Identification of Fusarium graminearum-responsive miRNAs and their targets in wheat by sRNA sequencing and degradome analysis

Noncoding elements in wheat defence response to fusarium head blight

Wheat (Triticum aestivum L.) is a major source of global food security while various stressors, including biotic and abiotic factors, directly affect its production. Among these stressors, Fusarium infection poses a significant risk, leading to severe yield losses, and compromising the overall quality of the crop. To understand the regulatory mechanisms modulating wheat's response against Fusarium Head Blight (FHB) stress, a comprehensive analysis of the noncoding RNA profiles of two wheat varieties, Vida and Hank, was conducted. A dataset has been generated utilizing high throughput RNA sequencing (RNAseq) and small RNA sequencing (sRNAseq) technologies for identifying and characterizing microRNA (miRNA) and long noncoding RNA (lncRNA) profiles of these cultivars and the changes upon Fusarium infection. Our analysis revealed not only common but also cultivar- and condition-specific miRNAs and lncRNA transcripts, showing the unique regulatory responses exhibited by these wheat varieties under Fusarium stress. Furthermore, the functional properties of the identified miRNAs were investigated by identifying their putative coding sequence (CDS) targets. Additionally, the regulatory relationships between the putative miRNAs and lncRNAs were explored, providing a view of the complex molecular networks coordinating wheat's response against Fusarium infection. The proposed regulatory network includes the dynamic interplay between miRNAs, CDS targets, and lncRNAs, offering insights into potential key players in the adaptive responses of wheat to biotic stressors.

Transcriptomic analysis of two Chinese wheat landraces with contrasting Fusarium head blight resistance reveals miRNA-mediated defense mechanisms

Introduction

Fusarium head blight (FHB), caused primarily by Fusarium graminearum (Fg), poses a significant threat to wheat production. It is necessary to deeply understand the molecular mechanisms underlying FHB resistance in wheat breeding.

Methods

In this study, the transcriptomic responses of two Chinese wheat landraces-Wuyangmai (WY, resistant) and Chinese Spring (CS, susceptible)-to F. graminearum infection were examined using RNA sequencing (RNA-seq). Differential expression of mRNAs, long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs) was analyzed at 3 and 5 days post-Fg inoculation (dpi).

Results

The results showed that WY exhibited a targeted miRNA response, primarily modulating defense-related pathways such as glutathione metabolism and phenylpropanoid biosynthesis, which are crucial for oxidative stress regulation and pathogen defense response. In contrast, CS displayed a broader transcriptional response, largely linked to general metabolic processes rather than immune activation. Notably, the up-regulation of genes involved in oxidative stress and immune defense in WY confirmed its enhanced resistance to FHB. The integrated analysis of miRNA-mRNA interactions highlighted miRNAs as central regulators of defense mechanisms in WY, particularly at later stages of infection. These miRNAs targeted genes involved in immune responses, while lncRNAs and circRNAs played a more limited role in the regulation of defense responses. The GO and KEGG pathway enrichment analyses further revealed that WY enriched for plant-pathogen interaction and secondary metabolite biosynthesis pathways, which are crucial for pathogen resistance. In contrast, CS prioritized metabolic homeostasis, suggesting a less effective defense strategy.

Discussion

Overall, this study underscores the critical role of miRNA-mediated regulation in FHB resistance in WY. These insights into miRNA-mediated regulatory mechanisms provide a molecular basis for breeding FHB-resistant wheat varieties and highlight miRNA-mRNA interactions as promising targets for enhancing disease resilience.

An in - silico perspective on the role of methylation-related genes in wheat - Fusarium graminearum interaction

Wheat (Triticum aestivum L.), a vital cereal crop, provides over 20% of the total calories and protein in the human diet. However, Fusarium graminearum, the pathogen responsible for Fusarium head blight (FHB), poses a significant threat to wheat production by contaminating grains with harmful mycotoxins. Although Fusarium head blight is currently a minor disease in India, it has the potential to cause substantial yield and quality losses, especially if rain occurs during mid-anthesis. Epigenetic mechanisms, including DNA methylation and sRNA accumulation, are crucial in regulating gene expression and enabling plants to adapt to environmental stresses. Previous studies investigating wheat's response to F. graminearum through transcriptome analysis of lines differing in 2DL FHB resistance QTLs did not fully explore the role of methylation-related genes. To address this gap, we re-analyzed RNA-Seq data to uncover the response of methylation-related genes to pathogen infection. Our analysis revealed that 16 methylation-related genes were down-regulated in the susceptible line 2-2890, with Gene Ontology (GO) analysis linking these genes to L-methionine salvage from methylthioadenosine (GO:0019509), S-adenosylmethionine metabolism (GO:0033353), and steroid biosynthesis (GO:0006694) (p-value = 0.001). Co-expression analysis identified a negative correlation (-0.82) between methionine S-methyl-transferase (MSM; TraesCS1A02G013800) and 3-hydroxy-3-methyl-glutaryl coenzyme A reductase (HMGCR; TraesCS5A02G269300). HMGCR also showed negative correlations (-1.00) with genes encoding pathogenesis-related, detoxification proteins, and xylanase inhibitors, with GO associating these genes with methionine S-methyl transferase activity (p-value = 0.001). In pathogen-inoculated samples, the elevated expression of HMGCR (Log2 3.25-4.00) and the suppression of MSM (Log2 1.25-3.25) suggest a dual role in stress response and susceptibility, potentially linked to disrupted DNA methylation and isoprenoid biosynthesis pathways. Furthermore, 43 genes down-regulated by miR9678 were associated with biotic stimulus responses and glucan endo-1,4-beta-glucanase activity, highlighting the complex regulatory networks involved in wheat's defense against F. graminearum. This study reveals the roles of methylation-related genes in susceptible wheat lines 2-2890, providing new insights into their potential impact on pathogen response and plant susceptibility.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-04179-0.

Genome-Wide Transcriptional Response of Avocado to Fusarium sp. Infection

The avocado crop is relevant for its economic importance and because of its unique evolutionary history. However, there is a lack of information regarding the molecular processes during the defense response against fungal pathogens. Therefore, using a genome-wide approach in this work, we investigated the transcriptional response of the Mexican horticultural race of avocado (Persea americana var. drymifolia), including miRNAs profile and their possible targets. For that, we established an avocado-Fusarium hydroponic pathosystem and studied the response for 21 days. To guarantee robustness in the analysis, first, we improved the avocado genome assembly available for this variety, resulting in 822.49 Mbp in length with 36,200 gene models. Then, using an RNA-seq approach, we identified 13,778 genes differentially expressed in response to the Fusarium infection. According to their expression profile across time, these genes can be clustered into six groups, each associated with specific biological processes. Regarding non-coding RNAs, 8 of the 57 mature miRNAs identified in the avocado genome are responsive to infection caused by Fusarium, and the analysis revealed a total of 569 target genes whose transcript could be post-transcriptionally regulated. This study represents the first research in avocados to comprehensively explore the role of miRNAs in orchestrating defense responses against Fusarium spp. Also, this work provides valuable data about the genes involved in the intricate response of the avocado during fungal infection.

Analyzing the defense response mechanism of Atractylodes macrocephala to Fusarium oxysporum through small RNA and degradome sequencing

Introduction

Fusarium oxysporum is a significant soil-borne fungal pathogen that affects over 100 plant species, including crucial crops like tomatoes, bananas, cotton, cucumbers, and watermelons, leading to wilting, yellowing, growth inhibition, and ultimately plant death. The root rot disease of A. macrocephala, caused by F. oxysporum, is one of the most serious diseases in continuous cropping, which seriously affects its sustainable development.

Methods

In this study, we explored the interaction between A. macrocephala and F. oxysporum through integrated small RNA (sRNA) and degradome sequencing to uncover the microRNA (miRNA)-mediated defense mechanisms.

Results

We identified colonization of F. oxysporum in A. macrocephala roots on day 6. Nine sRNA samples were sequenced to examine the dynamic changes in miRNA expression in A. macrocephala infected by F. oxysporum at 0, 6, and 12 days after inoculation. Furthermore, we using degradome sequencing and quantitative real-time PCR (qRT-PCR), validated four miRNA/target regulatory units involved in A. macrocephala-F. oxysporum interactions.

Discussion

This study provides new insights into the molecular mechanisms underlying A. macrocephala's early defense against F. oxysporum infection, suggesting directions for enhancing resistance against this pathogen.

Genome-wide identification of Sclerotinia sclerotiorum small RNAs and their endogenous targets

BACKGROUND

Several phytopathogens produce small non-coding RNAs of approximately 18-30 nucleotides (nt) which post-transcriptionally regulate gene expression. Commonly called small RNAs (sRNAs), these small molecules were also reported to be present in the necrotrophic pathogen Sclerotinia sclerotiorum. S. sclerotiorum causes diseases in more than 400 plant species, including the important oilseed crop Brassica napus. sRNAs can further be classified as microRNAs (miRNAs) and short interfering RNAs (siRNAs). Certain miRNAs can activate loci that produce further sRNAs; these secondary sRNA-producing loci are called 'phased siRNA' (PHAS) loci and have only been described in plants. To date, very few studies have characterized sRNAs and their endogenous targets in S. sclerotiorum.

RESULTS

We used Illumina sequencing to characterize sRNAs from fungal mycelial mats of S. sclerotiorum spread over B. napus leaves. In total, eight sRNA libraries were prepared from in vitro, 12 h post-inoculation (HPI), and 24 HPI mycelial mat samples. Cluster analysis identified 354 abundant sRNA clusters with reads of more than 100 Reads Per Million (RPM). Differential expression analysis revealed upregulation of 34 and 57 loci at 12 and 24 HPI, respectively, in comparison to in vitro samples. Among these, 25 loci were commonly upregulated. Altogether, 343 endogenous targets were identified from the major RNAs of 25 loci. Almost 88% of these targets were annotated as repeat element genes, while the remaining targets were non-repeat element genes. Fungal degradome reads confirmed cleavage of two transposable elements by one upregulated sRNA. Altogether, 24 milRNA loci were predicted with both mature and milRNA* (star) sequences; these are both criteria associated previously with experimentally verified miRNAs. Degradome sequencing data confirmed the cleavage of 14 targets. These targets were related to repeat element genes, phosphate acetyltransferases, RNA-binding factor, and exchange factor. A PHAS gene prediction tool identified 26 possible phased interfering loci with 147 phasiRNAs from the S. sclerotiorum genome, suggesting this pathogen might produce sRNAs that function similarly to miRNAs in higher eukaryotes.

CONCLUSIONS

Our results provide new insights into sRNA populations and add a new resource for the study of sRNAs in S. sclerotiorum.

Tae-miR397 Negatively Regulates Wheat Resistance to Blumeria graminis

MicroRNA (miRNA) plays a crucial role in the interactions between plants and pathogens, and identifying disease-related miRNAs could help us understand the mechanisms underlying plant disease pathogenesis and breed resistant varieties. However, the role of miRNA in wheat defense responses remains largely unexplored. The miR397 family is highly conserved in plants and involved in plant development and defense response. Therefore, the purpose of this study was to investigate the function of tae-miR397 in wheat resistance to powdery mildew. The expression pattern analysis revealed that tae-miR397 expression was higher in young leaves than in other tissues and was significantly decreased in wheat Bainong207 leaves after Blumeria graminis (Bgt) infection and chitin treatment. Additionally, the expression of tae-miR397 was significantly down-regulated by salicylic acid and induced under jasmonate treatment. The overexpression of tae-miR397 in common wheat Bainong207 enhanced the wheat's susceptibility to powdery mildew in the seedling and adult stages. The rate of Bgt spore germination and mycelial growth in transgenic wheat plants overexpressing tae-miR397 was faster than in the untransformed wild-type plants. The target gene of tae-miR397 was predicted to be a wound-induced protein (Tae-WIP), and the function was investigated. We demonstrated that silencing of Tae-WIP via barley-stripe-mosaic-virus-induced gene silencing enhanced wheat's susceptibility to powdery mildew. qRT-PCR indicated that tae-miR397 regulated wheat immunity by controlling pathogenesis-related gene expressions. Moreover, the transgenic plants overexpressing tae-miR397 exhibited more tillers than the wild-type plants. This work suggests that tae-miR397 is a negative regulator of resistance against powdery mildew and has great potential for breeding disease-resistant cultivars.

Genome-Wide Analysis and Identification of 1-Aminocyclopropane-1-Carboxylate Synthase (ACS) Gene Family in Wheat (Triticum aestivum L.)

Ethylene has an important role in regulating plant growth and development as well as responding to adversity stresses. The 1-aminocyclopropane-1-carboxylate synthase (ACS) is the rate-limiting enzyme for ethylene biosynthesis. However, the role of the ACS gene family in wheat has not been examined. In this study, we identified 12 ACS members in wheat. According to their position on the chromosome, we named them TaACS1-TaACS12, which were divided into four subfamilies, and members of the same subfamilies had similar gene structures and protein-conserved motifs. Evolutionary analysis showed that fragment replication was the main reason for the expansion of the TaACS gene family. The spatiotemporal expression specificity showed that most of the members had the highest expression in roots, and all ACS genes contained W box elements that were related to root development, which suggested that the ACS gene family might play an important role in root development. The results of the gene expression profile analysis under stress showed that ACS members could respond to a variety of stresses. Protein interaction prediction showed that there were four types of proteins that could interact with TaACS. We also obtained the targeting relationship between TaACS family members and miRNA. These results provided valuable information for determining the function of the wheat ACS gene, especially under stress.

Genome-Wide Characterization of the RNA Exosome Complex in Relation to Growth, Development, and Pathogenicity of Fusarium graminearum

The RNA exosome complex is a conserved, multisubunit RNase complex that contributes to the processing and degradation of RNAs in mammalian cells. However, the roles of the RNA exosome in phytopathogenic fungi and how it relates to fungal development and pathogenicity remain unclear. Herein, we identified 12 components of the RNA exosome in the wheat fungal pathogen Fusarium graminearum. Live-cell imaging showed that all the components of the RNA exosome complex are localized in the nucleus. FgEXOSC1 and FgEXOSCA were successfully knocked out; they are both involved in the vegetative growth, sexual reproduction, and pathogenicity of F. graminearum. Moreover, deletion of FgEXOSC1 resulted in abnormal toxisomes, decreased deoxynivalenol (DON) production, and downregulation of the expression levels of DON biosynthesis genes. The RNA-binding domain and N-terminal region of FgExosc1 are required for its normal localization and functions. Transcriptome sequencing (RNA-seq) showed that the disruption of FgEXOSC1 resulted in differential expression of 3,439 genes. Genes involved in processing of noncoding RNA (ncRNA), rRNA and ncRNA metabolism, ribosome biogenesis, and ribonucleoprotein complex biogenesis were significantly upregulated. Furthermore, subcellular localization, green fluorescent protein (GFP) pulldown, and coimmunoprecipitation (co-IP) assays demonstrated that FgExosc1 associates with the other components of the RNA exosome to form the RNA exosome complex in F. graminearum. Deletion of FgEXOSC1 and FgEXOSCA reduced the relative expression of some of the other subunits of the RNA exosome. Deletion of FgEXOSC1 affected the localization of FgExosc4, FgExosc6, and FgExosc7. In summary, our study reveals that the RNA exosome is involved in vegetative growth, sexual reproduction, DON production, and pathogenicity of F. graminearum. IMPORTANCE The RNA exosome complex is the most versatile RNA degradation machinery in eukaryotes. However, little is known about how this complex regulates the development and pathogenicity of plant-pathogenic fungi. In this study, we systematically identified 12 components of the RNA exosome complex in Fusarium head blight fungus Fusarium graminearum and first unveiled their subcellular localizations and established their biological functions in relation to the fungal development and pathogenesis. All the RNA exosome components are localized in the nucleus. FgExosc1 and FgExoscA are both required for the vegetative growth, sexual reproduction, DON production and pathogenicity in F. graminearum. FgExosc1 is involved in ncRNA processing, rRNA and ncRNA metabolism process, ribosome biogenesis and ribonucleoprotein complex biogenesis. FgExosc1 associates with the other components of RNA exosome complex and form the exosome complex in F. graminearum. Our study provides new insights into the role of the RNA exosome in regulating RNA metabolism, which is associated with fungal development and pathogenicity.

Genome-wide analysis and identification of light-harvesting chlorophyll a/b binding (LHC) gene family and BSMV-VIGS silencing TaLHC86 reduced salt tolerance in wheat

The discovery and identification of gene families by using wide-genome and public databases is an effective way to gain initial insight into gene function, which also is one of the current hot spots of research. Chlorophyll ab-binding proteins (LHC) are important for photosynthesis and widely involved in plant adversity stress. However, the study in wheat has not been reported. In this study, we identified 127 TaLHC members from common wheat which were unevenly distributed on all chromosomes except 3B and 3D. All members divided into three subfamilies, LHC a, LHC b and the LHC t which was only discovered in wheat. All of them had maximum expression in leaves and contained multiple light-responsive cis-acting element, which were evidence of the extensive involvement of LHC families in photosynthesis. In addition, we also analyzed their collinear relationship, targeting relationship with miRNA and their responses under different stresses. Based on these analyses, it was found that TaLHC86 was an excellent candidate gene for stress resistance. The full-length ORF of TaLHC86 was 792 bp and was localized on the chloroplasts. The salt tolerance of wheat was reduced when BSMV-VIGS silenced TaLHC86, and the photosynthetic rate and electron transport were also seriously affected. This study made a comprehensive analysis of the TaLHC family and found that TaLHC86 was a good gene for salt tolerance.

Wheat Long Noncoding RNAs from Organelle and Nuclear Genomes Carry Conserved microRNA Precursors Which May Together Comprise Intricate Networks in Insect Responses

Long noncoding RNAs (lncRNAs) are a diverse class of noncoding RNAs that are typically longer than 200 nucleotides but lack coding potentials. Advances in deep sequencing technologies enabled a better exploration of this type of noncoding transcripts. The poor sequence conservation, however, complicates the identification and annotation of lncRNAs at a large scale. Wheat is among the leading food staples worldwide whose production is threatened by both biotic and abiotic stressors. Here, we identified putative lncRNAs from durum wheat varieties that differ in stem solidness, a major source of defense against wheat stem sawfly, a devastating insect pest. We also analyzed and annotated lncRNAs from two bread wheat varieties, resistant and susceptible to another destructive pest, orange wheat blossom midge, with and without infestation. Several putative lncRNAs contained potential precursor sequences and/or target regions for microRNAs, another type of regulatory noncoding RNAs, which may indicate functional networks. Interestingly, in contrast to lncRNAs themselves, microRNAs with potential precursors within the lncRNA sequences appeared to be highly conserved at the sequence and family levels. We also observed a few putative lncRNAs that have perfect to near-perfect matches to organellar genomes, supporting the recent observations that organellar genomes may contribute to the noncoding transcript pool of the cell.

Degradome sequencing reveals an integrative miRNA-mediated gene interaction network regulating rice seed vigor

BACKGROUND

It is well known that seed vigor is essential for agricultural production and rice (Oryza sativa L.) is one of the most important crops in the world. Though we previously reported that miR164c regulates rice seed vigor, but whether and how other miRNAs cooperate with miR164c to regulate seed vigor is still unknown.

RESULTS

Based on degradome data of six RNA samples isolated from seeds of the wild-type (WT) indica rice cultivar 'Kasalath' as well as two modified lines in 'Kasalath' background (miR164c-silenced line [MIM164c] and miR164c overexpression line [OE164c]), which were subjected to either no aging treatment or an 8-day artificial aging treatment, 1247 different target transcripts potentially cleaved by 421 miRNAs were identified. The miRNA target genes were functionally annotated via GO and KEGG enrichment analyses. By STRING database assay, a miRNA-mediated gene interaction network regulating seed vigor in rice was revealed, which comprised at least four interconnected pathways: the miR5075-mediated oxidoreductase related pathway, the plant hormone related pathway, the miR164e related pathway, and the previously reported RPS27AA related pathway. Knockout and overexpression of the target gene Os02g0817500 of miR5075 decreased and enhanced seed vigor, respectively. By Y2H assay, the proteins encoded by five seed vigor-related genes, Os08g0295100, Os07g0633100, REFA1, OsPER1 and OsGAPC3, were identified to interact with Os02g0817500.

CONCLUSIONS

miRNAs cooperate to regulate seed vigor in rice via an integrative gene interaction network comprising miRNA target genes and other functional genes. The result provided a basis for fully understanding the molecular mechanisms of seed vigor regulation.

Expression Patterns of miR398, miR167, and miR159 in the Interaction between Bread Wheat (Triticum aestivum L.) and Pathogenic Fusarium culmorum and Beneficial Trichoderma Fungi

Bread wheat (Triticum aestivum L.) is an agronomically significant cereal cultivated worldwide. Wheat breeding is limited by numerous abiotic and biotic stresses. One of the most deleterious factors is biotic stress provoked by the Fusarium culmorum fungus. This pathogen is a causative agent of Fusarium root rot and Fusarium head blight. Beneficial fungi Trichoderma atroviride and T. cremeum are strong antagonists of mycotoxigenic Fusarium spp. These fungi promote plant growth and enhance their tolerance of negative environmental conditions. The aim of the study was to determine and compare the spatial (in above- and underground organs) and temporal (early: 6 and 22 hpi; and late: 5 and 7 dpi reactions) expression profiles of three mature miRNAs (miR398, miR167, and miR159) in wheat plants inoculated with two strains of F. culmorum (KF846 and EW49). Moreover, the spatial expression patterns in wheat response between plants inoculated with beneficial T. atroviride (AN35) and T. cremeum (AN392) were assessed. Understanding the sophisticated role of miRNAs in wheat-fungal interactions may initiate a discussion concerning the use of this knowledge to protect wheat plants from the harmful effects of fungal pathogens. With the use of droplet digital PCR (ddPCR), the absolute quantification of the selected miRNAs in the tested material was carried out. The differential accumulation of miR398, miR167, and miR159 in the studied groups was observed. The abundance of all analyzed miRNAs in the roots demonstrated an increase in the early and reduction in late wheat response to F. culmorum inoculation, suggesting the role of these particles in the initial wheat reaction to the studied fungal pathogen. The diverse expression patterns of the studied miRNAs between Trichoderma-inoculated or F. culmorum-inoculated plants and control wheat, as well as between Trichoderma-inoculated and F. culmorum-inoculated plants, were noticed, indicating the need for further analysis.