scholarly journals CRISPR-Cas systems in the plant pathogen Xanthomonas spp. and their impact on genome plasticity

2019 ◽  
Author(s):  
Paula Maria Moreira Martins ◽  
Andre da Silva Xavier ◽  
Marco Aurelio Takita ◽  
Poliane Alfemas-Zerbini ◽  
Alessandra Alves de Souza
Keyword(s):  
Phylogenetic Analysis ◽  
Plant Pathogen ◽  
Significant Variation ◽  
Crop Production ◽  
Plant Pathogens ◽  
Economic Losses ◽  
Genome Plasticity ◽  
Plant Pathogen Interactions ◽  
Cas Proteins

AbstractXanthomonas is one of the most important bacterial genera of plant pathogens causing economic losses in crop production worldwide. Despite its importance, many aspects of basic Xanthomonas biology remain unknown or understudied. Here, we present the first genus-wide analysis of CRISPR-Cas in Xanthomonas and describe specific aspects of its occurrence. Our results show that Xanthomonas genomes harbour subtype I-C and I-F CRISPR-Cas systems and that species belonging to distantly Xanthomonas-related genera in Xanthomonadaceae exhibit the same configuration of coexistence of the I-C and I-F CRISPR subtypes. Additionally, phylogenetic analysis using Cas proteins indicated that the CRISPR systems present in Xanthomonas spp. are the result of an ancient acquisition. Despite the close phylogeny of these systems, they present significant variation in both the number and targets of spacers. An interesting characteristic observed in this study was that the identified plasmid-targeting spacers were always driven toward plasmids found in other Xanthomonas strains, indicating that CRISPR-Cas systems could be very effective in coping with plasmidial infections. Since many effectors are plasmid encoded, CRISPR-Cas might be driving specific characteristics of plant-pathogen interactions.

scholarly journals Fungicide SYP-14288 Inducing Multidrug Resistance in Rhizoctonia solani

Plant Disease ◽  
2020 ◽  
Vol 104 (10) ◽  
pp. 2563-2570 ◽  
Author(s):  
Xingkai Cheng ◽  
Xuejing Man ◽  
Zitong Wang ◽  
Li Liang ◽  
Fan Zhang ◽  
...  
Keyword(s):  
Multidrug Resistance ◽  
Rhizoctonia Solani ◽  
Parental Strain ◽  
Crop Production ◽  
Plant Pathogens ◽  
Economic Losses ◽  
Cross Resistance ◽  
Baseline Sensitivity ◽  
Rice Plants ◽  
Type Strains

Rhizoctonia solani is a widely distributed soilborne plant pathogen, and can cause significant economic losses to crop production. In chemical controls, SYP-14288 is highly effective against plant pathogens, including R. solani. To examine the sensitivity to SYP-14288, 112 R. solani isolates were collected from infected rice plants. An established baseline sensitivity showed that values of effective concentration for 50% growth inhibition (EC50) ranged from 0.0003 to 0.0138 μg/ml, with an average of 0.0055 ± 0.0030 μg/ml. The frequency distribution of the EC50 was unimodal and the range of variation factor (the ratio of maximal over minimal EC50) was 46.03, indicating that all wild-type strains were sensitive to SYP-14288. To examine the risk of fungicide resistance, 20 SYP-14288-resistant mutants were generated on agar plates amended with SYP-14288. Eighteen mutants remained resistant after 10 transfers, and their fitness was significantly different from the parental strain. All of the mutants grew more slowly but showed high virulence to rice plants, though lower than the parental strain. A cross-resistance assay demonstrated that there was a positive correlation between SYP-14288 and fungicides having or not having the same mode of action with SYP-14288, including fluazinam, fentin chloride, fludioxonil, difenoconazole, cyazofamid, chlorothalonil, and 2,4-dinitrophen. This result showed a multidrug resistance induced by SYP-14288, which could be a concern in increasing the spectrum of resistance in R. solani to commonly used fungicides.

scholarly journals Co-Occurrence of Viruses, Plant Pathogens, and Symbionts in an Underexplored Hemipteran Clade

2021 ◽  
Vol 11 ◽  
Author(s):  
McKinlee M. Salazar ◽  
Mônica T. Pupo ◽  
Amanda M. V. Brown
Keyword(s):  
Plant Pathogen ◽  
Plant Pathogens ◽  
Plant Viruses ◽  
Metagenomic Sequencing ◽  
Base Pairs ◽  
Shotgun Metagenomic Sequencing ◽  
Data Clusters ◽  
Blast Database ◽  
Insect Symbionts ◽  
Plant Pathogen Interactions

Interactions between insect symbionts and plant pathogens are dynamic and complex, sometimes involving direct antagonism or synergy and sometimes involving ecological and evolutionary leaps, as insect symbionts transmit through plant tissues or plant pathogens transition to become insect symbionts. Hemipterans such as aphids, whiteflies, psyllids, leafhoppers, and planthoppers are well-studied plant pests that host diverse symbionts and vector plant pathogens. The related hemipteran treehoppers (family Membracidae) are less well-studied but offer a potentially new and diverse array of symbionts and plant pathogenic interactions through their distinct woody plant hosts and ecological interactions with diverse tending hymenopteran taxa. To explore membracid symbiont–pathogen diversity and co-occurrence, this study performed shotgun metagenomic sequencing on 20 samples (16 species) of treehopper, and characterized putative symbionts and pathogens using a combination of rapid blast database searches and phylogenetic analysis of assembled scaffolds and correlation analysis. Among the 8.7 billion base pairs of scaffolds assembled were matches to 9 potential plant pathogens, 12 potential primary and secondary insect endosymbionts, numerous bacteriophages, and other viruses, entomopathogens, and fungi. Notable discoveries include a divergent Brenneria plant pathogen-like organism, several bee-like Bombella and Asaia strains, novel strains of Arsenophonus-like and Sodalis-like symbionts, Ralstonia sp. and Ralstonia-type phages, Serratia sp., and APSE-type phages and bracoviruses. There were several short Phytoplasma and Spiroplasma matches, but there was no indication of plant viruses in these data. Clusters of positively correlated microbes such as yeast-like symbionts and Ralstonia, viruses and Serratia, and APSE phage with parasitoid-type bracoviruses suggest directions for future analyses. Together, results indicate membracids offer a rich palette for future study of symbiont–plant pathogen interactions.

scholarly journals Apoplastic Cell Death-Inducing Proteins of Filamentous Plant Pathogens: Roles in Plant-Pathogen Interactions

2020 ◽  
Vol 11 ◽  
Author(s):  
Ya Li ◽  
Yijuan Han ◽  
Mengyu Qu ◽  
Jia Chen ◽  
Xiaofeng Chen ◽  
...  
Keyword(s):  
Cell Death ◽  
Plant Pathogen ◽  
Plant Pathogens ◽  
Plant Pathogen Interactions

scholarly journals Functional Variation of Plant–Pathogen Interactions: New Concept and Methods for Virulence Data Analyses

2019 ◽  
Vol 109 (8) ◽  
pp. 1324-1330 ◽  
Author(s):  
E. Kosman ◽  
X. Chen ◽  
A. Dreiseitl ◽  
B. McCallum ◽  
A. Lebeda ◽  
...  
Keyword(s):  
Plant Pathogen ◽  
Plant Pathogens ◽  
Infection Type ◽  
Lesion Size ◽  
Data Sets ◽  
Functional Variation ◽  
Multiple Loci ◽  
Plant Pathogen Interaction ◽  
Few Data ◽  
Plant Pathogen Interactions

Classical virulence analysis is based on discovering virulence phenotypes of isolates with regard to a composition of resistance genes in a differential set of host genotypes. With such a vision, virulence phenotypes are usually treated in a genetic manner as one of two possible alleles, either virulence or avirulence in a binary locus. Therefore, population genetics metrics and methods have become prevailing tools for analyzing virulence data at multiple loci. However, a basis for resolving binary virulence phenotypes is infection type (IT) data of host–pathogen interaction that express functional traits of each specific isolate in a given situation (particular host, environmental conditions, cultivation practice, and so on). IT is determined by symptoms and signs observed (e.g., lesion type, lesion size, coverage of leaf or leaf segments by mycelium, spore production and so on), and assessed by IT scores at a generally accepted scale for each plant–pathogen system. Thus, multiple IT profiles of isolates are obtained and can be subjected to analysis of functional variation within and among operational units of a pathogen. Such an approach may allow better utilization of the information available in the raw data, and reveal a functional (e.g., environmental) component of pathogen variation in addition to the genetic one. New methods for measuring functional variation of plant–pathogen interaction with IT data were developed. The methods need an appropriate assessment scale and expert estimations of dissimilarity between IT scores for each plant–pathogen system (an example is presented). Analyses of a few data sets at different hierarchical levels demonstrated discrepancies in results obtained with IT phenotypes versus binary virulence phenotypes. The ability to measure functional IT-based variation offers promise as an effective tool in the study of epidemics caused by plant pathogens.

scholarly journals Comparative Proteomic Analysis of Plant–Pathogen Interactions in Resistant and Susceptible Poplar Ecotypes Infected with Botryosphaeria dothidea

2019 ◽  
Vol 109 (12) ◽  
pp. 2009-2021 ◽  
Author(s):  
Yongxia Li ◽  
Yuqian Feng ◽  
Quan Lü ◽  
Donghui Yan ◽  
Zhenyu Liu ◽  
...  
Keyword(s):  
Atp Synthase ◽  
Plant Pathogen ◽  
Molecular Mechanisms ◽  
Triosephosphate Isomerase ◽  
Hydrolytic Enzymes ◽  
Economic Losses ◽  
Botryosphaeria Dothidea ◽  
Bisphosphate Carboxylase ◽  
Populus Tomentosa Carr ◽  
Plant Pathogen Interactions

Poplar are important forestry species in China, but the Botryosphaeria dothidea pathogen causes serious economic losses worldwide. To identify candidate B. dothidea resistance proteins and explore the molecular mechanisms involved in poplar–pathogen interactions, proteomic responses of stem samples from resistant and susceptible poplar ecotypes to B. dothidea were investigated using nanoflow liquid chromatography-tandem mass spectrometry with label-free quantitative analysis. We identified 588 proteins, divided into 21 biological process categories including 48 oxidoreductases, 72 hydrolytic enzymes, 80 metabolic enzymes, and 29 proteins of unknown function. Differential proteome analysis revealed large differences between resistant Populus tomentosa Carr and susceptible Populus beijingensis Hsu ecotypes before and after inoculation. Among 102 identified proteins, 22 were highly upregulated in the resistant genotype but downregulated in the susceptible genotype. Proteins induced in P. tomentosa Carr in response to B. dothidea are associated with plant defenses including oxidoreductase activity (catalase, isocitrate dehydrogenase, and superoxide dismutase), phenylpropanoid biosynthesis and phenylalanine metabolism (alcohol dehydrogenase), photosynthesis (ATP synthase subunit alpha, ATP synthase gamma chain, photosystem I P700 chlorophyll a apoprotein A2, photosystem II CP47 chlorophyll apoprotein), carbon fixation (pyruvate kinase, triosephosphate isomerase, malic enzyme, phosphoglycerate kinase, ribulose-1,5-bisphosphate carboxylase, and ribulose bisphosphate carboxylase small chain), and glycolysis/gluconeogenesis (fructose-bisphosphate aldolase). Kyoto Encyclopedia of Genes and Genomes pathway analysis identified 168 proteins related to metabolic pathways, 41 proteins related to the biosynthesis of phenylpropanoids, and 36 proteins related to the biosynthesis of plant hormones, the biosynthesis of alkaloids derived from ornithine, lysine, and nicotinic acid, and photosynthesis in response to B. dothidea. Our findings provide insight into plant–pathogen interactions in resistant and susceptible poplar ecotypes infected with B. dothidea and could assist the development of novel strategies for fighting poplar canker disease.

scholarly journals Trick or Treat: Microbial Pathogens Evolved Apoplastic Effectors Modulating Plant Susceptibility to Infection

2018 ◽  
Vol 31 (1) ◽  
pp. 6-12 ◽  
Author(s):  
Yan Wang ◽  
Yuanchao Wang
Keyword(s):  
Immune Responses ◽  
Plant Pathogen ◽  
Plant Pathogens ◽  
Plant Cell Wall ◽  
Effector Proteins ◽  
Microbial Pathogens ◽  
Susceptibility To Infection ◽  
Plant Pathogen Interactions ◽  
Harsh Conditions ◽  
Plant Susceptibility

The apoplastic space between the plant cell wall and the plasma membrane constitutes a major battleground for plant-pathogen interactions. To survive in harsh conditions in the plant apoplast, pathogens must cope with various immune responses. During infection, plant pathogens secrete an arsenal of effector proteins into the apoplast milieu, some of which are detected by the plant surveillance system and, thus, activate plant innate immunity. Effectors that evade plant perception act in modulating plant apoplast immunity to favor successful pathogen infection. The concerted actions of apoplastic effectors often determine the outcomes of plant-pathogen interactions. In this review, we summarize current advances on the understanding of apoplastic effectors and highlight the strategies employed by pathogens to counter host apoplastic defense.

scholarly journals Plant Disease Sensing: Studying Plant-Pathogen Interactions at Scale

mSystems ◽  
2021 ◽  
Author(s):  
Kaitlin M. Gold
Keyword(s):  
Plant Pathogen ◽  
Crop Production ◽  
Plant Disease ◽  
Financial Sustainability ◽  
Crop Loss ◽  
Modern Agriculture ◽  
Plant Pathogen Interactions

Plant disease threatens the environmental and financial sustainability of crop production, causing $220 billion in annual losses. The dire threat disease poses to modern agriculture demands tools for better detection and monitoring to prevent crop loss and input waste.

scholarly journals Convergent Adaptation to Quantitative Host Resistance in a Major Plant Pathogen

mBio ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jean Carlier ◽  
François Bonnot ◽  
Véronique Roussel ◽  
Sébastien Ravel ◽  
Reina Teresa Martinez ◽  
...  
Keyword(s):  
Plant Pathogen ◽  
Genetic Basis ◽  
Plant Pathogens ◽  
Quantitative Resistance ◽  
Biological Data ◽  
Content Type ◽  
A Genome ◽  
Genomic Regions ◽  
Plant Pathogen Interactions ◽  
Pseudocercospora Fijiensis

ABSTRACT Plant pathogens can adapt to quantitative resistance, eroding its effectiveness. The aim of this work was to reveal the genomic basis of adaptation to such a resistance in populations of the fungus Pseudocercospora fijiensis, a major devastating pathogen of banana, by studying convergent adaptation on different cultivars. Samples from P. fijiensis populations showing a local adaptation pattern on new banana hybrids with quantitative resistance were compared, based on a genome scan approach, with samples from traditional and more susceptible cultivars in Cuba and the Dominican Republic. Whole-genome sequencing of pools of P. fijiensis isolates (pool-seq) sampled from three locations per country was conducted according to a paired population design. The findings of different combined analyses highly supported the existence of convergent adaptation on the study cultivars between locations within but not between countries. Five to six genomic regions involved in this adaptation were detected in each country. An annotation analysis and available biological data supported the hypothesis that some genes within the detected genomic regions may play a role in quantitative pathogenicity, including gene regulation. The results suggested that the genetic basis of fungal adaptation to quantitative plant resistance is at least oligogenic, while highlighting the existence of specific host-pathogen interactions for this kind of resistance. IMPORTANCE Understanding the genetic basis of pathogen adaptation to quantitative resistance in plants has a key role to play in establishing durable strategies for resistance deployment. In this context, a population genomic approach was developed for a major plant pathogen (the fungus Pseudocercospora fijiensis causing black leaf streak disease of banana) whereby samples from new resistant banana hybrids were compared with samples from more susceptible conventional cultivars in two countries. A total of 11 genomic regions for which there was strong evidence of selection by quantitative resistance were detected. An annotation analysis and available biological data supported the hypothesis that some of the genes within these regions may play a role in quantitative pathogenicity. These results suggested a polygenic basis of quantitative pathogenicity in this fungal pathogen and complex molecular plant-pathogen interactions in quantitative disease development involving several genes on both sides.

scholarly journals Genome Editing and Protoplast Regeneration to Study Plant–Pathogen Interactions in the Model Plant Nicotiana benthamiana

2021 ◽  
Vol 2 ◽  
Author(s):  
Chen-Tran Hsu ◽  
Wen-Chi Lee ◽  
Yu-Jung Cheng ◽  
Yu-Hsuan Yuan ◽  
Fu-Hui Wu ◽  
...  
Keyword(s):  
Plant Pathogen ◽  
Nicotiana Benthamiana ◽  
Gene Editing ◽  
Plant Pathogens ◽  
Cytidine Deaminase ◽  
Protoplast Regeneration ◽  
Francisella Novicida ◽  
Model Plant ◽  
Plant Pathogen Interactions

Biotic diseases cause substantial agricultural losses annually, spurring research into plant pathogens and strategies to mitigate them. Nicotiana benthamiana is a commonly used model plant for studying plant–pathogen interactions because it is host to numerous plant pathogens and because many research tools are available for this species. The clustered regularly interspaced short palindromic repeats (CRISPR) system is one of several powerful tools available for targeted gene editing, a crucial strategy for analyzing gene function. Here, we demonstrate the use of various CRISPR-associated (Cas) proteins for gene editing of N. benthamiana protoplasts, including Staphylococcus aureus Cas9 (SaCas9), Streptococcus pyogenes Cas9 (SpCas9), Francisella novicida Cas12a (FnCas12a), and nCas9-activation-induced cytidine deaminase (nCas9-Target-AID). We successfully mutated Phytoene Desaturase (PDS) and Ethylene Receptor 1 (ETR1) and the disease-associated genes RNA-Dependent RNA Polymerase 6 (RDR6), and Suppressor of Gene Silencing 3 (SGS3), and confirmed that the mutated alleles were transmitted to progeny. sgs3 mutants showed the expected phenotype, including absence of trans-acting siRNA3 (TAS3) siRNA and abundant expression of the GFP reporter. Progeny of both sgs3 and rdr6 null mutants were sterile. Our analysis of the phenotypes of the regenerated progeny indicated that except for the predicted phenotypes, they grew normally, with no unexpected traits. These results confirmed the utility of gene editing followed by protoplast regeneration in N. benthamiana. We also developed a method for in vitro flowering and seed production in N. benthamiana, allowing the regenerants to produce progeny in vitro without environmental constraints.

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