Pathogen challenge, salicylic acid, and jasmonic acid regulate expression of chitinase gene homologs in pine

Effect of elevated ammonium on biotic and abiotic stress defense responses and expression of related genes in cucumber (Cucumis sativus L.) plants

Ammonium (NH4+) enhances plant defense mechanisms but can be phytotoxic as the sole nitrogen source. To investigate the impact of a balanced NH4+ and NO3- ratio on plant defense parameters without adverse effects, cucumber plants (Cucumis sativus L.) were grown under control (14 mM NO3- + 2 mM NH4+) and elevated level of NH4+ (eNH4+, 8 mM NO3-+ 8 mM NH4+). Plants subjected to eNH4+ showed significantly increased shoot and root biomass by about 41% and 47%, respectively. Among the antioxidant enzymes studied, ascorbate peroxidase (EC 1.11.1.11) activity was increased up to 3.3 fold in eNH4+ compared with control plants, which was associated with enhanced resistance to paraquat. Upregulation of PATHOGENESIS RELATED PROTEIN 4 (PR4) and LIPOXYGENASE 1 (LOX1), accompanied by increased concentrations of salicylic acid and nitric oxide, conferred more excellent resistance of eNH4+ plants to powdery mildew infection. However, the expression levels of ACC OXIDASE 1 (ACO1) and RESPIRATORY BURST OXIDASE HOMOLOGS B (RBOHB) were lower in eNH4+ plants, which was consistent with decreased NADPH oxidase activity and lower leaf H2O2 levels. The biosynthesis of phenolics was enhanced, whereas the activities of polymerizing enzymes and lignin deposition were reduced by half in eNH4+ plants. Besides, a significant effect on plant biomass under salt or drought stress has not been observed between control and eNH4+ plants. These results showed that different defense pathways are distinctively affected by eNH4+ treatment, and the NH4+ to NO3- ratio may play a role in fine-tuning the plant defense response.

Systematic analysis and functional characterization of the chitinase gene family in Fagopyrum tataricum under salt stress

BACKGROUND

Chitinases (CHIs) are glycosidases that degrade chitin, playing critical roles in plant responses to both abiotic and biotic stress. Despite their importance, the CHI family's systematic analysis and evolutionary pattern in F. tataricum (Tartary buckwheat) yet to be explored.

RESULTS

This study analyzed their phylogenetic relationships, conserved motifs, gene structures, syntenic relationships, physiological functions, and biochemical properties. This research identified 26 FtCHIs and examined their expression patterns under different salt stress conditions and across various tissues. Differential expression analysis revealed a significant upregulation of multiple FtCHIs in response to salt stress, which RT-qPCR further validated. Additionally, subcellular localization experiments demonstrated that Ft_chitinaseIV-2 is localized in vacuoles. The results of transient·transformation showed that·overexpression of Ft_chitinaseIV-2 could·enhance the salt tolerance of plants.

CONCLUSIONS

The findings provide new insights into the role of CHIs in stress tolerance and lay the groundwork for future research on the functional characterization of FtCHIs. Understanding the molecular mechanisms of CHI-mediated stress responses could contribute to developing stress-resistant crops.

Unraveling Pinus massoniana's Defense Mechanisms Against Bursaphelenchus xylophilus Under Aseptic Conditions: A Transcriptomic Analysis

Pine wilt disease (PWD) is caused by the pine wood nematode (PWN, Bursaphelenchus xylophilus) and significantly impacts pine forest ecosystems globally. This study focuses on Pinus massoniana, an important timber and oleoresin resource in China, which is highly susceptible to PWN. However, the defense mechanism of pine trees in response to PWN remains unclear. Addressing the complexities of PWD, influenced by diverse factors such as bacteria, fungi, and environment, we established a reciprocal system between PWN and P. massoniana seedlings under aseptic conditions. Utilizing combined second- and third-generation sequencing technologies, we identified 3,718 differentially expressed genes post PWN infection. Transcript analysis highlighted the activation of defense mechanisms via stilbenes, salicylic acid and jasmonic acid pathways, terpene synthesis, and induction of pathogenesis-related proteins and resistance genes, predominantly at 72 h postinfection. Notably, terpene synthesis pathways, particularly the mevalonate pathway, were crucial in defense, suggesting their significance in P. massoniana's response to PWN. This comprehensive transcriptome profiling offers insights into P. massoniana's intricate defense strategies against PWN under aseptic conditions, laying a foundation for future functional analyses of key resistance genes. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Genome-Wide Identification of the Maize Chitinase Gene Family and Analysis of Its Response to Biotic and Abiotic Stresses

BACKGROUND/OBJECTIVES

Chitinases, enzymes belonging to the glycoside hydrolase family, play a crucial role in plant growth and stress response by hydrolyzing chitin, a natural polymer found in fungal cell walls. This study aimed to identify and analyze the maize chitinase gene family, assessing their response to various biotic and abiotic stresses to understand their potential role in plant defense mechanisms and stress tolerance.

METHODS

We employed bioinformatics tools to identify 43 chitinase genes in the maize B73_V5 genome. These genes were characterized for their chromosomal positions, gene and protein structures, phylogenetic relationships, functional enrichment, and collinearity. Based on previous RNA-seq data, the analysis assessed the expression patterns of these genes at different developmental stages and under multiple stress conditions.

RESULTS

The identified chitinase genes were unevenly distributed across maize chromosomes with a history of tandem duplications contributing to their divergence. The ZmChi protein family was predominantly hydrophilic and localized mainly in chloroplasts. Expression analysis revealed that certain chitinase genes were highly expressed at specific developmental stages and in response to various stresses, with ZmChi31 showing significant responsiveness to 11 different abiotic and biotic stresses.

CONCLUSIONS

This study provides new insights into the role of chitinase genes in maize stress response, establishing a theoretical framework for exploring the molecular basis of maize stress tolerance. The identification of stress-responsive chitinase genes, particularly ZmChi31, offers potential candidates for further study in enhancing maize resistance to environmental challenges.

A delayed response in phytohormone signaling and production contributes to pine susceptibility to Fusarium circinatum

BACKGROUND

Fusarium circinatum is the causal agent of pine pitch canker disease, which affects Pinus species worldwide, causing significant economic and ecological losses. In Spain, two Pinus species are most affected by the pathogen; Pinus radiata is highly susceptible, while Pinus pinaster has shown moderate resistance. In F. circinatum-Pinus interactions, phytohormones are known to play a crucial role in plant defense. By comparing species with different degrees of susceptibility, we aimed to elucidate the fundamental mechanisms underlying resistance to the pathogen. For this purpose, we used an integrative approach by combining gene expression and metabolomic phytohormone analyses at 5 and 10 days post inoculation.

RESULTS

Gene expression and metabolite phytohormone contents suggested that the moderate resistance of P. pinaster to F. circinatum is determined by the induction of phytohormone signaling and hormone rearrangement beginning at 5 dpi, when symptoms are still not visible. Jasmonic acid was the hormone that showed the greatest increase by 5 dpi, together with the active gibberellic acid 4 and the cytokinin dehydrozeatin; there was also an increase in abscisic acid and salicylic acid by 10 dpi. In contrast, P. radiata hormonal changes were delayed until 10 dpi, when symptoms were already visible; however, this increase was not as high as that in P. pinaster. Indeed, in P. radiata, no differences in jasmonic acid or salicylic acid production were found. Gene expression analysis supported the hormonal data, since the activation of genes related to phytohormone synthesis was observed earlier in P. pinaster than in the susceptible P. radiata.

CONCLUSIONS

We determine that the moderate resistance of P. pinaster to F. circinatum is in part a result of early and strong activation of plant phytohormone-based defense responses before symptoms become visible. We suggest that jasmonic acid signaling and production are strongly associated with F. circinatum resistance. In contrast, P. radiata susceptibility was attributed to a delayed response to the fungus at the moment when symptoms were visible. Our results contribute to a better understanding of the phytohormone-based defense mechanism involved in the Pinus-F. circinatum interactions and provide insight into the development of new strategies for disease mitigation.

The Growth-Promoting and Colonization of the Pine Endophytic Pseudomonas abietaniphila for Pine Wilt Disease Control

In this study, we focused on evaluating the impact of Pseudomonas abietaniphila BHJ04 on the growth of Pinus massoniana seedlings and its biocontrol efficacy against pine wilt disease (PWD). Additionally, the colonization dynamics of P. abietaniphila BHJ04 on P. massoniana were examined. The growth promotion experiment showed that P. abietaniphila BHJ04 significantly promoted the growth of the branches and roots of P. massoniana. Pot control experiments indicated that strain BHJ04 significantly inhibited the spread of PWD. There were significant changes in the expression of several genes related to pine wood nematode defense in P. massoniana, including chitinase, nicotinamide synthetase, and triangular tetrapeptide-like superfamily protein isoform 9. Furthermore, our results revealed significant upregulation of genes associated with the water stress response (dehydration-responsive proteins), genetic material replication (DNA/RNA polymerase superfamily proteins), cell wall hydrolase, and detoxification (cytochrome P450 and cytochrome P450 monooxygenase superfamily genes) in the self-regulation of P. massoniana. Colonization experiments demonstrated that strain BHJ04 can colonize the roots, shoots, and leaves of P. massoniana, and the colonization amount on the leaves was the greatest, reaching 160,000 on the 15th day. However, colonization of the stems lasted longer, with the highest level of colonization observed after 45 d. This study provides a preliminary exploration of the growth-promoting and disease-preventing mechanisms of P. abietaniphila BHJ04 and its ability to colonize pines, thus providing a new biocontrol microbial resource for the biological control of plant diseases.

Dissecting the role of salicylic acid in mediating stress response in mungbean cultivars concurrently exposed to Macrophomina phaseolina infection and drought stress

The combined stress studies provide fundamental knowledge that could assist in producing multiple stress resilient crops. The fungal phytopathogen, Macrophomina phaseolina is a major limiting factor in the productivity of the crop, Vigna radiata (mungbean). This fungal species tends to flourish under hot and dry conditions. Therefore, in this study the salicylic acid (SA) mediated stress responses in contrasting mungbean cultivars (Shikha and RMG-975) exposed to combined M. phaseolina infection (F) and drought stress (D) have been elucidated. The combined stress was applied to ten days seedlings in three orders i.e. drought followed by fungal infection (DF), drought followed by fungal infection with extended water deficit (DFD) and fungal infection followed by drought stress (FD). The severity of infection was analyzed using ImageJ analysis. Besides, the concentration of SA has been correlated with the phenylpropanoid pathway products, expression of pathogenesis-related proteins (β-1,3-glucanase and chitinase) and the specific activity of certain related enzymes (phenylalanine ammonia lyase, lipoxygenase and glutathione-S-transferase). The data revealed that the cultivar RMG-975 was relatively more tolerant than Shikha under individual stresses. However, the former became more susceptible to the infection under DFD treatment while the latter showed tolerance. Otherwise, the crown rot severity was reduced in both the cultivars under other combined treatments. The stress response analysis suggested that enhanced chitinase expression is vital for tolerance against both, the pathogen and drought stress. Also, it was noted that plants treat each stress combination differently and the role of SA was more prominently visible under individual stress conditions.

The impact of insect egg deposition on Pinus sylvestris transcriptomic and phytohormonal responses to larval herbivory

Plants can improve their resistance to feeding damage by insects if they have perceived insect egg deposition prior to larval feeding. Molecular analyses of these egg-mediated defence mechanisms have until now focused on angiosperm species. It is unknown how the transcriptome of a gymnosperm species responds to insect eggs and subsequent larval feeding. Scots pine (Pinus sylvestris L.) is known to improve its defences against larvae of the herbivorous sawfly Diprion pini L. if it has previously received sawfly eggs. Here, we analysed the transcriptomic and phytohormonal responses of Scots pine needles to D. pini eggs (E-pine), larval feeding (F-pine) and to both eggs and larval feeding (EF-pine). Pine showed strong transcriptomic responses to sawfly eggs and-as expected-to larval feeding. Many egg-responsive genes were also differentially expressed in response to feeding damage, and these genes play an important role in biological processes related to cell wall modification, cell death and jasmonic acid signalling. EF-pine showed fewer transcriptomic changes than F-pine, whereas EF-treated angiosperm species studied so far showed more transcriptional changes to the initial phase of larval feeding than only feeding-damaged F-angiosperms. However, as with responses of EF-angiosperms, EF-pine showed higher salicylic acid concentrations than F-pine. Based on the considerable overlap of the transcriptomes of E- and F-pine, we suggest that the weaker transcriptomic response of EF-pine than F-pine to larval feeding damage is compensated by the strong, egg-induced response, which might result in maintained pine defences against larval feeding.

Transcriptional survey of abiotic stress response in maize (Zea mays) in the level of gene co-expression network and differential gene correlation analysis

Abstract. Maize may be exposed to several abiotic stresses in the field. Therefore, identifying the tolerance mechanisms of natural field stress is mandatory. Gene expression data of maize upon abiotic stress were collected, and 560 differentially expressed genes (DEGs) were identified through meta-analysis. The most significant gene ontology terms in up-regulated genes were 'response to abiotic stress' and 'chitinase activity'. 'Phosphorelay signal transduction system' was the most significant enriched biological process in down-regulated DEGs. The co-expression analysis unveiled seven modules of DEGs, with a notable positive correlation between the modules and abiotic stress. Furthermore, the statistical significance was strikingly high for the turquoise, green and yellow modules. The turquoise group played a central role in orchestrating crucial adaptations in metabolic and stress response pathways in maize when exposed to abiotic stress. Within three up-regulated modules, Zm.7361.1.A1_at, Zm.10386.1.A1_a_at and Zm.10151.1.A1_at emerged as hub genes. These genes might introduce novel candidates implicated in stress tolerance mechanisms, warranting further comprehensive investigation and research. In parallel, the R package glmnet was applied to fit a logistic LASSO regression model on the DEGs profile to select candidate genes associated with abiotic responses in maize. The identified hub genes and LASSO regression genes were validated on an independent microarray dataset. Additionally, Differential Gene Correlation Analysis (DGCA) was performed on LASSO and hub genes to investigate the gene-gene regulatory relationship. The P value of DGCA of 16 pairwise gene comparisons was lower than 0.01, indicating a gene-gene significant change in correlation between control and abiotic stress. Integrated weighted gene correlation network analysis and logistic LASSO analysis revealed Zm.11185.1.S1_at, Zm.2331.1.S1_x_at and Zm.17003.1.S1_at. Notably, these 3 genes were identified in the 16 gene-pair comparisons. This finding highlights the notable significance of these genes in the abiotic stress response. Additional research into maize stress tolerance may focus on these three genes.

The Bursaphelenchus xylophilus candidate effector BxLip-3 targets the class I chitinases to suppress immunity in pine

Lipase is involved in lipid hydrolysis, which is related to nematodes' energy reserves and stress resistance. However, the role of lipases in Bursaphelenchus xylophilus, a notorious plant-parasitic nematode responsible for severe damage to pine forest ecosystems, remains largely obscure. Here, we characterized a class III lipase as a candidate effector and named it BxLip-3. It was transcriptionally up-regulated in the parasitic stages of B. xylophilus and specifically expressed in the oesophageal gland cells and the intestine. In addition, BxLip-3 suppressed cell death triggered by the pathogen-associated molecular patterns PsXEG1 and BxCDP1 in Nicotiana benthamiana, and its Lipase-3 domain is essential for immunosuppression. Silencing of the BxLip-3 gene resulted in a delay in disease onset and increased the activity of antioxidant enzymes and the expression of pathogenesis-related (PR) genes. Plant chitinases are thought to be PR proteins involved in the defence system against pathogen attack. Using yeast two-hybrid and co-immunoprecipitation assays, we identified two class I chitinases in Pinus thunbergii, PtChia1-3 and PtChia1-4, as targets of BxLip-3. The expression of these two chitinases was up-regulated during B. xylophilus inoculation and inhibited by BxLip-3. Overall, this study illustrated that BxLip-3 is a crucial virulence factor that plays a critical role in the interaction between B. xylophilus and host pine.

Bioinformatics and Expression Analysis of the Chitinase Genes in Strawberry (Fragaria vesca) and Functional Study of FvChi-14

Plant chitinases (EC 3.2.1.14) are pathogenesis-related (PR) proteins and are well studied in many plant species. However, little is known about the genomic organization and expression of chitinase genes in strawberries (Fragaria vesca). Here, 23 FvChi genes were identified in the genome of strawberry (F. vesca) and divided into GH18 and GH19 subfamilies based on phylogenetic relationships. A detailed bioinformatics analysis of the FvChi genes was performed, including gene physicochemical properties, chromosomal location, exon-intron distribution, domain arrangement, and subcellular localization. Twenty-two FvChi genes showed upregulation after Colletotrichum gloeosporioides infection. Following the exogenous application of SA, FvChi-3, 4, and 5 showed significant changes in expression. The ectopic expression of FvChi-14 in Arabidopsis thaliana increased resistance to C. higginsianum via controlling the SA and JA signaling pathway genes (AtPR1, AtICS1, AtPDF1.2, and AtLOX3). The FvChi-14 protein location was predicted in the cell wall or extracellular matrix. We speculate that FvChi-14 is involved in disease resistance by regulating the SA and JA signaling pathways. The findings of this study provide a theoretical reference for the functional studies of FvChi genes and new candidates for strawberry stress resistance breeding programs.

A chitinase CsChi23 promoter polymorphism underlies cucumber resistance against Fusarium oxysporum f. sp. cucumerinum

Fusarium wilt disease, caused by Fusarium oxysporum f. sp. cucumerinum (Foc), leads to widespread yield loss and quality decline in cucumber. However, the molecular mechanisms underlying Foc resistance remain poorly understood. We report the mapping and functional characterisation of CsChi23, encoding a cucumber class I chitinase with antifungal properties. We assessed sequence variations at CsChi23 and the associated defence response against Foc. We functionally characterised CsChi23 using transgenic assay and expression analysis. The mechanism regulating CsChi23 expression was assessed by genetic and molecular approaches. CsChi23 was induced by Foc infection, which led to rapid upregulation in resistant cucumber lines. Overexpressing CsChi23 enhanced fusarium wilt resistance and reduced fungal biomass accumulation, whereas silencing CsChi23 causes loss of resistance. CsHB15, a homeodomain leucine zipper (HD-Zip) III transcription factor, was found to bind to the CsChi23 promoter region and activate its expression. Furthermore, silencing of CsHB15 reduces CsChi23 expression. A single-nucleotide polymorphism variation -400 bp upstream of CsChi23 abolished the HD-Zip III binding site in a susceptible cucumber line. Collectively, our study indicates that CsChi23 is sufficient to enhance fusarium wilt resistance and reveals a novel function of an HD-Zip III transcription factor in regulating chitinase expression in cucumber defence against fusarium wilt.

Transcriptome changes associated with apple (Malus domestica) root defense response after Fusarium proliferatum f. sp. malus domestica infection

BACKGROUND

Apple replant disease is a soilborne disease caused by Fusarium proliferatum f. sp. malus domestica strain MR5 (abbreviated hereafter as Fpmd MR5) in China. This pathogen causes root tissue rot and wilting leaves in apple seedlings, leading to plant death. A comparative transcriptome analysis was conducted using the Illumina Novaseq platform to identify the molecular defense mechanisms of the susceptible M.26 and the resistant M9T337 apple rootstocks to Fpmd MR5 infection.

RESULTS

Approximately 518.1 million high-quality reads were generated using RNA sequencing (RNA-seq). Comparative analysis between the mock-inoculated and Fpmd MR5 infected apple rootstocks revealed 28,196 significantly differentially expressed genes (DEGs), including 14,572 up-regulated and 13,624 down-regulated genes. Among them, the transcriptomes in the roots of the susceptible genotype M.26 were reflected by overrepresented DEGs. MapMan analysis indicated that a large number of DEGs were involved in the response of apple plants to Fpmd MR5 stress. The important functional groups identified via gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were responsible for fundamental biological regulation, secondary metabolism, plant-pathogen recognition, and plant hormone signal transduction (ethylene and jasmonate). Furthermore, the expression of 33 up-regulated candidate genes (12 related to WRKY DNA-binding proteins, one encoding endochitinase, two encoding beta-glucosidases, ten related to pathogenesis-related proteins, and eight encoding ethylene-responsive transcription factors) were validated by quantitative real-time PCR.

CONCLUSION

RNA-seq profiling was performed for the first time to analyze response of apple root to Fpmd MR5 infection. We found that the production of antimicrobial compounds and antioxidants enhanced plant resistance to pathogens, and pathogenesis-related protein (PR10 homologs, chitinase, and beta-glucosidase) may play unique roles in the defense response. These results provide new insights into the mechanisms of the apple root response to Fpmd MR5 infection.

Transcriptomic changes during the establishment of long-term methyl jasmonate-induced resistance in Norway spruce

Norway spruce (Picea abies) is an economically and ecologically important tree species that grows across northern and central Europe. Treating Norway spruce with jasmonate has long-lasting beneficial effects on tree resistance to damaging pests, such as the European spruce bark beetle Ips typographus and its fungal associates. The (epi)genetic mechanisms involved in such long-lasting jasmonate induced resistance (IR) have gained much recent interest but remain largely unknown. In this study, we treated 2-year-old spruce seedlings with methyl jasmonate (MeJA) and challenged them with the I. typographus vectored necrotrophic fungus Grosmannia penicillata. MeJA treatment reduced the extent of necrotic lesions in the bark 8 weeks after infection and thus elicited long-term IR against the fungus. The transcriptional response of spruce bark to MeJA treatment was analysed over a 4-week time course using mRNA-seq. This analysis provided evidence that MeJA treatment induced a transient upregulation of jasmonic acid, salicylic acid and ethylene biosynthesis genes and downstream signalling genes. Our data also suggests that defence-related genes are induced while genes related to growth are repressed by methyl jasmonate treatment. These results provide new clues about the potential underpinning mechanisms and costs associated with long-term MeJA-IR in Norway spruce.

Studying tree response to biotic stress using a multi-disciplinary approach: The pine pitch canker case study

In an era of climate change and global trade, forests sustainability is endangered by several biotic threats. Pine pitch canker (PPC), caused by Fusarium circinatum, is one of the most important disease affecting conifers worldwide. To date, no effective control measures have been found for this disease. Earlier studies on PPC were mainly focused on the pathogen itself or on determining the levels of susceptibility of different hosts to F. circinatum infection. However, over the last years, plenty of information on the mechanisms that may explain the susceptibility or resistance to PPC has been published. This data are useful to better understand tree response to biotic stress and, most importantly, to aid the development of innovative and scientific-based disease control measures. This review gathers and discusses the main advances on PPC knowledge, especially focusing on multi-disciplinary studies investigating the response of pines with different levels of susceptibility to PPC upon infection. After an overview of the general knowledge of the disease, the importance of integrating information from physiological and Omics studies to unveil the mechanisms behind PPC susceptibility/resistance and to develop control strategies is explored. An extensive review of the main host responses to PPC was performed, including changes in water relations, signalling (ROS and hormones), primary metabolism, and defence (resin, phenolics, and PR proteins). A general picture of pine response to PPC is suggested according to the host susceptibility level and the next steps and gaps on PPC research are pointed out.

Comparative proteomics of Pinus-Fusarium circinatum interactions reveal metabolic clues to biotic stress resistance

Fusarium circinatum, causing pine pitch canker (PPC), affects conifers productivity and health worldwide. Selection and breeding for resistance arises as the most promising approach to fight PPC. Therefore, it is crucial to explore the response of hosts with varying levels of susceptibility to PPC to unveil the genes/pathways behind these phenotypes. We evaluated the dynamics of the needle proteome of a susceptible (Pinus radiata) and a relatively resistant (Pinus pinea) species upon F. circinatum inoculation by GeLC-MS/MS. Integration with physiological data and validation of key genes by qPCR allowed to identify core pathways regulating these contrasting responses. In P. radiata, the pathogen may target both the secondary metabolism to negatively regulate immune response and chloroplast redox proteins to increase energy-producing pathways for amino acid production in its favour. In contrast, chloroplast redox regulation may assure redox homeostasis in P. pinea, as well as nonenzymatic antioxidants. The presence of membrane trafficking-related proteins exclusively in P. pinea likely explains its defence response against F. circinatum. A crosstalk between abscisic acid and epigenetic regulation of gene expression is also proposed in PPC response. These results are useful to support breeding programs aiming to achieve PPC resistance.

Insights Into the Mechanisms Implicated in Pinus pinaster Resistance to Pinewood Nematode

Pine wilt disease (PWD), caused by the plant-parasitic nematode Bursaphelenchus xylophilus, has become a severe environmental problem in the Iberian Peninsula with devastating effects in Pinus pinaster forests. Despite the high levels of this species' susceptibility, previous studies reported heritable resistance in P. pinaster trees. Understanding the basis of this resistance can be of extreme relevance for future programs aiming at reducing the disease impact on P. pinaster forests. In this study, we highlighted the mechanisms possibly involved in P. pinaster resistance to PWD, by comparing the transcriptional changes between resistant and susceptible plants after infection. Our analysis revealed a higher number of differentially expressed genes (DEGs) in resistant plants (1,916) when compared with susceptible plants (1,226). Resistance to PWN is mediated by the induction of the jasmonic acid (JA) defense pathway, secondary metabolism pathways, lignin synthesis, oxidative stress response genes, and resistance genes. Quantification of the acetyl bromide-soluble lignin confirmed a significant increase of cell wall lignification of stem tissues around the inoculation zone in resistant plants. In addition to less lignified cell walls, susceptibility to the pine wood nematode seems associated with the activation of the salicylic acid (SA) defense pathway at 72 hpi, as revealed by the higher SA levels in the tissues of susceptible plants. Cell wall reinforcement and hormone signaling mechanisms seem therefore essential for a resistance response.

Dual RNA-Sequencing Analysis of Resistant (Pinus pinea) and Susceptible (Pinus radiata) Hosts during Fusarium circinatum Challenge

Fusarium circinatum causes one of the most important diseases of conifers worldwide, the pine pitch canker (PPC). However, no effective field intervention measures aiming to control or eradicate PPC are available. Due to the variation in host genetic resistance, the development of resistant varieties is postulated as a viable and promising strategy. By using an integrated approach, this study aimed to identify differences in the molecular responses and physiological traits of the highly susceptible Pinus radiata and the highly resistant Pinus pinea to F. circinatum at an early stage of infection. Dual RNA-Seq analysis also allowed to evaluate pathogen behavior when infecting each pine species. No significant changes in the physiological analysis were found upon pathogen infection, although transcriptional reprogramming was observed mainly in the resistant species. The transcriptome profiling of P. pinea revealed an early perception of the pathogen infection together with a strong and coordinated defense activation through the reinforcement and lignification of the cell wall, the antioxidant activity, the induction of PR genes, and the biosynthesis of defense hormones. On the contrary, P. radiata had a weaker response, possibly due to impaired perception of the fungal infection that led to a reduced downstream defense signaling. Fusarium circinatum showed a different transcriptomic profile depending on the pine species being infected. While in P. pinea, the pathogen focused on the degradation of plant cell walls, active uptake of the plant nutrients was showed in P. radiata. These findings present useful knowledge for the development of breeding programs to manage PPC.

Temporal physiological response of pine to Fusarium circinatum infection is dependent on host susceptibility level: the role of ABA catabolism

Pine pitch canker (PPC), caused by Fusarium circinatum Nirenberg and O'Donnell, represents an important threat to conifer forests worldwide, being associated with significant economic losses. Although essential to develop disease mitigation strategies, little research focused on host susceptibility/resistance mechanisms has been conducted. We aimed to explore the response of a highly susceptible (Pinus radiata D. Don) and a relatively resistant (Pinus pinea L.) species to F. circinatum infection at different stages of infection. Morpho-physiological, hormonal and oxidative stress-related changes were assessed for each pine species and sampling point. Most of the changes found occurred in symptomatic P. radiata, for which an increased susceptibility to photoinhibition was detected together with decreased superoxide dismutase activity. Abscisic acid catabolism was activated by F. circinatum inoculation in both pine species, leading to the accumulation of the inactive dihydrophaseic acid in P. radiata and of the less-active phaseic acid in P. pinea. Hormone confocal analysis revealed that this strategy may be of particular importance at 6 d.p.i. in P. pinea, which together with photosynthesis maintenance to fuel defense mechanism, could in part explain the species resistance to PPC. These results are of great interest for the development of hormone-based breeding strategies or for the use of hormone application as inducers of resistance to F. circinatum infection.

Genome-wide identification and expression analysis of the Brassica oleracea L. chitin-binding genes and response to pathogens infections

Chitinase family genes were involved in the response of Brassica oleracea to Fusarium wilt, powdery mildew, black spot and downy mildew. Abstract Chitinase, a category of pathogenesis-related proteins, is believed to play an important role in defending against external stress in plants. However, a comprehensive analysis of the chitin-binding gene family has not been reported to date in cabbage (Brassica oleracea L.), especially regarding the roles that chitinases play in response to various diseases. In this study, a total of 20 chitinase genes were identified using a genome-wide search method. Phylogenetic analysis was employed to classify these genes into two groups. The genes were distributed unevenly across six chromosomes in cabbage, and all of them contained few introns (≤ 2). The results of collinear analysis showed that the cabbage genome contained 1-5 copies of each chitinase gene (excluding Bol035470) identified in Arabidopsis. The heatmap of the chitinase gene family showed that these genes were expressed in various tissues and organs. Two genes (Bol023322 and Bol041024) were relatively highly expressed in all of the investigated tissues under normal conditions, exhibiting the expression characteristics of housekeeping genes. In addition, under four different stresses, namely, Fusarium wilt, powdery mildew, black spot and downy mildew, we detected 9, 5, 8 and 8 genes with different expression levels in different treatments, respectively. Our results may help to elucidate the roles played by chitinases in the responses of host plants to various diseases.

Roles of ethylene, jasmonic acid, and salicylic acid and their interactions in frankincense resin production in Boswellia sacra Flueck. trees

The roles of ethylene, jasmonic acid, and salicylic acid and their interactions in frankincense resin production in Boswellia sacra trees growing in the drylands of Oman were studied. On March 18 (Experiment 1) and September 17 (Experiment 2), 2018, 32-year-old B. sacra trees with multiple trunks were selected at the Agricultural Experiment Station, Sultan Qaboos University, Oman. Various lanolin pastes containing Ethrel, an ethylene-releasing compound; methyl jasmonate; sodium salicylate; and combinations of these compounds were applied to debarked wounds 15 mm in diameter on the trunks. After a certain period, the frankincense resin secreted from each wound was harvested and weighed. The anatomical characteristics of the resin ducts were also studied in the bark tissue near the upper end of each wound. The combination of Ethrel and methyl jasmonate greatly enhanced frankincense resin production within 7 days in both seasons. The application of methyl jasmonate alone, sodium salicylate alone or a combination of both did not affect resin production. These findings suggest a high possibility of artificial enhancement of frankincense resin production by the combined application of Ethrel and methyl jasmonate to B. sacra trees.

Genotoxic effects and proteomic analysis on Allium cepa var. agrogarum L. root cells under Pb stress

Ionic lead (Pb) in the environment has accumulated due to anthropogenic activities, causing a potential threat to plants and plant consumers. We conducted this study to reveal the molecular mechanism of Pb stress response in plants. The effects of Pb (5.0 and 15.0 μM) on mitosis, DNA replication, gene expression and proteins in root-tip cells of Allium cepa var. agrogarum L. were addressed. The results indicated that root growth was inhibited dramatically in Pb treatment groups. Chromosomal aberrations were observed and the mitotic index decreased during Pb treatments at different concentrations. The accumulation of reactive oxygen species (ROS) in onion roots was induced by Pb stress. Pb increased DNA damage and suppressed cell cycle progression. The above toxic effects got more serious with increasing Pb concentration and prolonging exposure time. A total of 17 proteins were expressed differentially between control and Pb exposure groups. Under Pb treatment, the decreased expression of Anx D1 indicated decreased defensive response; the decreased expression of SHMT1 indicated decreased respiration; the decreased expression of COMT2 indicated decreased response of other funtions; the increased expression of NDPK indicated increased transcription and protein synthesis; the increased expression of PR1 and CHI1 indicated increased pathogen invasion; the increased expression of ORC5 and MPK5 indicated the reduced DNA replicating activity; the decreased expression of POLD1 indicated the reduced DNA repair activity. Our results provide new insights at the proteomic level into the Pb-induced responses, defensive responses and toxic effects, and provide new molecular markers of the early events of plant responses to Pb toxicity.

The transcriptome of Pinus pinaster under Fusarium circinatum challenge

BACKGROUND

Fusarium circinatum, the causal agent of pitch canker disease, poses a serious threat to several Pinus species affecting plantations and nurseries. Although Pinus pinaster has shown moderate resistance to F. circinatum, the molecular mechanisms of defense in this host are still unknown. Phytohormones produced by the plant and by the pathogen are known to play a crucial role in determining the outcome of plant-pathogen interactions. Therefore, the aim of this study was to determine the role of phytohormones in F. circinatum virulence, that compromise host resistance.

RESULTS

A high quality P. pinaster de novo transcriptome assembly was generated, represented by 24,375 sequences from which 17,593 were full length genes, and utilized to determine the expression profiles of both organisms during the infection process at 3, 5 and 10 days post-inoculation using a dual RNA-sequencing approach. The moderate resistance shown by Pinus pinaster at the early time points may be explained by the expression profiles pertaining to early recognition of the pathogen, the induction of pathogenesis-related proteins and the activation of complex phytohormone signaling pathways that involves crosstalk between salicylic acid, jasmonic acid, ethylene and possibly auxins. Moreover, the expression of F. circinatum genes related to hormone biosynthesis suggests manipulation of the host phytohormone balance to its own benefit.

CONCLUSIONS

We hypothesize three key steps of host manipulation: perturbing ethylene homeostasis by fungal expression of genes related to ethylene biosynthesis, blocking jasmonic acid signaling by coronatine insensitive 1 (COI1) suppression, and preventing salicylic acid biosynthesis from the chorismate pathway by the synthesis of isochorismatase family hydrolase (ICSH) genes. These results warrant further testing in F. circinatum mutants to confirm the mechanism behind perturbing host phytohormone homeostasis.

Comprehensive Analysis of the Chitinase Gene Family in Cucumber (Cucumis sativus L.): From Gene Identification and Evolution to Expression in Response to Fusarium oxysporum

Chitinases, a subgroup of pathogenesis-related proteins, are responsible for catalyzing the hydrolysis of chitin. Accumulating reports indicate that chitinases play a key role in plant defense against chitin-containing pathogens and are therefore good targets for defense response studies. Here, we undertook an integrated bioinformatic and expression analysis of the cucumber chitinases gene family to identify its role in defense against Fusarium oxysporum f. sp. cucumerinum. A total of 28 putative chitinase genes were identified in the cucumber genome and classified into five classes based on their conserved catalytic and binding domains. The expansion of the chitinase gene family was due mainly to tandem duplication events. The expression pattern of chitinase genes was organ-specific and 14 genes were differentially expressed in response to F. oxysporum challenge of fusarium wilt-susceptible and resistant lines. Furthermore, a class I chitinase, CsChi23, was constitutively expressed at high levels in the resistant line and may play a crucial role in building a basal defense and activating a rapid immune response against F. oxysporum. Whole-genome re-sequencing of both lines provided clues for the diverse expression patterns observed. Collectively, these results provide useful genetic resource and offer insights into the role of chitinases in cucumber-F. oxysporum interaction.

Pinus Susceptibility to Pitch Canker Triggers Specific Physiological Responses in Symptomatic Plants: An Integrated Approach

Fusarium circinatum, the causal agent of pine pitch canker (PPC), is an emergent and still understudied risk that threatens Pinus forests worldwide, with potential production and sustainability losses. In order to explore the response of pine species with distinct levels of susceptibility to PPC, we investigated changes in physiology, hormones, specific gene transcripts, and primary metabolism occurring in symptomatic Pinus pinea, Pinus pinaster, and Pinus radiata upon inoculation with F. circinatum. Pinus radiata and P. pinaster exhibiting high and intermediate susceptibility to PPC, respectively, suffered changes in plant water status and photosynthetic impairment. This was associated with sink metabolism induction, a general accumulation of amino acids and overexpression of pathogenesis-related genes. On the other hand, P. pinea exhibited the greatest resistance to PPC and stomatal opening, transpiration increase, and glycerol accumulation were observed in inoculated plants. A stronger induction of pyruvate decarboxylase transcripts and differential hormones regulation were also found for inoculated P. pinea in comparison with the susceptible Pinus species studied. The specific physiological changes reported herein are the first steps to understand the complex Pinus-Fusarium interaction and create tools for the selection of resistant genotypes thus contributing to disease mitigation.

Genome-wide identification and expression analysis of chitinase gene family in Brassica rapa reveals its role in clubroot resistance

Chitinases, a category of pathogenesis-related proteins, are responsible for catalyzing the hydrolysis of chitin into the N-acetyl-d-glucosamine. Therefore, chitinases are believed to function as a guardian against chitin-containing pathogens. Here, we examined the role of the Brassica rapa chitinase family genes in clubroot disease. A total of 33 chitinase genes were identified and grouped into five classes based on their conserved domain. They were distributed unevenly across eight chromosomes in B. rapa, and 31 of them contained few introns (≤2). In addition, the expression of these genes was organ-specific, and 14 genes were expressed differentially in response to Plasmodiophora brassicae challenge of clubroot-susceptible (CS NIL) and resistant (CR NIL) lines. Furthermore, reduced pathogen DNA content and clubroot symptoms were observed in the CS NILs after their treatment with chitin oligosaccharides 24 h prior to inoculation with P. brassicae. The findings indicate that chitinases play a crucial role in pathogen resistance of the host plants. The results offer an insight into the role of chitinase in B. rapa-P. brassicae interaction.

Drought stress leads to systemic induced susceptibility to a nectrotrophic fungus associated with mountain pine beetle in Pinus banksiana seedlings

Conifers have complex defense responses to initial attacks by insects and pathogens that can have cascading effects on success of subsequent colonizers. However, drought can affect a plant's ability to respond to biotic agents by potentially altering the resources needed for the energetically costly production of induced defense chemicals. We investigated the impact of reduced water on induced chemical defenses of jack pine (Pinus banksiana) seedlings from initial attack by biotic agents and resistance to subsequent challenge inoculation with a pathogenic fungal associate of mountain pine beetle (Dendroctonus ponderosae), Grosmannia clavigera. Applications of phytohormones (methyl salicylate and methyl jasmonate) and G. clavigera were used for initial induction of defenses. Monoterpene concentrations varied with initial induction from fungal and phytohormone application while watering treatment had no effect. Seedlings treated with G. clavigera and methyl jasmonate had the greatest monoterpene concentrations compared to the control and methyl salicylate-treated seedlings. However, the monoterpene response to the challenge inoculation varied with watering treatments, not with prior induction treatments, with lower monoterpene concentrations in fungal lesions on seedlings in the low to moderate watering treatments compared to normal watering treatment. Furthermore, prior induction from phytohormones resulted in systemic cross-induction of resistance to G. clavigera under normal watering treatment but susceptibility under low watering treatment. Seedlings stressed by low water conditions, which also had lower stomatal conductance than seedlings in the normal watering treatment, likely allocated resources to initial defense response but were left unable to acquire further resources for subsequent responses. Our results demonstrate that drought can affect interactions among tree-infesting organisms through systemic cross-induction of susceptibility.

Phosphatidic acid synthesis, octadecanoic pathway and fatty acids content as lipid markers of exogeneous salicylic acid-induced elicitation in wheat

Activators of plant defence responses against pathogens are a potential alternative to fungicides, and the well-known resistance inducer salicylic acid (SA) protects wheat (Triticum aestivum L.) against powdery mildew. The aim of our work was to investigate through biochemical and molecular approaches whether lipid metabolism alteration could be considered as a characteristic feature of induced resistance in wheat upon SA infiltration. Expression levels of lox, PI-PLC2 and ltp genes encoding for a lipoxygenase (LOX), a phospholipase C2 and a lipid-transfer protein, respectively, were investigated. Increase of phosphatidic acid (PA) content 48h after SA infiltration in wheat leaves, upregulation of PI-PLC2 gene expression and increased diacylglycerol content were recorded, indicating the involvement of the PLC pathway in the PA synthesis. The wheat octadecanoid pathway was shown to be highly responsive to SA infiltration through simultaneous increases in lox gene expression and LOX activity, as well as a reduction in the content of linolenic acid. Changes in several FA contents and increases of the ltp gene expression were also recorded during the latest hours after SA infiltration. The status of lipid metabolism, as well as the connections between its components as markers of SA-induced resistance in wheat, are discussed.

Identification, phylogeny, and transcript of chitinase family genes in sugarcane

Chitinases are pathogensis-related proteins, which play an important role in plant defense mechanisms. The role of the sugarcane chitinase family genes remains unclear due to the highly heterozygous and aneuploidy chromosome genetic background of sugarcane. Ten differentially expressed chitinase genes (belonging to class I~VII) were obtained from RNA-seq analysis of both incompatible and compatible sugarcane genotypes during Sporisorium scitamineum challenge. Their structural properties and expression patterns were analyzed. Seven chitinases (ScChiI1, ScChiI2, ScChiI3, ScChiIII1, ScChiIII2, ScChiIV1 and ScChiVI1) showed more positive with early response and maintained increased transcripts in the incompatible interaction than those in the compatible one. Three (ScChiII1, ScChiV1 and ScChiVII1) seemed to have no significant difference in expression patterns between incompatible and compatible interactions. The ten chitinases were expressed differentially in response to hormone treatment as well as having distinct tissue specificity. ScChiI1, ScChiIV1 and ScChiVII1 were induced by various abiotic stresses (NaCl, CuCl2, PEG and 4 °C) and their involvement in plant immunity was demonstrated by over-expression in Nicotiana benthamiana. The results suggest that sugarcane chitinase family exhibit differential responses to biotic and abiotic stress, providing new insights into their function.

Influence of water deficit on the molecular responses of Pinus contorta × Pinus banksiana mature trees to infection by the mountain pine beetle fungal associate, Grosmannia clavigera

Conifers exhibit a number of constitutive and induced mechanisms to defend against attack by pests and pathogens such as mountain pine beetle (Dendroctonus ponderosae Hopkins) and their fungal associates. Ecological studies have demonstrated that stressed trees are more susceptible to attack by mountain pine beetle than their healthy counterparts. In this study, we tested the hypothesis that water deficit affects constitutive and induced responses of mature lodgepole pine × jack pine hybrids (Pinus contorta Dougl. ex Loud. var. latifolia Engelm. ex S. Wats. × Pinus banksiana Lamb.) to inoculation with the mountain pine beetle fungal associate Grosmannia clavigera (Robinson-Jeffrey and Davidson) Zipfel, de Beer and Wingfield. The degree of stress induced by the imposed water-deficit treatment was sufficient to reduce photosynthesis. Grosmannia clavigera-induced lesions exhibited significantly reduced dimensions in water-deficit trees relative to well-watered trees at 5 weeks after inoculation. Treatment-associated cellular-level changes in secondary phloem were also observed. Quantitative RT-PCR was used to analyze transcript abundance profiles of 18 genes belonging to four families classically associated with biotic and abiotic stress responses: aquaporins (AQPs), dehydration-responsive element binding (DREB), terpene synthases (TPSs) and chitinases (CHIs). Transcript abundance profiles of a TIP2 AQP and a TINY-like DREB decreased significantly in fungus-inoculated trees, but not in response to water deficit. One TPS, Pcb(+)-3-carene synthase, and the Class II CHIs PcbCHI2.1 and PcbCHI2.2 showed increased expression under water-deficit conditions in the absence of fungal inoculation, while another TPS, Pcb(E)-β-farnesene synthase-like, and two CHIs, PcbCHI1.1 and PcbCHI4.1, showed attenuated expression under water-deficit conditions in the presence of fungal inoculation. The effects were observed both locally and systemically. These results demonstrate that both constitutive and induced carbon- and nitrogen-based defenses are affected by water deficit, suggesting potential consequences for mountain pine beetle dynamics, particularly in novel environments.

Cloning and characterization of chitinases from interior spruce and lodgepole pine

Chitinases have been implicated in the defence of conifers against insects and pathogens. cDNA for six chitinases were cloned from interior spruce (Picea glauca x engelmannii) and four from lodgepole pine (Pinus contorta). The cloned interior spruce chitinases were annotated class I PgeChia1-1 and PgeChia1-2, class II PgeChia2-1, class IV PgeChia4-1, and class VII PgeChia7-1 and PgeChia7-2; lodgepole pine chitinases were annotated class I PcChia1-1, class IV PcChia4-1, and class VII PcChia7-1 and PcChia7-2. Chitinases were expressed in Escherichia coli with maltose-binding-protein tags and soluble proteins purified. Functional characterization demonstrated chitinolytic activity for the three class I chitinases PgeChia1-1, PgeChia1-2 and PcChia1-1. Transcript analysis established strong induction of most of the tested chitinases, including all three class I chitinases, in interior spruce and lodgepole pine in response to inoculation with bark beetle associated fungi (Leptographium abietinum and Grosmannia clavigera) and in interior spruce in response to weevil (Pissodes strobi) feeding. Evidence of chitinolytic activity and inducibility by fungal and insect attack support the involvement of these chitinases in conifer defense.

Characterization of Withania somnifera leaf transcriptome and expression analysis of pathogenesis-related genes during salicylic acid signaling

Withania somnifera (L.) Dunal is a valued medicinal plant with pharmaceutical applications. The present study was undertaken to analyze the salicylic acid induced leaf transcriptome of W. somnifera. A total of 45.6 million reads were generated and the de novo assembly yielded 73,523 transcript contig with average transcript contig length of 1620 bp. A total of 71,062 transcripts were annotated and 53,424 of them were assigned GO terms. Mapping of transcript contigs to biological pathways revealed presence of 182 pathways. Seventeen genes representing 12 pathogenesis-related (PR) families were mined from the transcriptome data and their pattern of expression post 17 and 36 hours of salicylic acid treatment was documented. The analysis revealed significant up-regulation of all families of PR genes by 36 hours post treatment except WsPR10. The relative fold expression of transcripts ranged from 1 fold to 6,532 fold. The two families of peroxidases including the lignin-forming anionic peroxidase (WsL-PRX) and suberization-associated anionic peroxidase (WsS-PRX) recorded maximum expression of 377 fold and 6532 fold respectively, while the expression of WsPR10 was down-regulated by 14 fold. Additionally, the most stable reference gene for normalization of qRT-PCR data was also identified. The effect of SA on the accumulation of major secondary metabolites of W. somnifera including withanoside V, withaferin A and withanolide A was also analyzed and an increase in content of all the three metabolites were detected. This is the first report on expression patterns of PR genes during salicylic acid signaling in W. somnifera.

Spatial and temporal dynamics of the colonization of Pinus radiata by Fusarium circinatum, of conidiophora development in the pith and of traumatic resin duct formation

· Fusarium circinatum causes pitch canker disease in a wide range of pine trees, including Pinus radiata, with devastating economic consequences. · To assess the spatial and temporal dynamics of growth of this pathogen in radiata pine, we examined the process of infection using both real-time PCR to quantify fungal biomass inside the plant host, and confocal microscopy using a green fluorescent protein (GFP)-tagged strain of F. circinatum. · Pathogen growth exhibited three distinct phases: an initial exponential increase in fungal biomass, concomitant with pathogen colonization of the cortex and phloem; a slowdown in fungal growth coincident with sporulating hyphae deep within the host; and stabilization of the fungal biomass when the first wilting symptoms appeared. The number of resin ducts in the xylem was found to increase in response to infection and the fungus grew inside both constitutive and traumatic resin ducts. · These results indicate that conidiation may contribute to the spatial or temporal dissemination of the pathogen. Moreover, the present findings raise the intriguing possibility that the generation of traumatic resin ducts may be of more benefit to the fungus than to the plant.

Signaling cross-talk in plant disease resistance

Hormone signaling crosstalk plays a major role in plant defense against a wide range of both biotic and abiotic stresses. While many reviews on plant-microbe interactions have well described the general trends of signaling pathways in shaping host responses to pathogens, few discussions have considered a synthesis of positive versus negative interactions among such pathways, or variations in the signaling molecules themselves. This review deals with the interaction trends between salicylic, jasmonic, and abscisic acids in the signaling pathways, as well as exceptions to such trends. Here we focused on antagonistic versus cooperative interactions between salicylic and jasmonic acids, two major disease resistance signaling molecules, and some interactions with abscisic acid, a known abiotic stress hormone, and another player in plant defense mechanisms. We provide a set of examples materializing either antagonism or cooperation for each interaction between two pathways, thereby showing the trends and pinpointing the exceptions. Such analyses are practical for researchers working on the subject and essential for a better exploitation of the data already available in plant disease resistance signaling, both in Arabidopsis and crop species, toward the development of better disease management strategies for economically important crops.

Transcriptome analysis of symptomatic and recovered leaves of geminivirus-infected pepper (Capsicum annuum)

BACKGROUND

Geminiviruses are a large and important family of plant viruses that infect a wide range of crops throughout the world. The Begomovirus genus contains species that are transmitted by whiteflies and are distributed worldwide causing disease on an array of horticultural crops. Symptom remission, in which newly developed leaves of systemically infected plants exhibit a reduction in symptom severity (recovery), has been observed on pepper (Capsicum annuum) plants infected with Pepper golden mosaic virus (PepGMV). Previous studies have shown that transcriptional and post-transcriptional gene silencing mechanisms are involved in the reduction of viral nucleic acid concentration in recovered tissue. In this study, we employed deep transcriptome sequencing methods to assess transcriptional variation in healthy (mock), symptomatic, and recovered pepper leaves following PepGMV infection.

RESULTS

Differential expression analyses of the pepper leaf transcriptome from symptomatic and recovered stages revealed a total of 309 differentially expressed genes between healthy (mock) and symptomatic or recovered tissues. Computational prediction of differential expression was validated using quantitative reverse-transcription PCR confirming the robustness of our bioinformatic methods. Within the set of differentially expressed genes associated with the recovery process were genes involved in defense responses including pathogenesis-related proteins, reactive oxygen species, systemic acquired resistance, jasmonic acid biosynthesis, and ethylene signaling. No major differences were found when compared the differentially expressed genes in symptomatic and recovered tissues. On the other hand, a set of genes with novel roles in defense responses was identified including genes involved in histone modification. This latter result suggested that post-transcriptional and transcriptional gene silencing may be one of the major mechanisms involved in the recovery process. Genes orthologous to the C. annuum proteins involved in the pepper-PepGMV recovery response were identified in both Solanum lycopersicum and Solanum tuberosum suggesting conservation of components of the viral recovery response in the Solanaceae.

CONCLUSION

These data provide a valuable source of information for improving our understanding of the underlying molecular mechanisms by which pepper leaves become symptomless following infection with geminiviruses. The identification of orthologs for the majority of genes differentially expressed in recovered tissues in two major solanaceous crop species provides the basis for future comparative analyses of the viral recovery process across related taxa.

Differential effects of plant ontogeny and damage type on phloem and foliage monoterpenes in jack pine (Pinus banksiana)

Coniferous trees have both constitutive and inducible defences that deter or kill herbivores and pathogens. We investigated constitutive and induced monoterpene responses of jack pine (Pinus banksiana Lamb.) to a number of damage types: a fungal associate of the mountain pine beetle (Dendroctonus ponderosae Hopkins), Grosmannia clavigera (Robinson-Jeffrey & R.W. Davidson); two phytohormones, methyl jasmonate (MJ) and methyl salicylate (MS); simulated herbivory; and mechanical wounding. We only included the fungal, MJ and mechanical wounding treatments in the field experiments while all treatments were part of the greenhouse studies. We focused on both constitutive and induced responses between juvenile and mature jack pine trees and differences in defences between phloem and needles. We found that phytohormone applications and fungal inoculation resulted in the greatest increase in monoterpenes in both juvenile and mature trees. Additionally, damage types differentially affected the proportions of individual monoterpenes: MJ-treated mature trees had higher myrcene and β-pinene than fungal-inoculated mature trees, while needles of juveniles inoculated with the fungus contained higher limonene than MJ- or MS-treated juveniles. Although the constitutive monoterpenes were higher in the phloem of juveniles than mature jack pine trees, the phloem of mature trees had a much higher magnitude of induction. Further, induced monoterpene concentrations in juveniles were higher in phloem than in needles. There was no difference in monoterpene concentration between phytohormone applications and G. clavigera inoculation in mature trees, while in juvenile trees MJ was different from both G. clavigera and simulated herbivory in needle monoterpenes, but there was no difference between phytohormone applications and simulated herbivory in the phloem.

Root herbivory: molecular analysis of the maize transcriptome upon infestation by Southern corn rootworm, Diabrotica undecimpunctata howardi

While many studies have characterized changes to the transcriptome of plants attacked by shoot-eating insect pests, few have examined transcriptome-level effects of root pests. Maize (Zea mays) seedlings were subjected to infestation for approximately 2 weeks by the root herbivore southern corn rootworm (SCR) Diabrotica undecimpunctata howardi, and changes in transcript abundance within both roots and shoots were analyzed using a 57K element microarray. A total of 541 genes showed statistically significant changes in transcript abundance in infested roots, including genes encoding many pathogenesis-related proteins such as chitinases, proteinase inhibitors, peroxidases and β-1,3-glucanases. Several WRKY transcription factors--often associated with biotic responses--exhibited increased transcript abundance upon SCR feeding. Differentially expressed (DE) genes were also detected in shoots of infested vs control plants. Quantitative Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) was used to confirm patterns of transcript abundance for several significant DE genes using an independent experiment with a 2-6 day period of SCR infestation. Because of the well-documented roles that jasmonic acid (JA) or salicylic acid (SA) play in herbivory responses, the effect of exogenous JA or SA application on transcript abundance corresponding to the same subset of SCR-responsive genes was assessed. The response of these genes at the level of transcript abundance to SA and JA differed between roots and shoots and also differed among the genes that were examined. These data suggested that SA- and JA-dependent and independent signals contributed to the transcriptome-level changes in maize roots and shoots in response to SCR infestation.

Ammonium secretion during Colletotrichum coccodes infection modulates salicylic and jasmonic acid pathways of ripe and unripe tomato fruit

The postharvest pathogens Colletotrichum coccodes remains quiescent after infection of unripe fruit. However, during fruit ripening, the pathogen assumes a necrotrophic life style, rapidly colonizing the tissue. C. coccodes secretes ammonium during germination and colonization of host tissue that induces host programmed cell death. We further examined the role of ammonia in the infection process by analyzing transcriptome expression from infected and ammonia-treated fruit tissue compared with healthy tissue. The analysis revealed 82 and 237 common upregulated and downregulated genes, respectively. Quantitative reverse-transcriptase polymerase chain reaction analysis of select transcripts in normal and transgenic NADPH oxidase antisense plants revealed that their expression was NADPH oxidase dependent. Common-upregulated genes showed overrepresentation of salicylic acid (SA)-dependent genes as well as genes related to biotic stress. The downregulated genes showed overrepresentation of jasmonic acid (JA)-dependent genes. Indeed, direct application of SA to the fruit enhanced C. coccodes necrotrophic colonization, whereas the application of JA delayed colonization. Importantly, green fruit and red fruit displayed similar gene expression patterns although only red fruit is susceptible to colonization. Thus, it is likely that the resistance of green fruit to C. coccodes colonization is due to additional factors.

The pathogenic white-rot fungus Heterobasidion parviporum triggers non-specific defence responses in the bark of Norway spruce

Norway spruce [Picea abies (L.) Karst.] is one of the economically most important conifer species in Europe. The major pathogen on Norway spruce is Heterobasidion parviporum (Fr.) Niemelä & Korhonen. To achieve a better understanding of Norway spruce's defence mechanisms, transcriptional responses in bark to H. parviporum infection were compared with the response to wounding using cDNA-amplified fragment length polymorphism. The majority of the recovered transcript-derived fragments (TDFs) showed a similar expression pattern for infection and wounding treatment, although inoculated samples showed an enhanced reaction. Genes related to systemic acquired resistance, e.g., PR1, accumulated after H. parviporum infection. Simultaneously, several transcripts involved in various aspects of jasmonic acid (JA)- and ethylene (ET)-mediated signalling accumulated. Genes involved in the ubiquitin/proteasome system were also regulated. Expression patterns have been confirmed by quantitative polymerase chain reaction. The expression patterns of the isolated TDFs suggest that infection with H. parviporum in Norway spruce induces a broad defence, with many similarities to non-specific defence responses in angiosperms. The parallel induction of salicylic acid- and JA/ET-mediated pathways implies spatially separated responses in different cell layers, with and without hyphal contact. A set of TDFs were analysed in an independent experiment with unrelated material treated with wounding or with inoculation with H. parviporum or Phlebiopsis gigantea, verifying the original observations and underlining the non-specific defence responses. In addition, our data suggest that rerouting of carbon in secondary metabolism is an integral part of Norway spruce induced defence. We report the sequences of three 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase genes (PaDAHP1, PaDAHP2 and PaDAHP3) and their relative expression in response to wounding and infection with H. parviporum and P. gigantea. The results clearly indicate differential regulation of the three DAHPs in the induced defence responses in Norway spruce. This study gives insights into the central mechanisms in the induced defences in Norway spruce.

Expression and β-glucan binding properties of Scots pine (Pinus sylvestris L.) antimicrobial protein (Sp-AMP)

Scots pine (Pinus sylvestris) secretes a number of small, highly-related, disulfide-rich proteins (Sp-AMPs) in response to challenges with fungal pathogens such as Heterobasidion annosum, although their biological role has been unknown. Here, we examined the expression patterns of these genes, as well as the structure and function of the encoded proteins. Northern blots and quantitative real time PCR showed increased levels of expression that are sustained during the interactions of host trees with pathogens, but not non-pathogens, consistent with a function in conifer tree defenses. Furthermore, the genes were up-regulated after treatment with salicylic acid and an ethylene precursor, 1-aminocyclopropane-1-carboxylic-acid, but neither methyl jasmonate nor H(2)O(2) induced expression, indicating that Sp-AMP gene expression is independent of the jasmonic acid signaling pathways. The cDNA encoding one of the proteins was cloned and expressed in Pichia pastoris. The purified protein had antifungal activity against H. annosum, and caused morphological changes in its hyphae and spores. It was directly shown to bind soluble and insoluble β-(1,3)-glucans, specifically and with high affinity. Furthermore, addition of exogenous glucan is linked to higher levels of Sp-AMP expression in the conifer. Homology modeling and sequence comparisons suggest that a conserved patch on the surface of the globular Sp-AMP is a carbohydrate-binding site that can accommodate approximately four sugar units. We conclude that these proteins belong to a new family of antimicrobial proteins (PR-19) that are likely to act by binding the glucans that are a major component of fungal cell walls.

Root secretion of defense-related proteins is development-dependent and correlated with flowering time

Proteins found in the root exudates are thought to play a role in the interactions between plants and soil organisms. To gain a better understanding of protein secretion by roots, we conducted a systematic proteomic analysis of the root exudates of Arabidopsis thaliana at different plant developmental stages. In total, we identified 111 proteins secreted by roots, the majority of which were exuded constitutively during all stages of development. However, defense-related proteins such as chitinases, glucanases, myrosinases, and others showed enhanced secretion during flowering. Defense-impaired mutants npr1-1 and NahG showed lower levels of secretion of defense proteins at flowering compared with the wild type. The flowering-defective mutants fca-1, stm-4, and co-1 showed almost undetectable levels of defense proteins in their root exudates at similar time points. In contrast, root secretions of defense-enhanced cpr5-2 mutants showed higher levels of defense proteins. The proteomics data were positively correlated with enzymatic activity assays for defense proteins and with in silico gene expression analysis of genes specifically expressed in roots of Arabidopsis. In conclusion, our results show a clear correlation between defense-related proteins secreted by roots and flowering time.

Identification, characterization, and expression analyses of class II and IV chitinase genes from Douglas-fir seedlings infected by Phellinus sulphurascens

Laminated root rot (LRR) disease, caused by the fungus Phellinus sulphurascens, is a major threat to coastal Douglas-fir (DF) (Pseudotsuga menziesii) forests in western North America. Understanding host-pathogen interactions of this pathosystem is essential to manage this important conifer root disease. Our research objectives were to identify DF pathogenesis-related (PR) genes and analyze their expression patterns over the course of infection. We constructed a cDNA library of Phellinus sulphurascens-infected DF seedling roots and sequenced a total of 3,600 random cDNA clones from this library. One of the largest groups of identified genes (203 cDNA clones) matched with chitinase genes reported in other plant species. We identified at least three class II and six class IV chitinase genes from DF seedlings. Quantitative reverse-transcriptase polymerase chain reaction analyses showed significant differential expression patterns locally in root tissues and systemically in needle tissues after fungal invasion. Nonetheless, there was a common trend in gene expression patterns for most of the chitinase genes: an upregulation within 12 h of pathogen inoculation followed by down-regulation within 2 to 3 days postinoculation (dpi), and then further upregulation within 5 to 7 dpi. Western immunoblot data showed differential accumulation of class IV chitinases in Phellinus sulphurascens-infected DF seedlings. Further detailed functional analyses will help us to understand the specific role of DF chitinases in defense against Phellinus sulphurascens infection.

Identification and characterization of differentially expressed genes from Fagus sylvatica roots after infection with Phytophthora citricola

Phytophthora species are major plant pathogens infecting herbaceous and woody plants including European beech, the dominant or co-dominant tree in temperate Europe and an economically important species. For the analysis of the interaction of Phytophthora citricola with Fagus sylvatica suppression subtractive hybridization was used to isolate transcripts induced during infection and 1,149 sequences were generated. Hybridizations with driver and tester populations demonstrated differential expression in infected roots as compared to controls and verify efficient enrichment of these cDNAs during subtraction. Up regulation of selected genes during pathogenesis demonstrated using RT-PCR is consistent with these results. Pathogenesis-related proteins formed the largest group among functionally categorized transcripts. Cell wall proteins and protein kinases were also frequently found. Several transcription factors were isolated that are reactive to pathogens or wounding in other plants. The library contained a number of jasmonic acid, salicylic acid and ethylene responsive genes as well as genes directly involved in signaling pathways. Besides a mechanistic interconnection among signaling pathways another factor explaining the activation of different pathways could be the hemibiotrophic life style of Phytophthora triggering different signals in both stages.

Two poplar methyl salicylate esterases display comparable biochemical properties but divergent expression patterns

Two genes encoding proteins of 98% sequence identity that are highly homologous to tobacco methyl salicylate (MeSA) esterase (SABP2) were identified and cloned from poplar. Proteins encoded by these two genes displayed specific esterase activities towards MeSA to produce salicylic acid, and are named PtSABP2-1 and PtSABP2-2, respectively. Recombinant PtSABP2-1 and PtSABP2-2 exhibited apparent Km values of 68.2+/-3.8microM and 24.6+/-1microM with MeSA, respectively. Structural modeling using the three-dimensional structure of tobacco SABP2 as a template indicated that the active sites of PtSABP2-1 and PtSABP2-2 were highly similar to that of tobacco SABP2. Under normal growing conditions, PtSABP2-1 showed the highest level of expression in leaves and PtSABP2-2 was most highly expressed in roots. In leaf tissues of poplar plants under stress conditions, the expression of PtSABP2-1 was significantly down-regulated by two stress factors, whereas the expression of PtSABP2-2 was significantly up-regulated by four stress factors. The plausible mechanisms leading to these two highly homologous MeSA esterase genes involved in divergent biological processes in poplar are discussed.

Poplar defense against insect herbivoresThis review is one of a selection of papers published in the Special Issue on Poplar Research in Canada

The availability of a poplar ( Populus trichocarpa Torr & A. Gray, black cottonwood) genome sequence is enabling new research approaches in angiosperm tree biology. Much of the recent genomics research in poplars has been on wood formation, growth and development, resistance to abiotic stress and pathogens, motivated, at least in part, by the fact that poplars provide an important system for large-scale, short-rotation plantation forestry in the Northern Hemisphere. To sustain productivity and ecosystem health of natural and planted poplar forests it is of critical importance to also develop a better understanding of the molecular mechanisms of defense and resistance of poplars against insect pests. Previous research has established a solid foundation of the chemical ecology of poplar defense against insects. This review summarizes some of the relevant literature on defense against insect herbivores in poplars with an emphasis on molecular, biochemical, and emerging genomic research in this important field within forest biotechnology and chemical ecology. Following a general introduction, we provide a brief overview of some of the most relevant insect pests of poplars; we then describe some of the general defense strategies of poplars along with selected examples of their activities. We conclude with a summary of emerging results and perspectives from recent advances in genomics research on poplar defense against insects.

Cross-induction of systemic induced resistance between an insect and a fungal pathogen in Austrian pine over a fertility gradient

Evidence for cross-induction of systemic resistance or susceptibility in plant-fungus-herbivore interactions is mostly derived from herbaceous model systems and not perennial woody plants. Furthermore, the effects of environmental variables such as soil fertility on these tripartite interactions are generally unknown. This study examined cross-induction of systemic resistance in Pinus nigra (Austrian pine) to infection by Sphaeropsis sapinea (a fungal pathogen), or feeding by Neodiprion sertifer (European pine sawfly), by prior induction with either S. sapinea or N. sertifer, over a fertility gradient. In a replicated 3-year study, cross-induction of systemic induced resistance (SIR) was found to be both asymmetric within a single year and variable between years. Prior induction with insect defoliation induced SIR to subsequent fungal challenge in 2006 but not in 2005. In 2005, a fertility-independent negative systemic effect of the fungal infection on herbivore growth was detected while herbivore survival was affected by a significant interaction between induction treatment and fertility level in 2006. Prior infection by the fungus induced SIR against the same fungus in both years regardless of fertility levels. This is the first report of whole-plant SIR against a defoliating insect induced by a fungal pathogen and vice versa, under variable nutrient availability, in a conifer or any other tree.

Differential expression of two class III chitinases in two types of roots of Quercus robur during pre-mycorrhizal interactions with Piloderma croceum

Expression of two plant chitinase genes, representing members of class III chitinases, was studied in Quercus robur roots during interactions in a pre-mycorrhizal stage with the ectomycorrhizal fungus Piloderma croceum. Chitinase gene expression was compared in lateral roots destined to form ectomycorrhiza, and in principal roots that are not directly involved in mycorrhizal interactions. The transcript level of the first chitinase (QrchitIII-1) was upregulated in lateral roots, whereas no significant differential expression was observed in principal roots. The second chitinase (QrchitIII-2) was regulated neither in lateral nor in principal roots in presence of the fungus. Because P. croceum did not induce significant chitinase responses in principal roots, the enhanced expression of QrchitIII-1 in lateral roots after inoculation may be related to some steps in symbiosis ontogenesis.