Orobanchaceae parasite-host interactions

Machine Learning-Based identification of resistance genes associated with sunflower broomrape

BACKGROUND

Sunflowers (Helianthus annuus L.), a vital oil crop, are facing a severe challenge from broomrape (Orobanche cumana), a parasitic plant that seriously jeopardizes the growth and development of sunflowers, limits global production and leads to substantial economic losses, which urges the development of resistant sunflower varieties.

RESULTS

This study aims to identify resistance genes from a comprehensive transcriptomic profile of 103 sunflower varieties based on gene expression data and then constructs predictive models with the key resistant genes. The least absolute shrinkage and selection operator (LASSO) regression and random forest feature importance ranking method were used to identify resistance genes. These genes were considered as biomarkers in constructing machine learning models with Support Vector Machine (SVM), K-Nearest Neighbours (KNN), Logistic Regression (LR), and Gaussian Naive Bayes (GaussianNB). The SVM model constructed with the 24 key genes selected by the LASSO method demonstrated high classification accuracy (0.9514) and a robust AUC value (0.9865), effectively distinguishing between resistant and susceptible varieties based on gene expression data. Furthermore, we discovered a correlation between key genes and differential metabolites, particularly jasmonic acid (JA).

CONCLUSION

Our study highlights a novel perspective on screening sunflower varieties for broomrape resistance, which is anticipated to guide future biological research and breeding strategies.

Proteomic profiling of spleen in rat infected with clonorchis sinensis using liquid chromatography tandem mass spectrometry analysis

Clonorchiasis, caused by Clonorchis sinensis, remains a significant neglected tropical disease with substantial global health implications. As the largest immune organ in mammals, the spleen plays a crucial role in defending against C. sinensis infection; however, the molecular mechanisms underlying spleen pathogenesis during such infections remain poorly understood. To address this gap, quantitative Tandem Mass Tags (TMT) liquid chromatography-tandem mass spectrometry was employed to profile protein changes in the spleens of rats infected with C. sinensis. This analysis identified 40,664 peptides from 6817 proteins, including 371 and 464 differentially expressed proteins at 4 and 8 weeks post-infection (wpi) compared to the control groups, respectively. Clustering analysis revealed distinct proteomic profiles among the groups, while gene ontology analysis associated the differentially expressed proteins with biological binding activities and metabolic processes. KEGG analysis revealed significant enrichment of immune-related and metabolic pathways, including AMPK, IL-17, and p53 signaling pathways. These findings reveal dynamic proteomic alterations in the spleen during C. sinensis infection, offering valuable insights into the biomarker candidates for early diagnosis. Further studies are warranted to validate these potential biomarkers and explore their utility for early diagnosis of clonorchiasis.

Resistance to Striga parasitism through reduction of strigolactone exudation

Parasitism with Striga poses a major threat to global food production. Striga germination and growth rely on strigolactones (SLs) exuded by crop roots under phosphate (Pi)-deficient conditions, although the mechanism of this host-parasite interaction remains elusive. In this study, transcriptomic and functional analyses of sorghum treated with Pi deficiency or the SL GR245DS identify two ABC transporter G (ABCG) transporters of SL, Sorghum biocolor strigolactones transporter 1 (SbSLT1) and SbSLT2. Using AlphaFold2 and amino acid conversion mutants, we identify highly conserved amino acids in SL transport channels essential for transport function. Sorghum lines with single or double knockouts of these transporters exhibit significantly reduced SL secretion from roots, leading to decreased Striga germination and parasitism in field experiments and consequently reducing the grain loss under Striga infestation. This study thus describes the mechanism of SL exudation in monocots and defines conserved residues essential for SL transporter function, offering a potential strategy for enhancing crop resistance to Striga parasitism.

The Biopotential of Bellardia trixago in Replacing Synthetic Compounds for Health-Promoting Applications: Is It a Promising Candidate?

Bellardia trixago (L.) All. (family Orobanchaceae) is a facultative hemiparasitic plant used traditionally to cure many diseases. The present study was designed to evaluate the phenolic constituents, antioxidant, enzyme inhibitory, and cytotoxic properties of the aerial parts of B. trixago. Ethyl acetate (EtOAc), ethanol (EtOH), and 70% EtOH extracts were prepared by maceration, while the aqueous extract was prepared by infusion. Rutin, 4-hydroxy benzoic acid, ferulic acid, p-coumaric acid, hyperoside, delphinidin 3,5 diglucoside, kaempferol, and isoquercitrin were identified in most extracts with variable concentrations, but generally, the EtOH or 70% EtOH accumulated the highest contents. The 70% EtOH extract displayed the best antiradical (DPPH = 13.55 mg TE/g; ATBS = 53.78 mg TE/g) and ion-reducing (CUPRAC = 50.09 mg TE/g; FRAP = 24.73 mg TE/g) properties. The aqueous extract recorded the highest chelating iron power (12.91 mg EDTAE/g) while EtOAc and EtOH exerted the highest total antioxidant activity (2.29 and 2.49 mmol TE/g, p > 0.05). The best cholinesterase (anti-AChE = 2.91 mg GALAE/g; and anti-BchE = 2.62 mg GALAE/g) and α-glucosidase (1.19 mmol ACAE/g) inhibition activity was recorded from the EtOH extract, while that against the α-amylase was obtained from the EtOAc extract (0.69 mmol ACAE/g). The plant was most cytotoxic toward the HT-29 cell line, where the best effect was exerted by the 70% EtOH (IC50 38.42 μg/mL) extract. Furthermore, network pharmacology analysis revealed critical gene targets and pathways associated with the bioactive compounds. Molecular docking studies revealed favorable binding modes and interaction patterns of major compounds with key colon cancer-related proteins, which were further supported by molecular dynamics simulations. As the first investigation into the phenolic composition and pharmacological effects of B. trixago, this study highlights its potential as a promising source of bioactive compounds with therapeutic relevance for oxidative stress-related conditions.

Manipulation of a strigolactone transporter in tomato confers resistance to the parasitic weed broomrape

Parasitic weeds of the Orobanchaceae family cause substantial economic losses and pose significant threats to global agriculture. However, management of such parasitism is challenging, and very few resistance genes have been cloned and characterized in depth. Here, we performed a genome-wide association study using 152 tomato accessions and identified SlABCG45 as a key gene that mediates host resistance to Phelipanche aegyptiaca by affecting the level of strigolactones (SLs) in root exudates. SLs are synthesized and released by host plants and act as germination stimulants for parasitic weeds. We found that SlABCG45 and its close homolog SlABCG44 were membrane-localized SL transporters with essential roles in exudation of SLs to the rhizosphere, resistance to Phelipanche and Orobanche, and upward transport of SLs from roots to shoots. As a predominant environmental stimulant exacerbates parasitism, phosphorus deficiency dramatically induced SlABCG45 expression and weakly induced SlABCG44 expression via the transcription factors SlNSP1 and SlNSP2. Knockout of SlABCG45 in tomato had little effect on yield traits in a broomrape-free field, but conferred increased resistance to different Phelipanche and Orobanche species, resulting in an ∼30% yield increase in a Phelipanche-infested field. Our findings reveal that targeting a single gene by genome editing can confer broad-spectrum parasite resistance in tomato, providing an effective strategy for the sustainable control of parasitic plants in agriculture.

Pseudomonas produce various metabolites displaying herbicide activity against broomrape

Pseudomonads are well-known for their plant growth-promoting properties and biocontrol capabilities against microbial pathogens. Recently, their potential to protect crops from parasitic plants has garnered attention. This study investigates the potential of different Pseudomonas strains to inhibit broomrape growth and to protect host plants against weed infestation. Four Pseudomonas strains, two P. fluorescens JV391D17 and JV391D10, one P. chlororaphis JV395B and one P. ogarae F113 were cultivated using various carbon sources, including fructose, pyruvate, fumarate, and malate, to enhance the diversity of potential Orobanche growth inhibition (OGI)-specialized metabolites produced by Pseudomonas strains. Both global and targeted metabolomic approaches were utilized to identify specific OGI metabolites. Both carbon sources and Pseudomonas genetic diversity significantly influenced the production of OGI metabolites. P. chlororaphis JV395B and P. ogarae F113 produced unique OGI metabolites belonging to different chemical families, such as hydroxyphenazines and phloroglucinol compounds, respectively. Additionally, metabolomic analyses identified an unannotated potential OGI ion, M375T65. This ion was produced by all Pseudomonas strains but was found to be over-accumulated in JV395B, which likely explains its superior OGI activity. Then, greenhouse experiments were performed to evaluate the biocontrol efficacy of selected strains: they showed the efficacy of these strains, particularly JV395B, in reducing broomrape infestation in rapeseed. These findings suggest that certain Pseudomonas strains, through their metabolite production, can offer a sustainable biocontrol strategy against parasitic plants. This biocontrol activity can be optimized by environmental factors, such as carbon amendments. Ultimately, this approach presents a promising alternative to chemical herbicides.

Highly Sensitive Strigolactone Perception by a Divergent Clade KAI2 Receptor in a Facultative Root Parasitic Plant, Phtheirospermum japonicum

Phtheirospermum japonicum, a member of the Orobanchaceae family, is a facultative root parasitic plant that can survive without parasitizing the host. In contrast, obligate root parasitic plants, such as Striga and Orobanche, which are also members of the Orobanchaceae family, cannot survive in the absence of the host. The germination of obligate root parasitic plants is typically induced by host root-derived strigolactones (SLs) at very low concentrations. The KAI2/HTL family proteins have been found to be involved in the perception of karrikin (KAR), a smoke-derived germination inducer and unidentified endogenous ligand, in non-parasitic plants. Obligate root parasitic plants possess uniquely diverged KAI2 clade genes, which are collectively referred to as KAI2d. Many of those have been shown to function as SL receptors. Intriguingly, the KAI2d clade genes are also conserved in P. japonicum, even though this plant does not require SLs for germination. The biochemical and physiological functions of the KAI2d proteins in P. japonicum remain unclear. Here, we report that some of these proteins can function as SL receptors in P. japonicum. Moreover, we found that one of them, PjKAI2d4, is highly sensitive to SLs when expressed in Arabidopsis, and it is similar to the sensitive SL receptors found in Striga and Orobanche. These results suggest that the KAI2d clade SL receptors play a crucial role not only in obligate parasites but also in facultative parasitic plants.

Dominant-Negative KAI2d Paralogs Putatively Attenuate Strigolactone Responses in Root Parasitic Plants

Many root parasitic plants in the Orobanchaceae use host-derived strigolactones (SLs) as germination cues. This adaptation facilitates attachment to a host and is particularly important for the success of obligate parasitic weeds that cause substantial crop losses globally. Parasite seeds sense SLs through 'divergent' KARRIKIN INSENSITIVE2 (KAI2d)/HYPOSENSITIVE TO LIGHT α/β-hydrolases that have undergone substantial duplication and diversification in Orobanchaceae genomes. After germination, chemotropic growth of parasite roots toward a SL source also occurs in some species. We investigated which of the seven KAI2d genes found in a facultative hemiparasite, Phtheirospermum japonicum, may enable chemotropic responses to SLs. To do so, we developed a triple mutant Nbd14a,b kai2i line of Nicotiana benthamiana in which SL-induced degradation of SUPPRESSOR OF MORE AXILLARY GROWTH2 (MAX2) 1 (SMAX1), an immediate downstream target of KAI2 signaling, is disrupted. In combination with a transiently expressed, ratiometric reporter of SMAX1 protein abundance, this mutant forms a system for the functional analysis of parasite KAI2d proteins in a plant cellular context. Using this system, we unexpectedly found three PjKAI2d proteins that do not trigger SMAX1 degradation in the presence of SLs. Instead, these PjKAI2d proteins inhibit the perception of low SL concentrations by SL-responsive PjKAI2d in a dominant-negative manner that depends upon an active catalytic triad. Similar dominant-negative KAI2d paralogs were identified in an obligate hemiparasitic weed, Striga hermonthica. These proteins suggest a mechanism for attenuating SL signaling in parasites, which might be used to enhance the perception of shallow SL gradients during root growth toward a host or to restrict germination responses to specific SLs.

Mapping an avirulence gene in the sunflower parasitic weed Orobanche cumana and characterization of host selection based on virulence alleles

BACKGROUND

Sunflower broomrape (Orobanche cumana Wallr.) is a holoparasitic plant that jeopardizes sunflower production in most areas of Europe and Asia. Recently, populations with increased virulence, classified as race GGV, have been identified in Southern Spain's Guadalquivir Valley gene pool. These populations overcome resistance genes in hybrids resistant to the predominant race FGV. This study aimed to (i) determine the inheritance and map the avirulence trait segregating in a cross between O. cumana individuals from populations EK23 (FGV) and IN201 (GGV), and (ii) characterize the host effect on the IN201 parental population allelic diversity.

RESULTS

A segregating population consisting of 144 F2:3 families was evaluated for virulence using a differential sunflower genotype (Hybrid 1, resistant to race FGV and susceptible to race GGV) and genotyped with SNP markers. The ratio of avirulent to virulent F2:3 families was not significantly different to 1:3 (χ2 = 0.93; P = 0.34), indicating monogenic control of the avirulence/virulence trait. The AvrG-GV locus was mapped on the upper end of O. cumana chromosome 2, 9.2 cM distal from the SNP markers OS04791 and OS02805. Secretome analysis in the AvrG-GV region revealed a cysteine-rich CAP superfamily- and a glucan 1,3-beta-glucosidase family 3-encoding genes as possible candidates for AvrG-GV. SNP allelic analysis on the IN201 population parasitizing a highly susceptible genotype or the differential genotype Hybrid 1 showed that (i) IN201 structure was shaped towards virulent alleles at SNP loci linked to AvrG-GV (ii) there were significant allelic frequency differences associated with the host genotype at AvrG-GV-linked loci.

CONCLUSIONS

This study mapped for the first time an avirulence gene in parasitic plants using a classical genetic approach, confirmed a gene-for-gene model in the O.cumana -sunflower system, and showed the implication of this single avirulence gene in determining the structure of broomrape populations subjected to selection pressure posed by a resistant genotype. The results will contribute to a better understanding of the interaction between crops and weedy parasitic plants, and to effectively manage evolution of virulence by sustainable control strategies based on host genetic resistance.

Broomrape-host interaction: host morphology and physiology as metrics for infestation

MAIN CONCLUSION

In contrast to other plant pests, broomrape, parasitic plant, rely on maintaining the productivity of the host plant to complete their life cycle. Parasitic plants, particularly those in the Orobanchaceae family, rely on their host plants to complete their life cycle. Unlike other plant parasites such as fungi and bacteria, which exploit their hosts regardless of their physiological status, parasitic plants development is linked to the host productivity due to their mutual physiological dependence on water availability and sugar metabolism. Presently, most research focuses on the damage caused to the host after the parasite completes its life cycle, including inflorescence emergence and seed dispersal. However, the interaction between parasite and host begins long before these stages. This implies that certain physiological adaptations are necessary to sustain the parasite's development while maintaining the host's productivity. In this review, I compile existing knowledge regarding changes in host physiology during the early developmental stages of parasitic plants, spanning from attachment to inflorescence emergence. Additionally, I highlight knowledge gaps that should be addressed to understand how hosts sustain themselves throughout extended periods of parasitism.

Secretory Proteins Are Involved in the Parasitism of Melon by Phelipanche aegyptiaca During the Attachment Stage

Parasitic plants represent a significant challenge in global agriculture, with Broomrape (Orobanche/Phelipanche spp.) being a notable example of a holoparasitic species that targets the roots of host plants. This study employed comparative transcriptomics to investigate the mechanisms underlying the parasitism of P. aegyptiaca on melon, focusing on both resistant and susceptible interactions. The findings indicate that the critical phase of P. aegyptiaca parasitism occurs during the post-attachment stage. It is suggested that peptidases may play a role in the development of invasive cells, while cell wall-degrading enzymes (CWDEs) are likely involved in cell wall modification and degradation, and transferases, elicitors, and effectors may play a role in immune regulation. In this study, 25 tobacco rattle virus (TRV) recombinant vectors were successfully constructed and functionally validated using a host-induced gene silencing assay to explore the functions of candidate-secreted effector proteins. The results revealed that silencing Cluster-107894.0, Cluster-11592.0, and Cluster-12482.0 significantly decreased the parasitism rate of P. aegyptiaca on Nicotiana benthamiana. Notably, Cluster-107849.0 encodes a cellulase with hydrolase activity, Cluster-11592.0 encodes a periodic-dependent kinase inhibitor with phosphoprotein activity, and Cluster-12482.0 encodes a glucan 1,3-β-glucosidase with hydrolase activity. These findings potentially offer a novel theoretical framework and justification for understanding host-parasite plant interactions, and suggest new avenues for developing crop varieties resistant to parasitic infestation.

Chromosome-level assembly of Lindenbergia philippensis and comparative genomic analyses shed light on genome evolution in Lamiales

Lamiales, comprising over 23,755 species across 24 families, stands as a highly diverse and prolific plant group, playing a significant role in the cultivation of horticultural, ornamental, and medicinal plant varieties. Whole-genome duplication (WGD) and its subsequent post-polyploid diploidization (PPD) process represent the most drastic type of karyotype evolution, injecting significant potential for promoting the diversity of this lineage. However, polyploidization histories, as well as genome and subgenome fractionation following WGD events in Lamiales species, are still not well investigated. In this study, we constructed a chromosome-level genome assembly of Lindenbergia philippensis (Orobanchaceae) and conducted comparative genomic analyses with 14 other Lamiales species. L. philippensis is positioned closest to the parasitic lineage within Orobanchaceae and has a conserved karyotype. Through a combination of Ks analysis and syntenic depth analysis, we reconstructed and validated polyploidization histories of Lamiales species. Our results indicated that Primulina huaijiensis underwent three rounds of diploidization events following the γ-WGT event, rather than two rounds as reported. Besides, we reconfirmed that most Lamiales species shared a common diploidization event (L-WGD). Subsequently, we constructed the Lamiales Ancestral Karyotype (LAK), comprising 11 proto-chromosomes, and elucidated its evolutionary trajectory, highlighting the highly flexible reshuffling of the Lamiales paleogenome. We identified biased fractionation of subgenomes following the L-WGD event across eight species, and highlighted the positive impacts of non-WGD genes on gene family expansion. This study provides novel genomic resources and insights into polyploidy and karyotype remodeling of Lamiales species, essential for advancing our understanding of species diversification and genome evolution.

Rising from the shadows: Selective foraging in model shoot parasitic plants

Despite being sessile, plants nonetheless forage for resources by modulating their growth. Adaptative foraging in response to changes in resource availability and presence of neighbours has strong implications for performance and fitness. It is an even more pressing issue for parasitic plants, which draw resources directly from other plants. Indeed, parasitic plants were demonstrated over the years to direct their growth towards preferred hosts and invest resources in parasitism relative to host quality. In contrast to root parasites that rely mostly on chemical cues, some shoot parasites seem to profit from the ability to integrate different types of abiotic and biotic cues. While significant progress in this field has been made recently, there are still many open questions regarding the molecular perception and the integration of diverse signalling pathways under different ecological contexts. Addressing how different cues are integrated in parasitic plants will be important when unravelling variations in plant interaction pathways, and essential to predict the spread of parasites in natural and agricultural environments. In this review, we discuss this with a focus on Cuscuta species as an emerging parasitic model, and provide research perspectives based on the recent advances in the topic and plant-plant interactions in general.

An improved method for the highly specific detection of transcription start sites

Precise detection of the transcriptional start site (TSS) is a key for characterizing transcriptional regulation of genes and for annotation of newly sequenced genomes. Here, we describe the development of an improved method, designated 'TSS-seq2.' This method is an iterative improvement of TSS-seq, a previously published enzymatic cap-structure conversion method to detect TSSs in base sequences. By modifying the original procedure, including by introducing split ligation at the key cap-selection step, the yield and the accuracy of the reaction has been substantially improved. For example, TSS-seq2 can be conducted using as little as 5 ng of total RNA with an overall accuracy of 96%; this yield a less-biased and more precise detection of TSS. We then applied TSS-seq2 for TSS analysis of four plant species that had not yet been analyzed by any previous TSS method.

Inhibition of broomrape germination by 2,4-diacetylphloroglucinol produced by environmental Pseudomonas

Parasitic weeds such as broomrapes (Phelipanche ramosa and Orobanche cumana) cause severe damage to crops and their development must be controlled. Given that phloroglucinol compounds (PGCs) produced by environmental Pseudomonas could be toxic towards certain plants, we assessed the potential herbicidal effect of the bacterial model Pseudomonas ogarae F113, a PGCs-producing bacterium, on parasitic weed. By combining the use of a mutagenesis approach and of pure PGCs, we evaluated the in vitro effect of PGC-produced by P. ogarae F113 on broomrape germination and assessed the protective activity of a PGC-producing bacteria on oilseed rape (Brassica napus) against P. ramosa in non-sterile soils. We showed that the inhibition of the germination depends on the PGCs molecular structure and their concentrations as well as the broomrape species and pathovars. This inhibition caused by the PGCs is irreversible, causing a brown coloration of the broomrape seeds. The inoculation of PGCs-producing bacteria limited the broomrape infection of P. ramosa, without affecting the host growth. Moreover, elemental profiling analysis of oilseed rape revealed that neither F113 nor applied PGCs affected the nutrition capacity of the oilseed rape host. Our study expands the knowledge on plant-beneficial Pseudomonas as weed biocontrol agents and opens new avenues for the development of natural bioherbicides to enhance crop yield.

Strigolactones in Rhizosphere Communication: Multiple Molecules With Diverse Functions

Strigolactones (SLs) are root-secreted small molecules that influence organisms living in the rhizosphere. While SLs are known as germination stimulants for root parasitic plants and as hyphal branching factors for arbuscular mycorrhizal fungi, recent studies have also identified them as chemoattractants for parasitic plants, sensors of neighboring plants and key players in shaping the microbiome community. Furthermore, the discovery of structurally diverged SLs, including so-called canonical and non-canonical SLs in various plant species, raises the question of whether the same SLs are responsible for their diverse functions 'in planta' and the rhizosphere or whether different molecules play different roles. Emerging evidence supports the latter, with each SL exhibiting different activities as rhizosphere signals and plant hormones. The evolution of D14/KAI2 receptors has enabled the perception of various SLs or SL-like compounds to control downstream signaling, highlighting the complex interplay between plants and their rhizosphere environment. This review summarizes the recent advances in our understanding of the diverse functions of SLs in the rhizosphere.

Plant polygalacturonase structures specify enzyme dynamics and processivities to fine-tune cell wall pectins

Polygalacturonases (PGs) fine-tune pectins to modulate cell wall chemistry and mechanics, impacting plant development. The large number of PGs encoded in plant genomes leads to questions on the diversity and specificity of distinct isozymes. Herein, we report the crystal structures of 2 Arabidopsis thaliana PGs, POLYGALACTURONASE LATERAL ROOT (PGLR), and ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE2 (ADPG2), which are coexpressed during root development. We first determined the amino acid variations and steric clashes that explain the absence of inhibition of the plant PGs by endogenous PG-inhibiting proteins (PGIPs). Although their beta helix folds are highly similar, PGLR and ADPG2 subsites in the substrate binding groove are occupied by divergent amino acids. By combining molecular dynamic simulations, analysis of enzyme kinetics, and hydrolysis products, we showed that these structural differences translated into distinct enzyme-substrate dynamics and enzyme processivities: ADPG2 showed greater substrate fluctuations with hydrolysis products, oligogalacturonides (OGs), with a degree of polymerization (DP) of ≤4, while the DP of OGs generated by PGLR was between 5 and 9. Using the Arabidopsis root as a developmental model, exogenous application of purified enzymes showed that the highly processive ADPG2 had major effects on both root cell elongation and cell adhesion. This work highlights the importance of PG processivity on pectin degradation regulating plant development.

Detection of Secreted Effector Proteins from Phelipanche aegyptiaca During Invasion of Melon Roots

Parasites can interact with their host plants through the induction and delivery of secreted effector proteins that facilitate plant colonization by decomposing plant cell walls and inhibiting plant immune response to weaken the defense ability of the host. Yet effectors mediating parasitic plant-host interactions are poorly understood. Phelipanche aegyptiaca is an obligate root parasite plant causing severe yield and economic losses in agricultural fields worldwide. Host resistance against P. aegyptiaca occurred during the attachment period of parasitism. Comparative transcriptomics was used to assess resistant and susceptible interactions simultaneously between P. aegyptiaca and two contrasting melon cultivars. In total, 2,740 secreted proteins from P. aegyptiaca were identified here. Combined with transcriptome profiling, 209 candidate secreted effector proteins (CSEPs) were predicted, with functional annotations such as cell wall degrading enzymes, protease inhibitors, transferases, kinases, and elicitor proteins. A heterogeneous expression system in Nicotiana benthamiana was used to investigate the functions of 20 putatively effector genes among the CSEPs. Cluster 15140.0 can suppress BAX-triggered programmed cell death in N. benthamiana. These findings showed that the prediction of P. aegyptiaca effector proteins based on transcriptomic analysis and multiple bioinformatics software is effective and more accurate, providing insights into understanding the essential molecular nature of effectors and laying the foundation of revealing the parasite mechanism of P. aegyptiaca, which is helpful in understanding parasite-host plant interaction.

Conferring resistance to parasitic witchweed by shifting strigolactone biosynthesis

Strigolactones from the exudates of maize root induce germination of the parasitic witchweed Striga. Recently, Li et al. characterized the biosynthesis pathway of two strigolactones, zealactol and zealactonoic acid, which induce less Striga germination than the major maize strigolactone, zealactone. This study provides a promising strategy for plant protection against parasitic witchweed.

Rethinking convergence in plant parasitism through the lens of molecular and population genetic processes

The autotrophic lifestyle of photosynthetic plants has profoundly shaped their body plan, physiology, and gene repertoire. Shifts to parasitism and heterotrophy have evolved at least 12 times in more than 4000 species, and this transition has consequently left major evolutionary footprints among these parasitic lineages. Features that are otherwise rare at the molecular level and beyond have evolved repetitively, including reduced vegetative bodies, carrion-mimicking during reproduction, and the incorporation of alien genetic material. Here, I propose an integrated conceptual model, referred to as the funnel model, to define the general evolutionary trajectory of parasitic plants and provide a mechanistic explanation for their convergent evolution. This model connects our empirical understanding of gene regulatory networks in flowering plants with classical theories of molecular and population genetics. It emphasizes that the cascading effects brought about by the loss of photosynthesis may be a major force constraining the physiological capacity of parasitic plants and shaping their genomic landscapes. Here I review recent studies on the anatomy, physiology, and genetics of parasitic plants that lend support to this photosynthesis-centered funnel model. Focusing on nonphotosynthetic holoparasites, I elucidate how they may inevitably reach an evolutionary terminal status (i.e., extinction) and highlight the utility of a general, explicitly described and falsifiable model for future studies of parasitic plants.

Phenotypic and histological analyses on the resistance of melon to Phelipanche aegyptiaca

Melon (Cucumis melo L.) is an economically important crop in Xinjiang, China, but its production is constrained by the parasitic plant Phelipanche aegyptiaca that attaches to the roots of many crops and causes severe stunting and loss of yield. Rhizotron, pot, and field experiments were employed to evaluate the resistance of 27 melon cultivars to P. aegyptiaca. Then, the resistant and susceptible cultivars were inoculated with P. aegyptiaca from six populations to assess their resistance stability and broad spectrum. Further microscopic and histological analyses were used to clarify the resistance phenotypes and histological structure. The results showed that Huangpi 9818 and KR1326 were more resistant to P. aegyptiaca compared to other cultivars in the rhizotron, pot, and field experiments. In addition, compared to the susceptible cultivar K1076, Huangpi 9818 and KR1326 showed broad-spectrum resistance to six P. aegyptiaca populations. These two resistant cultivars had lower P. aegyptiaca biomass and fewer and smaller P. aegyptiaca attachments on their roots compared to susceptible cultivar K1076. KR1326 (resistant) and K1076 (susceptible) were selected to further study resistance phenotypes and mechanisms. Germination-inducing activity of root exudates and microscopic analysis showed that the resistance in KR1326 was not related to low induction of P. aegyptiaca germination. The tubercles of parasite on KR1326 were observed slightly brown at 14 days after inoculation (DAI), the necrosis and arrest of parasite development occurred at 23 DAI. Histological analysis of necrosis tubercles showed that the endophyte of parasite had reached host central cylinder, connected with host xylem, and accumulation of secretions and callose were detected in neighbouring cells. We concluded that KR1326 is an important melon cultivar for P. aegyptiaca resistance that could be used to expand the genetic basis of cultivated muskmelon for resistance to the parasite.

Host root exudates initiate a foraging preference by the root parasite Santalum album

Haustoria of root-parasitic plants draw nutrients from the roots of host species. While recent studies have assessed host preferences of parasitic plants, how root-exuded chemicals can mediate host tropism and selection by root-parasitic plants is poorly understood. Under greenhouse conditions, we performed two pot experiments to determine whether the root parasite Santalum album selectively forages for superior hosts (N2-fixing Acacia confusa Merr. or Dalbergia odorifera T. Chen) rather than for inferior hosts (non-N2-fixing Bischofia polycarpa (levl.) Airy Shaw or Dracontomelon duperreranum Pierre), and whether S. album uses host root exudates and/or specific chemicals in these root exudates to locate and trigger haustorium formation. Lateral roots and haustoria of S. album seedlings exhibited greater growth in the direction of D. odorifera roots than toward roots from the other three hosts. Comparative metabolic analysis revealed that D. odorifera root exudates were enriched in isoflavonoid, flavonoid and flavone/flavonol biosynthesis pathways, and that the relative contents of flavonoids were significantly greater in the root exudates of D. odorifera than in those of the other three hosts. Root exudates from D. odorifera significantly promoted S. album root growth, haustorium formation and reactive oxygen species accumulation in haustoria. Our results demonstrate that the key step in plant parasitism by S. album is based on root exudation by a host plant; the exudates function as a metabolite signal that activate lateral root growth and haustorium formation. Our results also indicate that flavonoids in the root exudates could play an important role in S. album foraging activity. Information on the responses of root parasites to host root exudates and/or haustorium-inducing chemicals may be useful for selecting superior host species to plant with valuable species of root parasites.

Protein Profiling of Psittacanthus calyculatus during Mesquite Infection

Psittacanthus calyculatus is a hemiparasite mistletoe that represents an ecological problem due to the impacts caused to various tree species of ecological and commercial interest. Although the life cycle for the Psittacanthus genus is well established in the literature, the development stages and molecular mechanism implicated in P. calyculatus host infection are poorly understood. In this study, we used a manageable infestation of P. laevigata with P. calyculatus to clearly trace the infection, which allowed us to describe five phenological infective stages of mistletoe on host tree branches: mature seed (T1), holdfast formation (T2), haustorium activation (T3), haustorium penetration (T4), and haustorium connection (T5) with the host tree. Proteomic analyses revealed proteins with a different accumulation and cellular processes in infective stages. Activities of the cell wall-degrading enzymes cellulase and β-1,4-glucosidase were primarily active in haustorium development (T3), while xylanase, endo-glucanase, and peptidase were highly active in the haustorium penetration (T4) and xylem connection (T5). Patterns of auxins and cytokinin showed spatial concentrations in infective stages and moreover were involved in haustorium development. These results are the first evidence of proteins, cell wall-degrading enzymes, and phytohormones that are involved in early infection for the Psittacanthus genus, and thus represent a general infection mechanism for other mistletoe species. These results could help to understand the molecular dialogue in the establishment of P. calyculatus parasitism.

Strigol induces germination of the facultative parasitic plant Phtheirospermum japonicum in the absence of nitrate ions

Root parasitic plants in the family Orobanchaceae, such as Striga and Orobanche spp., infest major crops worldwide, leading to a multibillion-dollar loss annually. Host-derived strigolactones (SLs), recognized by a group of α/β hydrolase receptors (KAI2d) in these parasites, are important determinants for germinating root parasitic plants near the roots of host plants. Phtheirospermum japonicum, a facultative hemiparasitic Orobanchaceae plant, can germinate and grow in the presence or absence of the host and can also exhibit root chemotropism to host-derived SLs that are perceived via KAI2d. However, the importance of SLs in P. japonicum germination remains unclear. In this study, we found that germination of P. japonicum was suppressed in the absence of nitrate ions and that germination of P. japonicum was promoted by exogenous strigol, an SL, under such conditions. We propose a model in which P. japonicum may select either independent living or parasitism in response to ambient nitrogen conditions and host presence.

Silencing of a mannitol transport gene in Phelipanche aegyptiaca by the tobacco rattle virus system reduces the parasite germination on the host root

Root parasitic weed Phelipanche aegyptiaca is an obligate plant parasite that causes severe damage to host crops. Agriculture crops mainly belong to the Brassicaceae, Leguminosae, Cruciferae, and Solanaceae plant families affected by this parasitic weed, leading to the devastating loss of crop yield and economic growth. This root-specific parasitic plant is not able to complete its life cycle without a suitable host and is dependent on the host plant for nutrient uptake and germination. Therefore, selected parasitic genes of P. aegyptiaca which were known to be upregulated upon interaction with the host were chosen. These genes are essential for parasitism, and reduced activity of these genes could affect host-parasitic interaction and provide resistance to the host against these parasitic weeds. To check and examine the role of these parasitic genes which can affect the development of host resistance, we silenced selected genes in the P. aegyptiaca using the tobacco rattle virus (TRV) based virus-induced gene silencing (VIGS) method. Our results demonstrated that the total number of P. aegyptiaca parasite tubercles attached to the root of the host plant Nicotiana benthamiana was substantially decreased in all the silenced plants. However, silencing of the P. aegyptiaca MNT1 gene which encodes the mannitol transporter showed a significantly reduced number of germinated shoots and tubercles. Thus, our study indicates that the mannitol transport gene of P. aegyptiaca plays a crucial role in parasitic germination, and silencing of the PaMNT1 gene abolishes the germination of parasites on the host roots.

Phenolic signals for prehaustorium formation in Striga hermonthica

Striga hermonthica is a root parasitic plant that causes considerable crop yield losses. To parasitize host plants, parasitic plants develop a specialized organ called the haustorium that functions in host invasion and nutrient absorption. The initiation of a prehaustorium, the primitive haustorium structure before host invasion, requires the perception of host-derived compounds, collectively called haustorium-inducing factors (HIFs). HIFs comprise quinones, phenolics, flavonoids and cytokinins for S. hermonthica; however, the signaling pathways from various HIFs leading to prehaustorium formation remain largely uncharacterized. It has been proposed that quinones serve as direct signaling molecules for prehaustorium induction and phenolic compounds originating from the host cell wall are the oxidative precursors, but the overlap and distinction of their downstream signaling remain unknown. Here we show that quinone and phenolic-triggered prehaustorium induction in S. hermonthica occurs through partially divergent signaling pathways. We found that ASBr, an inhibitor of acetosyringone in virulence gene induction in the soil bacterium Agrobacterium, compromised prehaustorium formation in S. hermonthica. In addition, LGR-991, a competitive inhibitor of cytokinin receptors, inhibited phenolic-triggered but not quinone-triggered prehaustorium formation, demonstrating divergent signaling pathways of phenolics and quinones for prehaustorium formation. Comparisons of genome-wide transcriptional activation in response to either phenolic or quinone-type HIFs revealed markedly distinct gene expression patterns specifically at the early initiation stage. While quinone DMBQ triggered rapid and massive transcriptional changes in genes at early stages, only limited numbers of genes were induced by phenolic syringic acid. The number of genes that are commonly upregulated by DMBQ and syringic acid is gradually increased, and many genes involved in oxidoreduction and cell wall modification are upregulated at the later stages by both HIFs. Our results show kinetic and signaling differences in quinone and phenolic HIFs, providing useful insights for understanding how parasitic plants interpret different host signals for successful parasitism.

Cytokinins Induce Prehaustoria Coordinately with Quinone Signals in the Parasitic Plant Striga hermonthica

Orobanchaceae parasitic plants are major threats to global food security, causing severe agricultural damage worldwide. Parasitic plants derive water and nutrients from their host plants through multicellular organs called haustoria. The formation of a prehaustorium, a primitive haustorial structure, is provoked by host-derived haustorium-inducing factors (HIFs). Quinones, including 2,6-dimethoxy-p-benzoquinone (DMBQ), are of the most potent HIFs for various species in Orobanchaceae, but except non-photosynthetic holoparasites, Phelipanche and Orobanche spp. Instead, cytokinin (CK) phytohormones were reported to induce prehaustoria in Phelipanche ramosa. However, little is known about whether CKs act as HIFs in the other parasitic species to date. Moreover, the signaling pathways for quinones and CKs in prehaustorium induction are not well understood. This study shows that CKs act as HIFs in the obligate parasite Striga hermonthica but not in the facultative parasite Phtheirospermum japonicum. Using chemical inhibitors and marker gene expression analysis, we demonstrate that CKs activate prehaustorium formation through a CK-specific signaling pathway that overlaps with the quinone HIF pathway at downstream in S. hermonthica. Moreover, host root exudates activated S. hermonthica CK biosynthesis and signaling genes, and DMBQ and CK inhibitors perturbed the prehaustorium-inducing activity of exudates, indicating that host root exudates include CKs. Our study reveals the importance of CKs for prehaustorium formation in obligate parasitic plants.

Microbial community roles and chemical mechanisms in the parasitic development of Orobanche cumana

Orobanche cumana Wallr. is a holoparasite weed that extracts water and nutrients from its host the sunflower, thereby causing yield reductions and quality losses. However, the number of O. cumana parasites in the same farmland is distinctly different. The roots of some hosts have been heavily parasitized, while others have not been parasitized. What are the factors contributing to this phenomenon? Is it possible that sunflower interroot microorganisms are playing a regulatory role in this phenomenon? The role of the microbial community in this remains unclear. In this study, we investigated the rhizosphere soil microbiome for sunflowers with different degrees of O. cumana parasitism, that is, healthy, light infection, moderate infection, and severe infection on the sunflower roots. The microbial structures differed significantly according to the degree of parasitism, where Xanthomonadaceae was enriched in severe infections. Metagenomic analyses revealed that amino acid, carbohydrate, energy, and lipid metabolism were increased in the rhizosphere soils of severely infected sunflowers, which were attributed to the proliferation of Lysobacter. Lysobacter antibioticus (HX79) was isolated and its capacity to promote O. cumana seed germination and increase the germ tube length was confirmed by germination and pot experiments. Cyclo(Pro-Val), an active metabolite of strain HX79, was identified and metabolomic and molecular docking approaches confirmed it was responsible for promoting O. cumana seed germination and growth. And we found that Pseudomonas mandelii HX1 inhibited the growth of O. cumana in the host rhizosphere soil. Our findings clarify the role of rhizosphere microbiota in regulating the parasite O. cumana to possibly facilitate the development of a new weed suppression strategy.

Strigolactones are chemoattractants for host tropism in Orobanchaceae parasitic plants

Parasitic plants are worldwide threats that damage major agricultural crops. To initiate infection, parasitic plants have developed the ability to locate hosts and grow towards them. This ability, called host tropism, is critical for parasite survival, but its underlying mechanism remains mostly unresolved. To characterise host tropism, we used the model facultative root parasite Phtheirospermum japonicum, a member of the Orobanchaceae. Here, we show that strigolactones (SLs) function as host-derived chemoattractants. Chemotropism to SLs is also found in Striga hermonthica, a parasitic member of the Orobanchaceae, but not in non-parasites. Intriguingly, chemotropism to SLs in P. japonicum is attenuated in ammonium ion-rich conditions, where SLs are perceived, but the resulting asymmetrical accumulation of the auxin transporter PIN2 is diminished. P. japonicum encodes putative receptors that sense exogenous SLs, whereas expression of a dominant-negative form reduces its chemotropic ability. We propose a function for SLs as navigators for parasite roots.

Parasitic Plants: An Overview of Mechanisms by Which Plants Perceive and Respond to Parasites

In contrast to most autotrophic plants, which produce carbohydrates from carbon dioxide using photosynthesis, parasitic plants obtain water and nutrients by parasitizing host plants. Many important crop plants are infested by these heterotrophic plants, leading to severe agricultural loss and reduced food security. Understanding how host plants perceive and resist parasitic plants provides insight into underlying defense mechanisms and the potential for agricultural applications. In this review, we offer a comprehensive overview of the current understanding of host perception of parasitic plants and the pre-attachment and post-attachment defense responses mounted by the host. Since most current research overlooks the role of organ specificity in resistance responses, we also summarize the current understanding and cases of cross-organ parasitism, which indicates nonconventional haustorial connections on other host organs, for example, when stem parasitic plants form haustoria on their host roots. Understanding how different tissue types respond to parasitic plants could provide the potential for developing a universal resistance mechanism in crops against both root and stem parasitic plants.

Living with a giant, flowering parasite: metabolic differences between Tetrastigma loheri Gagnep. (Vitaceae) shoots uninfected and infected with Rafflesia (Rafflesiaceae) and potential applications for propagation

Metabolites in Rafflesia-infected and non-infected Tetrastigma were compared which may have applications in Rafflesia propagation. Benzylisoquinoline alkaloids, here reported for the first time in Vitaceae, were abundant in non-infected shoots and may be a form of defense. In Rafflesia-infected shoots, oxylipins, which mediate immune response, were elevated. Endemic to the forests of Southeast Asia, Rafflesia (Rafflesiaceae) is a genus of holoparasitic plants producing the largest flowers in the world, yet completely dependent on its host, the tropical grape vine, Tetrastigma. Rafflesia species are threatened with extinction, making them an iconic symbol of plant conservation. Thus far, propagation has proved challenging, greatly decreasing efficacy of conservation efforts. This study compared the metabolites in the shoots of Rafflesia-infected and non-infected Tetrastigma loheri to examine how Rafflesia infection affects host metabolomics and elucidate the Rafflesia infection process. Results from LC-MS-based untargeted metabolomics analysis showed benzylisoquinoline alkaloids were naturally more abundant in non-infected shoots and are here reported for the first time in the genus Tetrastigma, and in the grape family, Vitaceae. These metabolites have been implicated in plant defense mechanisms and may prevent a Rafflesia infection. In Rafflesia-infected shoots, oxygenated fatty acids, or oxylipins, and a flavonoid, previously shown involved in plant immune response, were significantly elevated. This study provides a preliminary assessment of metabolites that differ between Rafflesia-infected and non-infected Tetrastigma hosts and may have applications in Rafflesia propagation to meet conservation goals.

Large-scale sequencing paves the way for genomic and genetic analyses in parasitic plants

Parasitic plants pose a serious agricultural threat, but are also precious resources for valuable metabolites. The heterotrophic nature of these plants has resulted in the development of several morphological and physiological features that are of evolutionary significance. Recent advances in large-scale sequencing technology have provided insights into the evolutionary and molecular mechanisms of plant parasitism. Genome sequencing has revealed gene losses and horizontal gene transfers in parasitic plants. Mobile signals traveling between the parasite and host may have contributed to the increased fitness of parasitic life styles. Transcriptome analyses implicate shared processes among various parasitic species and the establishment of functional analysis is beginning to reveal molecular mechanisms during host and parasite interactions.

Molecular dissection of haustorium development in Orobanchaceae parasitic plants

Characterizing molecular aspects of haustorium development by parasitic plants in the Orobanchaceae family has identified hormone signaling/transport and specific genes as major players.

Using biotechnological approaches to develop crop resistance to root parasitic weeds

New transgenic and biotechnological approaches may serve as a key component in achieving crop resistance to root parasitic weeds. Root parasitic weeds inflict severe damage to numerous crops, reducing yield quantity and quality. A lack of new sources of resistance limits our ability to manage newly developing, more virulent races. Having no effective means to control the parasites in most crops, innovative biotechnological solutions are needed. Several novel biotechnological strategies using regulatory RNA molecules, the CRISPR/Cas9 system, and T-DNA insertions have been acknowledged for engineering resistance against parasitic weeds. Significant breakthroughs have been made over the years in deciphering the plant genome and its functions, including the genomes of parasitic weeds. However, the basis of biotechnological strategies to generate host resistance to root parasitic weeds needs to be further developed. Gene-silencing and editing tools should be used to target key processes of host-parasite interactions, such as strigolactone biosynthesis and signaling, haustorium development, and degradation and penetration of the host cell wall. In this review, we summarize and discuss the main areas of research leading to the discovery and functional analysis of genes involved in host-induced gene silencing that target key parasite genes, transgenic host modification, and host gene editing to generate sustainable resistance to root parasitic weeds.