MicroRNAs in loblolly pine (Pinus taeda L.) and their association with fusiform rust gall development

Differential microRNA and Target Gene Expression in Scots Pine (Pinus sylvestris L.) Needles in Response to Methyl Jasmonate Treatment

Background/objectives: Methyl jasmonate is a plant signaling molecule involved in a wide range of functions, including stress responses. This study investigates the relative differential expression of microRNAs and their target genes in response to methyl jasmonate treatment of Scots pine needles. Methods: A combined strategy of high-throughput sequencing and in silico prediction of potential target genes was implemented. Results: a total of 58 differentially expressed (DE) microRNAs (miRNAs) (43 up-regulated and 15 down-regulated), belonging to 29 miRNA families, were identified. The 41 DE miRNAs from 17 families were conifer-specific miRNA families-miR946, miR947, miR950, miR1312, miR1313, miR1314, miR3693, miR3107, miR11452, miR11466, miR11487, miR11490, miR11504, miR11511, miR11532, miR11544, and miR11551. The other DE miRNAs (miR159, miR164, miR169, miR396, miR397, miR398, miR408, miR535) were conserved miRNAs, which are also found in angiosperm species. Transcriptome analysis identified 389 gene transcripts with 562 miRNA-target sites targeted by 57 of the 58 DE miRNAs. Of these, 250 target genes with 138 different GO annotations were found for the 41 DE conifer-specific conserved miRNAs. Conclusions: The 26 DE miRNAs from 14 DE miRNA families, of which almost all (12 families, 24 miRNAs) are conifer specific, and were associated with 68 disease resistance and TMV resistance proteins, TIR-NBS-LRR, LRR receptor-like serine/threonine-protein kinase, putative CC-NBS-LRR protein, and putative NBS-LRR protein target transcripts with 29 target gene GO term descriptions. Some of the genes targeted by conifer-specific miRNAs have been previously reported to be targeted by other miRNAs in angiosperms, indicating that the miRNA-target gene regulation system can vary between species.

Genome-Wide Identification and Characterization of miRNAs and Natural Antisense Transcripts Show the Complexity of Gene Regulatory Networks for Secondary Metabolism in Aristolochia contorta

Aristolochia contorta Bunge is an academically and medicinally important plant species. It belongs to the magnoliids, with an uncertain phylogenetic position, and is one of the few plant species lacking a whole-genome duplication (WGD) event after the angiosperm-wide WGD. A. contorta has been an important traditional Chinese medicine material. Since it contains aristolochic acids (AAs), chemical compounds with nephrotoxity and carcinogenicity, the utilization of this plant has attracted widespread attention. Great efforts are being made to increase its bioactive compounds and reduce or completely remove toxic compounds. MicroRNAs (miRNAs) and natural antisense transcripts (NATs) are two classes of regulators potentially involved in metabolism regulation. Here, we report the identification and characterization of 223 miRNAs and 363 miRNA targets. The identified miRNAs include 51 known miRNAs belonging to 20 families and 172 novel miRNAs belonging to 107 families. A negative correlation between the expression of miRNAs and their targets was observed. In addition, we identified 441 A. contorta NATs and 560 NAT-sense transcript (ST) pairs, of which 12 NATs were targets of 13 miRNAs, forming 18 miRNA-NAT-ST modules. Various miRNAs and NATs potentially regulated secondary metabolism through the modes of miRNA-target gene-enzyme genes, NAT-STs, and NAT-miRNA-target gene-enzyme genes, suggesting the complexity of gene regulatory networks in A. contorta. The results lay a solid foundation for further manipulating the production of its bioactive and toxic compounds.

The roles of miR156 in abiotic and biotic stresses in plants

MicroRNAs (miRNAs), known as a kind of non-coding RNA, can negatively regulate its target genes. To date, the roles of various miRNAs in plant development and resistance to abiotic and biotic stresses have been widely explored. The present review summarized and discussed the functions of miR156 or miR156-SPL module in abiotic and biotic stresses, such as drought, salt, heat, cold stress, UV-B radiation, heavy mental hazards, nutritional starvation, as well as plant viruses, plant diseases, etc. Based on this, the regulation of miR156-involved stress tolerance was better understood, thus, it would be much easier for plant biologists to carry out suitable strategies to help plants suffer from unfavorable living environments.

Genome-wide identification of xylan glucuronosyltransferase family in cotton and function characterization of GhGUX5 in regulating Verticillium wilt resistance

Xylan glucuronosyltransferase (GUX) is widely involved in a variety of physiological processes in plants, including plant development, growth and the defense response to pathogens. However, the function of GUX regulators in Verticillium dahliae (V. dahliae) infection has not been considered previously in cotton. Overall, 119 GUX genes were identified from multiple species and were phylogenetically categorized into seven classes. Duplication event analysis indicated that GUXs in Gossypium hirsutum primarily originated from segmental duplication. GhGUXs promoter analysis indicated cis-regulatory elements capable of reacting to several different stresses. RNA-Seq data and qRT-PCR analysis both indicated that most GhGUXs were associated with V. dahliae infection. Gene interaction network analysis showed that GhGUX5 interacted with 11 proteins, and the relative expression of these 11 proteins changed significantly following V. dahliae infection. In addition, silencing and overexpression of GhGUX5 results to enhance and reduce plant's susceptibility to V. dahliae. Further study showed that TRV: GhGUX5 silenced cotton plants exhibited a decrease in the degree of lignification, total lignin content, gene expression levels involved in lignin biosynthesis, and enzyme activity compared with TRV: 00. The above results indicate that GhGUX5 enhances Verticillium wilt resistance through the lignin biosynthesis pathway.

Comparative transcriptome analysis of juniper branches infected by Gymnosporangium spp. highlights their different infection strategies associated with cytokinins

BACKGROUND

Gymnosporangium asiaticum and G. yamadae can share Juniperus chinensis as the telial host, but the symptoms are completely different. The infection of G. yamadae causes the enlargement of the phloem and cortex of young branches as a gall, but not for G. asiaticum, suggesting that different molecular interaction mechanisms exist the two Gymnosporangium species with junipers.

RESULTS

Comparative transcriptome analysis was performed to investigate genes regulation of juniper in responses to the infections of G. asiaticum and G. yamadae at different stages. Functional enrichment analysis showed that genes related to transport, catabolism and transcription pathways were up-regulated, while genes related to energy metabolism and photosynthesis were down-regulated in juniper branch tissues after infection with G. asiaticum and G. yamadae. The transcript profiling of G. yamadae-induced gall tissues revealed that more genes involved in photosynthesis, sugar metabolism, plant hormones and defense-related pathways were up-regulated in the vigorous development stage of gall compared to the initial stage, and were eventually repressed overall. Furthermore, the concentration of cytokinins (CKs) in the galls tissue and the telia of G. yamadae was significantly higher than in healthy branch tissues of juniper. As well, tRNA-isopentenyltransferase (tRNA-IPT) was identified in G. yamadae with highly expression levels during the gall development stages.

CONCLUSIONS

In general, our study provided new insights into the host-specific mechanisms by which G. asiaticum and G. yamadae differentially utilize CKs and specific adaptations on juniper during their co-evolution.

Characterization of microRNAs and Target Genes in Musa acuminata subsp. burmannicoides, var. Calcutta 4 during Interaction with Pseudocercospora musae

Endogenous microRNAs (miRNAs) are small non-coding RNAs that perform post-transcriptional regulatory roles across diverse cellular processes, including defence responses to biotic stresses. Pseudocercospora musae, the causal agent of Sigatoka leaf spot disease in banana (Musa spp.), is an important fungal pathogen of the plant. Illumina HiSeq 2500 sequencing of small RNA libraries derived from leaf material in Musa acuminata subsp. burmannicoides, var. Calcutta 4 (resistant) after inoculation with fungal conidiospores and equivalent non-inoculated controls revealed 202 conserved miRNAs from 30 miR-families together with 24 predicted novel miRNAs. Conserved members included those from families miRNA156, miRNA166, miRNA171, miRNA396, miRNA167, miRNA172, miRNA160, miRNA164, miRNA168, miRNA159, miRNA169, miRNA393, miRNA535, miRNA482, miRNA2118, and miRNA397, all known to be involved in plant immune responses. Gene ontology (GO) analysis of gene targets indicated molecular activity terms related to defence responses that included nucleotide binding, oxidoreductase activity, and protein kinase activity. Biological process terms associated with defence included response to hormone and response to oxidative stress. DNA binding and transcription factor activity also indicated the involvement of miRNA target genes in the regulation of gene expression during defence responses. sRNA-seq expression data for miRNAs and RNAseq data for target genes were validated using stem-loop quantitative real-time PCR (qRT-PCR). For the 11 conserved miRNAs selected based on family abundance and known involvement in plant defence responses, the data revealed a frequent negative correlation of expression between miRNAs and target host genes. This examination provides novel information on miRNA-mediated host defence responses, applicable in genetic engineering for the control of Sigatoka leaf spot disease.

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.

Further Mining and Characterization of miRNA Resource in Chinese Fir (Cunninghamia lanceolata)

In this study, we aimed to expand the current miRNA data bank of Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) regarding its potential value for further genetic and genomic use in this species. High-throughput small RNA sequencing successfully captured 140 miRNAs from a Chinese fir selfing family harboring vigor and depressed progeny. Strikingly, 75.7% (n = 106) of these miRNAs have not been documented previously, and most (n = 105) of them belong to the novel set with 6858 putative target genes. The new datasets were then integrated with the previous information to gain insight into miRNA genetic architecture in Chinese fir. Collectively, a relatively high proportion (62%, n = 110) of novel miRNAs were found. Furthermore, we identified one MIR536 family that has not been previously documented in this species and four overlapped miRNA families (MIR159, MIR164, MIR171_1, and MIR396) from new datasets. Regarding the stability, we calculated the secondary structure free energy and found a relatively low R2 value (R2 < 0.22) between low minimal folding free energy (MFE) of pre-miRNAs and MFE of its corresponding mature miRNAs in most datasets. When in view of the conservation aspect, the phylogenetic trees showed that MIR536 and MIR159 sequences were highly conserved in gymnosperms.

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.

MicroRNA-mediated post-transcriptional regulation of Pinus pinaster response and resistance to pinewood nematode

Pine wilt disease (PWD), caused by the parasitic nematode Bursaphelenchus xylophilus, or pinewood nematode (PWN), is a serious threat to pine forests in Europe. Pinus pinaster is highly susceptible to the disease and it is currently the most affected European pine species. In this work, we investigated the role of small RNAs (sRNAs) in regulating P. pinaster–PWN interaction in an early stage of infection. After performing an artificial PWN inoculation assay, we have identified 105 plant microRNAs (miRNAs) responsive to PWN. Based on their predicted targets, part of these miRNAs was associated with roles in jasmonate-response pathway, ROS detoxification, and terpenoid biosynthesis. Furthermore, by comparing resistant and susceptible plants, eight miRNAs with putative functions in plant defence and resistance to PWN have been identified. Finally, we explored the possibility of bidirectional trans-kingdom RNA silencing, identifying several P. pinaster genes putatively targeted by PWN miRNAs, which was supported by degradome analysis. Targets for P. pinaster miRNAs were also predicted in PWN, suggesting a role for trans-kingdom miRNA transfer and gene silencing both in PWN parasitism as in P. pinaster resistance to PWD. Our results provide new insights into previously unexplored roles of sRNA post-transcriptional regulation in P. pinaster response and resistance to PWN.

Differential expression profiling of microRNAs and their target genes during wheat-Bipolaris sorokiniana pathosystem

Wheat spot blotch, caused by Bipolaris sorokiniana, is a serious constraint to wheat production, reducing grain yield and consequently having severe economic impact. Several plant miRNAs have recently been discovered as regulators of gene expression involved in cellular and metabolic functions. So far reports on the roles of miRNAs in B. sorokiniana infection response of wheat are scanty. To further understand the defence mechanism of miRNAs- regulated cellular functions, we examined the expression patterns of 17 miRNAs and their targets involved in the interaction between wheat and B. sorokiniana in two contrasting wheat genotypes, Chiriya-1 and WH-147. All of the miRNAs and target genes were shown to be expressed differentially in both genotypes after B. sorokiniana infection. Seven and nine miRNAs were observed as up-regulated in the resistant genotype Chiriya-1 and the susceptible genotype WH147, respectively. Among the up-regulated miRNAs, ptc-miR901 (~ 10.21 times) accumulated the most in Chiriya-1 followed by ptc-miR1450 (~ 7.6 times) in WH-147. Furthermore, only two miRNAs, tae-miR156 and ptc-miR482c showed a complete inverse relation with their target genes, SPL and NBS-LRR, respectively. This research sheds light on the temporal differential regulation of miRNAs and their targets, which may play a role in wheat adaptation to B. sorokiniana infection.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01092-1.

Molecular mechanism of modulating miR482b level in tomato with botrytis cinerea infection

BACKGROUND

Plant miRNAs are involved in the response to biotic and abiotic stresses by altering their expression levels, and they play an important role in the regulation of plant resistance to stress. However, the molecular mechanism that regulates the expression levels of miRNAs in plants with biotic and abiotic stress still needs to be explored. Previously, we found that the expression of the miR482 family was changed in tomato infected by Botrytis cinerea. In this study, we investigated and uncovered the mechanism underlying the response of miR482 to B. cinerea infection in tomato.

RESULTS

First, RT-qPCR was employed to detect the expression patterns of miR482b in tomato infected by B. cinerea, and results showed that miR482b primary transcripts (pri-miR482b) were up-regulated in B. cinerea-infected leaves, but the mature miR482b was down-regulated. Subsequently, we used rapid amplification cDNA end method to amplify the full-length of pri-miR482b. Result showed that the pri-miR482b had two isoforms, with the longer one (consisting 300 bp) having an extra fragment of 53 bp in the 3'-end compared with the shorter one. In vitro Dicer assay indicated that the longer isoform pri-miR482b-x1 had higher efficiency in the post-transcriptional splicing of miRNA than the shorter isoform pri-miR482b-x2. In addition, the transcription level of mature miR482b was much higher in transgenic Arabidopsis overexpressing pri-miR482b-x1 than that in OE pri-miR482b-x2 Arabidopsis. These results confirmed that this extra 53 bp in pri-miR482b-x1 might play a key role in the miR482b biogenesis of post-transcription processing.

CONCLUSIONS

Extra 53 bp in pri-miR482b-x1 enhanced miR482b biogenesis, which elevated the transcription level of miR482b. This study clarified the response of miR482 to B. cinerea infection in tomato, thereby helping us further understand the molecular mechanisms that regulate the expression levels of other miRNAs.

Identification and Characterization of Downy Mildew-Responsive microRNAs in Indian Vitis vinifera by High-Throughput Sequencing

Downy mildew (DM) is one of the most devastating diseases disturbing viticulture, mainly during temperate and humid climates. The DM pathogen can attack grapevine leaves and berries differentially, and the disease is managed with recurring applications of fungicides that direct pathogen pressure, develop of resistant strains, and lead to residual soil toxicity and increased pollution effects. Plant microRNAs (miRNAs) are important candidates in physiological regulatory roles in response to biotic stress in plants. In this study, high-throughput sequencing and MiRDeep-P were employed to identify miRNAs in Vitis vinifera. Altogether, 22,492,910, 25,476,471, and 22,448,438 clean reads from the sterile distilled water (SDW)-control, bio-pesticide Trichoderma harzianum (TriH_JSB36)-treated, and downy mildew Plasmopara viticola pathogen libraries, respectively, were obtained. On the basis of the sequencing results and analysis (differential expression analysis), we observed significant differences in 15 miRNAs (5 novel upregulated, and 10 known downregulated) in the pathogen-infected sample (Test) in comparison to the SDW-control sample, with majority of the reads beingin the range of 20-24 bp. This study involves the identification and characterization of vvi-miRNAs that are involved in resistance against downy mildew disease in grapes.

MicroRNAs in Woody Plants

MicroRNAs (miRNAs) are small (∼21-nucleotides) non-coding RNAs found in plant and animals. MiRNAs function as critical post-transcriptional regulators of gene expression by binding to complementary sequences in their target mRNAs, leading to mRNA destabilization and translational inhibition. Plant miRNAs have some distinct characteristics compared to their animal counterparts, including greater evolutionary conservation and unique miRNA processing methods. The lifecycle of a plant begins with embryogenesis and progresses through seed germination, vegetative growth, reproductive growth, flowering and fruiting, and finally senescence and death. MiRNAs participate in the transformation of plant growth and development and directly monitor progression of these processes and the expression of certain morphological characteristics by regulating transcription factor genes involved in cell growth and differentiation. In woody plants, a large and rapidly increasing number of miRNAs have been identified, but their biological functions are largely unknown. In this review, we summarize the progress of miRNA research in woody plants to date. In particular, we discuss the potential roles of these miRNAs in growth, development, and biotic and abiotic stresses responses in woody plants.

Roles of small RNAs in crop disease resistance

Small RNAs (sRNAs) are a class of short, non-coding regulatory RNAs that have emerged as critical components of defense regulatory networks across plant kingdoms. Many sRNA-based technologies, such as host-induced gene silencing (HIGS), spray-induced gene silencing (SIGS), virus-induced gene silencing (VIGS), artificial microRNA (amiRNA) and synthetic trans-acting siRNA (syn-tasiRNA)-mediated RNA interference (RNAi), have been developed as disease control strategies in both monocot and dicot plants, particularly in crops. This review aims to highlight our current understanding of the roles of sRNAs including miRNAs, heterochromatic siRNAs (hc-siRNAs), phased, secondary siRNAs (phasiRNAs) and natural antisense siRNAs (nat-siRNAs) in disease resistance, and sRNAs-mediated trade-offs between defense and growth in crops. In particular, we focus on the diverse functions of sRNAs in defense responses to bacterial and fungal pathogens, oomycete and virus in crops. Further, we highlight the application of sRNA-based technologies in protecting crops from pathogens. Further research perspectives are proposed to develop new sRNAs-based efficient strategies to breed non-genetically modified (GMO), disease-tolerant crops for sustainable agriculture.

Biotic stress-associated microRNA families in plants

Plants and animals utilize various regulatory mechanisms for control of gene expression during development in different tissues and cell types. About 30 years ago, a new mechanism of gene regulation, termed RNA interference (RNAi), was discovered and proved revolutionary for the mechanistic understanding of gene regulation. Noncoding RNAs, including short, 21-24 nucleotide (nt) long microRNAs (miRNAs), endogenously-generated from MIR genes, are key components of RNAi processes, by post-transcriptionally controlling transcripts with antisense complementarity through either translational repression or mRNA degradation. Since their discovery, important roles in regulation of ontogenetic development, cell differentiation, proliferation, and apoptosis in eukaryotes have been elucidated. In plants, miRNAs are known regulatory elements of basic endogenous functions and responses to the environmental stimuli. While the role of miRNAs in regulation of nutrient uptake, circadian clock and general response to abiotic stress is already well understood, a comprehensive understanding of their immune-regulatory roles in response to various biotic stress factors has not yet been achieved. This review summarizes the current understanding of the function of miRNAs and their targets in plants during interaction with microbial pathogens and symbionts. Additionally, we provide a consensus conclusion regarding the typical induction or repression response of conserved miRNA families to pathogenic and beneficial fungi, bacteria, and oomycetes, as well as an outlook of agronomic application of miRNAs in plants. Further investigation of plant miRNAs responsive to microbes, aided with novel sequencing and bioinformatics approaches for discovery and prediction in non-model organisms holds great potential for development of new forms of plant protection.

Clubroot in Brassica: recent advances in genomics, breeding, and disease management

Clubroot disease, caused by Plasmodiophora brassicae, affects Brassica oilseed and vegetable production worldwide. This review is focused on various aspects of clubroot disease and its management, including understanding the pathogen and resistance in the host plants. Advances in genetics, molecular biology techniques, and omics research have helped to identify several major loci, QTL, and genes from the Brassica genomes involved in the control of clubroot resistance. Transcriptomic studies have helped to extend our understanding of the mechanism of infection by the pathogen and the molecular basis of resistance/susceptibility in the host plants. A comprehensive understanding of the clubroot disease and host resistance would allow developing a better strategy by integrating the genetic resistance with cultural practices to manage this disease from a long-term perspective.

Comprehensive analysis of the isomiRome in the vegetative organs of the conifer Pinus pinaster under contrasting water availability

An increasing number of microRNAs (miRNAs) and miRNA-related sequences produced during miRNA biogenesis, comprising the isomiRome, have been recently highlighted in different species as critical mediators of environmental stress responses. Conifers have some of the largest known genomes but an extensive characterization of the isomiRome from any conifer species has been lacking. We provide here a comprehensive overview of the Pinus pinaster isomiRome expressed in roots, stem and needles under well-watered and drought conditions. From the 13,441 unique small RNA sequences identified, 2,980 were annotated as canonical miRNAs or miRNA* and the remaining were classified as isomiRNA or miRNA-like sequences. A survey of their expression patterns highlighted roots as the most responsive organ under drought, where specific sequences of which a 24-nt novel miRNA stood out, were strongly down-regulated. Given the putative roles of the miRNA-targeted transcripts validated specifically in root tissues, some of the miRNAs, conserved and novel, are shortlisted as potential regulators of drought response. These results provide a valuable resource for comparative studies between gymnosperms and angiosperms. Furthermore, it evidences high transferability of the isomiRome between pine species being a useful basis for further molecular regulation and physiological studies, and especially those focused on adaptation to drought conditions.

Plant miR397 and its functions

MicroRNAs (miRNAs) are noncoding, small RNAs of 20-24 nucleotides (nt) and function critically at the post-transcriptional level to regulate gene expression through cleaving mRNA targets or interfering with translation of the target mRNAs. They are broadly involved in many biological processes in plants. The miR397 family in plants contains several conserved members either in 21-nt or in 22-nt that mainly target the laccase (LAC) genes functioning in lignin synthesis and are involved in the development of plants under various conditions. Recent findings showed that miR397b in Arabidopsis could also target to Casein Kinase II Subunit Beta 3 (CKB3) and mediate circadian regulation and plant flowering. This review aims to summarise recent updates on miR397 and provides the available basis for understanding the functional mechanisms of miR397 in plant growth and development regulation and in response to external adverse stimulation.

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

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

Biotic stress triggered small RNA and RNAi defense response in plants

The yield of crops is largely affected by different types of biotic stresses. To minimize the damage, crop plants adapted themselves to overcome the stress conditions through gene expression reprogramming at transcriptional and post-transcriptional levels. With a better knowledge of plants' responses in adverse environments, new methodologies and strategies have been applied to develop better stress-tolerant plants. In this manner, small RNAs (micro RNA and small-interfering RNA) are reported to play a central role to combat biotic stresses in plants. Depending upon the stress stimuli, these small RNAs can up or down regulate the genes expression, that indicate their potential role in overcoming the stress. These stress-induced small RNAs may reduce the expression of the target gene(s) that might negatively influence plants' response to the adverse conditions. Contrariwise, miRNA, a class of small RNA, can downregulate its expression to upregulate the expression of the target gene(s), which might positively aid to the stress adaptation. Along with this, benefits of RNA interference (RNAi) have also been stated in functional genomic research on insects, fungi and plant pathogens. RNAi is involved in the safe transport of dsRNA to the targeted mRNA(s) in the biotic stress-causing agents (for example fungi and insects) and saves the plant from damage, which is a safer approach compared to use of chemical pesticides. The current review summarizes the role of small RNAs and the use of RNAi to save the plants from biotic stress conditions.

The lre-miR159a-LrGAMYB pathway mediates resistance to grey mould infection in Lilium regale

Grey mould is one of the most determinative factors of lily growth and plays a major role in limiting lily productivity. MicroRNA159 (miR159) is a highly conserved microRNA in plants, and participates in the regulation of plant development and stress responses. Our previous studies revealed that lre-miR159a participates in the response of Lilium regale to Botrytis elliptica according to deep sequencing analyses; however, the response mechanism remains unknown. Here, lre-miR159a and its target LrGAMYB gene were isolated from L. regale. Transgenic Arabidopsis overexpressing lre-MIR159a exhibited larger leaves and smaller necrotic spots on inoculation with Botrytis than those of wild-type and overexpressing LrGAMYB plants. The lre-MIR159a overexpression also led to repressed expression of two targets of miR159, AtMYB33 and AtMYB65, and enhanced accumulation of hormone-related genes, including AtPR1, AtPR2, AtNPR1, AtPDF1.2, and AtLOX for both the jasmonic acid and salicylic acid pathways. Moreover, lower levels of H₂ O₂ and O2- were observed in lre-MIR159a transgenic Arabidopsis, which reduced the damage from reactive oxygen species accumulation. Taken together, these results indicate that lre-miR159a positively regulates resistance to grey mould by repressing the expression of its target LrGAMYB gene and activating a defence response.

Identification of lncRNAs and their regulatory relationships with target genes and corresponding miRNAs in melon response to powdery mildew fungi

Melon (Cucumis melo L.), an economically beneficial crop widely cultivated around the world, is vulnerable to powdery mildew (PM). However, the studies on molecular mechanism of melon response to PM fungi is still limited. Long non coding RNAs (lncRNAs) have emerged as new regulators in plants response to biotic stresses. We predicted and identified the intricate regulatory roles of lncRNAs in melon response to PM fungi. A total of 539 lncRNAs were identified from PM-resistant (MR-1) and susceptible melon (Top Mark), in which 254 were significantly altered after PM fungi infection. Multiple target genes of lncRNAs were found to be involved in the hydrolysis of chitin, callose deposition and cell wall thickening, plant-pathogen interaction and plant hormone signal transduction pathway. Additionally, a total of 42 lncRNAs possess the various functions with microRNAs (miRNAs), including lncRNAs that are targeted by miRNAs and function as miRNA precursors or miRNA sponges. These findings provide a comprehensive view of potentially functional lncRNAs, corresponding target genes and related lncRNA-miRNA pairs, which will greatly increase our knowledge of the mechanism underlying susceptibility and resistance to PM in melon.

Colonisation of Oncidium orchid roots by the endophyte Piriformospora indica restricts Erwinia chrysanthemi infection, stimulates accumulation of NBS-LRR resistance gene transcripts and represses their targeting micro-RNAs in leaves

BACKGROUND

Erwinia chrysanthemi (Ec) is a destructive pathogen which causes soft-rot diseases in diverse plant species including orchids. We investigated whether colonization of Oncidium roots by the endophytic fungus Piriformospora indica (Pi) restricts Ec-induced disease development in leaves, and whether this might be related to the regulation of nucleotide binding site-leucine rich repeat (NBS-LRR) Resistance (R) genes.

RESULTS

Root colonization of Oncidium stackings by Pi restricts progression of Ec-induced disease development in the leaves. Since Pi does not inhibit Ec growth on agar plates, we tested whether NBS-LRR R gene transcripts and the levels of their potential target miRNAs in Oncidium leaves might be regulated by Pi. Using bioinformatic tools, we first identified NBS-LRR R gene sequences from Oncidium, which are predicted to be targets of miRNAs. Among them, the expression of two R genes was repressed and the accumulation of several regulatory miRNA stimulated by Ec in the leaves of Oncidium plants. This correlated with the progression of disease development, jasmonic and salicylic acid accumulation, ethylene synthesis and H₂O₂ production after Ec infection of Oncidium leaves. Interestingly, root colonization by Pi restricted disease development in the leaves, and this was accompanied by higher expression levels of several defense-related R genes and lower expression level of their target miRNA.

CONCLUSION

Based on these data we propose that Pi controls the levels of NBS-LRR R mRNAs and their target miRNAs in leaves. This regulatory circuit correlates with the protection of Oncidium plants against Ec infection, and molecular and biochemical investigations will demonstrate in the future whether, and if so, to what extent these two observations are related to each other.

RNAi-Mediated Resistance Against Viruses in Perennial Fruit Plants

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

Identification of Regulatory Networks of MicroRNAs and Their Targets in Response to Colletotrichum gloeosporioides in Tea Plant (Camellia sinensis L.)

Anthracnose disease is caused by Colletotrichum gloeosporioides, and is common in leaves of the tea plant (Camellia sinensis). MicroRNAs (miRNAs) have been known as key modulators of gene expression in response to environmental stresses, disease resistance, defense responses, and plant immunity. However, the role of miRNAs in responses to C. gloeosporioides remains unexplored in tea plant. Therefore, in the present study, six miRNA sequencing data sets and two degradome data sets were generated from C. gloeosporioides-inoculated and control tea leaves. A total of 485 conserved and 761 novel miRNAs were identified. Of those, 239 known and 369 novel miRNAs exhibited significantly differential expression under C. gloeosporioides stress. One thousand one hundred thirty-four and 596 mRNAs were identified as targets of 389 conserved and 299 novel miRNAs by degradome analysis, respectively. Based on degradome analysis, most of the predicted targets are negatively correlated with their corresponding conserved and novel miRNAs. The expression levels of 12 miRNAs and their targets were validated by quantitative real-time PCR. A negative correlation between expression profiles of five miRNAs (PC-5p-80764_22, csn-miR160c, csn-miR828a, csn-miR164a, and csn-miR169e) and their targets (WRKY, ARF, MYB75, NAC, and NFY transcription factor) was observed. The predicted targets of five interesting miRNAs were further validated through 5'RLM-RACE. Furthermore, Gene Ontology and metabolism pathway analysis revealed that most of the target genes were involved in the regulation of auxin pathway, ROS scavenging pathway, salicylic acid mediated pathway, receptor kinases, and transcription factors for plant growth and development as well as stress responses in tea plant against C. gloeosporioides stress. This study enriches the resources of stress-responsive miRNAs and their targets in C. sinensis and thus provides novel insights into the miRNA-mediated regulatory mechanisms, which could contribute to the enhanced susceptibility of C. gloeosporioides in tea plant.

Identification of miRNAs and their target genes in Larix olgensis and verified of differential expression miRNAs

BACKGROUND

MiRNAs (microRNA) are 18-24 nt endogenous noncoding RNAs that regulate gene expression at the post-transcriptional level, including tissue-specific, developmental timing and evolutionary conservation gene expression.

RESULTS

This study used high-throughput sequencing technology for the first time in Larix olgensis, predicted 78 miRNAs, including 12,229,003 reads sRNA, screened differentially expressed miRNAs. Predicting target genes was helpful for understanding the miRNA regulation function and obtained 333 corresponding target genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation were analysed, mostly including nucleic acid binding, plant hormone signal transduction, pantothenate and CoA biosynthesis, and cellulose synthase. This study will lay the foundation for clarifying the complex miRNA-mediated regulatory network for growth and development. In view of this, spatio-temporal expression of miR396, miR950, miR164, miR166 and miR160 were analysed in Larix olgensis during the growth stages of not lignified, beginning of lignification, and completely lignified in different tissues (root, stem, and leaf) by quantitative real-time PCR (qRT-PCR). There were differences in the expression of miRNAs in roots, stems and leaves in the same growth period. At 60 days, miR160, miR166 and miR396-2 exhibited the highest expression in leaves. At 120 days, most miRNAs in roots and stems decreased significantly. At 180 days, miRNAs were abundantly expressed in roots and stems. Meanwhile, analysis of the expression of miRNAs in leaves revealed that miR396-2 was reduced as time went on, whereas other miRNAs increased initially and then decreased. On the other hand, in the stems, miR166-1 was increase, whereas other miRNAs, especially miR160, miR164, miR396 and miR950-1, first decreased and then increased. Similarly, in the roots, miR950-2 first decreased and then increased, whereas other miRNAs exhibited a trend of continuous increase.

CONCLUSIONS

The present investigation included rapid isolation and identification of miRNAs in Larix olgensis through construction of a sRNA library using Solexa and predicted 78 novel miRNAs, which showed differential expression levels in different tissues and stages. These results provided a theoretical basis for further revealing the genetic regulation mechanism of miRNA in the growth and development of conifers and the verification of function in target genes.

Quantitative expression of microRNAs in Brassica oleracea infected with Xanthomonas campestris pv. campestris

Brassica oleracea var. capitata (cabbage) is an economically important crop affected by black rot disease caused by Xanthomonas campestris pv. campestris (Xcc). MicroRNAs (miRNAs) play an important role in plant defense modulation and therefore the analysis of these molecules can help better understand plant-pathogen interactions. In this study, we report the differential expression of four miRNAs that seem to participate in the plant response to Xcc infection. Northern Blot and RT-qPCR techniques were used to measure miRNA expression in resistant (União) and susceptible (Kenzan) cultivars. From 6 miRNAs analyzed, 4 were detected and differentially expressed, showing a down- and upregulated expression profile in susceptible and resistant cultivars, respectively. These results suggest that miR156, miR167, miR169, and miR390 could play a role in B. oleracea resistance enhancement against Xcc and could be explored as potential resistance markers in B. oleracea-Xcc interaction.

miR156/SPL9 Regulates Reactive Oxygen Species Accumulation and Immune Response in Arabidopsis thaliana

The functions of microRNA156 (miR156) and its targeted SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factor genes in plant development have been widely investigated. However, the role of the miR156/SPLs regulatory network in plant immune systems remains obscure. Here, we found that the accumulation of reactive oxygen species (ROS) and the transcripts of basal salicylic acid (SA) signaling pathway genes were lower in Arabidopsis Pro35S:MIR156 seedlings (miR156 overexpression mutants) but higher in Pro35S:MIM156 (miR156 repression mutants) and ProSPL9:rSPL9 (SPL9 overexpression mutants) seedlings compared with wild-type Col-0 plants (WT). As a result, Pro35S:MIR156 mutants induced greater susceptibility to Pseudomonas syringae pv. tomato DC3000 following syringe infiltration than WT, while Pro35S:MIM156 and ProSPL9:rSPL9 mutants showed enhanced resistance. In addition, foliar H₂O₂ application resulted in activation of SA-mediated defense response and ablation of miR156-induced susceptibility to P. syringae pv. tomato DC3000 infection. Collectively, our results provide new insights into the function of the miR156/SPL network in Arabidopsis immune response by regulating ROS accumulation and activating the SA signaling pathway.

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

BACKGROUND

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

OBJECTIVES

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

METHODS

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

RESULTS

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

CONCLUSION

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

Novel and Conserved miRNAs Among Brazilian Pine and Other Gymnosperms

The knowledge about plant miRNAs has increased exponentially, with thousands of miRNAs been reported in different plant taxa using high throughput sequencing technologies and bioinformatic tools. Nevertheless, several groups of plants remain unexplored, and the gap of knowledge about conifer miRNAs is considerable. There is no sequence or functional information available on miRNAs in Araucariaceae. This group is represented in Brazil by only one species, Araucaria angustifolia, an endangered species known as Brazilian pine. In the present study, Brazilian pine has its transcriptome explored with respect to small RNAs, representing the first description in a member of the Araucariaceae family. The screening for conserved miRNAs in Brazilian pine revealed 115 sequences of 30 miRNA families. A total of 106 precursors sequences were predicted. Forty one comprised conserved miRNAs from 16 families, whereas 65 were annotated as novel miRNAs. The comparison of Brazilian pine precursors with sRNA libraries of other five conifer species indicates that 9 out 65 novel miRNAs are conserved among gymnosperms, while 56 seems to be specific for Brazilian pine or restricted to Araucariaceae family. Analysis comparing novel Brazilian pine miRNAs precursors and Araucaria cunninghamii RNA-seq data identified seven orthologs between both species. Mature miRNA identified by bioinformatics predictions were validated using stem-loop RT-qPCR assays. The expression pattern of conserved and novel miRNAs was analyzed in five different tissues of 3-month-old Araucaria seedlings. The present study provides insights about the nature and composition of miRNAs in an Araucariaceae species, with valuable information on miRNAs diversity and conservation in this taxon.

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

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

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

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

Identification and characterization of differentially expressed Phaseolus vulgaris miRNAs and their targets during mungbean yellow mosaic India virus infection reveals new insight into Phaseolus-MYMIV interaction

Phaseolus vulgaris is an economically important legume in tropical and subtropical regions of Asia, Africa, Latin-America and parts of USA and Europe. However, its production gets severely affected by mungbean yellow mosaic India virus (MYMIV). We aim to identify and characterize differentially expressed miRNAs during MYMIV-infection in P. vulgaris. A total of 422 miRNAs are identified of which 292 are expressed in both MYMIV-treated and mock-treated samples, 109 are expressed only in MYMIV-treated and 21 are expressed only in mock-treated samples. Selected up- and down-regulated miRNAs are validated by RT-qPCR. 3367 target ORFs are identified for 270 miRNAs. Selected targets are validated by 5' RLM-RACE. Differentially expressed miRNAs regulate transcription factors and are involved in improving stress tolerance to MYMIV. These findings will provide an insight into the role of miRNAs during MYMIV infection in P. vulgaris in particular and during any biotic stress conditions in Leguminosae family in general.

Transcript-level expression control of plant NLR genes

Plant NLR genes encode sensitive immune receptors that can mediate the specific recognition of pathogen avirulence effectors and activate a strong defence response, termed effector-triggered immunity. The expression of NLRs requires strict regulation, as their ability to trigger immunity is dependent on their dose, and overexpression of NLRs results in autoimmunity and massive fitness costs. An elaborate interplay of different mechanisms controlling NLR transcript levels allows plants to maximize their defence capacity, whilst limiting negative impact on their fitness. Global suppression of NLR transcripts may be a prerequisite for the fast evolution of new NLR variants and the expansion of this gene family. Here, we summarize recent progress made towards a comprehensive understanding of NLR transcript-level expression control. Multiple mechanistic steps, including transcription as well as co-/post-transcriptional processing and transcript turn-over, contribute to balanced base levels of NLR transcripts and allow for dynamic adjustments to defence situations.

MiRNA160 is associated with local defense and systemic acquired resistance against Phytophthora infestans infection in potato

To combat pathogen infection, plants employ local defenses in infected sites and elicit systemic acquired resistance (SAR) in distant tissues. MicroRNAs have been shown to play a significant role in local defense, but their association with SAR is unknown. In addition, no such studies of the interaction between potato and Phytophthora infestans have been reported. We investigated the role of miR160 in local and SAR responses to P. infestans infection in potato. Expression analysis revealed induced levels of miR160 in both local and systemic leaves of infected wild-type plants. miR160 overexpression and knockdown plants exhibited increased susceptibility to infection, suggesting that miR160 levels equivalent to those of wild-type plants may be necessary for mounting local defense responses. Additionally, miR160 knockdown lines failed to elicit SAR, and grafting assays indicated that miR160 is required in both local and systemic leaves to trigger SAR. Consistently, SAR-associated signals and genes were dysregulated in miR160 knockdown lines. Furthermore, analysis of the expression of defense and auxin pathway genes and direct regulation of StGH3.6, a mediator of salicylic acid-auxin cross-talk, by the miR160 target StARF10 revealed the involvement of miR160 in antagonistic cross-talk between salicylic acid-mediated defense and auxin-mediated growth pathways. Overall, our study demonstrates that miR160 plays a crucial role in local defense and SAR responses during the interaction between potato and P. infestans.

Plant microRNAs: Front line players against invading pathogens

Plants are attacked by a large number of pathogens. To defend against these pathogens, plants activate or repress a vast array of genes. For genetic expression and reprogramming, host endogenous small RNAs (sRNAs) are the key factors. Among these sRNAs, microRNAs (miRNAs) mediate gene regulation through RNA silencing at the post-transcriptional level and play an essential role in the defense responses to biotic and abiotic stress. In the recent years, high-throughput sequencing has enabled the researchers to uncover the role of plant miRNAs during pathogen invasion. So here we have reviewed the recent research findings illustrating the plant miRNAs active involvement in various defense processes during fungal, bacterial, viral and nematode infections. However, rapid validation of direct targets of miRNAs is the dire need of time, which can be very helpful in improving the plant resistance against various pathogenic diseases.

Plant Responses to Pathogen Attack: Small RNAs in Focus

Small RNAs (sRNA) are a significant group of gene expression regulators for multiple biological processes in eukaryotes. In plants, many sRNA silencing pathways produce extensive array of sRNAs with specialized roles. The evidence on record advocates for the functions of sRNAs during plant microbe interactions. Host sRNAs are reckoned as mandatory elements of plant defense. sRNAs involved in plant defense processes via different pathways include both short interfering RNA (siRNA) and microRNA (miRNA) that actively regulate immunity in response to pathogenic attack via tackling pathogen-associated molecular patterns (PAMPs) and other effectors. In response to pathogen attack, plants protect themselves with the help of sRNA-dependent immune systems. That sRNA-mediated plant defense responses play a role during infections is an established fact. However, the regulations of several sRNAs still need extensive research. In this review, we discussed the topical advancements and findings relevant to pathogen attack and plant defense mediated by sRNAs. We attempted to point out diverse sRNAs as key defenders in plant systems. It is hoped that sRNAs would be exploited as a mainstream player to achieve food security by tackling different plant diseases.

In Silico Analysis of Small RNAs Suggest Roles for Novel and Conserved miRNAs in the Formation of Epigenetic Memory in Somatic Embryos of Norway Spruce

Epigenetic memory in Norway spruce affects the timing of bud burst and bud set, vitally important adaptive traits for this long-lived forest species. Epigenetic memory is established in response to the temperature conditions during embryogenesis. Somatic embryogenesis at different epitype inducing (EpI) temperatures closely mimics the natural processes of epigenetic memory formation in seeds, giving rise to epigenetically different clonal plants in a reproducible and predictable manner, with respect to altered bud phenology. MicroRNAs (miRNAs) and other small non-coding RNAs (sRNAs) play an essential role in the regulation of plant gene expression and may affect this epigenetic mechanism. We used NGS sequencing and computational in silico methods to identify and profile conserved and novel miRNAs among small RNAs in embryogenic tissues of Norway spruce at three EpI temperatures (18, 23 and 28°C). We detected three predominant classes of sRNAs related to a length of 24 nt, followed by a 21–22 nt class and a third 31 nt class of sRNAs. More than 2100 different miRNAs within the prevailing length 21–22 nt were identified. Profiling these putative miRNAs allowed identification of 1053 highly expressed miRNAs, including 523 conserved and 530 novels. 654 of these miRNAs were found to be differentially expressed (DEM) depending on EpI temperature. For most DEMs, we defined their putative mRNA targets. The targets represented mostly by transcripts of multiple-repeats proteins, like TIR, NBS-LRR, PPR and TPR repeat, Clathrin/VPS proteins, Myb-like, AP2, etc. Notably, 124 DE miRNAs targeted 203 differentially expressed epigenetic regulators. Developing Norway spruce embryos possess a more complex sRNA structure than that reported for somatic tissues. A variety of the predicted miRNAs showed distinct EpI temperature dependent expression patterns. These putative EpI miRNAs target spruce genes with a wide range of functions, including genes known to be involved in epigenetic regulation, which in turn could provide a feedback process leading to the formation of epigenetic marks. We suggest that TIR, NBS and LRR domain containing proteins could fulfill more general functions for signal transduction from external environmental stimuli and conversion them into molecular response. Fine-tuning of the miRNA production likely participates in both developmental regulation and epigenetic memory formation in Norway spruce.

Malus hupehensis miR168 Targets to ARGONAUTE1 and Contributes to the Resistance against Botryosphaeria dothidea Infection by Altering Defense Responses

MicroRNA (miRNA)-mediated post-transcriptional regulation plays a fundamental role in various plant physiological processes, including responses to pathogens. MicroRNA168 has been implicated as an essential factor of miRNA pathways by targeting ARGONAUTE1 (AGO1), the core component of the RNA-induced silencing complex (RISC). A fluctuation in AGO1 expression influences various plant-pathogen interactions, and the homeostasis of AGO1 and miR168 accumulation is maintained by a complicated feedback regulatory loop. In this study, the connection between miR168 and the resistance of Malus hupehensis to Botryosphaeria dothidea is revealed. The induction of both the mature miR168 and its precursor in plants subjected to B. dothidea infection indicate the transcriptional activation of MIR168a. MIR168a promoter analysis demonstrates that the promoter can be activated by B. dothidea and salicylic acid (SA). However, the direct target of miR168, M. hupehensis ARGONAUTE1 (MhAGO1), is shown to be induced under the infection. Expression and transcription activity analysis demonstrate the transcriptional activation and the post-transcriptional suppression of MhAGO1 in response to B. dothidea infection. By inhibiting reactive oxygen species (ROS) production and enhancing SA-mediated defense responses, miR168a delays the symptom development of leaves inoculated with B. dothidea and impedes the pathogen growth, while MhAGO1 is found to have the opposite effects. Collectively, these findings suggest that the expression of miR168 and MhAGO1 in M. hupehensis in response to B. dothidea infection is regulated by a complicated mechanism. Targeting to MhAGO1, a negative regulator, miR168 plays a positive role in the resistance by alterations in diverse defense responses.

Tight regulation of the interaction between Brassica napus and Sclerotinia sclerotiorum at the microRNA level

MicroRNAs (miRNAs) are multifunctional non-coding short nucleotide molecules. Nevertheless, the role of miRNAs in the interactions between plants and necrotrophic pathogens is largely unknown. Here, we report the identification of the miRNA repertoire of the economically important oil crop oilseed rape (Brassica napus) and those involved in interacting with its most devastating necrotrophic pathogen Sclerotinia sclerotiorum. We identified 280 B. napus miRNA candidates, including 53 novel candidates and 227 canonical members or variants of known miRNA families, by high-throughput deep sequencing of small RNAs from both normal and S. sclerotiorum-inoculated leaves. Target genes of 15 novel candidates and 222 known miRNAs were further identified by sequencing of degradomes from the two types of samples. MiRNA microarray analysis revealed that 68 miRNAs were differentially expressed between S. sclerotiorum-inoculated and uninoculated leaves. A set of these miRNAs target genes involved in plant defense to S. sclerotiorum and/or other pathogens such as nucleotide binding site-leucine-rich repeat (NBS-LRR) R genes and nitric oxygen and reactive oxygen species related genes. Additionally, three miRNAs target AGO1 and AGO2, key components of post-transcriptional gene silencing (PTGS). Expression of several viral PTGS suppressors reduced resistance to S. sclerotiorum. Arabidopsis mutants of AGO1 and AGO2 exhibited reduced resistance while transgenic lines over-expressing AGO1 displayed increased resistance to S. sclerotiorum in an AGO1 expression level-dependent manner. Moreover, transient over-expression of miRNAs targeting AGO1 and AGO2 decreased resistance to S. sclerotiorum in oilseed rape. Our results demonstrate that the interactions between B. napus and S. sclerotiorum are tightly regulated at miRNA level and probably involve PTGS.

Transcriptional regulation of vascular cambium activity during the transition from juvenile to mature stages in Cunninghamia lanceolata

Cunninghamia lanceolata (Lamb.) Hook., an evergreen conifer distributed in southern China, has been recognized as the most commercially important timber species due to its rapid growth. However, the molecular mechanisms underlying growth alternation due to vascular cambium activity are poorly understood. Here, we used cryosectioning to isolate the vascular cambium tissue of C. lanceolata at three stages, namely, juvenile, transition and mature (3-, 13-, and 35-year-old trees respectively) for transcriptome-wide analysis. Through assembling and annotation of transcripts, 108,767 unigenes and some potential growth-regulated genes were identified. A total of 5213, 4873 and 2541 differentially expressed genes (DEGs) were identified in the three stages. DEGs related to cambial activity, cell division and cell wall modification were detected at various developmental stages of the vascular cambium. In addition, some putative genes involved in plant hormone biosynthesis were also differentially regulated. These results indicate that various cambium-related molecular activities result in alterations in the growth of C. lanceolata, particularly during the transition from juvenile to mature stages. The findings of the present study improve our understanding of cambium development and may aid in studies of the molecular mechanisms of wood production and provide fundamental insights into the establishment of the optimal rotation period for silvicultural trees.

Small RNAs regulate plant responses to filamentous pathogens

Small RNAs are central players of RNA silencing in eukaryotes. These short RNA molecules (20-25 nucleotides in length) repress target gene expression based on sequence complementarity. While small RNAs are well-known for their essential function in regulating growth and development, recent research has revealed that they also influence plant immunity. Extensive changes in small RNA accumulation have been observed during infection. This review focuses on specific small RNA changes that are involved in plant responses to filamentous eukaryotic pathogens including fungi and oomycetes. We describe how changes in small RNA accumulation influence plant immunity and summarize the cellular processes affected by these small RNAs. In particular, we discuss secondary small interfering RNAs that directly modulate the expression of defense-related genes.

Large-scale rewiring of innate immunity circuitry and microRNA regulation during initial rice blast infection

Rice blast is a recurrent fungal disease, and resistance to fungal infection is a complex trait. Therefore, a comprehensive examination of rice transcriptome and its variation during fungal infection is necessary to understand the complex gene regulatory networks. In this study, adopting Next-Generation Sequencing we profiled the transcriptomes and microRNAomes of rice varieties, one susceptible and the other resistant to M. oryzae, at multiple time points during the fungal infection. Our results revealed a substantial variation in the plant transcriptome and microRNAome as well as change to rice innate immunity during fungal infection. A number of putative R gene candidates were identified from a perturbed rice transcriptome analysis. The expression of genes and non-coding RNA molecules changed in both fungal resistant and susceptible plants during M. oryzae invasion discovered distinct pathways triggered in the susceptible and resistant plants. In addition, a number of fungus genes in the susceptible and resistant plants were constantly expressed at different time points, suggesting that they were likely to be the potential AVR genes. Our results revealed large-scale rewiring of innate immunity circuitry and microRNA regulation during initial rice blast infection, which would help to develop more robust blast-resistant rice plants.

Plastoquinone and Ubiquinone in Plants: Biosynthesis, Physiological Function and Metabolic Engineering

Plastoquinone (PQ) and ubiquinone (UQ) are two important prenylquinones, functioning as electron transporters in the electron transport chain of oxygenic photosynthesis and the aerobic respiratory chain, respectively, and play indispensable roles in plant growth and development through participating in the biosynthesis and metabolism of important chemical compounds, acting as antioxidants, being involved in plant response to stress, and regulating gene expression and cell signal transduction. UQ, particularly UQ₁₀, has also been widely used in people's life. It is effective in treating cardiovascular diseases, chronic gingivitis and periodontitis, and shows favorable impact on cancer treatment and human reproductive health. PQ and UQ are made up of an active benzoquinone ring attached to a polyisoprenoid side chain. Biosynthesis of PQ and UQ is very complicated with more than thirty five enzymes involved. Their synthetic pathways can be generally divided into two stages. The first stage leads to the biosynthesis of precursors of benzene quinone ring and prenyl side chain. The benzene quinone ring for UQ is synthesized from tyrosine or phenylalanine, whereas the ring for PQ is derived from tyrosine. The prenyl side chains of PQ and UQ are derived from glyceraldehyde 3-phosphate and pyruvate through the 2-C-methyl-D-erythritol 4-phosphate pathway and/or acetyl-CoA and acetoacetyl-CoA through the mevalonate pathway. The second stage includes the condensation of ring and side chain and subsequent modification. Homogentisate solanesyltransferase, 4-hydroxybenzoate polyprenyl diphosphate transferase and a series of benzene quinone ring modification enzymes are involved in this stage. PQ exists in plants, while UQ widely presents in plants, animals and microbes. Many enzymes and their encoding genes involved in PQ and UQ biosynthesis have been intensively studied recently. Metabolic engineering of UQ₁₀ in plants, such as rice and tobacco, has also been tested. In this review, we summarize and discuss recent research progresses in the biosynthetic pathways of PQ and UQ and enzymes and their encoding genes involved in side chain elongation and in the second stage of PQ and UQ biosynthesis. Physiological functions of PQ and UQ played in plants as well as the practical application and metabolic engineering of PQ and UQ are also included.

Small RNA Regulators of Plant-Hemipteran Interactions: Micromanagers with Versatile Roles

Non-coding small RNAs (sRNAs) in plants have important roles in regulating biological processes, including development, reproduction, and stress responses. Recent research indicates significant roles for sRNA-mediated gene silencing during plant-hemipteran interactions that involve all three of these biological processes. Plant responses to hemipteran feeding are determined by changes in the host transcriptome that appear to be fine-tuned by sRNAs. The role of sRNA in plant defense responses is complex. Different forms of sRNAs, with specific modes of action, regulate changes in the host transcriptome primarily through post-transcriptional gene silencing and occasionally through translational repression. Plant genetic resistance against hemipterans provides a model to explore the regulatory roles of sRNAs in plant defense. Aphid-induced sRNA expression in resistance genotypes delivers a new paradigm in understanding the regulation of R gene-mediated resistance in host plants. Unique sRNA profiles, including changes in sRNA biogenesis and expression can also provide insights into susceptibility to insect herbivores. Activation of phytohormone-mediated defense responses against insect herbivory is another hallmark of this interaction, and recent studies have shown that regulation of phytohormone signaling is under the control of sRNAs. Hemipterans feeding on resistant plants also show changes in insect sRNA profiles, possibly influencing insect development and reproduction. Changes in insect traits such as fecundity, host range, and resistance to insecticides are impacted by sRNAs and can directly contribute to the success of certain insect biotypes. In addition to causing direct damage to the host plant, hemipteran insects are often vectors of viral pathogens. Insect anti-viral RNAi machinery is activated to limit virus accumulation, suggesting a role in insect immunity. Virus-derived long sRNAs strongly resemble insect piRNAs, leading to the speculation that the piRNA pathway is induced in response to viral infection. Evidence for robust insect RNAi machinery in several hemipteran species is of immense interest and is being actively pursued as a possible tool for insect control. RNAi-induced gene silencing following uptake of exogenous dsRNA was successfully demonstrated in several hemipterans and the presence of sid-1 like genes support the concept of a systemic response in some species.

MicroRNA Expression Profile during Aphid Feeding in Chrysanthemum (Chrysanthemum morifolium)

MicroRNAs (miRNAs) are important regulators of gene expression, affecting many biological processes. As yet, their roles in the response of chrysanthemum to aphid feeding have not been explored. Here, the identity and abundance of miRNAs induced by aphid infestation have been obtained using high-throughput Illumina sequencing platform. Three leaf small RNA libraries were generated, one from plants infested with the aphid Macrosiphoniella sanbourni (library A), one from plants with mock puncture treatment (library M), and the third from untreated control plants (library CK). A total of 7,944,797, 7,605,251 and 9,244,002 clean unique reads, ranging from 18 to 30 nucleotides (nt) in length, were obtained from library CK, A and M, respectively. As a result, 303 conserved miRNAs belonging to 276 miRNAs families and 234 potential novel miRNAs were detected in chrysanthemum leaf, out of which 80, 100 and 79 significantly differentially expressed miRNAs were identified in the comparison of CK-VS-A, CK-VS-M and M-VS-A, respectively. Several of the differentially abundant miRNAs (in particular miR159a, miR160a, miR393a) may be associated with the plant's response to aphid infestation.