Pathogen Invasion Research Articles

Commensal microbiome and gastrointestinal mucosal immunity: Harmony and conflict with our closest neighbor.

The gastrointestinal tract contains a wide range of microorganisms that have evolved alongside the immune system of the host. The intestinal mucosa maintains balance within the intestines by utilizing the mucosal immune system, which is controlled by the complex gut mucosal immune network. This review aims to comprehensively introduce current knowledge of the gut mucosal immune system, focusing on its interaction with commensal bacteria. The gut mucosal immune network includes gut-associated lymphoid tissue, mucosal immune cells, cytokines, and chemokines. The connection between microbiota and the immune system occurs through the engagement of bacterial components with pattern recognition receptors found in the intestinal epithelium and antigen-presenting cells. This interaction leads to the activation of both innate and adaptive immune responses. The interaction between the microbial community and the host is vital for maintaining the balance and health of the host's mucosal system. The gut mucosal immune network maintains a delicate equilibrium between active immunity, which defends against infections and damaging non-self antigens, and immunological tolerance, which allows for the presence of commensal microbiota and dietary antigens. This balance is crucial for the maintenance of intestinal health and homeostasis. Disturbance of gut homeostasis leads to enduring or severe gastrointestinal ailments, such as colorectal cancer and inflammatory bowel disease. Utilizing these factors can aid in the development of cutting-edge mucosal vaccines that have the ability to elicit strong protective immune responses at the primary sites of pathogen invasion.

Ultralong‐lasting plasma‐activated water inhibits pathogens and improves plant disease resistance in soft rot‐infected hydroponic lettuce

AbstractTo address the short lifetime of plasma‐activated water (PAW), this work reports on the application of ultralong‐lasting PAW for plant disease treatment. Compared with lettuce without ultralong‐lasting PAW treatment, the treated lettuce solution showed c. 1 log10 colony forming units mL−1 decrease in pathogens, as well as improvements in leaf area, leaf weight, root length, and root weight by 75%, 20%, 108.33%, and 150%, respectively. The leaf withering/root mortality rate of PAW‐treated plants was significantly lower than those of non‐PAW‐treated plants. Besides, disease defense‐related enzymes, such as catalase and β−1,3‐glucanase, were respectively enhanced by 112.5% and 5.13% in PAW‐treated lettuce, while the plant defense‐related genes were upregulated to respond to the pathogen's invasion.

Hotspot shelters stimulate frog resistance to chytridiomycosis.

Many threats to biodiversity cannot be eliminated; for example, invasive pathogens may be ubiquitous. Chytridiomycosis is a fungal disease that has spread worldwide, driving at least 90 amphibian species to extinction, and severely affecting hundreds of others1-4. Once the disease spreads to a new environment, it is likely to become a permanent part of that ecosystem. To enable coexistence with chytridiomycosis in the field, we devised an intervention that exploits host defences and pathogen vulnerabilities. Here we show that sunlight-heated artificial refugia attract endangered frogs and enable body temperatures high enough to clear infections, and that having recovered in this way, frogs are subsequently resistant to chytridiomycosis even under cool conditions that are optimal for fungal growth. Our results provide a simple, inexpensive and widely applicable strategy to buffer frogs against chytridiomycosis in nature. The refugia are immediately useful for the endangered species we tested and will have broader utility for amphibian species with similar ecologies. Furthermore, our concept could be applied to other wildlife diseases in which differences in host and pathogen physiologies can be exploited. The refugia are made from cheap and readily available materials and therefore could be rapidly adopted by wildlife managers and the public. In summary, habitat protection alone cannot protect species that are affected by invasive diseases, but simple manipulations to microhabitat structure could spell the difference between the extinction and the persistence of endangered amphibians.

Advances in analytical techniques for assessing volatile organic compounds in pulse crops: a comprehensive review

Pulse crops, including beans, peas, chickpeas, and lentils, are vital sources of protein, fiber, and essential nutrients worldwide. They serve not only as staple foods but also as key components of sustainable agricultural practices, contributing to soil fertility through nitrogen fixation and enhancing overall productivity. However, pulse crops face numerous abiotic and biotic stresses mainly insect pest attack and pathogen invasion, which pose significant threats to pulse crops, impacting both production and food security. To overcome these challenges, plants have evolved diverse defense mechanisms, including the emission of specific volatile organic compounds (VOCs). These volatiles play crucial roles in plant communication, protection, and real-time health status indication. Monitoring VOCs offers a promising approach for early detection of pest infestations or pathogen infections, enabling the grower to take early action and decide on the proper control measure to minimize losses. The identification of plant-emitted VOCs requires robust and sensitive analytical techniques such as gas chromatography and mass spectrometry, which are the mainly used techniques for in pulse crops studies. However, traditional methods have limitations, prompting the need for advanced, portable, and real-time detection alternatives, such as gas-sensing technologies. This paper provides a comprehensive review of VOC measuring methods, including extraction, separation, and analytical techniques, focusing on their application in pulse crops. Recent advancements in gas-sensing technologies are also discussed, highlighting their potential in enhancing crop protection and agricultural sustainability.

Cy3-Based Nanoviscosity Determination of Mucus: Effect of Mucus Collection Methods and Antibiotics Treatment.

The integrity of the protective mucus layer as a primary defense against pathogen invasion and microbial leakage into the intestinal epithelium can be compromised by the effects of antibiotics on the commensal microbiome. Changes in mucus integrity directly affect the solvent viscosity in the immediate vicinity of the mucin network, that is, the nanoviscosity, which in turn affects both biochemical reactions and selective transport. To assess mucus nanoviscosity, a reliable readout via the viscosity-dependent fluorescence lifetime of the molecular rotor dye cyanine 3 is established and nanoviscosities from porcine and murine ex vivo mucus are determined. To account for different mucin concentrations due to the removal of digestive residues during mucus collection, the power law dependence of mucin concentration on viscosity is used. The impact of antibiotics combinations (meropenem/vancomycin, gentamycin/ampicillin) on ex vivo intestinal mucus nanoviscosity is presented. The significant increase in viscosity of murine intestinal mucus after treatment suggests an effect of antibiotics on the microbiota that affects mucus integrity. This method will be a useful tool to assess how drugs, directly or indirectly, affect mucus integrity. Additionally, the method can be utilized to analyze the role of mucus nanoviscosity in health and disease, as well as in drug development.

AIM2 enhances Candida albicans infection through promoting macrophage apoptosis via AKT signaling

Candida albicans is among the most prevalent invasive fungal pathogens for immunocompromised individuals and novel therapeutic approaches that involve immune response modulation are imperative. Absent in melanoma 2 (AIM2), a pattern recognition receptor for DNA sensing, is well recognized for its involvement in inflammasome formation and its crucial role in safeguarding the host against various pathogenic infections. However, the role of AIM2 in host defense against C. albicans infection remains uncertain. This study reveals that the gene expression of AIM2 is induced in human and mouse innate immune cells or tissues after C. albicans infection. Furthermore, compared to their wild-type (WT) counterparts, Aim2−/− mice surprisingly exhibit resistance to C. albicans infection, along with reduced inflammation in the kidneys post-infection. The resistance of Aim2−/− mice to C. albicans infection is not reliant on inflammasome or type I interferon production. Instead, Aim2−/− mice display lower levels of apoptosis in kidney tissues following infection than WT mice. The deficiency of AIM2 in macrophages, but not in dendritic cells, results in a phenocopy of the resistance observed in Aim2−/− mice against C. albican infection. The treatment of Clodronate Liposome, a reagent that depletes macrophages, also shows the critical role of macrophages in host defense against C. albican infection in Aim2−/− mice. Furthermore, the reduction in apoptosis is observed in Aim2−/− mouse macrophages following infection or treatment of DNA from C. albicans in comparison with controls. Additionally, higher levels of AKT activation are observed in Aim2−/− mice, and treatment with an AKT inhibitor reverses the host resistance to C. albicans infection. The findings collectively demonstrate that AIM2 exerts a negative regulatory effect on AKT activation and enhances macrophage apoptosis, ultimately compromising host defense against C. albicans infection. This suggests that AIM2 and AKT may represent promising therapeutic targets for the management of fungal infections.

Continuum of global to local dispersal frameworks highlights the increasing threat of pine wilt disease in China

The global introduction of human-mediated trade and local dispersal through transport or natural pathways are major processes and contributors to biological invasion. To effectively prevent and manage biological invasion, global introduction pathways and local dispersal processes of biological invasions need to be considered as a continuum of global to local dispersal (CGLD). However, there has been no unified CGLD framework developed that simultaneously considers global introduction pathway dynamics and multiple local dispersal processes with human-mediated and natural pathways to guide the development of effective management priority strategies for pine wilt disease. In this study, we constructed a CGLD framework to evaluate the global introduction and local dispersal risks of pine wilt disease. This is an invasive forest pathogen caused by the pine wood nematode (PWN) Bursaphelenchus xylophilus, which causes severe harm to forestry ecosystems worldwide. The global introduction network dynamics has indicated that the introduction pressure of PWN continually increased during 2003–2016. The highest-risk source country and entry port were the United States and Jiangsu ports, respectively. The local dispersal modes of PWN were mainly presented a random structure with lots of “in-filling” dispersal events during 2010–2021. The PWN populations in China have gradually dispersed to non-analogous climatic regions compared to those in the native and other invasive ranges. The dispersal risk areas of PWN primarily cover southwestern, eastern, central, and northeastern China. Such integration can facilitate more accurate prediction of global introduction and local dispersal pathway risk of biological invasion and provide vital guidance for designing management priority strategies to prevent invasion.

Higher tree species richness and diversity in urban areas than in forests: Implications for host availability for invasive tree pests and pathogens

Urban and forest trees provide valuable ecosystem services. However, they are increasingly threatened by invasive forest pests and pathogens. Trees in urban areas are often the first potential hosts non-native tree-feeding insects and tree pathogens (“pests”) encounter after introduction in a novel region. If the trees encountered are suitable hosts, these pests can establish and become invasive – eventually also in surrounding forests. Here, we compared tree species and genus composition between urban areas and surrounding forests and examined the implications for host availability for forest pests and potential effects on invasibility. We compiled and standardised 26 urban tree inventories, containing ∼ 500.000 individual trees. We used multivariate analyses to compare urban tree composition with forest tree composition from forests surrounding each municipality (10 km radius), derived from the Swiss National Forest Inventory. With > 1300 different tree species, species richness of urban trees was 17 times higher than species richness in surrounding forests. Linear models and multivariate analyses revealed that host availability for forest quarantine pests is significantly higher in urban areas than in forests, with large differences in host suitability for different quarantine pests between urban and forest tree assemblages. This indicates that differences in species composition in urban and forest trees can result in increased host availability, possibly facilitating the establishment of quarantine forest pests.

Evaluating the impact of an invasive pathogen on tree population decline: An evidence based modelling approach

An upsurge of invasive forest pathogens (IFPs) has been causing widespread damage to forest ecosystems worldwide. Modelling future forest loss caused by IFPs is challenging, as it requires a sophisticated understanding of the pathogen-hosts-surrounding interactions. We developed a complexity-appropriate model using an evidence-based approach to predict the decline of the European ash (Fraxinus excelsior L.) population caused by ash dieback (Hymenoscyphus fraxineus) in a British deciduous woodland. Our model predicts that (1) the ash population will decline by ∼26 % in the next 10 year; (2) an ±10 % relative error in mortality survey would cause a ∼8 % bias in 10-year population decline; and (3) a 5 % increase in resistant trees would save ∼3 % population over 10 years. Our research demonstrates the merit of systematic reviews in balancing model complexity against generalisation. By scaling up the methodology to other IFPs, it is possible to forecast forest health with various management scenarios.

Pan-drug resistance and hypervirulence in a human fungal pathogen are enabled by mutagenesis induced by mammalian body temperature.

The continuing emergence of invasive fungal pathogens poses an increasing threat to public health. Here, through the China Hospital Invasive Fungal Surveillance Net programme, we identified two independent cases of human infection with a previously undescribed invasive fungal pathogen, Rhodosporidiobolus fluvialis, from a genus in which many species are highly resistant to fluconazole and caspofungin. We demonstrate that R. fluvialis can undergo yeast-to-pseudohyphal transition and that pseudohyphal growth enhances its virulence, revealed by the development of a mouse model. Furthermore, we show that mouse infection or mammalian body temperature induces its mutagenesis, allowing the emergence of hypervirulent mutants favouring pseudohyphal growth. Temperature-induced mutagenesis can also elicit the development of pan-resistance to three of the most commonly used first-line antifungals (fluconazole, caspofungin and amphotericin B) in different Rhodosporidiobolus species. Furthermore, polymyxin B was found to exhibit potent activity against the pan-resistant Rhodosporidiobolus mutants. Collectively, by identifying and characterizing a fungal pathogen in the drug-resistant genus Rhodosporidiobolus, we provide evidence that temperature-dependent mutagenesis can enable the development of pan-drug resistance and hypervirulence in fungi, and support the idea that global warming can promote the evolution of new fungal pathogens.

A dual function of the IDA peptide in regulating cell separation and modulating plant immunity at the molecular level.

The abscission of floral organs and emergence of lateral roots in Arabidopsis is regulated by the peptide ligand inflorescence deficient in abscission (IDA) and the receptor protein kinases HAESA (HAE) and HAESA-like 2 (HSL2). During these cell separation processes, the plant induces defense-associated genes to protect against pathogen invasion. However, the molecular coordination between abscission and immunity has not been thoroughly explored. Here, we show that IDA induces a release of cytosolic calcium ions (Ca2+) and apoplastic production of reactive oxygen species, which are signatures of early defense responses. In addition, we find that IDA promotes late defense responses by the transcriptional upregulation of genes known to be involved in immunity. When comparing the IDA induced early immune responses to known immune responses, such as those elicited by flagellin22 treatment, we observe both similarities and differences. We propose a molecular mechanism by which IDA promotes signatures of an immune response in cells destined for separation to guard them from pathogen attack.

A dual function of the IDA peptide in regulating cell separation and modulating plant immunity at the molecular level

The abscission of floral organs and emergence of lateral roots in Arabidopsis is regulated by the peptide ligand inflorescence deficient in abscission (IDA) and the receptor protein kinases HAESA (HAE) and HAESA-like 2 (HSL2). During these cell separation processes, the plant induces defense-associated genes to protect against pathogen invasion. However, the molecular coordination between abscission and immunity has not been thoroughly explored. Here, we show that IDA induces a release of cytosolic calcium ions (Ca2+) and apoplastic production of reactive oxygen species, which are signatures of early defense responses. In addition, we find that IDA promotes late defense responses by the transcriptional upregulation of genes known to be involved in immunity. When comparing the IDA induced early immune responses to known immune responses, such as those elicited by flagellin22 treatment, we observe both similarities and differences. We propose a molecular mechanism by which IDA promotes signatures of an immune response in cells destined for separation to guard them from pathogen attack.

Identification and characterization of circular RNAs in the skin of rainbow trout (Oncorhynchus mykiss) infected with infectious hematopoietic necrosis virus

Rainbow trout (Oncorhynchus mykiss) is an economically significant freshwater-farmed fish worldwide, and the frequent outbreaks of infectious hematopoietic necrosis (IHN) in recent years have gravely compromised the healthy growth of the rainbow trout aquaculture industry. Fish skin is an essential immune barrier against the invasion of external pathogens, but it is poorly known about the role of circRNAs in rainbow trout skin. Therefore, we examined the expression profiles of circRNAs in rainbow trout skin following IHNV infection using RNA-seq. A total of 6607 circRNAs were identified, of which 34 circRNAs were differentially expressed (DE) and these DE circRNA source genes were related to immune-related pathways such as Toll-like receptor signaling pathway, NOD-like receptor signaling pathway, Cytokine-cytokine receptor interaction, ubiquitin mediated proteolysis, and ferroptosis. We used qRT-PCR, Sanger sequencing, and subcellular localization to validate the chosen DE circRNAs, confirming their localization and expression patterns in rainbow trout skin. Further, 12 DE circRNAs were selected to construct the circRNA-miRNA-mRNA regulatory network, finding one miRNA could connect one or more circRNAs and mRNAs, and some miRNAs were reported to be associated with antiviral immunity. The functional prediction findings revealed that novel_circ_002779 and novel_circ_004118 may act as sponges for miR-205-z and miR-155-y to regulate the expression of target genes TLR8 and PIK3R1, respectively, and participated in the antiviral immune responses in rainbow trout. These results shed light on the immunological mechanism of circRNAs in rainbow trout skin and offer fundamental information for further research on the innate immune system and breeding rainbow trout resistant to disease.

Characterization of the transmembrane C-type lectin reveals a novel phagocytic receptor for hemocytes of Tegillarca granosa

C-type lectins (CTLs), a superfamily of calcium-dependent carbohydrate binding proteins, which remain uncharacterized in bivalve mollusks such as blood clam Tegillarca granosa, plays a pivotal role in non-self-recognition and pathogen clearance within the innate immune system. In this study, we identified a CTL as a potential marker gene for immune cells in T. granosa using single-cell RNA-sequence (scRNA-seq). Structural predictions confirmed TgCTL as a functional protein, being characterized by a classic C-type lectin domain (CTLD) and a stable transmembrane structure. Furthermore, the Vibrio parahaemolyticus challenge experiment indicated that the TgCTL gene can significantly respond to pathogen invasion as a marker of immune response and can effectively eliminate pathogens. Results of RNA interference (RNAi) showed that TgCTL knockdown led to a significant decrease in hemocytes phagocytic activity (P < 0.05). Taken together, the results of this study revealed that TgCTL, a marker for immune response, could participate in immune defense against pathogens by enhancing phagocytosis of hemocytes, providing new insights into the antimicrobial immune response of T. granosa.

Intersection of the microbiome and immune metabolism in lupus.

Systemic lupus erythematosus is a complex autoimmune disease resulting from a dysregulation of the immune system that involves gut dysbiosis and an altered host cellular metabolism. This review highlights novel insights and expands on the interactions between the gut microbiome and the host immune metabolism in lupus. Pathobionts, invasive pathogens, and even commensal microbes, when in dysbiosis, can all trigger and modulate immune responses through metabolic reprogramming. Changes in the microbiota's global composition or individual taxa may trigger a cascade of metabolic changes in immune cells that may, in turn, reprogram their functions. Factors contributing to dysbiosis include changes in intestinal hypoxia, competition for glucose, and limited availability of essential nutrients, such as tryptophan and metal ions, all of which can be driven by host metabolism changes. Conversely, the accumulation of some host metabolites, such as itaconate, succinate, and free fatty acids, could further influence the microbial composition and immune responses. Overall, mounting evidence supports a bidirectional relationship between host immunometabolism and the microbiota in lupus pathogenesis.

Commensal E. coli limits Salmonella gut invasion during inflammation by producing toxin-bound siderophores in a tonB-dependent manner.

The gastrointestinal tract is densely colonized by a polymicrobial community known as the microbiota which serves as primary line of defence against pathogen invasion. The microbiota can limit gut-luminal pathogen growth at different stages of infection. This can be traced to specific commensal strains exhibiting direct or indirect protective functions. Although these mechanisms hold the potential to develop new approaches to combat enteric pathogens, they remain far from being completely described. In this study, we investigated how a mouse commensal Escherichia coli can outcompete Salmonella enterica serovar Typhimurium (S. Tm). Using a salmonellosis mouse model, we found that the commensal E. coli 8178 strain relies on a trojan horse trap strategy to limit S. Tm expansion in the inflamed gut. Combining mutants and reporter tools, we demonstrated that inflammation triggers the expression of the E. coli 8178 antimicrobial microcin H47 toxin which, when fused to salmochelin siderophores, can specifically alter S. Tm growth. This protective function was compromised upon disruption of the E. coli 8178 tonB-dependent catecholate siderophore uptake system, highlighting a previously unappreciated crosstalk between iron intake and microcin H47 activity. By identifying the genetic determinants mediating S. Tm competition, our work not only provides a better mechanistic understanding of the protective function displayed by members of the gut microbiota but also further expands the general contribution of microcins in bacterial antagonistic relationships. Ultimately, such insights can open new avenues for developing microbiota-based approaches to better control intestinal infections.

High variation of virulence in Aphanomyces astaci strains lacks association with pathogenic traits and mtDNA haplogroups

Introduced into Europe from North America 150 years ago alongside its native crayfish hosts, the invasive pathogen Aphanomyces astaci is considered one of the main causes of European crayfish population decline. For the past two centuries, this oomycete pathogen has been extensively studied, with the more recent efforts focused on containing and monitoring its spread across the continent. However, after the recent introduction of new strains, the newly-discovered diversity of A. astaci in North America and several years of coevolution with its European host, a new assessment of the traits linked to the pathogen’s virulence is much needed. To fill this gap, we investigated the presence of phenotypic patterns (i.e., in vitro growth and sporulation rates) possibly associated with the pathogen’s virulence (i.e., induced mortality in crayfish) in a collection of 14 A. astaci strains isolated both in North America and in Europe. The results highlighted a high variability in virulence, growth rate and motile spore production among the different strains, while the total-sporulation rate was more similar across strains. Surprisingly, growth and sporulation rates were not significantly correlated with virulence. Furthermore, none of the analysed parameters, including virulence, was significantly different among the major A. astaci haplogroups. These results indicate that each strain is defined by a characteristic combination of pathogenic features, specifically assembled for the environment and host faced by each strain. Thus, canonical mitochondrial markers, often used to infer the pathogen’s virulence, are not accurate tools to deduce the phenotype of A. astaci strains. As the diversity of A. astaci strains in Europe is bound to increase due to translocations of new carrier crayfish species from North America, there is an urgent need to deepen our understanding of A. astaci’s virulence variability and its ability to adapt to new hosts and environments.

Pyroptosis: A major trigger of excessive immune response in the gingiva.

The gingival mucosal barrier, an important oral cavity barrier, plays a significant role in preventing pathogenic microorganism invasion and maintaining periodontal tissue health. Pathogenic microorganism invasion of the gingival mucosa produces a large number of cytokines. Among them, pyroptosis is an important player in exacerbating immune-inflammatory responses, leading to tissue destruction. However, the mechanism of pyroptosis and the immune response it triggers have not been fully elucidated. We provide an overview of recent advances in understanding gingival physical barrier pyroptosis and inflammation-induced hyperimmunity. PubMed, Web of Science databases were searched for articles, reviews, and clinical studies published until March 2024. We summarised the importance of the gingival barrier in terms of the functions of different cells, described the progress in research on gingival epithelial cell and gingival fibroblast pyroptosis and the immune-inflammatory response it induces, and discussed the relationship between pyroptosis and systemic diseases, association of multiple cell death systems. Finally, we propose future directions for pyroptosis research. Pyroptosis often triggers a range of inflammatory immune responses that lead to associated diseases. Therefore, further study of the molecular mechanisms of pyroptosis and the immune responses is warranted.

Molecular Basis of Plant-Pathogen Interactions in the Agricultural Context.

Biotic stressors pose significant threats to crop yield, jeopardizing food security and resulting in losses of over USD 220 billion per year by the agriculture industry. Plants activate innate defense mechanisms upon pathogen perception and invasion. The plant immune response comprises numerous concerted steps, including the recognition of invading pathogens, signal transduction, and activation of defensive pathways. However, pathogens have evolved various structures to evade plant immunity. Given these facts, genetic improvements to plants are required for sustainable disease management to ensure global food security. Advanced genetic technologies have offered new opportunities to revolutionize and boost plant disease resistance against devastating pathogens. Furthermore, targeting susceptibility (S) genes, such as OsERF922 and BnWRKY70, through CRISPR methodologies offers novel avenues for disrupting the molecular compatibility of pathogens and for introducing durable resistance against them in plants. Here, we provide a critical overview of advances in understanding disease resistance mechanisms. The review also critically examines management strategies under challenging environmental conditions and R-gene-based plant genome-engineering systems intending to enhance plant responses against emerging pathogens. This work underscores the transformative potential of modern genetic engineering practices in revolutionizing plant health and crop disease management while emphasizing the importance of responsible application to ensure sustainable and resilient agricultural systems.

Whole-Genome Sequencing and Analysis of Tumour-Forming Radish (Raphanus sativus L.) Line.

Spontaneous tumour formation in higher plants can occur in the absence of pathogen invasion, depending on the plant genotype. Spontaneous tumour formation on the taproots is consistently observed in certain inbred lines of radish (Raphanus sativus var. radicula Pers.). In this paper, using Oxford Nanopore and Illumina technologies, we have sequenced the genomes of two closely related radish inbred lines that differ in their ability to spontaneously form tumours. We identified a large number of single nucleotide variants (amino acid substitutions, insertions or deletions, SNVs) that are likely to be associated with the spontaneous tumour formation. Among the genes involved in the trait, we have identified those that regulate the cell cycle, meristem activity, gene expression, and metabolism and signalling of phytohormones. After identifying the SNVs, we performed Sanger sequencing of amplicons corresponding to SNV-containing regions to validate our results. We then checked for the presence of SNVs in other tumour lines of the radish genetic collection and found the ERF118 gene, which had the SNVs in the majority of tumour lines. Furthermore, we performed the identification of the CLAVATA3/ESR (CLE) and WUSCHEL (WOX) genes and, as a result, identified two unique radish CLE genes which probably encode proteins with multiple CLE domains. The results obtained provide a basis for investigating the mechanisms of plant tumour formation and also for future genetic and genomic studies of radish.