Plants versus pathogens: an evolutionary arms race

Metabolome profiling dissects the oat (Avena sativa L.) innate immune response to Pseudomonas syringae pathovars

One of the most important characteristics of successful plant defence is the ability to rapidly identify potential threats in the surrounding environment. Plants rely on the perception of microbe-derived molecular pattern chemicals for this recognition, which initiates a number of induced defence reactions that ultimately increase plant resistance. The metabolome acts as a metabolic fingerprint of the biochemical activities of a biological system under particular conditions, and therefore provides a functional readout of the cellular mechanisms involved. Untargeted metabolomics was applied to decipher the biochemical processes related to defence responses of oat plants inoculated with pathovars of Pseudomonas syringae (pathogenic and non-pathogenic on oat) and thereby identify signatory markers that are involved in host or nonhost defence responses. The strains were P. syringae pv. coronafaciens (Ps-c), P. syringae pv. tabaci, P. syringae pv. tomato DC3000 and the hrcC mutant of DC3000. At the seedling growth stage, metabolic alterations in the Dunnart oat cultivar (tolerant to Ps-c) in response to inoculation with the respective P. syringae pathovars were examined following perception and response assays. Following inoculation, plants were monitored for symptom development and harvested at 2-, 4- and 6 d.p.i. Methanolic leaf extracts were analysed by ultra-high-performance liquid chromatography (UHPLC) connected to high-definition mass spectrometry. Chemometric modelling and multivariate statistical analysis indicated time-related metabolic reconfigurations that point to host and nonhost interactions in response to bacterial inoculation/infection. Metabolic profiles derived from further multivariate data analyses revealed a range of metabolite classes involved in the respective defence responses, including fatty acids, amino acids, phenolic acids and phenolic amides, flavonoids, saponins, and alkaloids. The findings in this study allowed the elucidation of metabolic changes involved in oat defence responses to a range of pathovars of P. syringae and ultimately contribute to a more comprehensive view of the oat plant metabolism under biotic stress during host vs nonhost interactions.

Luciferase-mediated assay to detect the PAMP-triggered gene expression in transgenic Nicotiana benthamiana

Luciferase is one of the bioluminescence-producing agents, which was widely used as a reporter enzyme for constructing bioassay systems to study gene expression with high accuracy and within a broad dynamic spectrum. Perception of pathogen associated molecular patterns (PAMPs) in plants often lead to significant transcriptional changes. The transcriptional changes of defense-related genes are often used as a marker to assay PAMP-triggered plant immune response. In this study, we showed that the marker gene CYP71D20 was rapidly activated in Nicotiana benthamiana upon treatment with the bacterial PAMP flg22 and the Phytophthora elicitin INF1. In addition, we generated transgenic N. benthamiana using the luciferase as a reporter gene to analyze CYP71D20 gene expression upon PAMP treatment. The transgenic line carrying the luciferase gene driven by CYP71D20 promoter was treated with the bacterial PAMP flg22 or Phytophthora elicitin INF1. Transcriptional activation of CYP71D20 was measured by monitoring the luciferase activity. The results showed that the LUC activity was increased after treatment with different PAMPs, indicating that the CYP71D20-promotor luciferase assay can be used to study the PAMP-triggered gene expression in N. benthamiana.

Carbohydrate-active enzymes involved in rice cell wall metabolism

Plant cell walls are complex, multifunctional structures, built up of polysaccharides and proteins. The configuration and abundance of cell wall constituents determine cellular elongation and plant growth. The emphasis of this review is on rice, a staple crop with economic importance, serving as model for grasses/cereals. Recent advancements have contributed to a better understanding of the grass/cereal cell wall. This review brings together current knowledge of the organization and metabolism of the rice cell wall, and addresses gaps in the information regarding the cell wall and enzymes involved. Several cell wall fractions, including cellulose, mixed-linkage glucans, and glucuronoarabinoxylans, are well understood in rice and other grasses/grains. Conversely, there are still open questions and missing links in relation to xyloglucans, glucomannans, pectin, lignin, and arabinogalactan proteins. There is still a large and untapped potential to identify carbohydrate-active enzymes (CAZymes), to characterize their activity, and to elucidate their involvement in the metabolism of the mentioned cell wall fractions. This review highlights the involvement of carbohydrate-active enzymes in rice cell wall metabolism, providing an update of current understanding with the aim of demarcating research areas with potential for further investigations.

Assessing Biofungicides and Host Resistance against Rhizoctonia Large Patch in Zoysiagrass

Rhizoctonia large patch (Rhizoctonia solani AG2-2 LP) significantly reduces turfgrass quality, aesthetics, and playability. Synthetic fungicides are commonly used for managing this disease, but they present high costs, potential for fungicide resistance, and environmental concerns. We conducted in vitro assays to test the effectiveness of three biofungicides, seven synthetic fungicides, and ten combinations against R. solani. We then assessed seven spray programs that included Bacillus subtilis QST713 and propiconazole, either alone or tank-mixed, on zoysiagrass 'El Toro' in a growth chamber and in field trials. Biofungicide B. subtilis QST713 reduced pathogen growth by up to 100% in vitro. B. subtilis QST713 alone or combined with synthetic fungicides and/or in rotation was as effective as the standalone synthetic fungicide, reducing disease severity and AUDPC by 81 and 77% (growth chamber) and by 71 and 52% (field), respectively, while maintaining acceptable turfgrass quality. Additionally, we screened zoysiagrass genotypes and advanced breeding lines against three R. solani isolates in growth chamber studies. Five genotypes and two breeding lines demonstrated resistance to Rhizoctonia large patch across isolates, highlighting their potential for developing disease-resistant cultivars. Our findings suggest that integrating biofungicides, resistant cultivars with chemical controls offer sustainable and effective strategies for managing Rhizoctonia large patch.

Reduction of Phytophthora palmivora plant root infection in weak electric fields

The global food security crisis is partly caused by significant crop losses due to pests and pathogens, leading to economic burdens. Phytophthora palmivora, an oomycete pathogen, affects many plantation crops and costs over USD 1 billion each year. Unfortunately, there is currently no prevention plan in place, highlighting the urgent need for an effective solution. P. palmivora produces motile zoospores that respond to weak electric fields. Here, we show that external electric fields can be used to reduce root infection in two plant species. We developed two original essays to study the effects of weak electric fields on the interaction between P. palmivora's zoospores and roots of Arabidopsis thaliana and Medicago truncatula. In the first configuration, a global artificial electric field is set up to induce ionic currents engulfing the plant roots while, in the second configuration, ionic currents are induced only locally and at a distance from the roots. In both cases, we found that weak ionic currents (250-550 μA) are sufficient to reduce zoospore attachment to Arabidopsis and Medicago roots, without affecting plant health. Moreover, we show that the same configurations decrease P. palmivora mycelial growth in Medicago roots after 24 h. We conclude that ionic currents can reduce more than one stage of P. palmivora root infection in hydroponics. Overall, our findings suggest that weak external electric fields can be used as a sustainable strategy for preventing P. palmivora infection, providing innovative prospects for agricultural crop protection.

A suite of selective pressures supports the maintenance of alleles of a Drosophila immune peptide

The innate immune system provides hosts with a crucial first line of defense against pathogens. While immune genes are often among the fastest evolving genes in the genome, in Drosophila , antimicrobial peptides (AMPs) are notable exceptions. Instead, AMPs may be under balancing selection, such that over evolutionary timescales multiple alleles are maintained in populations. In this study, we focus on the Drosophila antimicrobial peptide Diptericin A, which has a segregating amino acid polymorphism associated with differential survival after infection with the Gram-negative bacteria Providencia rettgeri . Diptericin A also helps control opportunistic gut infections by common Drosophila gut microbes, especially those of Lactobacillus plantarum . In addition to genotypic effects on gut immunity, we also see strong sex-specific effects that are most prominent in flies without functional diptericin A . To further characterize differences in microbiomes between different diptericin genotypes, we used 16S metagenomics to look at the microbiome composition. We used both lab reared and wild caught flies for our sequencing and looked at overall composition as well as the differential abundance of individual bacterial families. Overall, we find flies that are homozygous for one allele of diptericin A are better equipped to survive a systemic infection from P. rettgeri , but in general have a shorter lifespans after being fed common gut commensals. Our results suggest a possible mechanism for the maintenance of genetic variation of diptericin A through the complex interactions of sex, systemic immunity, and the maintenance of the gut microbiome.

Fusarium Tropical Race 4 in Latin America and the Caribbean: status and global research advances towards disease management

Fusarium wilt of banana (FWB), caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense (Foc), poses an undeniable threat to global banana production. This disease has intensified in recent years, with the tropical race 4 (TR4) strain spreading rapidly. Since 2018, the number of affected countries has increased from 16 to 23, presenting a significant challenge to researchers, producers, and National Plant Protection Organizations (NPPOs) worldwide. The potential impact of TR4 in Latin America and the Caribbean (LAC) is particularly concerning. This region boasts seven of the top ten banana-exporting countries, and bananas and plantains are crucial for food security and income generation. In Colombia, where TR4 was detected in 2019, the disease has already spread from La Guajira to Magdalena, and it is currently affecting 20 large commercial export farms. In Peru, the disease was detected in 2021 and although still restricted to the northern region, flood irrigation and heavy rains associated with the Yaku cyclone, boosted pathogen spread, and more than 400 small organic banana farmers are currently affected. In Venezuela, TR4 detection occurred in 2023, with plantations across three states and five municipalities now affected. Worryingly, TR4 has also been confirmed in plantains, a staple food in the region. Current national responses in LAC primarily rely on preventive and reactive measures: preventing initial incursions and containing outbreaks to avoid further spread. However, the disease's relentless progression suggests that its eventual presence in all banana-producing areas is likely. Therefore, exploring alternative management approaches beyond pathogen exclusion becomes crucial, both in affected and disease-free regions. This paper examines the current spread of TR4, focusing on epidemiological aspects and recent research-based management options. Key epidemiological features were highlighted, drawing practical examples from various scales (plots to landscapes) and utilizing experiences from LAC's fight against TR4. The paper also reviews field-tested approaches in biosecurity, biological control, resistant varieties, soil health, and integrated disease management, acknowledging the specific challenges faced by smallholder settings. In each section research initiatives were analyzed, identifying gaps, and proposing directions to minimize TR4 impact and accelerate the development of sustainable solutions for managing this devastating disease.

Plant-microbe interactions through a lens: tales from the mycorrhizosphere

BACKGROUND

The soil microbiome plays a pivotal role in maintaining ecological balance, supporting food production, preserving water quality and safeguarding human health. Understanding the intricate dynamics within the soil microbiome necessitates unravelling complex bacterial-fungal interactions (BFIs). BFIs occur in diverse habitats, such as the phyllosphere, rhizosphere and bulk soil, where they exert substantial influence on plant-microbe associations, nutrient cycling and overall ecosystem functions. In various symbiotic associations, fungi form mycorrhizal connections with plant roots, enhancing nutrient uptake through the root and mycorrhizal pathways. Concurrently, specific soil bacteria, including mycorrhiza helper bacteria, play a pivotal role in nutrient acquisition and promoting plant growth. Chemical communication and biofilm formation further shape plant-microbial interactions, affecting plant growth, disease resistance and nutrient acquisition processes.

SCOPE

Promoting synergistic interactions between mycorrhizal fungi and soil microbes holds immense potential for advancing ecological knowledge and conservation. However, despite the significant progress, gaps remain in our understanding of the evolutionary significance, perception, functional traits and ecological relevance of BFIs. Here we review recent findings obtained with respect to complex microbial communities - particularly in the mycorrhizosphere - and include the latest advances in the field, outlining their profound impacts on our understanding of ecosystem dynamics and plant physiology and function.

CONCLUSIONS

Deepening our understanding of plant BFIs can help assess their capabilities with regard to ecological and agricultural safe-guarding, in particular buffering soil stresses, and ensuring sustainable land management practices. Preserving and enhancing soil biodiversity emerge as critical imperatives in sustaining life on Earth amidst pressures of anthropogenic climate change. A holistic approach integrates scientific knowledge on bacteria and fungi, which includes their potential to foster resilient soil ecosystems for present and future generations.

NIT24 and NIT29-mediated IAA synthesis of Xanthomonas oryzae pv. oryzicola suppresses immunity and boosts growth in rice

Auxin plays a pivotal role in the co-evolution of plants and microorganisms. Xanthomonas oryzae pv. oryzicola (Xoc) stands as a significant factor that affects rice yield and quality. However, the current understanding of Xoc's capability for indole 3-acetic acid (IAA) synthesis and its mechanistic implications remains elusive. In this study, we performed a comprehensive genomic analysis of Xoc strain RS105, leading to the identification of two nitrilase enzyme family (NIT) genes, designated as AKO15524.1 and AKO15829.1, subsequently named NIT24 and NIT29, respectively. Our investigation unveiled that the deletion of NIT24 and NIT29 resulted in a notable reduction in IAA synthesis capacity within RS105, thereby impacting extracellular polysaccharide production. This deficiency was partially ameliorated through exogenous IAA supplementation. The study further substantiated that NIT24 and NIT29 have nitrilase activity and the ability to catalyse IAA production in vitro. The lesion length and bacterial population statistics experiments confirmed that NIT24 and NIT29 positively regulated the pathogenicity of RS105, suggesting that NIT24 and NIT29 may regulate Xoc invasion by affecting IAA synthesis. Furthermore, our analysis corroborated mutant strains, RS105_ΔNIT24 and RS105_ΔNIT29, which elicited the outbreak of reactive oxygen species, the deposition of callose and the upregulation of defence-related gene expression in rice. IAA exerted a significant dampening effect on the immune responses incited by these mutant strains in rice. In addition, the absence of NIT24 and NIT29 affected the growth-promoting effect of Xoc on rice. This implies that Xoc may promote rice growth by secreting IAA, thus providing a more suitable microenvironment for its own colonization. In summary, our study provides compelling evidence for the existence of a nitrilase-dependent IAA biosynthesis pathway in Xoc. IAA synthesis-related genes promote Xoc colonization by inhibiting rice immune defence response and affecting rice growth by increasing IAA content in Xoc.

Meta-QTL analysis in wheat: progress, challenges and opportunities

Wheat, an important cereal crop globally, faces major challenges due to increasing global population and changing climates. The production and productivity are challenged by several biotic and abiotic stresses. There is also a pressing demand to enhance grain yield and quality/nutrition to ensure global food and nutritional security. To address these multifaceted concerns, researchers have conducted numerous meta-QTL (MQTL) studies in wheat, resulting in the identification of candidate genes that govern these complex quantitative traits. MQTL analysis has successfully unraveled the complex genetic architecture of polygenic quantitative traits in wheat. Candidate genes associated with stress adaptation have been pinpointed for abiotic and biotic traits, facilitating targeted breeding efforts to enhance stress tolerance. Furthermore, high-confidence candidate genes (CGs) and flanking markers to MQTLs will help in marker-assisted breeding programs aimed at enhancing stress tolerance, yield, quality and nutrition. Functional analysis of these CGs can enhance our understanding of intricate trait-related genetics. The discovery of orthologous MQTLs shared between wheat and other crops sheds light on common evolutionary pathways governing these traits. Breeders can leverage the most promising MQTLs and CGs associated with multiple traits to develop superior next-generation wheat cultivars with improved trait performance. This review provides a comprehensive overview of MQTL analysis in wheat, highlighting progress, challenges, validation methods and future opportunities in wheat genetics and breeding, contributing to global food security and sustainable agriculture.

Crossing the Gateless Barriers: Factors Involved in the Movement of Circulative Bacteria Within Their Insect Vectors

Plant bacterial pathogens transmitted by hemipteran vectors pose a large threat to the agricultural industry worldwide. Although virus-vector relationships have been widely investigated, a significant gap exists in our understanding of the molecular interactions between circulative bacteria and their insect vectors, mainly leafhoppers and psyllids. In this review, we will describe how these bacterial pathogens adhere, invade, and proliferate inside their insect vectors. We will also highlight the different transmission routes and molecular factors of phloem-limited bacteria that maintain an effective relationship with the insect host. Understanding the pathogen-vector relationship at the molecular level will help in the management of vector-borne bacterial diseases.

Microgravity and evasion of plant innate immunity by human bacterial pathogens

Spaceflight microgravity and modeled-microgravity analogs (MMA) broadly alter gene expression and physiology in both pathogens and plants. Research elucidating plant and bacterial responses to normal gravity or microgravity has shown the involvement of both physiological and molecular mechanisms. Under true and simulated microgravity, plants display differential expression of pathogen-defense genes while human bacterial pathogens exhibit increased virulence, antibiotic resistance, stress tolerance, and reduced LD50 in animal hosts. Human bacterial pathogens including Salmonella enterica and E. coli act as cross-kingdom foodborne pathogens by evading and suppressing the innate immunity of plants for colonization of intracellular spaces. It is unknown if evasion and colonization of plants by human pathogens occurs under microgravity and if there is increased infection capability as demonstrated using animal hosts. Understanding the relationship between microgravity, plant immunity, and human pathogens could prevent potentially deadly outbreaks of foodborne disease during spaceflight. This review will summarize (1) alterations to the virulency of human pathogens under microgravity and MMA, (2) alterations to plant physiology and gene expression under microgravity and MMA, (3) suppression and evasion of plant immunity by human pathogens under normal gravity, (4) studies of plant-microbe interactions under microgravity and MMA. A conclusion suggests future study of interactions between plants and human pathogens under microgravity is beneficial to human safety, and an investment in humanity's long and short-term space travel goals.

Impact of the fungal pathogen Fusarium oxysporum on the taxonomic and functional diversity of the common bean root microbiome

BACKGROUND

Plants rely on their root microbiome as the first line of defense against soil-borne fungal pathogens. The abundance and activities of beneficial root microbial taxa at the time prior to and during fungal infection are key to their protective success. If and how invading fungal root pathogens can disrupt microbiome assembly and gene expression is still largely unknown. Here, we investigated the impact of the fungal pathogen Fusarium oxysporum (fox) on the assembly of rhizosphere and endosphere microbiomes of a fox-susceptible and fox-resistant common bean cultivar.

RESULTS

Integration of 16S-amplicon, shotgun metagenome as well as metatranscriptome sequencing with community ecology analysis showed that fox infections significantly changed the composition and gene expression of the root microbiome in a cultivar-dependent manner. More specifically, fox infection led to increased microbial diversity, network complexity, and a higher proportion of the genera Flavobacterium, Bacillus, and Dyadobacter in the rhizosphere of the fox-resistant cultivar compared to the fox-susceptible cultivar. In the endosphere, root infection also led to changes in community assembly, with a higher abundance of the genera Sinorhizobium and Ensifer in the fox-resistant cultivar. Metagenome and metatranscriptome analyses further revealed the enrichment of terpene biosynthesis genes with a potential role in pathogen suppression in the fox-resistant cultivar upon fungal pathogen invasion.

CONCLUSION

Collectively, these results revealed a cultivar-dependent enrichment of specific bacterial genera and the activation of putative disease-suppressive functions in the rhizosphere and endosphere microbiome of common bean under siege.

Comparative genomics of the Liberibacter genus reveals widespread diversity in genomic content and positive selection history

'Candidatus Liberibacter' is a group of bacterial species that are obligate intracellular plant pathogens and cause Huanglongbing disease of citrus trees and Zebra Chip in potatoes. Here, we examined the extent of intra- and interspecific genetic diversity across the genus using comparative genomics. Our approach examined a wide set of Liberibacter genome sequences including five pathogenic species and one species not known to cause disease. By performing comparative genomics analyses, we sought to understand the evolutionary history of this genus and to identify genes or genome regions that may affect pathogenicity. With a set of 52 genomes, we performed comparative genomics, measured genome rearrangement, and completed statistical tests of positive selection. We explored markers of genetic diversity across the genus, such as average nucleotide identity across the whole genome. These analyses revealed the highest intraspecific diversity amongst the 'Ca. Liberibacter solanacearum' species, which also has the largest plant host range. We identified sets of core and accessory genes across the genus and within each species and measured the ratio of nonsynonymous to synonymous mutations (dN/dS) across genes. We identified ten genes with evidence of a history of positive selection in the Liberibacter genus, including genes in the Tad complex, which have been previously implicated as being highly divergent in the 'Ca. L. capsica' species based on high values of dN.

In Silico Characterization of the Secretome of the Fungal Pathogen Thielaviopsis punctulata, the Causal Agent of Date Palm Black Scorch Disease

The black scorch disease of date palm caused by Thielaviopsis punctulata is a serious threat to the cultivation and productivity of date palm in Arabian Peninsula. The virulence factors that contribute to pathogenicity of T. punctulata have not been identified yet. In the present study, using bioinformatics approach, secretory proteins of T. punctulata were identified and functionally characterized. A total of 197 putative secretory proteins were identified, of which 74 were identified as enzymes for carbohydrate degradation (CAZymes), 25 were proteases, and 47 were predicted as putative effectors. Within the CAZymes, 50 cell wall-degrading enzymes, potentially to degrade cell wall components such as cellulose, hemicellulose, lignin, and pectin, were identified. Of the 47 putative effectors, 34 possessed at least one functional domain. The secretome of T. punctulata was compared to the predicted secretome of five closely related species (T. musarum, T. ethacetica, T. euricoi, T. cerberus, and T. populi) and identified species specific CAZymes and putative effector genes in T. punctulata, providing a valuable resource for the research aimed at understanding the molecular mechanism underlying the pathogenicity of T. punctulata on Date palm.

Climate change impedes plant immunity mechanisms

Rapid climate change caused by human activity is threatening global crop production and food security worldwide. In particular, the emergence of new infectious plant pathogens and the geographical expansion of plant disease incidence result in serious yield losses of major crops annually. Since climate change has accelerated recently and is expected to worsen in the future, we have reached an inflection point where comprehensive preparations to cope with the upcoming crisis can no longer be delayed. Development of new plant breeding technologies including site-directed nucleases offers the opportunity to mitigate the effects of the changing climate. Therefore, understanding the effects of climate change on plant innate immunity and identification of elite genes conferring disease resistance are crucial for the engineering of new crop cultivars and plant improvement strategies. Here, we summarize and discuss the effects of major environmental factors such as temperature, humidity, and carbon dioxide concentration on plant immunity systems. This review provides a strategy for securing crop-based nutrition against severe pathogen attacks in the era of climate change.

Progress and prospectus in genetics and genomics of Phytophthora root and stem rot resistance in soybean (Glycine max L.)

Soybean is one of the largest sources of protein and oil in the world and is also considered a "super crop" due to several industrial advantages. However, enhanced acreage and adoption of monoculture practices rendered the crop vulnerable to several diseases. Phytophthora root and stem rot (PRSR) caused by Phytophthora sojae is one of the most prevalent diseases adversely affecting soybean production globally. Deployment of genetic resistance is the most sustainable approach for avoiding yield losses due to this disease. PRSR resistance is complex in nature and difficult to address by conventional breeding alone. Genetic mapping through a cost-effective sequencing platform facilitates identification of candidate genes and associated molecular markers for genetic improvement against PRSR. Furthermore, with the help of novel genomic approaches, identification and functional characterization of Rps (resistance to Phytophthora sojae) have also progressed in the recent past, and more than 30 Rps genes imparting complete resistance to different PRSR pathotypes have been reported. In addition, many genomic regions imparting partial resistance have also been identified. Furthermore, the adoption of emerging approaches like genome editing, genomic-assisted breeding, and genomic selection can assist in the functional characterization of novel genes and their rapid introgression for PRSR resistance. Hence, in the near future, soybean growers will likely witness an increase in production by adopting PRSR-resistant cultivars. This review highlights the progress made in deciphering the genetic architecture of PRSR resistance, genomic advances, and future perspectives for the deployment of PRSR resistance in soybean for the sustainable management of PRSR disease.

Roles of RNA silencing in viral and non-viral plant immunity and in the crosstalk between disease resistance systems

RNA silencing is a well-established antiviral immunity system in plants, in which small RNAs guide Argonaute proteins to targets in viral RNA or DNA, resulting in virus repression. Virus-encoded suppressors of silencing counteract this defence system. In this Review, we discuss recent findings about antiviral RNA silencing, including the movement of RNA through plasmodesmata and the differentiation between plant self and viral RNAs. We also discuss the emerging role of RNA silencing in plant immunity against non-viral pathogens. This immunity is mediated by transkingdom movement of RNA into and out of the infected plant cells in vesicles or as extracellular nucleoproteins and, like antiviral immunity, is influenced by the silencing suppressors encoded in the pathogens' genomes. Another effect of RNA silencing on general immunity involves host-encoded small RNAs, including microRNAs, that regulate NOD-like receptors and defence signalling pathways in the innate immunity system of plants. These RNA silencing pathways form a network of processes with both positive and negative effects on the immune systems of plants.

Using Genomes and Evolutionary Analyses to Screen for Host-Specificity and Positive Selection in the Plant Pathogen Xylella fastidiosa

Xylella fastidiosa infects several economically important crops in the Americas, and it also recently emerged in Europe. Here, using a set of Xylella genomes reflective of the genus-wide diversity, we performed a pan-genome analysis based on both core and accessory genes for two purposes: (i) to test associations between genetic divergence and plant host species and (ii) to identify positively selected genes that are potentially involved in arms-race dynamics. For the former, tests yielded significant evidence for the specialization of X. fastidiosa to plant host species. This observation contributes to a growing literature suggesting that the phylogenetic history of X. fastidiosa lineages affects the host range. For the latter, our analyses uncovered evidence of positive selection across codons for 5.3% (67 of 1,257) of the core genes and 5.4% (201 of 3,691) of the accessory genes. These genes are candidates to encode interacting factors with plant and insect hosts. Most of these genes had unknown functions, but we did identify some tractable candidates, including nagZ_2, which encodes a beta-glucosidase that is important for Neisseria gonorrhoeae biofilm formation; cya, which modulates gene expression in pathogenic bacteria, and barA, a membrane associated histidine kinase that has roles in cell division, metabolism, and pili formation.

IMPORTANCEXylella fastidiosa causes devasting diseases to several critical crops. Because X. fastidiosa colonizes and infects many plant species, it is important to understand whether the genome of X. fastidiosa has genetic determinants that underlie specialization to specific host plants. We analyzed genome sequences of X. fastidiosa to investigate evolutionary relationships and to test for evidence of positive selection on specific genes. We found a significant signal between genome diversity and host plants, consistent with bacterial specialization to specific plant hosts. By screening for positive selection, we identified both core and accessory genes that may affect pathogenicity, including genes involved in biofilm formation.

Effector-triggered inhibition of nodulation: A rhizobial effector protease targets soybean kinase GmPBS1-1

Type III protein secretion systems of nitrogen-fixing rhizobia deliver effector proteins into leguminous host cells to promote or inhibit the nodule symbiosis. However, mechanisms underlying effector-triggered inhibition of nodulation remain largely unknown. Nodulation outer protein T (NopT) of Sinorhizobium sp. NGR234 is an effector protease related to the Pseudomonas effector Avirulence protein Pseudomonas phaseolicola B (AvrPphB). Here, we constructed NGR234 mutants producing different NopT variants and found that protease activity of NopT negatively affects nodulation of smooth crotalaria (Crotalaria pallida). NopT variants lacking residues required for autocleavage and subsequent lipidation showed reduced symbiotic effects and were not targeted to the plasma membrane. We further noticed that Sinorhizobium fredii strains possess a mutated nopT gene. Sinorhizobium fredii USDA257 expressing nopT of NGR234 induced considerably fewer nodules in soybean (Glycine max) cv. Nenfeng 15 but not in other cultivars. Effector perception was further examined in NopT-expressing leaves of Arabidopsis (Arabidopsis thaliana) and found to be dependent on the protein kinase Arabidopsis AvrPphB Susceptible 1 (AtPBS1) and the associated resistance protein Arabidopsis Resistance to Pseudomonas syringae 5 (AtRPS5). Experiments with Nicotiana benthamiana plants indicated that the soybean homolog GmPBS1-1 associated with AtRPS5 can perceive NopT. Further analysis showed that NopT cleaves AtPBS1 and GmPBS1-1 and thus can activate these target proteins. Insertion of a DKM motif at the cleavage site of GmPBS1-1 resulted in increased proteolysis. Nodulation tests with soybeans expressing an autoactive GmPBS1-1 variant indicated that activation of a GmPBS1-1-mediated resistance pathway impairs nodule formation in cv. Nenfeng 15. Our findings suggest that legumes face an evolutionary dilemma of either developing effector-triggered immunity against pathogenic bacteria or establishing symbiosis with suboptimally adapted rhizobia producing pathogen-like effectors.

Microbial community succession in steam-sterilized greenhouses infected with Fusarium oxysporum

Fusarium is an economically important crop pathogen but spends a large part of its life cycle in bulk soil environments where it interacts with a diverse community of soil microbes. Antagonistic interactions (e.g. competition) between the resident microbial community and Fusarium could constrain the growth of Fusarium in soil, which might therefore slow or prevent Fusarium establishment. We tracked Fusarium oxysporum in floriculture greenhouses where the soil had been steam-sterilized to remove Fusarium. The data indicated a resurgence of soil bacteria and fungi during the first 90 days post-sterilization, followed by a rapid decline in subsequent weeks, which was associated with an increase in F. oxysporum abundance at 148 days post sterilization. These changes over time were associated with successional changes in the bacterial but not the fungal communities. The results illustrate that, although soil steaming clears Fusarium in the short term, it may exacerbate re-emergence as the resident community is continually depleted by the steaming process while Fusarium benefits from nutrients released by steaming. Observations suggest combining steaming with microbial inoculations could help reduce the recovery of Fusarium reducing the fungal load in the first instance and preventing subsequent build-up by giving a head start to its saprophytic competitors.

A Bacterial Type Three Secretion-Based Delivery System for Functional Characterization of Sporisorium scitamineum Plant Immune Suppressing Effector Proteins

The facultative biotrophic basidiomycete Sporisorium scitamineum causes smut disease in sugarcane. This study applied an assay to identify S. scitamineum candidate effectors (CEs) with plant immunity suppression activities by delivering them into Nicotiana benthamiana cells via the type-three secretion system of Pseudomonas fluorescens EtHAn. Six CEs were individually cloned into the pEDV6 vector and expressed by P. fluorescens EtHAn for translocation into the plant cells. Three CEs (g1052, g3890, and g5159) could suppress pattern-triggered immunity (PTI) responses with high reproducibility in different coinfiltration experiments with P. syringae pv. tomato DC3000. In addition, three CEs (g1052, g4549, and g5159) were also found to be AvrB-induced suppressors of effector-triggered immunity (ETI), demonstrating for the first time that S. scitamineum can defeat both PTI and ETI responses. A transcriptomic analysis at different stages of infection by the smut fungus of three sugarcane cultivars with contrasting responses to the pathogen revealed that suppressors g1052, g3890, g4549, and g5159 were induced at the early stage of infection. By contrast, the two CEs (g2666 and g6610) that did not exhibit suppression activities expressed only at the late stage of infection. Moreover, genomic structures of the CEs and searches for orthologs in other smut species suggested duplication events and further divergence in CEs evolution of S. scitamineum. Thus, the transient assay applied here demonstrated the potential of pEDV6 and P. fluorescens EtHAn as biological tools for identifying plant immune suppressors from S. scitamineum.

Review: Exploring possible approaches using ubiquitylation and sumoylation pathways in modifying plant stress tolerance

Ubiquitin and similar proteins, such as SUMO, are utilized by plants to modify target proteins to rapidly change their stability and activity in cells. This review will provide an overview of these crucial protein interactions with a focus on ubiquitylation and sumoylation in plants and how they contribute to stress tolerance. The work will also explore possibilities to use these highly conserved pathways for novel approaches to generate more robust crop plants better fit to cope with abiotic and biotic stress situations.

Partially Resistant Avocado Rootstock Dusa® Shows Prolonged Upregulation of Nucleotide Binding-Leucine Rich Repeat Genes in Response to Phytophthora cinnamomi Infection

Avocado is an important agricultural food crop in many countries worldwide. Phytophthora cinnamomi, a hemibiotrophic oomycete, remains one of the most devastating pathogens within the avocado industry, as it is near impossible to eradicate from areas where the pathogen is present. A key aspect to Phytophthora root rot disease management is the use of avocado rootstocks partially resistant to P. cinnamomi, which demonstrates an increased immune response following infection. In plant species, Nucleotide binding-Leucine rich repeat (NLR) proteins form an integral part of pathogen recognition and Effector triggered immune responses (ETI). To date, a comprehensive set of Persea americana NLR genes have yet to be identified, though their discovery is crucial to understanding the molecular mechanisms underlying P. americana-P. cinnamomi interactions. In this study, a total of 161 PaNLR genes were identified in the P. americana West-Indian pure accession genome. These putative resistance genes were characterized using bioinformatic approaches and grouped into 13 distinct PaNLR gene clusters, with phylogenetic analysis revealing high sequence similarity within these clusters. Additionally, PaNLR expression levels were analyzed in both a partially resistant (Dusa®) and a susceptible (R0.12) avocado rootstock infected with P. cinnamomi using an RNA-sequencing approach. The results showed that the partially resistant rootstock has increased expression levels of 84 PaNLRs observed up to 24 h post-inoculation, while the susceptible rootstock only showed increased PaNLR expression during the first 6 h post-inoculation. Results of this study may indicate that the partially resistant avocado rootstock has a stronger, more prolonged ETI response which enables it to suppress P. cinnamomi growth and combat disease caused by this pathogen. Furthermore, the identification of PaNLRs may be used to develop resistant rootstock selection tools, which can be employed in the avocado industry to accelerate rootstock screening programs.

Phenolic degradation by catechol dioxygenases is associated with pathogenic fungi with a necrotrophic lifestyle in the Ceratocystidaceae

Fungal species of the Ceratocystidaceae grow on their host plants using a variety of different lifestyles, from saprophytic to highly pathogenic. Although many genomes of fungi in the Ceratocystidaceae are publicly available, it is not known how the genes that encode catechol dioxygenases (CDOs), enzymes involved in the degradation of phenolic plant defense compounds, differ among members of the Ceratocystidaceae. The aim of this study was therefore to identify and characterize the genes encoding CDOs in the genomes of Ceratocystidaceae representatives. We found that genes encoding CDOs are more abundant in pathogenic necrotrophic species of the Ceratocystidaceae and less abundant in saprophytic species. The loss of the CDO genes and the associated 3-oxoadipate catabolic pathway appears to have occurred in a lineage-specific manner. Taken together, this study revealed a positive association between CDO gene copy number and fungal lifestyle in Ceratocystidaceae representatives.

Identification and characterization of genome-wide resistance gene analogs (RGAs) of durian (Durio zibethinus L.)

BACKGROUND

Durian (Durio zibethinus L.) is a tropical fruit crop which is popular in Southeast Asia but recently gaining popularity in other parts of the world. In this study, we analyzed the resistance gene analogs (RGAs) of durian through mining of the currently available reference genome of its 'Musang King' cultivar (PRJNA400310).

RESULTS

A total of 2586 RGAs were identified in the durian genome consisting of 47 nucleotide binding site proteins (NBS), 158 NBS-leucine rich repeat proteins (NL), 400 coiled-coil NBS-LRR (CNL), 72 toll/interleukin-1 receptor NBS-LRR (TNL), 54 coiled-coil NBS (CN), 10 toll/interleukin-1 receptor NBS (TN), 19 toll/interleukin-1 receptor with unknown domain (TX), 246 receptor-like proteins (RLP), 1,377 receptor-like kinases (RLK), 185 TM-CC, and 18 other NBS-containing proteins with other domains. These RGAs were functionally annotated and characterized via gene ontology (GO) analysis. Among the RGAs with the highest copies in durian genome include the putative disease resistance RPP13-like protein 1, disease resistance protein At4g27190, disease resistance protein RPS6, Probable disease resistance protein At4g27220, and putative disease resistance protein RGA3, while 35 RGAs were found to be novel. Phylogenetic analyses revealed that the genome-wide RGAs were broadly clustered into four major clades based on their domain classification.

CONCLUSION

To our knowledge, this is the most comprehensive analysis of durian RGAs which provides a valuable resource for genetic, agronomic, and other biological research of this important tropical fruit crop.

Medicago truncatula in Interaction with Fusarium and Rhizoctonia Phytopathogenic Fungi: Fungal Aggressiveness, Plant Response Biodiversity and Character Heritability Indices

Fusarium and Rhizoctonia genera are important pathogens of many field crops worldwide. They are constantly evolving and expanding their host range. Selecting resistant cultivars is an effective strategy to break their infection cycles. To this end, we screened a collection of Medicago truncatula accessions against Fusarium oxysporum, Fusarium solani, and Rhizoctonia solani strains isolated from different plant species. Despite the small collection, a biodiversity in the disease response of M. truncatula accessions ranging from resistant phenotypes to highly susceptible ones was observed. A17 showed relative resistance to all fungal strains with the lowest disease incidence and ratings while TN1.11 was among the susceptible accessions. As an initiation of the characterization of resistance mechanisms, the antioxidant enzymes' activities, at the early stages of infections, were compared between these contrasting accessions. Our results showed an increment of the antioxidant activities within A17 plants in leaves and roots. We also analyzed the responses of a population of recombinant inbred lines derived from the crossing of A17 and TN1.11 to the infection with the same fungal strains. The broad-sense heritability of measured traits ranged from 0.87 to 0.95, from 0.72 to 0.96, and from 0.14 to 0.85 under control, F. oxysporum, and R. solani conditions, respectively. This high estimated heritability underlines the importance of further molecular analysis of the observed resistance to identify selection markers that could be incorporated into a breeding program and thus improving soil-borne pathogens resistance in crops.

Plant volatile organic compound (E)-2-hexenal facilitates Botrytis cinerea infection of fruits by inducing sulfate assimilation

Investigation into plant-fungal pathogen interactions is one of the most interesting fields in plant sciences. However, the roles of plant volatile organic compounds in the arms race are still largely unknown. Based on precise quantification of plant volatiles, we discovered that the plant volatile organic compound (E)-2-hexenal, at concentrations that were similar to or lower than those in tissues of strawberry and tomato fruits, upregulates sulfate assimilation in spores and hyphae of the phytopathogenic fungus Botrytis cinerea. This upregulation is independent of the types of sulfur sources in the plant and can be achieved in the presence of inorganic sulfate and organic sulfur sources. Using the fungal deletion mutants, we further found that sulfate assimilation is involved in the infection of tomato and strawberry fruits by B. cinerea, and that the severity of the disease is proportional to the sulfate content in the fruits. Both before and during the infection, (E)-2-hexenal induced utilisation of plant sulfate by B. cinerea facilitates its pathogenesis through enhancing its tolerance to oxidative stress. This work provides novel insights into the role of plant volatiles in plant-fungal pathogen interaction and highlights the importance of sulfur levels in the host in the prevention of grey mould disease.

Amyloid Proteins in Plant-Associated Microbial Communities

Amyloids have proven to be a widespread phenomenon rather than an exception. Many proteins presenting the hallmarks of this characteristic beta sheet-rich folding have been described to date. Particularly common are functional amyloids that play an important role in the promotion of survival and pathogenicity in prokaryotes. Here, we describe important developments in amyloid protein research that relate to microbe-microbe and microbe-host interactions in the plant microbiome. Starting with biofilms, which are a broad strategy for bacterial persistence that is extremely important for plant colonization. Microbes rely on amyloid-based mechanisms to adhere and create a protective coating that shelters them from external stresses and promotes cooperation. Another strategy generally carried out by amyloids is the formation of hydrophobic surface layers. Known as hydrophobins, these proteins coat the aerial hyphae and spores of plant pathogenic fungi, as well as certain bacterial biofilms. They contribute to plant virulence through promoting dissemination and infectivity. Furthermore, antimicrobial activity is an interesting outcome of the amyloid structure that has potential application in medicine and agriculture. There are many known antimicrobial amyloids released by animals and plants; however, those produced by bacteria or fungi remain still largely unknown. Finally, we discuss amyloid proteins with a more indirect mode of action in their host interactions. These include virulence-promoting harpins, signaling transduction that functions through amyloid templating, and root nodule bacteria proteins that promote plant-microbe symbiosis. In summary, amyloids are an interesting paradigm for their many functional mechanisms linked to bacterial survival in plant-associated microbial communities.

QTL mapping in Fusarium graminearum identified an allele of FgVe1 involved in reduced aggressiveness

Fusarium graminearum is one of the most frequent causal agents of the Fusarium Head Blight, a cereal disease spread throughout the world, reducing grain production and quality. F. graminearum isolates are genetically and phenotypically highly diverse. Notably, remarkable variations of aggressiveness between isolates have been observed, which could reflect an adaptive potential of this pathogen. In this study, we aimed to characterize the genetic basis of aggressiveness variation observed in an F1 population (n = 94), for which genome sequences of both parental strains are available. Aggressiveness was assessed by a panel of in planta and in vitro proxies during two phenotyping trials including, among others, disease severity and mycotoxin accumulation in wheat spike. One major and single QTL was mapped for all the traits measured, on chromosome I, that explained up to 90% of the variance for disease severity. The confidence interval at the QTL spanned 1.2 Mb and contained 428 genes on the reference genome. Of these, four candidates were selected based on the postulate that a non-synonymous mutation affecting protein function may be responsible for phenotypic differences. Finally, a new mutation was identified and functionally validated in the gene FgVe1, coding for a velvet protein known to be involved in pathogenicity and secondary metabolism production in several fungi.

ALD1 accumulation in Arabidopsis epidermal plastids confers local and non-autonomous disease resistance

The Arabidopsis plastid-localized ALD1 protein acts in the lysine catabolic pathway that produces infection-induced pipecolic acid (Pip), Pip derivatives, and basal non-Pip metabolite(s). ALD1 is indispensable for disease resistance associated with Pseudomonas syringae infections of naïve plants as well as those previously immunized by a local infection, a phenomenon called systemic acquired resistance (SAR). Pseudomonas syringae is known to associate with mesophyll as well as epidermal cells. To probe the importance of epidermal cells in conferring bacterial disease resistance, we studied plants in which ALD1 was only detectable in the epidermal cells of specific leaves. Local disease resistance and many features of SAR were restored when ALD1 preferentially accumulated in the epidermal plastids at immunization sites. Interestingly, SAR restoration occurred without appreciable accumulation of Pip or known Pip derivatives in secondary distal leaves. Our findings establish that ALD1 has a non-autonomous effect on pathogen growth and defense activation. We propose that ALD1 is sufficient in the epidermis of the immunized leaves to activate SAR, but basal ALD1 and possibly a non-Pip metabolite(s) are also needed at all infection sites to fully suppress bacterial growth. Thus, epidermal plastids that contain ALD1 play a key role in local and whole-plant immune signaling.

Bayogenin 3-O-cellobioside confers non-cultivar-specific defence against the rice blast fungus Pyricularia oryzae

Rice cultivars from japonica and indica lineage possess differential resistance against blast fungus as a result of genetic divergence. Whether different rice cultivars also show distinct metabolomic changes in response to P. oryzae, and their role in host resistance, are poorly understood. Here, we examine the responses of six different rice cultivars from japonica and indica lineage challenged with P. oryzae. Both susceptible and resistant rice cultivars expressed several metabolites exclusively during P. oryzae infection, including the saponin Bayogenin 3-O-cellobioside. Bayogenin 3-O-cellobioside level in infected rice directly correlated with their resistant attributes. These findings reveal, for the first time to our knowledge that besides oat, other grass plants including rice produces protective saponins. Our study provides insight into the role of pathogen-mediated metabolomics reprogramming in host immunity. The correlation between Bayogenin 3-O-Cellobioside levels and blast resistance suggests that engineering saponin expression in cereal crops represents attractive and sustainable disease management.

Evolution of Disease Severity and Susceptibility in the Asteraceae to the Powdery Mildew Golovinomyces latisporus: Major Phylogenetic Structure Coupled With Highly Variable Disease Severity at Fine Scales

Pathogen host range and pathogen severity are dependent on interactions with their hosts and are hypothesized to have evolved as products of a coevolutionary arms race. An understanding of the factors that affect host range and pathogen severity is especially crucial in introduced pathogens that infect evolutionarily naïve hosts and cause substantial damage to ecosystems. Powdery mildews are detrimental pathogens found worldwide in managed and natural systems. Golovinomyces latisporus is a powdery mildew species that is especially damaging to plants within Asteraceae and to plants within the genus Helianthus in particular. In this study, we evaluated 126 species within Asteraceae to measure the role of host plant morphophysiological traits and evolutionary history on susceptibility to G. latisporus and disease severity. We observed phylogenetic signal in both susceptibility and severity within and among major clades of the Asteraceae. In general, there was a major phylogenetic structure of host severity to G. latisporus; however, there was some fine-scale phylogenetic variability. Phylogenetic statistical methods showed that chlorophyll content, biomass, stomatal index, and trichome density were not associated with disease severity, thus providing evidence that phylogenetic structure, rather than observed plant morphophysiological traits, is the most reliable predictor of pathogen severity. This work sheds light on the role that evolutionary history plays in plant susceptibility and severity to disease and underscores the relative unimportance of commonly assessed host plant traits in powdery mildew severity.

Transcriptomic Profiling of Populus Roots Challenged with Fusarium Reveals Differential Responsive Patterns of Invertase and Invertase Inhibitor-Like Families within Carbohydrate Metabolism

Fusarium solani (Fs) is one of the notorious necrotrophic fungal pathogens that cause root rot and vascular wilt, accounting for the severe loss of Populus production worldwide. The plant-pathogen interactions have a strong molecular basis. As yet, the genomic information and transcriptomic profiling on the attempted infection of Fs remain unavailable in a woody model species, Populus trichocarpa. We used a full RNA-seq transcriptome to investigate the molecular interactions in the roots with a time-course infection at 0, 24, 48, and 72 h post-inoculation (hpi) of Fs. Concomitantly, the invertase and invertase inhibitor-like gene families were further analyzed, followed by the experimental evaluation of their expression patterns using quantitative PCR (qPCR) and enzyme assay. The magnitude profiles of the differentially expressed genes (DEGs) were observed at 72 hpi inoculation. Approximately 839 genes evidenced a reception and transduction of pathogen signals, a large transcriptional reprogramming, induction of hormone signaling, activation of pathogenesis-related genes, and secondary and carbohydrate metabolism changes. Among these, a total of 63 critical genes that consistently appear during the entire interactions of plant-pathogen had substantially altered transcript abundance and potentially constituted suitable candidates as resistant genes in genetic engineering. These data provide essential clues in the developing new strategies of broadening resistance to Fs through transcriptional or translational modifications of the critical responsive genes within various analyzed categories (e.g., carbohydrate metabolism) in Populus.

Under fire-simultaneous volatilome and transcriptome analysis unravels fine-scale responses of tansy chemotypes to dual herbivore attack

BACKGROUND

Tansy plants (Tanacetum vulgare L.) are known for their high intraspecific chemical variation, especially of volatile organic compounds (VOC) from the terpenoid compound group. These VOCs are closely involved in plant-insect interactions and, when profiled, can be used to classify plants into groups known as chemotypes. Tansy chemotypes have been shown to influence plant-aphid interactions, however, to date no information is available on the response of different tansy chemotypes to simultaneous herbivory by more than one insect species.

RESULTS

Using a multi-cuvette system, we investigated the responses of five tansy chemotypes to feeding by sucking and/or chewing herbivores (aphids and caterpillars; Metopeurum fuscoviride Stroyan and Spodoptera littoralis Boisduval). Herbivory by caterpillars following aphid infestation led to a plant chemotype-specific change in the patterns of terpenoids stored in trichome hairs and in VOC emissions. The transcriptomic analysis of a plant chemotype represents the first de novo assembly of a transcriptome in tansy and demonstrates priming effects of aphids on a subsequent herbivory. Overall, we show that the five chemotypes do not react in the same way to the two herbivores. As expected, we found that caterpillar feeding increased VOC emissions, however, a priori aphid infestation only led to a further increase in VOC emissions for some chemotypes.

CONCLUSIONS

We were able to show that different chemotypes respond to the double herbivore attack in different ways, and that pre-treatment with aphids had a priming effect on plants when they were subsequently exposed to a chewing herbivore. If neighbouring chemotypes in a field population react differently to herbivory/dual herbivory, this could possibly have effects from the individual level to the group level. Individuals of some chemotypes may respond more efficiently to herbivory stress than others, and in a group environment these "louder" chemotypes may affect the local insect community, including the natural enemies of herbivores, and other neighbouring plants.

What is the Molecular Basis of Nonhost Resistance?

This article is part of the Top 10 Unanswered Questions in MPMI invited review series.Nonhost resistance is typically considered the ability of a plant species to repel all attempts of a pathogen species to colonize it and reproduce on it. Based on this common definition, nonhost resistance is presumed to be very durable and, thus, of great interest for its potential use in agriculture. Despite considerable research efforts, the molecular basis of this type of plant immunity remains nebulous. We here stress the fact that "nonhost resistance" is a phenomenological rather than a mechanistic concept that comprises more facets than typically considered. We further argue that nonhost resistance essentially relies on the very same genes and pathways as other types of plant immunity, of which some may act as bottlenecks for particular pathogens on a given plant species or under certain conditions. Thus, in our view, the frequently used term "nonhost genes" is misleading and should be avoided. Depending on the plant-pathogen combination, nonhost resistance may involve the recognition of pathogen effectors by host immune sensor proteins, which might give rise to host shifts or host range expansions due to evolutionary-conditioned gains and losses in respective armories. Thus, the extent of nonhost resistance also defines pathogen host ranges. In some instances, immune-related genes can be transferred across plant species to boost defense, resulting in augmented disease resistance. We discuss future routes for deepening our understanding of nonhost resistance and argue that the confusing term "nonhost resistance" should be used more cautiously in the light of a holistic view of plant immunity.

Genetic Diversity and Population Structure of Races of Fusarium oxysporum Causing Cotton Wilt

To better understand the evolution of virulence we are interested in identifying the genetic basis of this trait in pathogenic fungi and in developing tools for the rapid characterization of variation in virulence among populations associated with epidemics. Fusarium oxysporum f. sp. vasinfectum (FOV) is a haploid fungus that causes devastating outbreaks of Fusarium wilt of cotton wherever it is grown. In the United States, six nominal races and eleven genotypes of FOV have been characterized based on the translation elongation factor (EF-1α) gene and intergenic spacer region (IGS), but it is unclear how race or genotype based on these regions relates to population structure or virulence. We used genotyping-by-sequencing to identify SNPs and determine genetic diversity and population structure among 86 diverse FOV isolates. Six individuals of Fusarium oxysporum closely related to FOV were genotyped and included in some analyses. Between 193 and 354 SNPs were identified and included in the analyses depending on the pipeline and filtering criteria used. Phylogenetic trees, minimum spanning networks (MSNs), principal components analysis (PCA), and discriminant analysis of principal components (DAPC) demonstrated that races and genotypes of FOV are generally not structured by EF-1α genotype, nor are they monophyletic groups with the exception of race 4 isolates, which are distinct. Furthermore, DAPC identified between 11 and 14 genetically distinct clusters of FOV, whereas only eight EF-1α genotypes were represented among isolates; suggesting that FOV, especially isolates within the widely distributed and common race 1 genotype, is more genetically diverse than currently recognized.

Structural evolution drives diversification of the large LRR-RLK gene family

●Cells are continuously exposed to chemical signals that they must discriminate between and respond to appropriately. In embryophytes, the leucine-rich repeat receptor-like kinases (LRR-RLKs) are signal receptors critical in development and defense. LRR-RLKs have diversified to hundreds of genes in many plant genomes. Although intensively studied, a well-resolved LRR-RLK gene tree has remained elusive. ●To resolve the LRR-RLK gene tree, we developed an improved gene discovery method based on iterative hidden Markov model searching and phylogenetic inference. We used this method to infer complete gene trees for each of the LRR-RLK subclades and reconstructed the deepest nodes of the full gene family. ●We discovered that the LRR-RLK gene family is even larger than previously thought, and that protein domain gains and losses are prevalent. These structural modifications, some of which likely predate embryophyte diversification, led to misclassification of some LRR-RLK variants as members of other gene families. Our work corrects this misclassification. ●Our results reveal ongoing structural evolution generating novel LRR-RLK genes. These new genes are raw material for the diversification of signaling in development and defense. Our methods also enable phylogenetic reconstruction in any large gene family.

Bioinformatic Detection of Positive Selection Pressure in Plant Pathogens: The Neutral Theory of Molecular Sequence Evolution in Action

The genomes of plant pathogenic fungi and oomycetes are often exposed to strong positive selection pressure. During speciation, shifts in host range and preference can lead to major adaptive changes. Furthermore, evolution of total host resistance to most isolates can force rapid evolutionary changes in host-specific pathogens. Crop pathogens are subjected to particularly intense selective pressures from monocultures and fungicides. Detection of the footprints of positive selection in plant pathogen genomes is a worthwhile endeavor as it aids understanding of the fundamental biology of these important organisms. There are two main classes of test for detection of positively selected alleles. Tests based on the ratio of non-synonymous to synonymous substitutions per site detect the footprints of multiple fixation events between divergent lineages. Thus, they are well-suited to the study of ancient adaptation events spanning speciations. On the other hand, tests that scan genomes for local fluctuations in allelic diversity within populations are suitable for detection of recent positive selection in populations. In this review, I briefly describe some of the more widely used tests of positive selection and the theory underlying them. I then discuss various examples of their application to plant pathogen genomes, emphasizing the types of genes that are associated with signatures of positive selection. I conclude with a discussion of the practicality of such tests for identification of pathogen genes of interest and the important features of pathogen ecology that must be taken into account for accurate interpretation.

The PTI to ETI Continuum in Phytophthora-Plant Interactions

Phytophthora species are notorious pathogens of several economically important crop plants. Several general elicitors, commonly referred to as Pathogen-Associated Molecular Patterns (PAMPs), from Phytophthora spp. have been identified that are recognized by the plant receptors to trigger induced defense responses in a process termed PAMP-triggered Immunity (PTI). Adapted Phytophthora pathogens have evolved multiple strategies to evade PTI. They can either modify or suppress their elicitors to avoid recognition by host and modulate host defense responses by deploying hundreds of effectors, which suppress host defense and physiological processes by modulating components involved in calcium and MAPK signaling, alternative splicing, RNA interference, vesicle trafficking, cell-to-cell trafficking, proteolysis and phytohormone signaling pathways. In incompatible interactions, resistant host plants perceive effector-induced modulations through resistance proteins and activate downstream components of defense responses in a quicker and more robust manner called effector-triggered-immunity (ETI). When pathogens overcome PTI-usually through effectors in the absence of R proteins-effectors-triggered susceptibility (ETS) ensues. Qualitatively, many of the downstream defense responses overlap between PTI and ETI. In general, these multiple phases of Phytophthora-plant interactions follow the PTI-ETS-ETI paradigm, initially proposed in the zigzag model of plant immunity. However, based on several examples, in Phytophthora-plant interactions, boundaries between these phases are not distinct but are rather blended pointing to a PTI-ETI continuum.

The host generalist phytopathogenic fungus Sclerotinia sclerotiorum differentially expresses multiple metabolic enzymes on two different plant hosts

Sclerotinia sclerotiorum is a necrotrophic fungal pathogen that infects upwards of 400 plant species, including several economically important crops. The molecular processes that underpin broad host range necrotrophy are not fully understood. This study used RNA sequencing to assess whether S. sclerotiorum genes are differentially expressed in response to infection of the two different host crops canola (Brassica napus) and lupin (Lupinus angustifolius). A total of 10,864 of the 11,130 genes in the S. sclerotiorum genome were expressed. Of these, 628 were upregulated in planta relative to in vitro on at least one host, suggesting involvement in the broader infection process. Among these genes were predicted carbohydrate-active enzymes (CAZYmes) and secondary metabolites. A considerably smaller group of 53 genes were differentially expressed between the two plant hosts. Of these host-specific genes, only six were either CAZymes, secondary metabolites or putative effectors. The remaining genes represented a diverse range of functional categories, including several associated with the metabolism and efflux of xenobiotic compounds, such as cytochrome P450s, metal-beta-lactamases, tannases and major facilitator superfamily transporters. These results suggest that S. sclerotiorum may regulate the expression of detoxification-related genes in response to phytotoxins produced by the different host species. To date, this is the first comparative whole transcriptome analysis of S. sclerotiorum during infection of different hosts.

Molecular Logic and Evolution of Bitter Taste in Drosophila

Taste systems detect a vast diversity of toxins, which are perceived as bitter. When a species adapts to a new environment, its taste system must adapt to detect new death threats. We deleted each of six commonly expressed bitter gustatory receptors (Grs) from Drosophila melanogaster. Systematic analysis revealed that requirements for these Grs differed for the same tastant in different neurons and for different tastants in the same neuron. Responses to some tastants in some neurons required four Grs, including Gr39a. Deletions also produced increased or novel responses, supporting a model of Gr-Gr inhibitory interactions. Coexpression of four Grs conferred several bitter responses to a sugar neuron. We then examined bitter coding in three other Drosophila species. We found major evolutionary shifts. One shift depended on the concerted activity of seven Grs. This work shows how the complex logic of bitter coding provides the capacity to detect innumerable hazards and the flexibility to adapt to new ones.

PpCRN7 and PpCRN20 of Phythophthora parasitica regulate plant cell death leading to enhancement of host susceptibility

BACKGROUND

Phytophthora species secrete cytoplasmic effectors from a family named Crinkler (CRN), which are characterised by the presence of conserved specific domains in the N- and C-terminal regions. P. parasitica causes disease in a wide range of host plants, however the role of CRN effectors in these interactions remains unclear. Here, we aimed to: (i) identify candidate CRN encoding genes in P. parasitica genomes; (ii) evaluate the transcriptional expression of PpCRN (Phytophthora parasitica Crinkler candidate) during the P. parasitica interaction with Citrus sunki (high susceptible) and Poncirus trifoliata (resistant); and (iii) functionally characterize two PpCRNs in the model plant Nicotiana benthamiana.

RESULTS

Our in silico analyses identified 80 putative PpCRN effectors in the genome of P. parasitica isolate 'IAC 01/95.1'. Transcriptional analysis revealed differential gene expression of 20 PpCRN candidates during the interaction with the susceptible Citrus sunki and the resistant Poncirus trifoliata. We have also found that P. parasitica is able to recognize different citrus hosts and accordingly modulates PpCRNs expression. Additionally, two PpCRN effectors, namely PpCRN7 and PpCRN20, were further characterized via transient gene expression in N. benthamiana leaves. The elicitin INF-1-induced Hypersensitivity Response (HR) was increased by an additive effect driven by PpCRN7 expression, whereas PpCRN20 expression suppressed HR response in N. benthamiana leaves. Despite contrasting functions related to HR, both effectors increased the susceptibility of plants to P. parasitica.

CONCLUSIONS

PpCRN7 and PpCRN20 have the ability to increase P. parasitica pathogenicity and may play important roles at different stages of infection. These PpCRN-associated mechanisms are now targets of biotechnological studies aiming to break pathogen's virulence and to promote plant resistance.

Evolution of the Genes Encoding Effector Candidates Within Multiple Pathotypes of Magnaporthe oryzae

Magnaporthe oryzae infects rice, wheat, and many grass species in the Poaceae family by secreting protein effectors. Here, we analyzed the distribution, sequence variation, and genomic context of effector candidate (EFC) genes in 31 isolates that represent five pathotypes of M. oryzae, three isolates of M. grisea, a sister species of M. oryzae, and one strain each for eight species in the family Magnaporthaceae to investigate how the host range expansion of M. oryzae has likely affected the evolution of effectors. We used the EFC genes of M. oryzae strain 70-15, whose genome has served as a reference for many comparative genomics analyses, to identify their homologs in these strains. We also analyzed the previously characterized avirulence (AVR) genes and single-copy orthologous (SCO) genes in these strains, which showed that the EFC and AVR genes evolved faster than the SCO genes. The EFC and AVR repertoires among M. oryzae pathotypes varied widely probably because adaptation to individual hosts exerted different types of selection pressure. Repetitive DNA elements appeared to have caused the variation of some EFC genes. Lastly, we analyzed expression patterns of the AVR and EFC genes to test the hypothesis that such genes are preferentially expressed during host infection. This comprehensive dataset serves as a foundation for future studies on the genetic basis of the evolution and host specialization in M. oryzae.

Cause and Effectors: Whole-Genome Comparisons Reveal Shared but Rapidly Evolving Effector Sets among Host-Specific Plant-Castrating Fungi

Plant pathogens use molecular weapons to successfully infect their hosts, secreting a large portfolio of various proteins and enzymes. Different plant species are often parasitized by host-specific pathogens; however, it is still unclear whether the molecular basis of such host specialization involves species-specific weapons or different variants of the same weapons. We therefore compared the genes encoding secreted proteins in three plant-castrating pathogens parasitizing different host plants, producing their spores in plant anthers by replacing pollen. We validated our predictions for secretion signals for some genes and checked that our predicted secreted proteins were often highly expressed during plant infection. While we found few species-specific secreted proteins, numerous genes encoding secreted proteins showed signs of rapid evolution and of natural selection. Our study thus found that most changes among closely related host-specific pathogens involved rapid adaptive changes in shared molecular weapons rather than innovations for new weapons.

Plant pathogens utilize a portfolio of secreted effectors to successfully infect and manipulate their hosts. It is, however, still unclear whether changes in secretomes leading to host specialization involve mostly effector gene gains/losses or changes in their sequences. To test these hypotheses, we compared the secretomes of three host-specific castrating anther smut fungi (Microbotryum), two being sister species. To address within-species evolution, which might involve coevolution and local adaptation, we compared the secretomes of strains from differentiated populations. We experimentally validated a subset of signal peptides. Secretomes ranged from 321 to 445 predicted secreted proteins (SPs), including a few species-specific proteins (42 to 75), and limited copy number variation, i.e., little gene family expansion or reduction. Between 52% and 68% of the SPs did not match any Pfam domain, a percentage that reached 80% for the small secreted proteins, indicating rapid evolution. In comparison to background genes, we indeed found SPs to be more differentiated among species and strains, more often under positive selection, and highly expressed in planta; repeat-induced point mutations (RIPs) had no role in effector diversification, as SPs were not closer to transposable elements than background genes and were not more RIP affected. Our study thus identified both conserved core proteins, likely required for the pathogenic life cycle of all Microbotryum species, and proteins that were species specific or evolving under positive selection; these proteins may be involved in host specialization and/or coevolution. Most changes among closely related host-specific pathogens, however, involved rapid changes in sequences rather than gene gains/losses.