Identification and characterization of new plant microRNAs using EST analysis

Computational identification and experimental validation of novel Saccharum officinarum microRNAs along with their targets through RT-PCR approach

Various metabolic and cell signaling processes impact the functions of sugarcane plant cells. MicroRNAs (miRNAs) play critical regulatory roles in enhancing yield and providing protection against various stressors. This study seeks to identify and partially characterize several novel miRNAs in sugarcane using in silico tools, while also offering a preliminary assessment of their functions. This was accomplished by predicting novel conserved miRNAs in sugarcane plants using a variety of genomics-based techniques like BLASTn, MFOLD, psRNA Target, sequence logo, Weblogo, primer-3, etc. and annotated using miRBase and NCBI. For validation, RT-PCR method was used along with agarose gel. After the preparation of fourteen randomly chosen primers, they were validated by RT-PCR. Accordingly, they contain fifty specific targeted proteins with substantial targets in the structural, transcriptional protein, etc. Furthermore, the sof-miR5025a directs the heat repeat protein while the voltage-dependent anion is governed by sof-miR8005a. Similarly, the sof-miR7768b and sof-miR6249b monitor the pathogenesis-related protein and zinc finger, C2H2 type protein, which assist as transcription factors. Thus, the novel sugarcane miRNAs target a wide range of important genes help regulate the environment for sugarcane to generate a higher-quality crop.

'140R' Rootstock Regulates Resveratrol Content in 'Cabernet Sauvignon' Grapevine Leaves Through miRNA

Grafting is important for increasing the resistance of grapevines to environmental stress, improving fruit quality, and shortening the reproductive period. In this study, 'Cabernet Sauvignon' (CS) grafted on the resistant rootstock 140R (CS/140R), self-grafted grapevines of the resistant rootstock 140R (140R/140R), and self-grafted grapevines of CS (CS/CS) were subjected to high-throughput sequencing; small RNA (sRNA) libraries were constructed, and miRNAs responsive to the grafting process were identified. A total of 177 known miRNAs and 267 novel miRNAs were identified. Many miRNAs responsive to the grafting process were significantly down-regulated in CS/140R leaves relative to CS/CS leaves, such as vvi-miR171c, vvi-miR171e, et al., suggesting that the expression of these miRNAs might be affected by grafting. Kyoto Encyclopedia of Genes and Genomes analysis revealed that the differentially expressed miRNAs regulated the expression of genes in the phenylpropanoid synthesis pathway. Grapevine leaves transiently overexpressing vvi-miR171c were assayed, and the expression of the target gene, VvMYB154, and the resveratrol content were decreased, indicating that vvi-miR171c negatively regulates the expression of VvMYB154. In sum, 140R increased the resveratrol content of the scion by grafting, down-regulating the expression of vvi-miR171c. These results provide new information that will aid future analyses of the effects of grafting on the content of secondary metabolites.

Machine learning provides specific detection of salt and drought stresses in cucumber based on miRNA characteristics

BACKGROUND

Specific detection of the type and severity of plant abiotic stresses helps prevent yield loss by considering timely actions. This study introduces a novel method to detect the type and severity of stress in cucumber plants under salinity and drought conditions. Various features, i.e., morphological (image textural features), physiological/biochemical (relative water content, chlorophyll, catalase activity, anthocyanins, phenol content, and proline), as well as miRNA characteristics (the concentration of miRNA-156a, miRNA-166i, miRNA-399g, and miRNA-477b) were extracted from plant leaves, and machine learning methods were used to predict the type and severity of stress by having these features. Support vector machine (SVM) with parameters optimized by genetic algorithm (GA) and particle swarm optimization (PSO) was used for machine learning.

RESULTS

The coefficient of determination of predicting the stress type and severity in plants under both stresses was 0.61, 0.82, and 0.99 using morphological, physiological/biochemical, and miRNA characteristics, respectively. This reveals machine learning methods optimized by metaheuristic optimization techniques can provide specific detection of salt and drought stresses in cucumber plants based on miRNA characteristics. Among the study miRNAs, miRNA-477b and miRNA-399g had the highest and lowest contribution to salt and drought stresses, respectively.

CONCLUSIONS

Comapred to conventional plant traits, miRNAs are more reliable features for providing us with valuable information about plant abiotic diseases at early stages. Using an electrochemical miRNA biosensor similar to one used in this work to measure the miRNA concentration in plant leaves and using a machine learning algorithm such as SVM enable farmers to detect the salt and drought stress at early stages in cucumber plants with very high accuracy.

Characterization of Two-Component System gene (TCS) in melatonin-treated common bean under salt and drought stress

The two-component system (TCS) generally consists of three elements, namely the histidine kinase (HK), response regulator (RR), and histidine phosphotransfer (HP) gene families. This study aimed to assess the expression of TCS genes in P. vulgaris leaf tissue under salt and drought stress and perform a genome-wide analysis of TCS gene family members using bioinformatics methods. This study identified 67 PvTCS genes, including 10 PvHP, 38 PvRR, and 19 PvHK, in the bean genome. PvHK2 had the maximum number of amino acids with 1261, whilst PvHP8 had the lowest number with 87. In addition, their theoretical isoelectric points were between 4.56 (PvHP8) and 9.15 (PvPRR10). The majority of PvTCS genes are unstable. Phylogenetic analysis of TCS genes in A. thaliana, G. max, and bean found that PvTCS genes had close phylogenetic relationships with the genes of other plants. Segmental and tandem duplicate gene pairs were detected among the TCS genes and TCS genes have been subjected to purifying selection pressure in the evolutionary process. Furthermore, the TCS gene family, which has an important role in abiotic stress and hormonal responses in plants, was characterized for the first time in beans, and its expression of TCS genes in bean leaves under salt and drought stress was established using RNAseq and qRT-PCR analyses. The findings of this study will aid future functional and genomic studies by providing essential information about the members of the TCS gene family in beans.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01406-5.

An Integrated Analysis of microRNAs and the Transcriptome Reveals the Molecular Mechanisms Underlying the Regulation of Leaf Development in Xinyang Maojian Green Tea (Camellia sinensis)

Xinyang Maojian (XYMJ) tea is one of the world's most popular green teas; the development of new sprouts directly affects the yield and quality of tea products, especially for XYMJ, which has hairy tips. Here, we used transcriptome and small RNA sequencing to identify mRNAs and miRNAs, respectively, involved in regulating leaf development in different plant tissues (bud, leaf, and stem). We identified a total of 381 conserved miRNAs. Given that no genomic data for XYMJ green tea are available, we compared the sequencing data for XYMJ green tea with genomic data from a closely related species (Tieguanyin) and the Camellia sinensis var. sinensis database; we identified a total of 506 and 485 novel miRNAs, respectively. We also identified 11 sequence-identical novel miRNAs in the tissues of XYMJ tea plants. Correlation analyses revealed 97 miRNA-mRNA pairs involved in leaf growth and development; the csn-miR319-2/csnTCP2 and miR159-csnMYB modules were found to be involved in leaf development in XYMJ green tea. Quantitative real-time PCR was used to validate the expression levels of the miRNAs and mRNAs. The miRNAs and target genes identified in this study might shed new light on the molecular mechanisms underlying the regulation of leaf development in tea plants.

Evaluation of efficacy of non-coding RNA in abiotic stress management of field crops: Current status and future prospective

Abiotic stresses are responsible for the major losses in crop yield all over the world. Stresses generate harmful ROS which can impair cellular processes in plants. Therefore, plants have evolved antioxidant systems in defence against the stress-induced damages. The frequency of occurrence of abiotic stressors has increased several-fold due to the climate change experienced in recent times and projected for the future. This had particularly aggravated the risk of yield losses and threatened global food security. Non-coding RNAs are the part of eukaryotic genome that does not code for any proteins. However, they have been recently found to have a crucial role in the responses of plants to both abiotic and biotic stresses. There are different types of ncRNAs, for example, miRNAs and lncRNAs, which have the potential to regulate the expression of stress-related genes at the levels of transcription, post-transcription, and translation of proteins. The lncRNAs are also able to impart their epigenetic effects on the target genes through the alteration of the status of histone modification and organization of the chromatins. The current review attempts to deliver a comprehensive account of the role of ncRNAs in the regulation of plants' abiotic stress responses through ROS homeostasis. The potential applications ncRNAs in amelioration of abiotic stresses in field crops also have been evaluated.

microRNA biogenesis and stabilization in plants

MicroRNAs (miRNAs) are short endogenous non-coding RNAs that regulate gene expression at the post-transcriptional level in a broad range of eukaryotic species. In animals, it is estimated that more than 60% of mammalian genes are targets of miRNAs, with miRNAs regulating cellular processes such as differentiation and proliferation. In plants, miRNAs regulate gene expression and play essential roles in diverse biological processes, including growth, development, and stress responses. Arabidopsis mutants with defective miRNA biogenesis are embryo lethal, and abnormal expression of miRNAs can cause severe developmental phenotypes. It is therefore crucial that the homeostasis of miRNAs is tightly regulated. In this review, we summarize the key mechanisms of plant miRNA biogenesis and stabilization. We provide an update on nuclear proteins with functions in miRNA biogenesis and proteins linking miRNA biogenesis to environmental triggers.

Identification of conserved miRNAs and their targets in Jatropha curcas: an in silico approach

BACKGROUND

MicroRNAs (miRNAs) are small endogenous RNAs with an approximate length of 18-22 nucleotides and involved in the regulation of gene expression in transcriptional or post-transcriptional levels. They were found to be associated with leaf morphogenesis, flowering time, vegetative phase change, and response to environmental cues in plants, where they act as a critical regulatory factor. The nature of high conservancy of plant miRNAs within the plant species made it possible to detect the conserved miRNAs by computational approaches. Expressed Sequence Tags (EST) based comparative genomic approaches provide advantages over wet lab approaches as it is convenient, easy to carry out and less time consuming. EST-based in silico approach can unravel new conserved miRNAs in plants, even when the complete genome sequence is not available.

RESULTS

To identify the novel miRNAs, a total of 46,865 ESTs from Jatropha curcas were searched for homology to all available 6746 mature miRNAs of plant eudicotyledons. Finally, we ended up with 12 novel miRNAs in Jatropha that range from 18 to 19 nucleotides where their respective precursor miRNAs had 54.11-71.76% (A + U) content. The putative miRNAs belong to 12 individual miRNA family and most of them have higher (A + U) content ranging from 47.36 to 77.77% than their respective miRNA homologs. Many of the target genes by the newly identified miRNAs were associated with plant growth and development, stress response, defense and hormone signaling, and oil synthesis pathways.

CONCLUSION

These findings have the potential to speed up miRNA identification and expand our understanding of miRNA functions in J. curcas.

Recent Insights into Plant miRNA Biogenesis: Multiple Layers of miRNA Level Regulation

MicroRNAs are small RNAs, 20-22 nt long, the main role of which is to downregulate gene expression at the level of mRNAs. MiRNAs are fundamental regulators of plant growth and development in response to internal signals as well as in response to abiotic and biotic factors. Therefore, the deficiency or excess of individual miRNAs is detrimental to particular aspects of a plant's life. In consequence, the miRNA levels must be appropriately adjusted. To obtain proper expression of each miRNA, their biogenesis is controlled at multiple regulatory layers. Here, we addressed processes discovered to influence miRNA steady-state levels, such as MIR transcription, co-transcriptional pri-miRNA processing (including splicing, polyadenylation, microprocessor assembly and activity) and miRNA-encoded peptides synthesis. MiRNA stability, RISC formation and miRNA export out of the nucleus and out of the plant cell also define the levels of miRNAs in various plant tissues. Moreover, we show the evolutionary conservation of miRNA biogenesis core proteins across the plant kingdom.

Identification of Conserved and Novel MicroRNAs with their Targets in Garden Pea (Pisum Sativum L.) Leaves by High-Throughput Sequencing

MicroRNAs (miRNAs) are single-stranded, endogenous, non-coding RNAs of 20–24 nucleotides that play a significant role in post-transcriptional gene regulation. Various conserved and novel miRNAs have been characterized, especially from the plant species whose genomes were well-characterized; however, information on miRNA in economically important plants such as pea ( Pisum sativum L.) is limited. In this study, I have identified conserved and novel miRNA in garden pea plant leaves samples along with their targets by analyzing the next generation sequencing (NGS) data. The raw data obtained from NGS were processed and 1.38 million high-quality non-redundant reads were retained for analysis, this tremendous quantity of reads indicates a large and diverse small RNA population in pea leaves. After analyzing the deep sequencing data, 255 conserved and 11 novel miRNAs were identified in the garden pea leaves sample. Utilizing psRNATarget tool, the miRNA targets of conserved and novel miRNA were predicted. Further, the functional annotation of the miRNA targets were performed using blast2Go software and the target gene products were predicted. The miRNA target gene products along with GO_ID (Gene Ontology Identifier) were categorized into biological processes, cellular components, and molecular functions. The information obtained from this study will provide genomic resources that will help in understanding miRNA-mediated post-transcriptional gene regulation in garden peas.

Comprehensive, integrative genomic analysis of microRNA expression profiles in different tissues of two wheat cultivars with different traits

Wheat is one of the most important food sources on Earth. MicroRNAs (miRNA) play important roles in wheat productivity. To identify wheat miRNAs, we constructed and sequenced sRNA libraries from leaves and roots of two wheat cultivars (RAC875 and Kukri) with many different traits. Given that available miRNA wheat complement in the plant-specific database PmiREN ( https://pmiren.com ) does not include root tissues and root-associated miRNAs might thus be missing, we performed first the prediction of novel miRNAs using the sRNAbench tool. We found a total of 150 putatively novel miRNA genes with expression of both arms from 289 unique mature sequences and nearly 30% of all miRNA reads in roots corresponded to novel miRNAs. In contrast, this figure in leaves dropped to under 3%, confirming the undersampling of roots in the complement of known miRNAs. By using 120 publicly available wheat datasets, 598 Zea mays small RNA libraries, 64 plant species genomes, wheat degradome library, and functional enrichment analysis, a subset of novel miRNAs were confirmed as bona-fide miRNAs. Of the total 605 miRNAs identified in this study inclusive of 316 known miRNAs, 528 miRNAs were shared by both cultivars, 429 miRNAs were shared by both root tissues and 329 miRNAs were shared by both leaf tissues. In addition, 32 miRNAs were specific to Kukri while 45 miRNAs were specific to RAC875. These miRNAs had diverse functions, such as regulation of gene transcription, protein translation, energy metabolism, and cell cycle progression. Our data provide a genome-wide miRNA expression profile in these two wheat cultivars and help functional studies of wheat genomics.

Integrated miRNA, target mRNA, and metabolome profiling of Tinospora cordifolia with reference to berberine biosynthesis

MicroRNAs play a central role in gene regulation and emerge as novel targets for secondary metabolites improvement in plants. The crops thus can be improved through knowledge obtained by the study of miRNAs because of their conserved nature in gene regulation. The present study has been carried out on Tinospora cordifolia (T. cordifolia), because of its illimitable application for the treatment of various diseases. This plant has tremendous medicinal properties, yet unexplored at the molecular level, and has not received much recognition in the scientific field. Thus, here computational analysis was performed to identify T. cordifolia miRNAs using EST database. Using these miRNAs, we predicted their targets which were found to be associated with the regulation of diverse gene networks including 433 berberine biosynthesis genes in T. cordifolia. Further, selected miRNAs were validated and their expression was detected in different T. cordifolia tissues followed by expression analysis of their target mRNAs. These data were then compared with the metabolic profile of T. cordifolia with an emphasis on therapeutically important compound berberine. In this study, we did simultaneous miRNA/target gene expression and metabolome analysis which opens a new way for initiating new proposition and prioritization of miRNAs/genes/metabolites for targeted follow‑up metabolic engineering experimentations.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03342-9.

Roles of microRNAs in abiotic stress response and characteristics regulation of plant

MicroRNAs (miRNAs) are a class of non-coding endogenous small RNAs (long 20-24 nucleotides) that negatively regulate eukaryotes gene expression at post-transcriptional level via cleavage or/and translational inhibition of targeting mRNA. Based on the diverse roles of miRNA in regulating eukaryotes gene expression, research on the identification of miRNA target genes has been carried out, and a growing body of research has demonstrated that miRNAs act on target genes and are involved in various biological functions of plants. It has an important influence on plant growth and development, morphogenesis, and stress response. Recent case studies indicate that miRNA-mediated regulation pattern may improve agronomic properties and confer abiotic stress resistance of plants, so as to ensure sustainable agricultural production. In this regard, we focus on the recent updates on miRNAs and their targets involved in responding to abiotic stress including low temperature, high temperature, drought, soil salinity, and heavy metals, as well as plant-growing development. In particular, this review highlights the diverse functions of miRNAs on achieving the desirable agronomic traits in important crops. Herein, the main research strategies of miRNAs involved in abiotic stress resistance and crop traits improvement were summarized. Furthermore, the miRNA-related challenges and future perspectives of plants have been discussed. miRNA-based research lays the foundation for exploring miRNA regulatory mechanism, which aims to provide insights into a potential form of crop improvement and stress resistance breeding.

Understanding the Molecular Mechanisms of Betel miRNAs on Human Health

BACKGROUND

Since ancient times, "betel leaf" (Piper betle) has been revered for its religious, cultural, and medicinal properties. Phytochemicals from the Piper betle are effective in a variety of conditions, including cancer. To date, however, no genomic study or evidence has been found to elucidate the regulatory mechanism that underpins its therapeutic properties. This is the first study of its kind to predict Piper betle miRNAs and also the first genomics source representation of Piper betle. According to previous research, miRNAs from the plants we eat can regulate gene expression. In line with this, our in-silico study revealed that Piper betle and human cross-kingdom control occurs.

METHOD

This study demonstrates the prediction and in-silico validation of Piper betle miRNAs from NGS-derived transcript sequences. The cross-kingdom regulation which can also be understood as inter-species RNA regulation was studied to identify human mRNA targets being controlled by Piper betle miRNAs. Functional annotation and gene-disease association of human targets were performed to understand the role of Piper betle miRNAs in human health and disease. The protein-protein interaction and expression study of targets was further carried out to decipher their role in cancer development.

RESULTS

Identified six Piper betle miRNAs belonging to miR156, miR164, miR172, and miR535 families were discovered to target 198 human mRNAs involved in various metabolic and disease processes. Angiogenesis and the cell surface signaling pathway were the most enriched gene ontology correlated with targets, both of which play a critical role in disease mechanisms, especially in the case of carcinoma. In an analysis of gene-disease interactions, 40 genes were found to be related to cancer. According to a protein-protein interaction, the CDK6 gene, which is thought to be a central regulator of cell cycle progression, was found as a hub protein, affecting the roles of CBFB, SAMD9, MDM4, AXIN2, and NOTCH2 onco genes. Further investigation revealed that pbe-miRNA164a can be used as a regulator to minimise disease severity in Acute Myeloid Leukemia, where CDK6 expression is highest compared to normal cells.

CONCLUSION

The predicted pbe-miRNA164a in this study can be a promising suppressor of CDK6 gene involved in tumour angiogenesis. In vivo validation of the pbe-miRNA164a mimic could pave the way for new opportunities to fight cancer and leverage the potential of Piper betle in the healthcare sector.

Genome-wide investigation of microRNAs and expression profiles during rhizome development in ginger (Zingiber officinale Roscoe)

BACKGROUND

MicroRNAs (miRNAs) are endogenous, non-coding small functional RNAs that govern the post-transcriptional regulatory system of gene expression and control the growth and development of plants. Ginger is an herb that is well-known for its flavor and medicinal properties. The genes involved in ginger rhizome development and secondary metabolism have been discovered, but the genome-wide identification of miRNAs and their overall expression profiles and targets during ginger rhizome development are largely unknown. In this study, we used BGISEQ-500 technology to perform genome-wide identification of miRNAs from the leaf, stem, root, flower, and rhizome of ginger during three development stages.

RESULTS

In total, 104 novel miRNAs and 160 conserved miRNAs in 28 miRNA families were identified. A total of 181 putative target genes for novel miRNAs and 2772 putative target genes for conserved miRNAs were predicted. Transcriptional factors were the most abundant target genes of miRNAs, and 17, 9, 8, 4, 13, 8, 3 conserved miRNAs and 5, 7, 4, 5, 5, 15, 9 novel miRNAs showed significant tissue-specific expression patterns in leaf, stem, root, flower, and rhizome. Additionally, 53 miRNAs were regarded as rhizome development-associated miRNAs, which mostly participate in metabolism, signal transduction, transport, and catabolism, suggesting that these miRNAs and their target genes play important roles in the rhizome development of ginger. Twelve candidate miRNA target genes were selected, and then, their credibility was confirmed using qRT-PCR. As the result of qRT-PCR analysis, the expression of 12 candidate target genes showed an opposite pattern after comparison with their miRNAs. The rhizome development system of ginger was observed to be governed by miR156, miR319, miR171a_2, miR164, and miR529, which modulated the expression of the SPL, MYB, GRF, SCL, and NAC genes, respectively.

CONCLUSION

This is a deep genome-wide investigation of miRNA and identification of miRNAs involved in rhizome development in ginger. We identified 52 rhizome-related miRNAs and 392 target genes, and this provides an important basis for understanding the molecular mechanisms of the miRNA target genes that mediate rhizome development in ginger.

MicroRNAs Are Involved in Regulating Plant Development and Stress Response through Fine-Tuning of TIR1/AFB-Dependent Auxin Signaling

Auxin, primarily indole-3-acetic acid (IAA), is a versatile signal molecule that regulates many aspects of plant growth, development, and stress response. Recently, microRNAs (miRNAs), a type of short non-coding RNA, have emerged as master regulators of the auxin response pathways by affecting auxin homeostasis and perception in plants. The combination of these miRNAs and the autoregulation of the auxin signaling pathways, as well as the interaction with other hormones, creates a regulatory network that controls the level of auxin perception and signal transduction to maintain signaling homeostasis. In this review, we will detail the miRNAs involved in auxin signaling to illustrate its in planta complex regulation.

Identification of Long Non-coding RNA Transcripts in Glycyrrhiza uralensis

Background:

Chinese liquorice (Glycyrrhiza uralensis), an important medicinal plant, contains various valuable secondary metabolites. Secondary metabolites biosynthesis is very tightly regulated; therefore, elucidation and manipulation of the biosynthetic pathways are of great interest. Recent studies have shown that lncRNAs play important regulatory roles in many biological processes, thus identification and modification of their expression is essential to metabolic pathways for biosynthesis of secondary metabolites.

Objectives:

In this study we attempted to identify non-coding RNA transcripts (lncRNAs) that may act as important regulators of diverse biological processes, including stress responses and developmental programs in Glycyrrhiza uralensis.

Materials and Methods:

Identification of potential lncRNAs in Chinese liquorice was performed using a bioinformatics pipeline from the available EST dataset of G. uralensis.

Results:

Bioinformatics analysis revealed that 1365 identical sequences in the range of 200 to 1286 base pair are putative lncRNAs. Only less than one percent of the predicted lncRNAs display sequence conservation with lncRNAs from other species. Moreover, 13 lncRNAs were detected as the potential precursors of 16 miRNAs. From this analysis, we also detected possible target genes of 16 known miRNA genes. The majority of the predicted miRNA target genes have important role in response to plant disease and a couple of them contribute to signalling and metabolic pathways.

Conclusion:

This study demonstrates the existence of lncRNAs in G. uralensis which has not been found before and provides valuable resources for further understanding and characterizing of lncRNAs and also a basis for additional investigation to reveal specific roles of lncRNAs in various biological processes and particularly in response to plant diseases.

Plant RNA-mediated gene regulatory network

Not all transcribed RNAs are protein-coding RNAs. Many of them are non-protein-coding RNAs in diverse eukaryotes. However, some of them seem to be non-functional and are resulted from spurious transcription. A lot of non-protein-coding transcripts have a significant function in the translation process. Gene expressions depend on complex networks of diverse gene regulatory pathways. Several non-protein-coding RNAs regulate gene expression in a sequence-specific system either at the transcriptional level or post-transcriptional level. They include a significant part of the gene expression regulatory network. RNA-mediated gene regulation machinery is evolutionarily ancient. They well-evolved during the evolutionary time and are becoming much more complex than had been expected. In this review, we are trying to summarizing the current knowledge in the field of RNA-mediated gene silencing.

Global expression dynamics and miRNA evolution profile govern floral/fiber architecture in the modern cotton (Gossypium)

Majority of differentially expressed miRNAs with functional attributes have been recruited independently and parallelly during allopolyploidy followed by the millennia of human selection of both domesticated G. hirsutum and G. barbadense. The genus Gossypium is a marvelous evolutionary model for studying allopolyploidy and morpho-evolution of long-spinnable fibers from the ancestral wild-fuzz. Many genes, transcription factors, and notably, the regulatory miRNAs essentially govern such remarkable modern fiber phenotypes. To comprehend the impact of allopolyploidy on the evolutionary selection of transcriptional dynamicity of key miRNAs, comparative transcriptome profiling of vegetative and fiber tissues of domesticated diploid G. arboreum (A₂) and allopolyploid cotton species G. hirsutum (AD₁), and G. barbadense (AD₂) identified > 300 differentially expressed miRNAs (DEmiRs) within or between corresponding tissues of A₂, AD₁ and AD₂ species. Up to 49% and 32% DEmiRs were up- and down-regulated at fiber initiation stage of AD₁ and AD₂ species, respectively, whereas 50% and 18% DEmiRs were up- and down-regulated at fiber elongation stage of both the allopolyploid species. Interestingly, A-subgenome-specific DEmiRs exhibit expression dominance in the allopolyploid genetic backgrounds. Comparative spatio-temporal expression analyses of AD₁ and AD₂ species discovered that a majority of DEmiRs were recruited independently under millennia of human selection during domestication. Functional annotations of these DEmiRs revealed selection of associated molecular functions such as hormone-signaling, calcium-signaling and reactive oxygen species (ROS) signaling during fiber initiation and elongation. To validate the functional attributes of annotated DEmiRs, we demonstrated for the first time that the target-mimicry-based constitutive diminution of auxin-signaling associated miR167 directly affected the differentiation of floral and fiber tissues of transgenic cotton. These results strongly suggested that the evolutionarily favored DEmiRs including miR167 were involved in the transcriptional regulation of numerous genes during cotton evolution for enhanced fiber-associated agronomic traits.

One vector-based method to verify predicted plant miRNAs, target sequences, and function modes

Many microRNAs (miRNAs) have been predicted from small RNA sequencing data, but little was experimentally verified due to the lack of effective methods. Here, we developed a simple and reliable dual gene expression cassette vector-based method to verify predicted plant miRNAs. We cloned osa-miR528 as a known miRNA, hvu-miRX as a predicted miRNA and TaDREB3 open reading frame as a non-miRNA into the first gene expression cassette and fused their complementary or noncomplementary sequences as predicted target or nontarget sequences with the 3' untranslated region of green fluorescent protein (GFP) in the second one. When these constructs were bombarded into plant cells, only the construct containing both osa-miR528 or hvu-miRX and its complementary sequence did not generate green fluorescence. Stem-loop reverse-transcription polymerase chain reaction detected mature osa-miR528 or mature hvu-miRX in the cells, while northern analysis showed that GFP messenger RNA from the construct containing both osa-miR528 or hvu-miRX and its complementary sequence was degraded. Taken together, the results indicate that hvu-miRX is an authentic miRNA like osa-miR528, miRNA's complementary sequence is its target sequence, and both osa-miR528 and hvu-miRX silenced the GFP expression via a cleavage mode. Our method thus facilitates the verification of predicted plant miRNAs, target sequences, and function modes.

Hydrogen Sulfide Alleviates Alkaline Salt Stress by Regulating the Expression of MicroRNAs in Malus hupehensis Rehd. Roots

Malus hupehensis Rehd. var. pingyiensis Jiang (Pingyi Tiancha, PYTC) is an excellent apple rootstock and ornamental tree, but its tolerance to salt stress is weak. Our previous study showed that hydrogen sulfide (H₂S) could alleviate damage in M. hupehensis roots under alkaline salt stress. However, the molecular mechanism of H₂S mitigation alkaline salt remains to be elucidated. MicroRNAs (miRNAs) play important regulatory roles in plant response to salt stress. Whether miRNAs are involved in the mitigation of alkaline salt stress mediated by H₂S remains unclear. In the present study, through the expression analysis of miRNAs and target gene response to H₂S and alkaline salt stress in M. hupehensis roots, 115 known miRNAs (belonging to 37 miRNA families) and 15 predicted novel miRNAs were identified. In addition, we identified and analyzed 175 miRNA target genes. We certified the expression levels of 15 miRNAs and nine corresponding target genes by real-time quantitative PCR (qRT-PCR). Interestingly, H₂S pretreatment could specifically induce the downregulation of mhp-miR408a expression, and upregulated mhp-miR477a and mhp-miR827. Moreover, root architecture was improved by regulating the expression of mhp-miR159c and mhp-miR169 and their target genes. These results suggest that the miRNA-mediated regulatory network participates in the process of H₂S-mitigated alkaline salt stress in M. hupehensis roots. This study provides a further understanding of miRNA regulation in the H₂S mitigation of alkaline salt stress in M. hupehensis roots.

Computational Identification of miRNAs and Temperature-Responsive lncRNAs From Mango (Mangifera indica L.)

Mango is a major tropical fruit in the world and is known as the king of fruits because of its flavor, aroma, taste, and nutritional values. Although various regulatory roles of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) have been investigated in many plants, there is yet an absence of such study in mango. This is the first study to provide information on non-coding RNAs (ncRNAs) of mango with the aims of identifying miRNAs and lncRNAs and discovering their potential functions by interaction prediction of the miRNAs, lncRNAs, and their target genes. In this analysis, about a hundred miRNAs and over 7,000 temperature-responsive lncRNAs were identified and the target genes of these ncRNAs were characterized. According to these results, the newly identified mango ncRNAs, like other plant ncRNAs, have a potential role in biological and metabolic pathways including plant growth and developmental process, pathogen defense mechanism, and stress-responsive process. Moreover, mango lncRNAs can target miRNAs to reduce the stability of lncRNAs and can function as molecular decoys or sponges of miRNAs. This paper would provide information about miRNAs and lncRNAs of mango and would help for further investigation of the specific functions of mango ncRNAs through wet lab experiments.

Role of miRNAs in the host-pathogen interaction between sugarcane and Colletotrichum falcatum, the red rot pathogen

Sugarcane microRNAs specifically involved during compatible and incompatible interactions with red rot pathogen Colletotrichum falcatum were identified. We have identified how the miRNAs regulate their gene targets and elaborated evidently on the underlying molecular mechanism of sugarcane defense response to C. falcatum for the first time. Resistance against the fungal pathogen Colletotrichum falcatum causing red rot is one of the most desirable traits for sustainable crop cultivation in sugarcane. To gain new insight into the host defense mechanism against C. falcatum, we studied the role of sugarcane microRNAs during compatible and incompatible interactions by adopting the NGS platform. We have sequenced a total of 80 miRNA families that comprised 980 miRNAs, and the putative targets of the miRNAs include transcription factors, membrane-bound proteins, glutamate receptor proteins, lignin biosynthesis proteins, signaling cascade proteins, transporter proteins, mitochondrial proteins, ER proteins, defense-related, stress response proteins, translational regulation proteins, cell proliferation, and ubiquitination proteins. Further, qRT-PCR analyses of 8 differentially regulated miRNAs and 26 gene transcript targets expression indicated that these miRNAs have a regulatory effect on the expression of respective target genes in most of the cases. Also, the results suggest that certain miRNA regulates many target genes that are involved in inciting early responses to the pathogen infection, signaling pathways, endoplasmic reticulum stress, and resistance gene activation through feedback response from various cellular processes during the compatible and incompatible interaction with the red rot pathogen C. falcatum. The present study revealed the role of sugarcane miRNAs and their target genes during sugarcane-C. falcatum interaction and provided new insight into the miRNA-mediated defense mechanism in sugarcane for the first time.

In silico identification of conserved miRNAs in the genome of fibre biogenesis crop Corchorus capsularis

Corchorus capsularis, commonly known as jute occupies the leading position in the production of natural fibre alongside lower environmental threat. Small noncoding ~21 to 24 nucleotides long microRNAs play significant roles in regulating the gene expression as well as different functions in cellular growth and development. Here, the study adopted a comprehensive in silico approach to identify and characterize the conserved miRNAs in the genome of C. capsularis including functional annotation of specific gene targets. Expressed Sequence Tags (ESTs) based homology search of 3350 known miRNAs of dicotyledons were allowed against 763 non-redundant ESTs of jute genome, resulted in the prediction of 5 potential miRNA candidates belonging five different miRNA families (miR1536, miR9567-3p, miR4391, miR11300, and miR8689). The putative miRNAs were composed of 18 nucleotides having a range of -0.49 to -1.56 MFEI values and 55%–61% of (A + U) content in their pre-miRNAs. A total of 1052 gene targets of putative miRNAs were identified and their functions were extensively analyzed. Most of the gene targets were involved in plant growth, cell cycle regulation, organelle synthesis, developmental process and environmental responses. Five gene targets, namely, NAC Domain Containing Protein, WRKY DNA binding protein, 3-dehydroquinate synthase, S-adenosyl-L-Met–dependent methyl transferase and Vascular-related NAC-Domain were found to be involved in the lignin biosynthesis, phenylpropanoid pathways and secondary wall formation. The present study might accelerate the more miRNA discovery, strengthening the complete understanding of miRNAs association in the cellular basis of lignin biosynthesis towards the production of high standard jute products.

Novel approaches on identification of conserved miRNAs for broad-spectrum Potyvirus control measures

Potyviridae comprises more than 200 ssRNA viruses, many of which have a broad host range and geographical distributions. Potyvirids (members of Potyviridae) infect several economically important plants such as saffron, cardamom, cucumber, pepper, potato, tomato, yam, etc. Cumulatively, potyvirids cause a substantial economic loss. The major bottleneck in developing an efficient antiviral strategy is that viruses quickly evade host immunity owing to their higher mutation and recombination rates. Due to this reason, the emergence of newer and improved broad-spectrum approaches to combat viral infections is essential. The use of microRNA's (miRNA) to circumvent viral infection against animal viruses has been successfully employed. Fewer studies reported the development of efficient miRNA-based antivirus resistant strategies against plant viruses and none focused on multiple virus resistance. We focused on potyviruses since studies are limited and identification of conserved miRNAs among various host plants would be an initiative to design broad-spectrum antivirus strategies. In this study, we predicted evolutionarily conserved miRNAs by BLAST searching of reported miRNAs from 15 plants against the GSS and EST sequences of banana. A total of nine miRNAs were predicted and screened in nine diverse potyvirids' hosts (Banana, Tomato, Green gram, Jasmine, Chilli, Coriander, Onion, Rose and Colocasia) belonging to eight different orders (Zingiberales, Solanales, Fabales, Lamiales, Apiales, Asperagales, Rosales and Alismatales). Results suggested that miR168 and miR162 are conserved among all the selected plants. This comprehensive study laid the foundations to design broad-spectrum antivirus resistance using miRNAs. To conclude miR168 and miR162 are conserved among many plants and play a crucial role in evading virus infection which could be used as a potential candidate for developing antiviral strategies against potyvirid infections.

Study of expressions of miRNAs in the spikelets based on their spatial location on panicle in rice cultivars provided insight into their influence on grain development

Development of rice cultivars bearing numerous spikelets by breeding approach to increase the yearly production of rice to approximately 800 million metric tons to feed the ever increasing population of the world accompanies poor grain filling in the inferior spikelets preventing achievement of the yield potential. As the initial stages of caryopses development are of much importance for grain filling, spatio-temporal expressions of the miRNAs were studied during these periods in the spikelets of a compact-panicle rice cultivar, Oryza sativa cv. Mahalaxmi, bearing numerous spikelets per panicle to understand the reason of poor grain filling at the level of the initial biochemical events. Differential expression of several known miRNAs between the superior and inferior spikelets suggested great difference in metabolism related to grain filling in the spikelets based on their spatial location on compact panicle. Expressions of five known and four novel miRNAs were validated by Northern. Their targets included the enzymes directly involved in starch biosynthesis like sucrose synthase, starch synthase and pullulanase, besides others. Spatio-temporal expression studies of these miRNAs in the spikelets of Mahalaxmi revealed a pattern of mostly a greater expression in the inferior spikelets compared with the superior ones concomitant with an inverse expression of the target genes, which was not observed in the lax-panicle cultivar Upahar. The study thus revealed that the grain filling in rice is greatly regulated by miRNAs, and these miRNAs or their target genes could be considered for biotechnological interventions for improving grain filling in the rice cultivars of interest.

The Critical Role of Small RNAs in Regulating Plant Innate Immunity

Plants, due to their sessile nature, have an innate immune system that helps them to defend against different pathogen infections. The defense response of plants is composed of a highly regulated and complex molecular network, involving the extensive reprogramming of gene expression during the presence of pathogenic molecular signatures. Plants attain proper defense against pathogens through the transcriptional regulation of genes encoding defense regulatory proteins and hormone signaling pathways. Small RNAs are emerging as versatile regulators of plant development and act in different tiers of plant immunity, including pathogen-triggered immunity (PTI) and effector-triggered immunity (ETI). The versatile regulatory functions of small RNAs in plant growth and development and response to biotic and abiotic stresses have been widely studied in recent years. However, available information regarding the contribution of small RNAs in plant immunity against pathogens is more limited. This review article will focus on the role of small RNAs in innate immunity in plants.

RNAi Mediated Hypoxia Stress Tolerance in Plants

Small RNAs regulate various biological process involved in genome stability, development, and adaptive responses to biotic or abiotic stresses. Small RNAs include microRNAs (miRNAs) and small interfering RNAs (siRNAs). MicroRNAs (miRNAs) are regulators of gene expression that affect the transcriptional and post-transcriptional regulation in plants and animals through RNA interference (RNAi). miRNAs are endogenous small RNAs that originate from the processing of non-coding primary miRNA transcripts folding into hairpin-like structures. The mature miRNAs are incorporated into the RNA-induced silencing complex (RISC) and drive the Argonaute (AGO) proteins towards their mRNA targets. siRNAs are generated from a double-stranded RNA (dsRNA) of cellular or exogenous origin. siRNAs are also involved in the adaptive response to biotic or abiotic stresses. The response of plants to hypoxia includes a genome-wide transcription reprogramming. However, little is known about the involvement of RNA signaling in gene regulation under low oxygen availability. Interestingly, miRNAs have been shown to play a role in the responses to hypoxia in animals, and recent evidence suggests that hypoxia modulates the expression of various miRNAs in plant systems. In this review, we describe recent discoveries on the impact of RNAi on plant responses to hypoxic stress in plants.

Whole Aegilops tauschii Transcriptome Investigation Revealed Nine Novel miRNAs Involved in Stress Response

Background:

Aegilops tauschii is a wild relative of bread wheat. This species has been reported as the donor of bread wheat D genome. There are also several reports that mentioned the importance of Ae. tauschii in biotic and abiotic stress tolerance. On the other hands, miRNAs have been reported as the essential regulatory elements in stress response.

Objective:

Therefore, it is important to discover novel miRNAs involved in stress tolerance in this species. The aim of the current study was to predict novel miRNAs in Ae. tauschii and also uncover their potential role in stress response.

Methods:

For this purpose, ESTs, TSAs, and miRBase databases were obtained and used to predict new miRNAs.

Results:

Our results discovered nine novel stem-loop miRNAs. These predicted miRNAs could be introduced as the new members of previously identified miRNA families in Ae. tauschii, including miR156, miR168, miR169, and miR319. The result indicating that miR397 and miR530 are novel families in this species. Furthermore, several novel stem-loop miRNAs predicted for T. aestivum showed remarkable similarities to novel Ae. tauschii stem-loops.

Conclusion:

Our results demonstrated that predicted novel miRNAs could play a significant role in stress response.

Genome wide in-silico miRNA and target network prediction from stress responsive Horsegram (Macrotyloma uniflorum) accessions

Horsegram (Macrotyloma uniflorum (Lam.) Verdc.) is a drought hardy food and fodder legume of Indo-African continents with diverse germplasm sources demonstrating alternating mechanisms depicting contrasting adaptations to different climatic zones. Tissue specific expression of genes contributes substantially to location specific adaptations. Regulatory networks of such adaptive genes are elucidated for downstream translational research. MicroRNAs are small endogenous regulatory RNAs which alters the gene expression profiles at a particular time and type of tissue. Identification of such small regulatory RNAs in low moisture stress hardy crops can help in cross species transfer and validation confirming stress tolerance ability. This study outlined prediction of conserved miRNAs from transcriptome shotgun assembled sequences and EST sequences of horsegram. We could validate eight out of 15 of the identified miRNAs to demonstrate their role in deficit moisture stress tolerance mechanism of horsegram variety Paiyur1 with their target networks. The putative mumiRs were related to other food legumes indicating the presence of gene regulatory networks. Differential miRNA expression among drought specific tissues indicted the probable energy conservation mechanism. Targets were identified for functional characterization and regulatory network was constructed to find out the probable pathways of post-transcriptional regulation. The functional network revealed mechanism of biotic and abiotic stress tolerance, energy conservation and photoperiod responsiveness.

Computational Identification and Comparative Analysis of Conserved miRNAs and Their Putative Target Genes in the Juglans regia and J. microcarpa Genomes

MicroRNAs (miRNAs) are important factors for the post-transcriptional regulation of protein-coding genes in plants and animals. They are discovered either by sequencing small RNAs or computationally. We employed a sequence-homology-based computational approach to identify conserved miRNAs and their target genes in Persian (English) walnut, Juglans regia, and its North American wild relative, J. microcarpa. A total of 119 miRNA precursors (pre-miRNAs) were detected in the J. regia genome and 121 in the J. microcarpa genome and miRNA target genes were predicted and their functional annotations were performed in both genomes. In the J. regia genome, 325 different genes were targets; 87.08% were regulated by transcript cleavage and 12.92% by translation repression. In the J. microcarpa genome, 316 different genes were targets; 88.92% were regulated by transcript cleavage and 11.08% were regulated by translation repression. Totals of 1.3% and 2.0% of all resistance gene analogues (RGA) and 2.7% and 2.6% of all transcription factors (TFs) were regulated by miRNAs in the J. regia and J. microcarpa genomes, respectively. Juglans genomes evolved by a whole genome duplication (WGD) and consist of eight pairs of fractionated homoeologous chromosomes. Within each pair, the chromosome that has more genes with greater average transcription also harbors more pre-miRNAs and more target genes than its homoeologue. While only minor differences were detected in pre-miRNAs between the J. regia and J. microcarpa genomes, about one-third of the pre-miRNA loci were not conserved between homoeologous chromosome within each genome. Pre-miRNA and their corresponding target genes showed a tendency to be collocated within a subgenome.

miRDetect: A combinatorial approach for automated detection of novel miRNA precursors from plant EST data using homology and Random Forest classification

Identification of microRNAs from plants is a crucial step for understanding the mechanisms of pathways and regulation of genes. A number of tools have been developed for the detection of microRNAs from small RNA-seq data. However, there is a lack of pipeline for detection of miRNA from EST dataset even when a huge resource is publicly available and the method is known. Here we present miRDetect, a python implementation to detect novel miRNA precursors from plant EST data using homology and machine learning approach. 10-fold cross validation was applied to choose best classifier based on ROC, accuracy, MCC and F1-scores using 112 features. miRDetect achieved a classification accuracy of 93.35% on a Random Forest classifier and outperformed other precursor detection tools in terms of performance. The miRDetect pipeline aids in identifying novel plant precursors using a mixed approach and will be helpful to researchers with less informatics background.

Identification of novel microRNAs and their targets in Chlorophytum borivilianum by small RNA and degradome sequencing

Plant specific miRNAs (Novel miRNAs) are well known to perform distinctive functions in biological processes. Identification of new miRNAs is necessary to understand their gene regulation. Degradome provides an opportunity to explore the miRNA functions by comparing the miRNA population and their degraded products. In the present study, Small RNA sequencing data was used to identify novel miRNAs. Further, degradome sequencing was carried out to identify miRNAs targets in the plant, Chlorophytum borivilianum. The present study supplemented 40 more novel miRNAs correlating degradome data with smallRNAome. Novel miRNAs, complementary to mRNA partial sequences obtained from degradome sequencing were actually targeting the later. A big pool of miRNA was established by using Oryza sativa, Arabidopsis thaliana, Populus trichocarpa, Ricinus communis, and Vitis vinifera genomic data. Targets were identified for novel miRNAs and total 109 targets were predicted. BLAST2GO analysis elaborate about localization of novel miRNAs’ targets and their corresponding KEGG (Kyoto Encyclopedia for Genes and Genomes) pathways. Identified targets were annotated and were found to be involved in significant biological processes like Nitrogen metabolism, Pyruvate metabolism, Citrate cycle (TCA cycle), photosynthesis, and Glycolysis/Gluconeogenesis. The present study provides an overall view of the miRNA regulation in multiple metabolic pathways that are involved in plant growth, pathogen resistance and secondary metabolism of C. borivilianum.

A novel computational approach to the silencing of Sugarcane Bacilliform Guadeloupe A Virus determines potential host-derived MicroRNAs in sugarcane (Saccharum officinarum L.)

Sugarcane Bacilliform Guadeloupe A Virus (SCBGAV, genus Badnavirus, family Caulimoviridae) is an emerging, deleterious pathogen of sugarcane which presents a substantial barrier to producing high sugarcane earnings. Sugarcane bacilliform viruses (SCBVs) are one of the main species that infect sugarcane. During the last 30 years, significant genetic changes in SCBV strains have been observed with a high risk of disease incidence associated with crop damage. SCBV infection may lead to significant losses in biomass production in susceptible sugarcane cultivars. The circular, double-stranded (ds) DNA genome of SCBGAV (7.4 Kb) is composed of three open reading frames (ORFs) on the positive strand that replicate by a reverse transcriptase. SCBGAV can infect sugarcane in a semipersistent manner via the insect vectors sugarcane mealybug species. In the current study, we used miRNA target prediction algorithms to identify and comprehensively analyze the genome-wide sugarcane (Saccharum officinarum L.)-encoded microRNA (miRNA) targets against the SCBGAV. Mature miRNA target sequences were retrieved from the miRBase (miRNA database) and were further analyzed for hybridization to the SCBGAV genome. Multiple computational approaches—including miRNA-target seed pairing, multiple target positions, minimum free energy, target site accessibility, maximum complementarity, pattern recognition and minimum folding energy for attachments—were considered by all algorithms. Among them, sof-miR396 was identified as the top effective candidate, capable of targeting the vital ORF3 of the SCBGAV genome. miRanda, RNA22 and RNAhybrid algorithms predicted hybridization of sof-miR396 at common locus position 3394. The predicted sugarcane miRNAs against viral mRNA targets possess antiviral activities, leading to translational inhibition by mRNA cleavage. Interaction network of sugarcane-encoded miRNAs with SCBGAV genes, created using Circos, allow analyze new targets. The finding of the present study acts as a first step towards the creation of SCBGAV-resistant sugarcane through the expression of the identified miRNAs.

Small RNAs in eucaryotes: new clues for amplifying microRNA benefits

miRNAs, the smallest nucleotide molecules able to regulate gene expression at post transcriptional level, are found in both animals and plants being involved in fundamental processes for growth and development of living organisms. The number of miRNAs has been hypothesized to increase when some organisms specialized the process of mastication and grinding of food. Further to the vertical transmission, miRNAs can undergo horizontal transmission among different species, in particular between plants and animals. In the last years, an increasing number of studies reported that miRNA passage occurs through feeding, and that in animals, plant miRNAs can survive the gastro intestinal digestion and transferred by blood into host cells, where they can exert their functions modulating gene expression. The present review reports studies on miRNAs during evolution, with particular focus on biogenesis and mechanisms regulating their stability in plants and animals. The different biogenesis and post biogenesis modifications allow to discriminate miRNAs of plant origin from those of animal origin, and make it possible to better clarify the controversial question on whether a possible cross-kingdom miRNA transfer through food does exist. The majority of human medicines and supplements derive from plants and a regular consumption of plant food is suggested for their beneficial effects in the prevention of metabolic diseases, cancers, and dietary related disorders. So far, these beneficial effects have been generally attributed to the content of secondary metabolites, whereas mechanisms regarding other components remain unclear. Therefore, in light of the above reported studies miRNAs could result another component for the medical properties of plants. miRNAs have been mainly studied in mammals characterizing their sequences and molecular targets as available in public databases. The herein presented studies provide evidences that miRNA situation is much more complex than the static situation reported in databases. Indeed, miRNAs may have redundant activities, variable sequences, different methods of biogenesis, and may be differently influenced by external and environmental factors. In-depth knowledge of mechanisms of synthesis, regulation and transfer of plant miRNAs to other species can open new frontiers in the therapy of many human diseases, including cancer.

The interplay between miR156/SPL13 and DFR/WD40-1 regulate drought tolerance in alfalfa

BACKGROUND

Developing Medicago sativa L. (alfalfa) cultivars tolerant to drought is critical for the crop's sustainable production. miR156 regulates various plant biological functions by silencing SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors.

RESULTS

To understand the mechanism of miR156-modulated drought stress tolerance in alfalfa we used genotypes with altered expression levels of miR156, miR156-regulated SPL13, and DIHYDROFLAVONOL-4-REDUCTASE (DFR) regulating WD40-1. Previously we reported the involvement of miR156 in drought tolerance, but the mechanism and downstream genes involved in this process were not fully studied. Here we illustrate the interplay between miR156/SPL13 and WD40-1/DFR to regulate drought stress by coordinating gene expression with metabolite and physiological strategies. Low to moderate levels of miR156 overexpression suppressed SPL13 and increased WD40-1 to fine-tune DFR expression for enhanced anthocyanin biosynthesis. This, in combination with other accumulated stress mitigating metabolites and physiological responses, improved drought tolerance. We also demonstrated that SPL13 binds in vivo to the DFR promoter to regulate its expression.

CONCLUSIONS

Taken together, our results reveal that moderate relative miR156 transcript levels are sufficient to enhance drought resilience in alfalfa by silencing SPL13 and increasing WD40-1 expression, whereas higher miR156 overexpression results in drought susceptibility.

In silico determination of transposon-derived miRNAs and targets in Aegilops species

Transposable elements (TEs) are found almost in all living organism, shaping organisms' genomes. miRNAs are noncoding RNA types which are especially important in gene expression regulations. Many previously determined plant miRNAs are identical/homologous to transposons (TE-MIR). The aim of this study was computational characterization of novel TE-related miRNAs and their targets in Aegilops genome by using stringent criteria. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed by BLAST2GO. Seventeen novel TE-related miRNAs in Aegilops genome were identified for the first time. GO analyses indicated that 40 targets played different roles in biological processes, cellular components and molecular functions. Moreover, these genes were involved in 10 metabolic pathways such as purine metabolism, nitrogen metabolism, oxidative phosphorylation, etc. as a result of KEGG analyses. Identification of miRNAs and their targets are significant to understand miRNA-TEs relationships and even how TEs affect plant growth and development. Obtaining results of this study are expected to provide possible new insight into Aegilops and its related species, wheat, with respect to miRNAs evolution and domestication.Communicated by Ramaswamy H. Sarma.

Cytotoxic and apoptotic effects of different extracts of Moringa oleifera Lam on lymphoid and monocytoid cells

Moringa oleifera Lam. (MO) is one of the most well-known and widely distributed species of the Moringaceae family in African communities, and various preparations of M. oleifera are used for the treatment of several diseases. Due to the extensive worldwide use of MO products, and the use of MO aqueous extract in traditional African medicine, the aim of the present study was to investigate the anti-proliferative, cytotoxic and pro-apoptotic activities of different aqueous extracts from leaves and seeds of M. oleifera (MOE), which have been prepared using different protocols, in lymphoid and monocytoid cells. The results of the present study demonstrated the anti-proliferative and pro-apoptotic effects of the aqueous extracts obtained from M. oleifera leaves and seeds on tumour cells; however, not on peripheral blood mononuclear cells (PBMCs) from healthy donors. The pro-apoptotic effect of MO seed aqueous extract (MOE-S) was correlated with decreased B-cell lymphoma 2 (BCL2) and sirtuin-1 (SIRT1) protein expression, which are involved in apoptosis. Considering the effects of plant secondary metabolites on human cells and the role of plant microRNA in cross-kingdom interactions, the presence of secondary metabolites and microRNA in MOE was characterised. In conclusion, M. oleifera aqueous extracts appeared to be able to differentially regulate proliferation and apoptosis in healthy cells and cancer cells, and this ability could be associated with the microRNA present in the extracts. These results highlighted the possible use of MOE as an adjuvant in traditional cancer therapy.

Stress-responsive miRNAome of Glycine max (L.) Merrill: molecular insights and way forward

MAIN CONCLUSION

Analysis of stress-associated miRNAs of Glycine max (L.) Merrill reveals wider ramifications of small RNA-mediated (conserved and legume-specific miRNAs) gene regulatory foot prints in molecular adaptive responses. MicroRNAs (miRNAs) are indispensable components of gene regulatory mechanism of plants. Soybean is a crop of immense commercial potential grown worldwide for its edible oil and soy meal. Intensive research efforts, using the next generation sequencing and bioinformatics techniques, have led to the identification and characterization of numerous small RNAs, especially microRNAs (miRNAs), in soybean. Furthermore, studies have unequivocally demonstrated the significance of miRNAs during the developmental processes and various stresses in soybean. In this review, we summarize the current state of understanding of miRNA-based abiotic and biotic stress responses in soybean. In addition, the molecular insights gained from the stress-related soybean miRNAs have been compared to the miRNAs of other crops, especially legumes, and the core commonalities have been highlighted, though differences among them were not ignored. Nature of response of soybean-derived conserved miRNAs during various stresses was also analyzed to gain deeper insights regarding sRNAome-based defense responses. This review further provides way forward in legume small RNA transcriptomics based on the adaptive responses of soybean and other legume-derived miRNAs.

Identification and characterization of drought responsive miRNAs in a drought tolerant upland rice cultivar KMJ 1-12-3

Shortfall of rain that creates drought like situation in non-irrigated agriculture system often limits rice production, necessitating introduction of drought tolerance trait into the cultivar of interest. The mechanism governing drought tolerance is, however, largely unknown, particularly the involvement of miRNAs, the master regulators of biochemical events. In this regard, response study on a drought tolerant rice variety KMJ 1-12-3 to 20% PEG (osmolality- 315 mOsm/kg) as drought stress revealed significant changes in abundance of several conserved miRNAs targeting transcription factors like homeodomain-leucine zipper, MADS box family protein, C2H2 zinc finger protein and Myb, well known for their importance in drought tolerance in plants. The response study also revealed significant PEG-induced decrease in abundance of the miRNAs targeting cyclin A, cyclin-dependent kinase, guanine nucleotide exchange factor, GTPase-activating protein, 1-aminocyclopropane-1-carboxylic acid oxidase and indole-3-acetic beta-glucosyl transferase indicating miRNA-regulated role of the cell cycle regulators, G-protein signalling and the plant hormones ethylene and IAA in drought tolerance in plants. The study confirmed the existence of four novel miRNAs, including osa-miR12470, osa-miR12471, osa-miR12472 and osa-miR12473, and the targets of three of them could be successfully validated. The PEG-induced decrease in abundance of the novel miRNAs osa-miR12470 and osa-miR12473 targeting RNA dependent RNA polymerase and equilibrative nucleoside transporter, respectively suggested an overall increase in both degradation and synthesis of nucleic acids in plants challenged with drought stress. The drought-responsive miRNAs identified in the study may be proved useful in introducing the trait in the rice cultivars of choice by manipulation of their cellular abundance.

Exploring miRNAs for developing climate-resilient crops: A perspective review

Climate changes and environmental stresses have significant implications on global crop production and necessitate developing crops that can withstand an array of climate changes and environmental perturbations such as irregular water-supplies leading to drought or water-logging, hyper soil-salinity, extreme and variable temperatures, ultraviolet radiations and metal stress. Plants have intricate molecular mechanisms to cope with these dynamic environmental changes, one of the most common and effective being the reprogramming of expression of stress-responsive genes. Plant microRNAs (miRNAs) have emerged as key post-transcriptional and translational regulators of gene-expression for modulation of stress implications. Recent reports are establishing their key roles in epigenetic regulations of stress/adaptive responses as well as in providing plants genome-stability. Several stress responsive miRNAs are being identified from different crop plants and miRNA-driven RNA-interference (RNAi) is turning into a technology of choice for improving crop traits and providing phenotypic plasticity in challenging environments. Here we presents a perspective review on exploration of miRNAs as potent targets for engineering crops that can withstand multi-stress environments via loss-/gain-of-function approaches. This review also shed a light on potential roles plant miRNAs play in genome-stability and their emergence as potent target for genome-editing. Current knowledge on plant miRNAs, their biogenesis, function, their targets, and latest developments in bioinformatics approaches for plant miRNAs are discussed. Though there are recent reviews discussing primarily the individual miRNAs responsive to single stress factors, however, considering practical limitation of this approach, special emphasis is given in this review on miRNAs involved in responses and adaptation of plants to multi-stress environments including at epigenetic and/or epigenomic levels.

In Silico Identification of Conserved MiRNAs from Physcomitrella patens ESTs and their Target Characterization

Background:

MicroRNAs (miRNAs) are groups of small non-protein-coding endogenous single stranded RNAs with approximately 18-24 nucleotides in length. High evolutionary sequence conservation of miRNAs among plant species and availability of powerful computational tools allow identification of new orthologs and paralogs.

Methods:

New conserved miRNAs in P. patens were found by EST-based homology search approaches. All candidates were screened according to a series of miRNA filtering criteria. Unigene, DFCI Gene Index (PpspGI) databases and psRNATarget algorithm were applied to identify target transcripts using P. patens putative conserved miRNA sequences.

Results:

Nineteen conserved P. patens miRNAs were identified. The sequences were homologous to known reference plant mature miRNA from 10 miRNA families. They could be folded into the typical miRNA secondary structures. RepeatMasker algorithm demonstrated that ppt-miR2919e and pptmiR1533 had simple sequence repeats in their sequences. Target sites (49 genes) were identified for 7 out of 19 miRNAs. GO and KEGG analysis of targets indicated the involvement of some in important multiple biological and metabolic processes.

Conclusion:

The majority of the registered miRNAs in databases were predicted by computational approaches while many more have remained unknown. Due to the conserved nature of miRNAs in plant species from closely to distantly related, homology search-based approaches between plants species could lead to the identification of novel miRNAs in other plant species providing baseline information for further search about the biological functions and evolution of miRNAs.

Genome-wide identification and profiling of microRNAs in Paulownia tomentosa cambial tissues in response to seasonal changes

MicroRNAs (miRNAs), a group of endogenous small non-coding RNAs, have been shown to play essential roles in the regulation of gene expression at the post-transcriptional level. Although Paulownia tomentosa is an ecologically and economically important timber species due to its rapid growth, few efforts have focused on small RNAs (sRNAs) in the cambial tissues during winter and summer transition. In the present study, we identified 33 known miRNA families and 29 novel miRNAs which include 20 putative novel miRNAs* in P. tomentosa cambial tissues during winter and summer transition. Through differential expression analysis, we showed that 15 known miRNAs and 8 novel miRNAs were preferentially abundant in certain stage of cambial tissues. Based on the P. tomentosa mRNA transcriptome database, 1667 and 78 potential targets were predicted for 29 known and 20 novel miRNAs, respectively and the predicted targets are mostly transcription factors and functional genes. The targets of these miRNAs were enriched in "metabolic process" and "transcription regulation" by using Gene Ontology enrichment analysis. In addition, KEGG pathway analyses revealed the involvement of miRNAs in starch and sucrose metabolism and plant-pathogen interaction metabolism pathways. Noticeably, qRT-PCR expression analysis demonstrated that 9 miRNAs and their targets were existed a negative correlation in P. tomentosa cambial tissues. This study is the first to examine known and novel miRNAs and their potential targets in P. tomentosa cambial tissues during winter and summer transition and identify several candidate genes potentially regulating cambial phase transition, and thus provide a framework for further understanding of miRNAs functions in the regulation of cambial phase transition and wood formation in trees.

New insights into tomato microRNAs

Cultivated tomato, Solanum lycopersicum, is one of the most common fruits in the global food industry. Together with the wild tomato Solanum pennellii, it is widely used for developing better cultivars. MicroRNAs affect mRNA regulation, inhibiting its translation and/or promoting its degradation. Important proteins involved in these processes are ARGONAUTE and DICER. This study aimed to identify and characterize the genes involved in the miRNA processing pathway, miRNA molecules and target genes in both species. We validated the presence of pathway genes and miRNA in different NGS libraries and 6 miRNA families using quantitative RT-PCR. We identified 71 putative proteins in S. lycopersicum and 108 in S. pennellii likely involved in small RNAs processing. Of these, 29 and 32 participate in miRNA processing pathways, respectively. We identified 343 mature miRNAs, 226 pre-miRNAs in 87 families, including 192 miRNAs, which were not previously identified, belonging to 38 new families in S. lycopersicum. In S. pennellii, we found 388 mature miRNAs and 234 pre-miRNAs contained in 85 families. All miRNAs found in S. pennellii were unpublished, being identified for the first time in our study. Furthermore, we identified 2471 and 3462 different miRNA target in S. lycopersicum and S. pennellii, respectively.