regulate discrete sets of sRNAs in response to pathogen attack. Sclerotinia sclerotiorum is an economically important pathogen affecting hundreds of plant species, including the economically important oilseed B. napus. However, there are limited studies on how regulation of sRNAs occurs in the S. sclerotiorum and B. napus pathosystem.ResultsWe identified different classes of sRNAs from B. napus using high throughput sequencing of replicated mock and infected samples at 24 h post-inoculation (HPI). Overall, 3999 sRNA loci were highly expressed, of which 730 were significantly upregulated during infection. These 730 up-regulated sRNAs targeted 64 genes, including disease resistance proteins and transcriptional regulators. A total of 73 conserved miRNA families were identified in our dataset. Degradome sequencing identified 2124 cleaved mRNA products from these miRNAs from combined mock and infected samples. Among these, 50 genes were specific to infection. Altogether, 20 conserved miRNAs were differentially expressed and 8 transcripts were cleaved by the differentially expressed miRNAs miR159, miR5139, and miR390, suggesting they may have a role in the S. sclerotiorum response. A miR1885-triggered disease resistance gene-derived secondary sRNA locus was also identified and verified with degradome sequencing. We also found further evidence for silencing of a plant immunity related ethylene response factor gene by a novel sRNA using 5′-RACE and RT-qPCR.ConclusionsThe findings in this study expand the framework for understanding the molecular mechanisms of the S. sclerotiorum and B. napus pathosystem at the sRNA level.

Knockdown of miR393 Promotes the Growth and Biomass Production in Poplar.

Short tandem target mimic (STTM), which is composed of two short sequences mimicking small RNA target sites, separated by a linker of optimal size, can block the functions of all members in a miRNA family. microRNA393 (miR393), which is one of the conserved miRNA families in plants, can regulate plant root growth, leaf development, plant architecture, and stress resistance. In order to verify the role of miR393 in the secondary growth of trees, we created its STTM transgenic poplar lines (STTM393). The expression of miR393 in STTM393 lines was reduced by over 10 times compared with the control plants. STTM393 lines showed promoted growth with about 20% higher, 15% thicker, and 2–4 more internodes than the control plants after 3 months of growth. The cross-section of the stems showed that STTM393 lines had wider phloem, xylem, and more cambium cell layers than control plants, and the lignin content in STTM393 lines was also higher as revealed by staining and chemical determination. Based on the transcriptome analysis, the genes related to the auxin signaling pathway, cell cyclin, cell expansion, and lignin synthesis had higher expression in STTM393 lines than that in control plants. The higher expression levels of FBL family members suggested that the auxin signaling pathway was strengthened in STTM393 lines to promote plant growth. Therefore, the knockdown of miR393 using the STTM approach provides a way to improve poplar growth and biomass production.

Microrna Regulation of Nodule Zone-Specific Gene Expression In Soybean

Microrna Regulation of Nodule Zone-Specific Gene Expression In Soybean