Functional roles of effectors of plant-parasitic nematodes

Identification and characterization of specific motifs in effector proteins of plant parasites using MOnSTER

Plant pathogens cause billions of dollars of crop loss every year and are a major threat to global food security. Identifying and characterizing pathogens effectors is crucial towards their improved control. Because of their poor sequence conservation, effector identification is challenging, and current methods generate too many candidates without indication for prioritizing experimental studies. In most phyla, effectors contain specific sequence motifs which influence their localization and targets in the plant. Therefore, there is an urgent need to develop bioinformatics tools tailored for pathogen effectors. To circumvent these limitations, we have developed MOnSTER a specific tool that identifies clusters of motifs of protein sequences (CLUMPs). MOnSTER can be fed with motifs identified by de novo tools or from databases such as Pfam and InterProScan. The advantage of MOnSTER is the reduction of motif redundancy by clustering them and associating a score. This score encompasses the physicochemical properties of AAs and the motif occurrences. We built up our method to identify discriminant CLUMPs in oomycetes effectors. Consequently, we applied MOnSTER on plant parasitic nematodes and identified six CLUMPs in about 60% of the known nematode candidate parasitism proteins. Furthermore, we found co-occurrences of CLUMPs with protein domains important for invasion and pathogenicity. The potentiality of this tool goes beyond the effector characterization and can be used to easily cluster motifs and calculate the CLUMP-score on any set of protein sequences.

Pine wilt disease: what do we know from proteomics?

Pine wilt disease (PWD) is a devastating forest disease caused by the pinewood nematode (PWN), Bursaphelenchus xylophilus, a migratory endoparasite that infects several coniferous species. During the last 20 years, advances have been made for understanding the molecular bases of PWN-host trees interactions. Major advances emerged from transcriptomic and genomic studies, which revealed some unique features related to PWN pathogenicity and constituted fundamental data that allowed the development of postgenomic studies. Here we review the proteomic approaches that were applied to study PWD and integrated the current knowledge on the molecular basis of the PWN pathogenicity. Proteomics has been useful for understanding cellular activities and protein functions involved in PWN-host trees interactions, shedding light into the mechanisms associated with PWN pathogenicity and being promising tools to better clarify host trees PWN resistance/susceptibility.

Meloidogyne enterolobii MeMSP1 effector targets the glutathione-S-transferase phi GSTF family in Arabidopsis to manipulate host metabolism and promote nematode parasitism

Meloidogyne enterolobii is an emerging root-knot nematode species that overcomes most of the nematode resistance genes in crops. Nematode effector proteins secreted in planta are key elements in the molecular dialogue of parasitism. Here, we show the MeMSP1 effector is secreted into giant cells and promotes M. enterolobii parasitism. Using co-immunoprecipitation and bimolecular fluorescent complementation assays, we identified glutathione-S-transferase phi GSTFs as host targets of the MeMSP1 effector. This protein family plays important roles in plant responses to abiotic and biotic stresses. We demonstrate that MeMSP1 interacts with all Arabidopsis GSTF. Moreover, we confirmed that the N-terminal region of AtGSTF9 is critical for its interaction, and atgstf9 mutant lines are more susceptible to root-knot nematode infection. Combined transcriptome and metabolome analyses showed that MeMSP1 affects the metabolic pathways of Arabidopsis thaliana, resulting in the accumulation of amino acids, nucleic acids, and their metabolites, and organic acids and the downregulation of flavonoids. Our study has shed light on a novel effector mechanism that targets plant metabolism, reducing the production of plant defence-related compounds while favouring the accumulation of metabolites beneficial to the nematode, and thereby promoting parasitism.

Functional Modules in the Meristems: "Tinkering" in Action

BACKGROUND

A feature of higher plants is the modular principle of body organisation. One of these conservative morphological modules that regulate plant growth, histogenesis and organogenesis is meristems-structures that contain pools of stem cells and are generally organised according to a common principle. Basic content: The development of meristems is under the regulation of molecular modules that contain conservative interacting components and modulate the expression of target genes depending on the developmental context. In this review, we focus on two molecular modules that act in different types of meristems. The WOX-CLAVATA module, which includes the peptide ligand, its receptor and the target transcription factor, is responsible for the formation and control of the activity of all meristem types studied, but it has its own peculiarities in different meristems. Another regulatory module is the so-called florigen-activated complex, which is responsible for the phase transition in the shoot vegetative meristem (e.g., from the vegetative shoot apical meristem to the inflorescence meristem).

CONCLUSIONS

The review considers the composition and functions of these two functional modules in different developmental programmes, as well as their appearance, evolution and use in plant breeding.

Galls induced by a root-knot nematode in Petroselinum crispum (Mill.): impacts on host development, histology, and cell wall dynamics

Infection by the root-knot nematode (RKN), Meloidogyne incognita, impacts crop productivity worldwide, including parsley cultures (Petroselinum crispum). Meloidogyne infection involves a complex relationship between the pathogen and the host plant tissues, leading to the formation of galls and feeding sites that disorganize the vascular system, affecting the development of cultures. Herein, we sought to evaluate the impact of RKN on the agronomic traits, histology, and cell wall components of parsley, with emphasis on giant cell formation. The study consisted of two treatments: (i) control, where 50 individuals of parsley grew without M. incognita inoculation; and (ii) inoculated plants, where 50 individuals were exposed to juveniles (J2) of M. incognita. Meloidogyne incognita infection affected the development of parsley, reducing the growth of some agronomical characteristics such as root weight and shoot weight and height. Giant cell formation was noticed at 18 days after inoculation, promoting disorganization of the vascular system. Epitopes of HGs detected in giant cells reveal the continuous capacity of giant cells to elongate under the stimulus of RKN, essential processes for feeding site establishment. In addition, the detection of epitopes of HGs with low and high methyl-esterified groups indicates the PMEs activity despite biotic stress.

An Insight into Occurrence, Biology, and Pathogenesis of Rice Root-Knot Nematode Meloidogyne graminicola

Rice (Oryza sativa L.) is one of the most widely grown crops in the world, and is a staple food for more than half of the global total population. Root-knot nematodes (RKNs), Meloidogyne spp., and especially M. graminicola, seem to be significant rice pests, which makes them the most economically important plant-parasitic nematode in this crop. RKNs develop a feeding site in galls by causing host cells to differentiate into hypertrophied, multinucleate, metabolically active cells known as giant cells. This grazing framework gives the nematode a constant food source, permitting it to develop into a fecund female and complete its life cycle inside the host root. M. graminicola effector proteins involved in nematode parasitism, including pioneer genes, were functionally characterized in earlier studies. Molecular modelling and docking studies were performed on Meloidogyne graminicola protein targets, such as β-1,4-endoglucanase, pectate lyase, phospholipase B-like protein, and G protein-coupled receptor kinase, to understand the binding affinity of Beta-D-Galacturonic Acid, 2,6,10,15,19,23-hexamethyltetracosane, (2S)-2-amino-3-phenylpropanoic acid, and 4-O-Beta-D-Galactopyranosyl-Alpha-D-Glucopyranose against ligand molecules of rice. This study discovered important molecular aspects of plant-nematode interaction and candidate effector proteins that were regulated by M. graminicola-infected rice plants. To the best of our knowledge, this is the first study to describe M. graminicola's molecular adaptation to host parasitism.

Biotechnological Tools to Elucidate the Mechanism of Plant and Nematode Interactions

Plant-parasitic nematodes (PPNs) pose a threat to global food security in both the developed and developing worlds. PPNs cause crop losses worth a total of more than USD 150 billion worldwide. The sedentary root-knot nematodes (RKNs) also cause severe damage to various agricultural crops and establish compatible relationships with a broad range of host plants. This review aims to provide a broad overview of the strategies used to identify the morpho-physiological and molecular events that occur during RKN parasitism. It describes the most current developments in the transcriptomic, proteomic, and metabolomic strategies of nematodes, which are important for understanding compatible interactions of plants and nematodes, and several strategies for enhancing plant resistance against RKNs. We will highlight recent rapid advances in molecular strategies, such as gene-silencing technologies, RNA interference (RNAi), and small interfering RNA (siRNA) effector proteins, that are leading to considerable progress in understanding the mechanism of plant-nematode interactions. We also take into account genetic engineering strategies, such as targeted genome editing techniques, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) (CRISPR/Cas-9) system, and quantitative trait loci (QTL), to enhance the resistance of plants against nematodes.

Mutations in Selected ABA-Related Genes Reduce Level of Arabidopsis thaliana Susceptibility to the Beet Cyst Nematode Heterodera schachtii

Heterodera schachtii is a common parasite of many important crops such as beets and Brassicaceae (oilseed rape, cabbage or mustard). Arabidopsis thaliana is a model plant also used for studying defence responses to pathogens or pest infections. Defence responses of plants are often regulated and fine-tuned by stress phytohormones: salicylic acid (SA), jasmonic acid (JA), ethylene (Et) and abscisic acid (ABA), of which the role of ABA in these responses is the least examined. The aim of this study was to show, if and which genes related to ABA turnover can be modulated during the development of nematode-induced feeding sites in A. thaliana roots. To answer the question, we performed infection tests on wild type and ABA mutant roots and analysed the expression levels of selected ABA-related genes (ABI1, ABI2, ABI5, PYL5, PYL6, CYP707A1 and CYP707A4) at the early stage of root infection. Our results show that the expression of ABI2, ABI5 (ABA signalling) and CYP707A4 (ABA metabolism) genes was upregulated in feeding sites at 4 dpi, whereas the level of expression of PYL5 and PYL6 (ABA receptors) genes was decreased. Mutations in ABI1, ABI2, ABI5, CYP707A1 or CYP707A4 genes led to a decrease of A. thaliana susceptibility verbalised as the number of fully developed females, whereas mutations in PYL5 or PYL6 genes did not influence the number of females of the nematode. Based on the results, it can be concluded that the modifications of analysed ABA-related gene expression are required for the proper development of nematodes; however, further in-depth analyses are required.

Loss-of-function mutations in WRKY22 and WRKY25 impair stomatal-mediated immunity and PTI and ETI responses against Pseudomonas syringae pv. tomato

Plants defend themselves against pathogens using a two-layered immune system. The first response, pattern-triggered immunity (PTI), is activated upon recognition of microbe-associated molecular patterns (MAMPs). Virulent bacteria such as Pseudomonas syringae pv. tomato (Pst), deliver effector proteins into the plant cell to promote susceptibility. However, some plants possess resistance (R) proteins that recognize specific effectors leading to the activation of the second response, effector-triggered immunity (ETI). Resistant tomatoes such as Río Grande-PtoR recognize two Pst effectors (AvrPto and AvrPtoB) through the host Pto/Prf complex and activate ETI. We previously showed that the transcription factors (TF) WRKY22 and WRKY25 are positive regulators of plant immunity against bacterial and potentially non-bacterial pathogens in Nicotiana benthamiana. Here, the CRISPR-Cas9 technique was used to develop three knockout tomato lines for either one or both TFs. The single and double mutants were all compromised in Pto/Prf-mediated ETI and had a weaker PTI response. The stomata apertures in all of the mutant lines did not respond to darkness or challenge with Pst DC3000. The WRKY22 and WRKY25 proteins both localize in the nucleus, but we found no evidence of a physical interaction between them. The WRKY22 TF was found to be involved in the transcriptional regulation of WRKY25, supporting the idea that they are not functionally redundant. Together, our results indicate that both WRKY TFs play a role in modulating stomata and are positive regulators of plant immunity in tomato.

Effects of Methyl Jasmonate Fumigation on the Growth and Detoxification Ability of Spodoptera litura to Xanthotoxin

Methyl jasmonate (MeJA) is a volatile substance derived from jasmonic acid (JA), and it responds to interbiotic and abiotic stresses by participating in interplant communication. Despite its function in interplant communication, the specific role of MeJA in insect defense responses is poorly understood. In this study, we found that carboxylesterase (CarE) activities, glutathione-S-transferase (GSTs) activities, and cytochrome mono-oxygenases (P450s) content increased more after the feeding of diets containing xanthotoxin, while larvae exposed to MeJA fumigation also showed higher enzyme activity in a dose-dependent manner: lower and medium concentrations of MeJA induced higher detoxification enzyme activities than higher concentrations of MeJA. Moreover, MeJA improved the growth of larvae fed on the control diet without toxins and diets with lower concentrations of xanthotoxin (0.05%); however, MeJA could not protect the larvae against higher concentrations of xanthotoxin (0.1%, 0.2%). In summary, we demonstrated that MeJA is effective at inducing S. litura defense response, but the enhanced detoxifying ability could not overcome the strong toxins.

Host-delivered RNAi-mediated silencing using fusion cassettes of different functional groups of genes precludes Meloidogyne incognita multiplication in Nicotiana tabacum

This study demonstrates multi-gene silencing approach for simultaneous silencing of several functional genes through a fusion gene strategy for protecting plants against root-knot nematode, Meloidogyne incognita. The ability of root-knot nematode (RKN), Meloidogyne incognita, to cause extensive yield decline in a wide range of cultivated crops is well-documented. Due to the inadequacies of current management approaches, the alternatively employed contemporary RNA interference (RNAi)-based host-delivered gene silencing (HD-RNAi) strategy targeting different functional effectors/genes has shown substantial potential to combat RKNs. In this direction, we have explored the possibility of simultaneous silencing of four esophageal gland genes, six plant cell-wall modifying enzymes (PCWMEs) and a serine protease gene of M. incognita using the fusion approach. In vitro RNAi showed that combinatorial gene silencing is the most effective in affecting nematode behavior in terms of reduced attraction, penetration, development, and reproduction in tomato and adzuki beans. In addition, qRT-PCR analysis of M. incognita J2s soaked in fusion-dsRNA showed perturbed expression of all the genes comprising the fusion construct confirming successful dsRNA processing which is also supported by increased mRNA abundance of five key-RNAi pathway genes. In addition, hairpin RNA expressing constructs of multi-gene fusion cassettes were developed and used for generation of Nicotiana tabacum transgenic plants. The integration of gene constructs and expression of siRNAs in transgenic events were confirmed by Southern and Northern blot analyses. Besides, bio-efficacy analyses of transgenic events, conferred up to 87% reduction in M. incognita multiplication. Correspondingly, reduced transcript accumulation of the target genes in the M. incognita females extracted from transgenic events confirmed successful gene silencing.

Suspension cell secretome of the grain legume Lathyrus sativus (grasspea) reveals roles in plant development and defense responses

Plant secretomics has been especially important in understanding the molecular basis of plant development, stress resistance and biomarker discovery. In addition to sharing a similar role in maintaining cell metabolism and biogenesis with the animal secretome, plant-secreted proteins actively participate in signaling events crucial for cellular homeostasis during stress adaptation. However, investigation of the plant secretome remains largely overlooked, particularly in pulse crops, demanding urgent attention. To better understand the complexity of the secretome, we developed a reference map of a stress-resilient orphan legume, Lathyrus sativus (grasspea), which can be utilized as a potential proteomic resource. Secretome analysis of L. sativus led to the identification of 741 nonredundant proteins belonging to a myriad of functional classes, including antimicrobial, antioxidative and redox potential. Computational prediction of the secretome revealed that ∼29% of constituents are predicted to follow unconventional protein secretion (UPS) routes. We conducted additional in planta analysis to determine the localization of two secreted proteins, recognized as cell surface residents. Sequence-based homology comparison revealed that L. sativus shares ∼40% of the constituents reported thus far from in vitro and in planta secretome analysis in model and crop species. Significantly, we identified 571 unique proteins secreted from L. sativus involved in cell-to-cell communication, organ development, kinase-mediated signaling, and stress perception, among other critical roles. Conclusively, the grasspea secretome participates in putative crosstalk between genetic circuits that regulate developmental processes and stress resilience.

Host-delivered RNAi-mediated silencing of the root-knot nematode (Meloidogyne incognita) effector genes, Mi-msp10 and Mi-msp23, confers resistance in Arabidopsis and impairs reproductive ability of the root-knot nematode

Mi-msp10 and Mi-msp23 effector genes play a significant role during Meloidogyne incognita parasitism on Arabidopsis roots. The role of these genes was confirmed by demonstrating the decrease of the level of susceptibility of Arabidopsis by the  silencing of Mi-msp10 and Mi-msp23 genes using HD-RNAi technology. Root-knot nematodes (RKNs) are the most damaging pathogens severely affecting global food production. The sustainable options to minimize menace of nematode populations through economically feasible measures are limited. Thus, the development of innovative and target-specific strategies that aid in their management is imperative. RNAi technology has emerged as a sustainable and target-specific alternative to control phytonematodes. Here, we characterized two novel subventral gland and dorsal gland-specific effectors, Mi-msp10 and Mi-msp23, to determine their potential effectiveness in controlling M. incognita. Comparative developmental profiling using qRT-PCR revealed higher expression of both effectors in the adult nematode female. Furthermore, functional evaluation of Mi-msp10 and Mi-msp23 dsRNA cassettes was performed using host-delivered RNAi (HD-RNAi) in Arabidopsis. The transgenic lines were examined against M. incognita, and the phenotypic effect of HD-RNAi was evident with a 61% and 51% reduction in gall formation in the Mi-msp10 and Mi-msp23 RNAi lines, respectively. A significant drop in the nematode adult females by 59% for Mi-msp10 and 49% for Mi-msp23-RNAi lines was observed. Similarly, production in egg masses decreased significantly by 76% (Mi-msp10) and 60% (Mi-msp23) for the RNAi lines, which eventually decreased the reproductive factor by 92% and 75%, respectively. The gene expression analysis showed a significant decrease in the transcript level by up to 72% (Mi-msp10) and 66% (Mi-msp23) in M. incognita females feeding on RNAi lines, providing further evidence of effective gene silencing. Overall, our findings provide useful information and support further development of RNAi-based strategies to control M. incognita.

The effector MJ-10A08 of Meloidogyne javanica is required for parasitism that suppressed programmed cell death in Nicotiana benthamiana

Effectors synthesised in the pharyngeal glands are important in the successful invasion of root-knot nematodes. Meloidogyne javanica is among the nematodes that cause the most damage to various crops. In this study, an effector named MJ-10A08 of M. javanica was identified and investigated. Mj-10A08 was exclusively expressed in the dorsal pharyngeal gland cell and highly expressed in the parasitic second-juvenile stage of M. javanica. Transgenic tobaccos that over-expressed Mj-10A08 were more susceptible to M. javanica; however, host delivered RNAi of Mj-10A08 in tobacco significantly decreased the expression level of Mj-10A08 and the infection efficiency of M. javanica. Transient expression in tobacco leaves demonstrated that MJ-10A08 suppressed programmed cell death caused by BAX and Gpa2/RBP-1. Our results indicated that MJ-10A08 is implicated in the suppression of plant defence response during nematode infection and plays an important role in the parasitism of M. javanica.

A Three-Year Plant Study of Salt-Tolerant Transgenic Maize Showed No Effects on Soil Enzyme Activity and Nematode Community

The environmental effects of genetically modified crops are now a global concern. It is important to monitor the potential environmental impact of transgenic corn after commercial release. In rhizosphere soil, plant roots interact with soil enzymes and microfauna, which can be affected by the transgenes of genetically modified crops. To determine the long-term impact of transgenic plant cultivation, we conducted a field study for 3 consecutive years (2018–2020) and observed the enzyme activities and nematode populations in plots planted with transgenic maize BQ-2, non-transgenic wild-type maize (Qi319), and inbred line B73. We took soil samples from three cornfields at four different growth stages (V3, V9, R1, and R6 stages); determined soil dehydrogenase, urease, and sucrase activities; and collected and identified soil nematodes to the genus level. The results demonstrated seasonal variations in dehydrogenase, urease, and sucrase activities. However, there was a consistent trend of change. The generic composition and diversity indices of the soil nematodes did not significantly differ, although significant seasonal variation was found in the individual densities of the principal trophic groups and the diversity indices of the nematodes in all three cornfields. The results of the study suggest that a 3-year cultivation of transgenic corn had no significant effects on soil enzyme activity and the soil nematode community. This study provides a theoretical basis for the environmental impact monitoring of transgenic corn.

Meloidogyne-SP4 effector gene silencing reduces reproduction of root-knot nematodes in rice (Oryza sativa)

The root-knot nematodes (RKN) Meloidogyne graminicola and M. incognita are responsible for rice yield losses worldwide, particularly in Asia and Africa. Previous studies demonstrated that nematode-secreted proteins are crucial for root invasion and establishment in the host. We present some characteristics of a pioneer effector, M. incognita-secreted protein 4 (Mi-SP4), which is conserved in RKN and required for infection in compatible rice-RKN interactions. In situ hybridisation assays revealed Mi-SP4 expression in the dorsal pharyngeal gland of M. incognita second-stage juveniles (J2). Meloidogyne-SP4 transcripts strongly accumulated in pre-parasitic J2 and decreased in later parasitic stages of M. incognita and M. graminicola. Transient expression of the nematode effector gene in Nicotiana benthamiana leaves and onion cells indicated that GFP-tagged Mi-SP4 was present in the cytoplasm and accumulated in the nucleus of the plant cells. In vitro RNA interference (RNAi) gene silencing, obtained by soaking J2 with small-interfering (si)RNA si4-1, decreased Mi -SP4 expression in J2 by 35% and significantly reduced M. incognita reproduction in rice by at least 30%. Similarly, host-mediated gene silencing of the nematode SP4 effector candidate gene in transgenic rice plants significantly reduced M. graminicola reproduction by 26% to 47%. The data obtained demonstrate that Mi -SP4 is a pioneer virulence effector, which plays an essential role in both M. incognita and M. graminicola pathogenicity on rice.

Root-knot nematodes (Meloidogyne spp.) a threat to agriculture in Mexico: biology, current control strategies, and perspectives

Root-knot nematodes (RKN) are sedentary parasites of the roots of plants and are considered some of the most damaging pests in agriculture. Since RKN target the root vascular system, they provoke host nutrient deprivation and defective water transport, causing above-ground symptoms of growth stunting, wilting, chlorosis, and reduced crop yields. In Mexico RKN infestations are primarily dealt with by treating with synthetic chemically based nematicides that are preferred by farmers over available bioproducts. However, due to environmental and human health concerns chemical control is increasingly restricted. Biological control of RKNs can help reduce the use of chemical nematicides as it is achieved with antagonistic organisms, mainly bacteria, fungi, other nematodes, or consortia of diverse microorganisms, which control nematodes directly by predation and parasitism at different stages: eggs, juveniles, or adults; or indirectly by the action of toxic diffusible inhibitory metabolites. The need to increase agricultural production and reduce negative environmental impact creates an opportunity for optimizing biological control agents to suppress nematode populations, but this endeavour remains challenging as researchers around the world try to understand diverse control mechanisms, nematode and microbe life cycles, ecology, metabolite production, predatory behaviours, molecular and biochemical interactions, in order to generate attractive products with the approval of local regulatory bodies. Here, we provide a brief review of the biology of the genus Meloidogyne, biological control strategies, and a comparison between chemical and bioproducts in the Mexican market, and guidelines emitted by national agencies to ensure safety and effectiveness of new developments.

Meloidogyne graminicola-A Threat to Rice Production: Review Update on Distribution, Biology, Identification, and Management

Simple Summary

New risks to plant health are constantly emerging. Such is the case of the rice root knot nematode Meloidogyne graminicola, adapted to flooded conditions and representing a risk to all types of rice agro-systems. It has been recently detected in Italy and added to the European and Mediterranean Plant Protection Organization (EPPO) Alert List. The presence of this nematode in Europe poses a threat to rice production, as there is a high probability to spread, due to trade activities and climate changes. In view of its importance, an extensive updated review was carried out.

Abstract

Rice (Oryza sativa L.) is one of the main cultivated crops worldwide and represents a staple food for more than half of the world population. Root-knot nematodes (RKNs), Meloidogyne spp., and particularly M. graminicola, are serious pests of rice, being, probably, the most economically important plant-parasitic nematode in this crop. M. graminicola is an obligate sedentary endoparasite adapted to flooded conditions. Until recently, M. graminicola was present mainly in irrigated rice fields in Asia, parts of the Americas, and South Africa. However, in July 2016, it was found in northern Italy in the Piedmont region and in May 2018 in the Lombardy region in the province of Pavia. Following the first detection in the EPPO region, this pest was included in the EPPO Alert List as its wide host range and ability to survive during long periods in environments with low oxygen content, represent a threat for rice production in the European Union. Considering the impact of this nematode on agriculture, a literature review focusing on M. graminicola distribution, biology, identification, and management was conducted.

Constraints and Prospects of Improving Cowpea Productivity to Ensure Food, Nutritional Security and Environmental Sustainability

Providing safe and secure food for an increasing number of people globally is challenging. Coping with such a human population by merely applying the conventional agricultural production system has not proved to be agro-ecologically friendly; nor is it sustainable. Cowpea (Vigna unguiculata (L) Walp) is a multi-purpose legume. It consists of high-quality protein for human consumption, and it is rich in protein for livestock fodder. It enriches the soil in that it recycles nutrients through the fixation of nitrogen in association with nodulating bacteria. However, the productivity of this multi-functional, indigenous legume that is of great value to African smallholder farmers and the rural populace, and also to urban consumers and entrepreneurs, is limited. Because cowpea is of strategic importance in Africa, there is a need to improve on its productivity. Such endeavors in Africa are wrought with challenges that include drought, salinity, the excessive demand among farmers for synthetic chemicals, the repercussions of climate change, declining soil nutrients, microbial infestations, pest issues, and so forth. Nevertheless, giant strides have already been made and there have already been improvements in adopting sustainable and smart biotechnological approaches that are favorably influencing the production costs of cowpea and its availability. As such, the prospects for a leap in cowpea productivity in Africa and in the enhancement of its genetic gain are good. Potential and viable means for overcoming some of the above-mentioned production constraints would be to focus on the key cowpea producer nations in Africa and to encourage them to embrace biotechnological techniques in an integrated approach to enhance for sustainable productivity. This review highlights the spectrum of constraints that limit the cowpea yield, but looks ahead of the constraints and seeks a way forward to improve cowpea productivity in Africa. More importantly, this review investigates applications and insights concerning mechanisms of action for implementing eco-friendly biotechnological techniques, such as the deployment of bio inoculants, applying climate-smart agricultural (CSA) practices, agricultural conservation techniques, and multi-omics smart technology in the spheres of genomics, transcriptomics, proteomics, and metabolomics, for improving cowpea yields and productivity to achieve sustainable agro-ecosystems, and ensuring their stability.

Dialog between Kingdoms: Enemies, Allies and Peptide Phytohormones

Various plant hormones can integrate developmental and environmental responses, acting in a complex network, which allows plants to adjust their developmental processes to changing environments. In particular, plant peptide hormones regulate various aspects of plant growth and development as well as the response to environmental stress and the interaction of plants with their pathogens and symbionts. Various plant-interacting organisms, e.g., bacterial and fungal pathogens, plant-parasitic nematodes, as well as symbiotic and plant-beneficial bacteria and fungi, are able to manipulate phytohormonal level and/or signaling in the host plant in order to overcome plant immunity and to create the habitat and food source inside the plant body. The most striking example of such phytohormonal mimicry is the ability of certain plant pathogens and symbionts to produce peptide phytohormones of different classes. To date, in the genomes of plant-interacting bacteria, fungi, and nematodes, the genes encoding effectors which mimic seven classes of peptide phytohormones have been found. For some of these effectors, the interaction with plant receptors for peptide hormones and the effect on plant development and defense have been demonstrated. In this review, we focus on the currently described classes of peptide phytohormones found among the representatives of other kingdoms, as well as mechanisms of their action and possible evolutional origin.

A chromosomal assembly of the soybean cyst nematode genome

The soybean cyst nematode (Heterodera glycines) is a sedentary plant parasite that exceeds billion USD annually in yield losses. This problem is exacerbated by H. glycines populations overcoming the limited sources of natural resistance in soybean and by the lack of effective and safe alternative treatments. Although there are genetic determinants that render soybeans resistant to nematode genotypes, resistant soybeans are increasingly ineffective because their multiyear usage has selected for virulent H. glycines populations. Successful H. glycines infection relies on the comprehensive re-engineering of soybean root cells into a syncytium, as well as the long-term suppression of host defences to ensure syncytial viability. At the forefront of these complex molecular interactions are effectors, the proteins secreted by H. glycines into host root tissues. The mechanisms that control genomic effector acquisition, diversification, and selection are important insights needed for the development of essential novel control strategies. As a foundation to obtain this understanding, we created a nine-scaffold, 158 Mb pseudomolecule assembly of the H. glycines genome using PacBio, Chicago, and Hi-C sequencing. A Mikado consensus gene prediction produced an annotation of 22,465 genes using short- and long-read expression data. To evaluate assembly and annotation quality, we cross-examined synteny among H. glycines assemblies, and compared BUSCO across related species. To describe the predicted proteins involved in H. glycines' secretory pathway, we contrasted expression between preparasitic and parasitic stages with functional gene information. Here, we present the results from our assembly and annotation of the H. glycines genome and contribute this resource to the scientific community.

The Meloidogyne javanica effector Mj2G02 interferes with jasmonic acid signalling to suppress cell death and promote parasitism in Arabidopsis

Plant-parasitic nematodes can cause devastating damage to crops. These nematodes secrete effectors that suppress the host immune responses to enhance their survival. In this study, Mj2G02, an effector from Meloidogyne javanica, is described. In situ hybridization and transcriptional analysis showed that Mj2G02 was highly expressed in the early infection stages and exclusively expressed in the nematode subventral oesophageal gland cells. In planta RNA interference targeting Mj2G02 impaired M. javanica parasitism, and Mj2G02-transgenic Arabidopsis lines displayed more susceptibility to M. javanica. Using an Agrobacterium-mediated transient expression system and plant immune response assays, we demonstrated that Mj2G02 localized in the plant cell nuclei and could suppress Gpa2/RBP-1-induced cell death. Moreover, by RNA-Seq and quantitative reverse transcription PCR analyses, we showed that Mj2G02 was capable of interfering with the host jasmonic acid (JA) signalling pathway. Multiple jasmonate ZIM-domain (JAZ) genes were significantly upregulated, whereas the JAR1 gene and four JA-responsive genes, MYC3, UPI, THI2.1, and WRKY75, were significantly downregulated. In addition, HPLC analysis showed that the endogenous jasmonoyl-isoleucine (JA-Ile) level in Mj2G02-transgenic Arabidopsis lines was significantly decreased compared to that in wildtype plants. Our results indicate that the M. javanica effector Mj2G02 suppresses the plant immune response, therefore facilitating nematode parasitism. This process is probably mediated by a JA-Ile reduction and JAZ enhancement to repress JA-responsive genes.

Transcriptome analysis of resistant and susceptible mulberry responses to Meloidogyne enterolobii infection

BACKGROUND

Mulberry (Morus alba L.) is an important sericulture crop; however, root-knot nematode infection seriously limits its production. Understanding the mechanism of interaction between mulberry and nematode is important for control of infection.

RESULTS

Using sequencing and de novo transcriptome assembly, we identified 55,894 unigenes from root samples of resistant and susceptible mulberry cultivars at different stages after infection with the nematode Meloidogyne enterolobii; 33,987 of these were annotated in the Nr, SWISS-PROT, KEGG, and KOG databases. Gene ontology and pathway enrichment analyses of differentially expressed genes (DEGs) revealed key genes involved in hormone metabolic processes, plant hormone signal transduction, flavonoid biosynthesis, phenylpropanoid biosynthesis, and peroxisomal and photosynthetic pathways. Analysis of key trends in co-expression networks indicated that expression of unigenes 0,015,083, 0,073,272, 0,004,006, and 0,000,628 was positively correlated with resistance to M. enterolobii. Unigene 0015083 encodes tabersonine 16-O-methyltransferase (16OMT), which is involved in alkaloid biosynthesis. Unigene 0073272 encodes a transcription factor contributing to nitric oxide accumulation during plant immune responses. Unigenes 0,004,006 and 0,000,628 encode ERF and MYB transcription factors, respectively, involved in plant hormone signaling. We verified the accuracy of transcriptome sequencing results by RT-qPCR of 21 DEGs.

CONCLUSIONS

The results of this study increase our understanding of the resistance mechanisms and candidate genes involved in mulberry-M. enterolobii interaction. Thus, our data will contribute to the development of effective control measures against this pathogen.

Transcriptomic and Histological Analysis of the Response of Susceptible and Resistant Cucumber to Meloidogyne incognita Infection Revealing Complex Resistance via Multiple Signaling Pathways

The root-knot nematode (RKN), Meloidogyne incognita, is a devastating pathogen for cucumber (Cucumis sativus L.) specially in production under protected environments or continuous cropping. High level RKN resistance has been identified in African horned melon Cucumis metuliferus (CM). However, the resistance mechanism remains unclear. In this study, the comparative analysis on phenotypic and transcriptomic responses in the susceptible cucumber inbred line Q24 and the resistant CM, after M. incognita infection, was performed. The results showed that, in comparison with Q24, the CM was able to significantly reduce penetration numbers of second stage juveniles (J2), slow its development in the roots resulting in fewer galls and smaller giant cells suggesting the presence of host resistance in CM. Comparative transcriptomes analysis of Q24 and CM before and after M. incognita infection was conducted and differentially expressed genes (DEGs) associated with host resistance were identified in CM. Enrichment analyses revealed most enriched DEGs in Ca²⁺ signaling, salicylic acid (SA)/jamonate signaling (JA), as well as auxin (IAA) signaling pathways. In particular, in CM, DEGs in the Ca²⁺ signaling pathway such as those for the calmodulin and calcium-binding proteins were upregulated at the early stage of M. incognita infection; genes for SA/JA synthesis/signal transduction were markedly activated, whereas the IAA signaling pathway genes were inhibited upon infection suggesting the importance of SA/JA signaling pathways in mediating M. incognita resistance in CM. A model was established to explain the different molecular mechanisms on M. incognita susceptibility in cucumber and resistance to M. incognita infection in CM.

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.

Comparative transcriptomic analysis of candidate effectors to explore the infection and survival strategy of Bursaphelenchus xylophilus during different interaction stages with pine trees

BACKGROUND

The pine wood nematode (PWN), Bursaphelenchus xylophilus, is a devastating pathogen of many Pinus species in China. The aim of this study was to understand the interactive molecular mechanism of PWN and its host by comparing differentially expressed genes and candidate effectors from three transcriptomes of B. xylophilus at different infection stages.

RESULTS

In total, 62, 69 and 46 candidate effectors were identified in three transcriptomes (2.5 h postinfection, 6, 12 and 24 h postinoculation and 6 and 15 d postinfection, respectively). In addition to uncharacterized pioneers, other candidate effectors were involved in the degradation of host tissues, suppression of host defenses, targeting plant signaling pathways, feeding and detoxification, which helped B. xylophilus survive successfully in the host. Seven candidate effectors were identified in both our study and the B. xylophilus transcriptome at 2.5 h postinfection, and one candidate effector was identified in all three transcriptomes. These common candidate effectors were upregulated at infection stages, and one of them suppressed pathogen-associated molecular pattern (PAMP) PsXEG1-triggered cell death in Nicotiana benthamiana.

CONCLUSIONS

The results indicated that B. xylophilus secreted various candidate effectors, and some of them continued to function throughout all infection stages. These various candidate effectors were important to B. xylophilus infection and survival, and they functioned in different ways (such as breaking down host cell walls, suppressing host defenses, promoting feeding efficiency, promoting detoxification and playing virulence functions). The present results provide valuable resources for in-depth research on the pathogenesis of B. xylophilus from the perspective of effectors.

A Venom Allergen-Like Protein, RsVAP, the First Discovered Effector Protein of Radopholus similis That Inhibits Plant Defense and Facilitates Parasitism

Radopholus similis is a migratory endoparasitic nematode that is extremely harmful to host plants. Venom allergen-like proteins (VAPs) are members of the cysteine-rich secretory protein family that are widely present in plants and animals. In this study, we cloned a VAP gene from R. similis, designated as RsVAP. RsVAP contains an open reading frame of 1089 bp encoding 362 amino acids. RsVAP is specifically expressed in the esophageal gland, and the expression levels of RsVAP are significantly higher in juveniles than in other life stages of R. similis. This expression pattern of RsVAP was consistent with the biological characteristics of juveniles of R. similis, which have the ability of infection and are the main infection stages of R. similis. The pathogenicity and reproduction rate of R. similis in tomato was significantly attenuated after RsVAP was silenced. In tobacco leaves transiently expressing RsVAP, the pathogen-associated molecular pattern-triggered immunity (PTI) induced by a bacterial flagellin fragment (flg22) was inhibited, while the cell death induced by two sets of immune elicitors (BAX and Gpa2/RBP-1) was repressed. The RsVAP-interacting, ras-related protein RABA1d (LeRabA1d) was identified in tomato hosts by yeast two-hybrid and co-immunoprecipitation assays. RsVAP may interact with LeRabA1d to affect the host defense response, which in turn facilitates nematode infection. This study provides the first evidence for the inhibition of plant defense response by a VAP from migratory plant-parasitic nematodes, and, for the first time, the target protein of R. similis in its host was identified.

Biological control: a novel strategy for the control of the plant parasitic nematodes

Plant parasitic nematodes (Root-knot nematodes, Meloidogyne spp.) are rounded worms, microscopic, and cause many agricultural economic losses. Their attacks have a direct impact on the productivity of cultivated crops by reducing their fruit quantity. Chemical control is widespread all over the world, but biological control is the most effective way to reduce the number of pests that infect crops, particularly by the use of microorganisms like fungi and bacteria. Biological control is rapidly evolving, and more products are being sold worldwide over time. They can be produced by fungi, bacteria, or actinomycetes that can destruct plant parasite nematodes and feed on them. Nematophagous microorganisms as the natural enemies of nematodes have a promising way of controlling nematodes. Some of them create net-like substances and traps to take the worms from outside and finally kill them. Other parasites serve as internal parasites in order to produce toxins and to produce virulence to kill nematodes. Comprehension of the molecular basis for microbial nematode interactions gives important insights into how successful biological nematode control agents can be created. We discuss recent advances in our understanding of nematodes and nematophagous microorganisms, with an emphasis on molecular mechanisms that infect nematodes with nematophagous microorganisms and on nematode safety from pathogenic attacks. Finally, we addressed numerous key areas for future research and development, including possible approaches to the application of our recent expertise in the development of successful biocontrol strategies.

A Meloidogyne graminicola Pectate Lyase Is Involved in Virulence and Activation of Host Defense Responses

Plant-parasitic nematodes secrete an array of cell-wall-degrading enzymes to overcome the physical barrier formed by the plant cell wall. Here, we describe a novel pectate lyase gene Mg-PEL1 from M. graminicola. Quantitative real-time PCR assay showed that the highest transcriptional expression level of Mg-PEL1 occurred in pre-parasitic second-stage juveniles, and it was still detected during the early parasitic stage. Using in situ hybridization, we showed that Mg-PEL1 was expressed exclusively within the subventral esophageal gland cells of M. graminicola. The yeast signal sequence trap system revealed that it possessed an N-terminal signal peptide with secretion function. Recombinant Mg-PEL1 exhibited hydrolytic activity toward polygalacturonic acid. Rice plants expressing RNA interference vectors targeting Mg-PEL1 showed an increased resistance to M. graminicola. In addition, using an Agrobacterium-mediated transient expression system and plant immune response assays, we demonstrated that the cell wall localization of Mg-PEL1 was required for the activation of plant defense responses, including programmed plant cell death, reactive oxygen species (ROS) accumulation and expression of defense-related genes. Taken together, our results indicated that Mg-PEL1 could enhance the pathogenicity of M. graminicola and induce plant immune responses during nematode invasion into plants or migration in plants. This provides a new insight into the function of pectate lyases in plants-nematodes interaction.

Oxylipins are implicated as communication signals in tomato-root-knot nematode (Meloidogyne javanica) interaction

Throughout infection, plant-parasitic nematodes activate a complex host defense response that will regulate their development and aggressiveness. Oxylipins-lipophilic signaling molecules-are part of this complex, performing a fundamental role in regulating plant development and immunity. At the same time, the sedentary root-knot nematode Meloidogyne spp. secretes numerous effectors that play key roles during invasion and migration, supporting construction and maintenance of nematodes' feeding sites. Herein, comprehensive oxylipin profiling of tomato roots, performed using LC-MS/MS, indicated strong and early responses of many oxylipins following root-knot nematode infection. To identify genes that might respond to the lipidomic defense pathway mediated through oxylipins, RNA-Seq was performed by exposing Meloidogyne javanica second-stage juveniles to tomato protoplasts and the oxylipin 9-HOT, one of the early-induced oxylipins in tomato roots upon nematode infection. A total of 7512 differentially expressed genes were identified. To target putative effectors, we sought differentially expressed genes carrying a predicted secretion signal peptide. Among these, several were homologous with known effectors in other nematode species; other unknown, potentially secreted proteins may have a role as root-knot nematode effectors that are induced by plant lipid signals. These include effectors associated with distortion of the plant immune response or manipulating signal transduction mediated by lipid signals. Other effectors are implicated in cell wall degradation or ROS detoxification at the plant-nematode interface. Being an integral part of the plant's defense response, oxylipins might be placed as important signaling molecules underlying nematode parasitism.

Genomic Profiling of Virulence in the Soybean Cyst Nematode Using Single-Nematode Sequencing

Soybean cyst nematode (SCN) is one of the most important diseases in soybean. Currently, the main management strategy relies on planting resistant cultivars. However, the overuse of a single resistance source has led to the selection of virulent SCN populations, although the mechanisms by which the nematode overcomes the resistance genes remain unknown. In this study, we used a nematode-adapted single-cell RNA-seq approach to identify SCN genes potentially involved in resistance breakdown in Peking and PI 88788 parental soybean lines. We established for the first time the full transcriptome of single SCN individuals allowing us to identify a list of putative virulence genes against both major SCN resistance sources. Our analysis identified 48 differentially expressed putative effectors (secreted proteins required for infection) alongside 40 effectors showing evidence of novel structural variants, and 11 effector genes containing phenotype-specific sequence polymorphisms. Additionally, a differential expression analysis revealed an interesting phenomenon of coexpressed gene regions with some containing putative effectors. The selection of virulent SCN individuals on Peking resulted in a profoundly altered transcriptome, especially for genes known to be involved in parasitism. Several sequence polymorphisms were also specific to these virulent nematodes and could potentially play a role in the acquisition of nematode virulence. On the other hand, the transcriptome of virulent individuals on PI 88788 was very similar to avirulent ones with the exception of a few genes, which suggest a distinct virulence strategy to Peking.

Comparative Secretome and Functional Analyses Reveal Glycoside Hydrolase Family 30 and Cysteine Peptidase as Virulence Determinants in the Pinewood Nematode Bursaphelenchus xylophilus

Pine wilt disease, caused by the pinewood nematode, Bursaphelenchus xylophilus, is one of the world's most serious tree diseases. Although the B. xylophilus whole-genome sequence and comprehensive secretome profile have been determined over the past decade, it remains unclear what molecules are critical in pine wilt disease and govern B. xylophilus virulence in host pine trees. Here, a comparative secretome analysis among four isolates of B. xylophilus with distinct virulence levels was performed to identify virulence determinants. The four candidate virulence determinants of B. xylophilus highly secreted in virulent isolates included lipase (Bx-lip1), glycoside hydrolase family 30 (Bx-GH30), and two C1A family cysteine peptidases (Bx-CAT1 and Bx-CAT2). To validate the quantitative differences in the four potential virulence determinants among virulence groups at the protein level, we used real-time reverse-transcription polymerase chain reaction analysis to investigate these determinants at the transcript level at three time points: pre-inoculation, 3 days after inoculation (dai), and 7 dai into pine seedlings. The transcript levels of Bx-CAT1, Bx-CAT2, and Bx-GH30 were significantly higher in virulent isolates than in avirulent isolates at pre-inoculation and 3 dai. A subsequent leaf-disk assay based on transient overexpression in Nicotiana benthamiana revealed that the GH30 candidate virulent factor caused cell death in the plant. Furthermore, we demonstrated that Bx-CAT2 was involved in nutrient uptake for fungal feeding via soaking-mediated RNA interference. These findings indicate that the secreted proteins Bx-GH30 and Bx-CAT2 contribute to B. xylophilus virulence in host pine trees and may be involved in pine wilt disease.

The Genomic Impact of Selection for Virulence against Resistance in the Potato Cyst Nematode, Globodera pallida

Although the use of natural resistance is the most effective management approach against the potato cyst nematode (PCN) Globodera pallida, the existence of pathotypes with different virulence characteristics constitutes a constraint towards this goal. Two resistance sources, GpaV (from Solanum vernei) and H3 from S. tuberosum ssp. andigena CPC2802 (from the Commonwealth Potato Collection) are widely used in potato breeding programmes in European potato industry. However, the use of resistant cultivars may drive strong selection towards virulence, which allows the increase in frequency of virulent alleles in the population and therefore, the emergence of highly virulent nematode lineages. This study aimed to identify Avirulence (Avr) genes in G. pallida populations selected for virulence on the above resistance sources, and the genomic impact of selection processes on the nematode. The selection drive in the populations was found to be specific to their genetic background. At the genomic level, 11 genes were found that represent candidate Avr genes. Most of the variant calls determining selection were associated with H3-selected populations, while many of them seem to be organised in genomic islands facilitating selection evolution. These phenotypic and genomic findings combined with histological studies performed revealed potential mechanisms underlying selection in G. pallida.

Meloidogyne enterolobii, a Major Threat to Tomato Production: Current Status and Future Prospects for Its Management

The guava root-knot nematode, Meloidogyne enterolobii (Syn. M. mayaguensis), is an emerging pathogen to many crops in the world. This nematode can cause chlorosis, stunting, and reduce yields associated with the induction of many root galls on host plants. Recently, this pathogen has been considered as a global threat for tomato (Solanum lycopersicum L.) production due to the lack of known resistance in commercially accepted varieties and the aggressiveness of M. enterolobii. Both conventional morphological and molecular approaches have been used to identify M. enterolobii, an important first step in an integrated management. To combat root-knot nematodes, integrated disease management strategies such as crop rotation, field sanitation, biocontrol agents, fumigants, and resistant cultivars have been developed and successfully used in the past. However, the resistance in tomato varieties mediated by known Mi-genes does not control M. enterolobii. Here, we review the current knowledge on geographic distribution, host range, population biology, control measures, and proposed future strategies to improve M. enterolobii control in tomato.

Multi-copy alpha-amylase genes are crucial for Ditylenchus destructor to parasitize the plant host

Ditylenchus destructor is a migratory plant-parasitic nematode that causes huge damage to global root and tuber production annually. The main plant hosts of D. destructor contain plenty of starch, which makes the parasitic environment of D. destructor to be different from those of most other plant-parasitic nematodes. It is speculated that D. destructor may harbor some unique pathogenesis-related genes to parasitize the starch-rich hosts. Herein, we focused on the multi-copy alpha-amylase genes in D. destructor, which encode a key starch-catalyzing enzyme. Our previously published D. destructor genome showed that it has three alpha-amylase encoding genes, Dd_02440, Dd_11154, and Dd_13225. Comparative analysis of alpha-amylases from different species demonstrated that the other plant-parasitic nematodes, even Ditylenchus dipsaci in the same genus, harbor only one or no alpha-amylase gene, and the three genes from D. destructor were closely clustered in the phylogenetic tree, indicating that there was a unique expansion of the alpha-amylase gene in D. destructor. The enzymatic activity of the three alpha-amylase proteins was verified by an enzyme assay. Quantitative real-time PCR assay showed that the expression of the three alpha-amylase genes in the post-hatching stage of D. destructor was found to be significantly higher than that in eggs. In the in situ hybridization assay, the expression of the genes was localized to the intestine, implying the association of these genes with nematode digestion. An infection assay in sweet potato demonstrated that RNA interference of any one alpha-amylase gene had no influence on the infectivity of D. destructor. Using the multi-target dsRNA cocktail method, it was found that silencing of two of the three genes inhibited nematode infection, and the infectivity of worms treated with three dsRNA simultaneously changed the most, which decreased by 76.6%. Thus, the multi-copy alpha-amylase genes in D. destructor are compensatory and crucial for nematodes to parasitize the plant host.

Phytochemistry-mediated disruption of ant-aphid interactions by root-feeding nematodes

Plants link interactions between aboveground and belowground organisms. Herbivore-induced changes in plant chemistry are hypothesized to impact entire food webs by changing the strength of trophic cascades. Yet, few studies have explored how belowground herbivores affect the behaviors of generalist predators, nor how such changes may act through diverse changes to the plant metabolome. Using a factorial experiment, we tested whether herbivory by root-knot nematodes (Meloidogyne incognita) affected the aboveground interaction among milkweed plants (Asclepias fascicularis or Asclepias speciosa), oleander aphids (Aphis nerii), and aphid-tending ants (Linepithema humile). We quantified the behaviors of aphid-tending ants, and we measured the effects of herbivore treatments on aphid densities and on phytochemistry. Unexpectedly, ants tended aphids primarily on the leaves of uninfected plants, whereas ants tended aphids primarily at the base of the stem of nematode-infected plants. In nematode-infected plants, aphids excreted more sugar per capita in their ant-attracting honeydew. Additionally, although plant chemistry was species-specific, nematode infection generally decreased the richness of plant secondary metabolites while acting as a protein sink in the roots. Path analysis indicated that the ants' behavioral change was driven in part by indirect effects of nematodes acting through changes in plant chemistry. We conclude that belowground herbivores can affect the behaviors of aboveground generalist ant predators by multiple paths, including changes in phytochemistry, which may affect the attractiveness of aphid honeydew rewards.

Compounds Associated with Infection by the Root-Knot Nematode, Meloidogyne javanica, Influence the Ability of Infective Juveniles to Recognize Host Plants

Plant root chemistry is altered by the parasitism of plant-parasitic nematodes (PPN). Here, we investigated the influence of the infective stage juveniles (J2) of Meloidogyne javanica in inducing tomato (Solanum lycopersicum) root volatiles and chemotactic effect on conspecifics. In olfactometer assays, J2 avoided the roots of 2-day infected plants but preferred 7-day-infected tomato compared to healthy plants. Chemical analysis showed a 2-7-fold increase in the amounts of monoterpenes emitted from tomato roots infected with M. javanica relative to healthy roots. In further bioassays, the monoterpenes β-pinene, (+)-(2)-carene, α-phellandrene, and β-phellandrene differentially attracted (51-87%) J2 relative to control. Concurrent reduction and increase in the levels of methyl salicylate and (Z)-methyl dihydrojasmonate, respectively, in the root volatiles reduced J2 responses. These results demonstrate that the host plant can alter its root volatile composition to inhibit PPN attack. The observed plant-produced inhibition of J2 warrants further investigation as a potential management tool for growers.

Analyses of the Root-Knot Nematode (Meloidogyne graminicola) Transcriptome during Host Infection Highlight Specific Gene Expression Profiling in Resistant Rice Plants

The plant-parasitic nematode Meloidogyne graminicola causes considerable damages to rice (Oryza sativa) culture. Resistance to M. graminicola in the related species Oryza glaberrima reduces root penetration by juveniles and stops further nematode development. M. graminicola genes expressed during O. sativa infection were previously characterized but no information is available about the molecular dialogue established with a resistant plant. We compared the M. graminicola transcriptomes of stage-two juveniles (J2s) before and during infection of susceptible or resistant rice. Among 36,121 M. graminicola genes surveyed, 367 were differentially expressed during infection of resistant or susceptible plants. Genes encoding cell wall-degrading enzymes, peptidases and neuropeptides were expressed for a longer time in resistant plants compared to susceptible plants. Conversely, genes related to nematode development were not activated in the resistant host. The majority of M. graminicola effector genes had similar expression patterns, whatever the host genotype. However, two venom allergen-like protein (VAP)-encoding genes were specifically induced in resistant plants and Mg-VAP1 silencing in J2s reduced their ability to colonize roots. This study highlighted that M. graminicola adapts its gene expression to the host susceptibility. Further investigation is required to assess the role of Mg-VAPs in the rice-nematode interaction.

Transcriptome and Parasitome Analysis of Beet Cyst Nematode Heterodera schachtii

Beet cyst nematodes depend on a set of secretory proteins (effectors) for the induction and maintenance of their syncytial feeding sites in plant roots. In order to understand the relationship between the beet cyst nematode H. schachtii and its host, identification of H. schachtii effectors is crucial and to this end, we sequenced a whole animal pre-infective J2-stage transcriptome in addition to pre- and post-infective J2 gland cell transcriptome using Next Generation Sequencing (NGS) and identified a subset of sequences representing putative effectors. Comparison between the transcriptome of H. schachtii and previously reported related cyst nematodes and root-knot nematodes revealed a subset of esophageal gland related sequences and putative effectors in common across the tested species. Structural and functional annotation of H. schachtii transcriptome led to the identification of nearly 200 putative effectors. Six putative effector expressions were quantified using qPCR and three of them were functionally analyzed using RNAi. Phenotyping of the RNAi nematodes indicated that all tested genes decrease the level of nematodes pathogenicity and/or the average female size, thereby regulating cyst nematode parasitism. These discoveries contribute to further understanding of the cyst nematode parasitism.

Mediation of Potato-Potato Cyst Nematode, G. rostochiensis Interaction by Specific Root Exudate Compounds

Potato (Solanum tuberosum) is a widely consumed staple food crop worldwide whose production is threatened by potato cyst nematodes (PCN). To infect a host, PCN eggs first need to be stimulated to hatch by chemical components in the host root exudates, yet it remains unknown how most root exudate components influence PCN behavior. Here, we evaluated the influence of eight compounds identified by LC-QqQ-MS in the root exudate of potato on the hatching response of the PCN, Globodera rostochiensis at varying doses. The eight compounds included the amino acids tyrosine, tryptophan and phenylalanine; phytohormones zeatin and methyl dihydrojasmonate; steroidal glycoalkaloids α-solanine and α-chaconine and the steroidal alkaloid solanidine. We additionally tested two other Solanaceae steroidal alkaloids, solasodine and tomatidine, previously identified in the root exudates of tomato, an alternative host for PCN. In dose-response assays with the individual compounds, the known PCN hatching factors α-chaconine and α-solanine stimulated the highest number of eggs to hatch, ∼47 and ∼42%, respectively, whereas the steroidal alkaloids (aglycones), solanidine and solasodine and potato root exudate (PRE) were intermediate, 28% each and 21%, respectively, with tomatidine eliciting the lowest hatching response 13%. However, ∼60% of the hatched juveniles failed to emerge from the cyst, which was compound- and concentration-dependent. The amino acids, phytohormones and the negative control (1% DMSO in water), however, were generally non-stimulatory. The use of steroidal glycoalkaloids and their aglycones in the suicidal hatching of PCN offers promise as an environmentally sustainable approach to manage this pest.

A MIF-like effector suppresses plant immunity and facilitates nematode parasitism by interacting with plant annexins

Plant-parasitic nematodes secrete numerous effectors to facilitate parasitism, but detailed functions of nematode effectors and their plant targets remain largely unknown. Here, we characterized four macrophage migration inhibitory factors (MIFs) in Meloidogyne incognita resembling the MIFs secreted by human and animal parasites. Transcriptional data showed MiMIFs are up-regulated in parasitism. Immunolocalization provided evidence that MiMIF proteins are secreted from the nematode hypodermis to the parasite surface, detected in plant tissues and giant cells. In planta MiMIFs RNA interference in Arabidopsis decreased infection and nematode reproduction. Transient expression of MiMIF-2 could suppress Bax- and RBP1/Gpa2-induced cell death. MiMIF-2 ectopic expression led to higher levels of Arabidopsis susceptibility, suppressed immune responses triggered by flg22, and impaired [Ca2+]cyt influx induced by H2O2. The immunoprecipitation of MiMIF-2-interacting proteins, followed by co-immunoprecipitation and bimolecular fluorescence complementation validations, revealed specific interactions between MiMIF-2 and two Arabidopsis annexins, AnnAt1 and AnnAt4, involved in the transport of calcium ions, stress responses, and signal transduction. Suppression of expression or overexpression of these annexins modified nematode infection. Our results provide functional evidence that nematode effectors secreted from hypodermis to the parasite cuticle surface target host proteins and M. incognita uses MiMIFs to promote parasitism by interfering with the annexin-mediated plant immune responses.

Development of a Species-Specific PCR for Detection and Quantification of Meloidogyne hapla in Soil Using the 16D10 Root-Knot Nematode Effector Gene

The Northern root-knot nematode (Meloidogyne hapla) is an important soilborne pathogen of numerous agricultural crops in temperate regions. Accurate detection and quantification is vital to supporting informed pest management decisions. However, traditional methods of manual nematode extraction and morphology-based identification are time-consuming and require highly specialized training. Molecular methods may expand the diagnostician's toolkit beyond those methods that rely on this disappearing specialized skillset. However, molecular assays targeting the internal transcribed spacer region may lead to inaccurate results because of intraspecific variability. The Meloidogyne spp. effector gene 16D10 was assessed as a target for a SYBR Green I quantitative PCR (qPCR) assay for detection and quantification of M. hapla. M. hapla-specific qPCR primers were developed and evaluated for specificity against five M. hapla isolates and 14 other plant-parasitic nematodes. A standard curve was generated by relating the quantification cycle (Cq) to the log of M. hapla population densities artificially introduced into soil. The influence of soil inhibitors on quantitative amplification was assessed by generating a dilution series from DNA extracted from pure nematode cultures and inoculated soil. Extracts from soil produced significantly higher Cq values than those produced from pure culture extracts. The utility of the qPCR was evaluated using soil samples collected from three naturally infested potato fields, resulting in a significant positive relationship between populations estimated using qPCR and populations derived from manual counting. The qPCR developed in this study provides a useful method for detecting and quantifying M. hapla in soil and demonstrates the utility of effector genes in plant-parasitic nematode diagnostics. The ability to use effector genes as targets for qPCR and other molecular detection and quantification methods may open additional avenues of novel research and support development of improved species-level diagnostics.

What determines host specificity in hyperspecialized plant parasitic nematodes?

Background

In hyperspecialized parasites, the ability to grow on a particular host relies on specific virulence factors called effectors. These excreted proteins are involved in the molecular mechanisms of parasitism and distinguish virulent pathogens from non-virulent related species. The potato cyst nematodes (PCN) Globodera rostochiensis and G. pallida are major plant-parasitic nematodes developing on numerous solanaceous species including potato. Their close relatives, G. tabacum and G. mexicana are stimulated by potato root diffusate but unable to establish a feeding site on this plant host.

Results

RNA sequencing was used to characterize transcriptomic differences among these four Globodera species and to identify genes associated with host specificity. We identified seven transcripts that were unique to PCN species, including a protein involved in ubiquitination. We also found 545 genes that were differentially expressed between PCN and non-PCN species, including 78 genes coding for effector proteins, which represent more than a 6-fold enrichment compared to the whole transcriptome. Gene polymorphism analysis identified 359 homozygous non-synonymous variants showing a strong evidence for selection in PCN species.

Conclusions

Overall, we demonstrated that the determinant of host specificity resides in the regulation of essential effector gene expression that could be under the control of a single or of very few regulatory genes. Such genes are therefore promising targets for the development of novel and more sustainable resistances against potato cyst nematodes.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5853-4) contains supplementary material, which is available to authorized users.

Life-stage specific transcriptomes of a migratory endoparasitic plant nematode, Radopholus similis elucidate a different parasitic and life strategy of plant parasitic nematodes

Radopholus similis is an important migratory endoparasitic nematode, severely harms banana, citrus and many other commercial crops. Little is known about the molecular mechanism of infection and pathogenesis of R. similis. In this study, 64761 unigenes were generated from eggs, juveniles, females and males of R. similis. 11443 unigenes showed significant expression difference among these four life stages. Genes involved in host parasitism, anti-host defense and other biological processes were predicted. There were 86 and 102 putative genes coding for cell wall degrading enzymes and antioxidase respectively. The amount and type of putative parasitic-related genes reported in sedentary endoparasitic plant nematodes are variable from those of migratory parasitic nematodes on plant aerial portion. There were no sequences annotated to effectors in R. similis, involved in feeding site formation of sedentary endoparasites nematodes. This transcriptome data provides a new insight into the parasitic and pathogenic molecular mechanisms of the migratory endoparasitic nematodes. It also provides a broad idea for further research on R. similis.

Cereal Root Interactions with Soilborne Pathogens—From Trait to Gene and Back

Realizing the yield potential of crop plants in the presence of shifting pathogen populations, soil quality, rainfall, and other agro-environmental variables remains a challenge for growers and breeders worldwide. In this review, we discuss current approaches for combatting the soilborne phytopathogenic nematodes, Pratylenchus and Heterodera of wheat and barley, and Meloidogyne graminicola Golden and Birchfield, 1965 of rice. The necrotrophic fungal pathogens, Rhizoctonia solani Kühn 1858 AG-8 and Fusarium spp. of wheat and barley, also are discussed. These pathogens constitute major causes of yield loss in small-grain cereals of the Pacific Northwest, USA and throughout the world. Current topics include new sources of genetic resistance, molecular leads from whole genome sequencing and genome-wide patterns of hosts, nematode or fungal gene expression during root-pathogen interactions, host-induced gene silencing, and building a molecular toolbox of genes and regulatory sequences for deployment of resistance genes. In conclusion, improvement of wheat, barley, and rice will require multiple approaches.

Two venom allergen-like proteins, HaVAP1 and HaVAP2, are involved in the parasitism of Heterodera avenae

Despite the fact that venom allergen-like proteins (VAPs) have been identified in many animal- and plant-parasitic nematodes, studies on VAPs in Heterodera avenae, which is an important phytonematode, are still in their infancy. Here, we isolated, cloned and characterized two VAPs, named HaVAP1 and HaVAP2, from H. avenae. The two encoded proteins, HaVAP1 and HaVAP2, harbour an SCP-like domain each, but share only 38% identity with each other. HaVAP1 and HaVAP2 are expressed in subventral and dorsal oesophageal glands, respectively. HaVAP1 is expressed mainly at the early stages, whereas HaVAP2 accumulates principally at the late stages. Both HaVAP1 and HaVAP2 are secreted when expressed in Nicotiana benthamiana leaves, but HaVAP1 is delivered into chloroplasts, whereas HaVAP2 is translocated to the nucleus without signal peptides. Knocking down HaVAP1 increased the virulence of H. avenae. In contrast, silencing of HaVAP2 hampered the parasitism of H. avenae. Both HaVAP1 and HaVAP2 suppressed the cell death induced by BAX in N. benthamiana leaves. Moreover, HaVAP2 physically interacted with a CYPRO4-like protein (HvCLP) of Hordeum vulgare in the nucleus of the plant. It is reasonable to speculate that the changes in the transcript of HvCLP are associated with HaVAP2 during the parasitism of H. avenae. All results obtained in this study show that both HaVAP1 and HaVAP2 are involved in the parasitism of H. avenae, but they possess different functions, broadening our understanding of the parasitic mechanism of H. avenae.

An Effector, BxSapB1, Induces Cell Death and Contributes to Virulence in the Pine Wood Nematode Bursaphelenchus xylophilus

The pine wood nematode (PWN) Bursaphelenchus xylophilus has caused serious damage to pine forests in China. Effectors secreted by phytonematodes play a role in host infection. We identified and characterized an effector, BxSapB1, based on the B. xylophilus transcriptome at the early stages of infection and the transient expression of proteins in Nicotiana benthamiana. BxSapB1 triggered cell death in N. benthamiana when secreted into the apoplast, and this effect was independent of N. benthamiana brassinosteroid-insensitive 1-associated kinase 1 (NbBAK1) and suppressor of BIR1-1 (NbSOBIR1). The signal peptide of BxSapB1 was proven to be functional in yeast using the yeast signal sequence trap system and BxSapB1 was strongly expressed in the subventral gland cells of B. xylophilus, as revealed by in-situ hybridization. In addition, based on local BLAST analysis, the BxSapB1 showed 100% identity to BUX.s00139.62, which was identified from the B. xylophilus secretome during Pinus thunbergii infection. BxSapB1 was upregulated in a highly virulent strain and downregulated in a weakly virulent strain of PWN at the early stages of infection. RNA interference assays showed that silencing BxSapB1 resulted in decreased expression of pathogenesis-related genes (PtPR-1b, PtPR-3, and PtPR-5) as well as delayed onset of symptoms in P. thunbergii infected by B. xylophilus. The combined data suggest that BxSapB1 can trigger cell death in N. benthamiana and that it contributes to the virulence in B. xylophilus during parasitic interaction.

Interactions of endoparasitic and ectoparasitic nematodes within the plant root system

Root-knot and cyst nematodes have sophisticated mechanisms to invade their plant hosts to reprogram the plant developmental program to induce feeding structures essential for nematode survival and reproduction. This has a detrimental effect on the plant as this sedentary endoparasitic interaction affects the growth and yields of many crop plants. However, other migratory endoparasitic nematodes that do not establish root feeding sites are as aggressive on many crop plants. With new information gained from the genome and transcriptomes of the migratory endoparasitic nematode, Pratylenchus spp., this review compares the different lifestyles and the pathogenic interactions these nematodes have with their plant host. Pratylenchus spp. utilises a common arsenal of effectors involved in plant cell wall degradation and the manipulation of plant host innate immunity. The absence of specific cell reprogramming effector genes may explain its migratory endoparasitic lifestyle, making it relevant to pest management approaches in Australia.