The Experts below are selected from a list of 2166 Experts worldwide ranked by ideXlab platform
Bruce A Mcdonald - One of the best experts on this subject based on the ideXlab platform.
-
genetic architecture of oxidative stress tolerance in the fungal wheat pathogen Zymoseptoria tritici
bioRxiv, 2020Co-Authors: Javier Palmaguerrero, Ziming Zhong, Bruce A McdonaldAbstract:Reactive oxygen species are toxic byproducts of aerobic respiration produced during cell growth. They also are an important component of plant defenses to inhibit microbial pathogens. Tolerance to oxidative stress contributes to viability and pathogenicity of plant pathogens. However, the complex molecular network of oxidative stress responses hinders identification of the genes contributing to variation in this trait. Variation in genes affecting responses to oxidative stress is likely to affect the evolutionary potential of pathogen tolerance to host defences. Here, we employed a forward genetic approach to investigate the genetic architecture of oxidative stress tolerance in the fungal wheat pathogen Zymoseptoria tritici. By performing quantitative trait locus (QTL) mapping in two crosses, we identified several genomic regions associated with tolerance to oxidative stress, including a QTL having a large effect on growth under oxidative stress. We found evidence for a significant trade-off between growth under non-stressful conditions and growth inhibition under oxidative stress. We identified a large QTL associated with this trade-off and with growth under non-stressful conditions, suggesting that differences in fungal growth could result in different sensitivities to oxidative stress. Our results suggest that genes related to fungal growth could also contribute to variation in oxidative stress tolerance among fungal strains.
-
A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici
BMC Biology, 2020Co-Authors: Thomas Badet, Bruce A Mcdonald, Ursula Oggenfuss, Leen Abraham, Daniel CrollAbstract:Background The gene content of a species largely governs its ecological interactions and adaptive potential. A species is therefore defined by both core genes shared between all individuals and accessory genes segregating presence-absence variation. There is growing evidence that eukaryotes, similar to bacteria, show intra-specific variability in gene content. However, it remains largely unknown how functionally relevant such a pangenome structure is for eukaryotes and what mechanisms underlie the emergence of highly polymorphic genome structures. Results Here, we establish a reference-quality pangenome of a fungal pathogen of wheat based on 19 complete genomes from isolates sampled across six continents. Zymoseptoria tritici causes substantial worldwide losses to wheat production due to rapidly evolved tolerance to fungicides and evasion of host resistance. We performed transcriptome-assisted annotations of each genome to construct a global pangenome. Major chromosomal rearrangements are segregating within the species and underlie extensive gene presence-absence variation. Conserved orthogroups account for only ~ 60% of the species pangenome. Investigating gene functions, we find that the accessory genome is enriched for pathogenesis-related functions and encodes genes involved in metabolite production, host tissue degradation and manipulation of the immune system. De novo transposon annotation of the 19 complete genomes shows that the highly diverse chromosomal structure is tightly associated with transposable element content. Furthermore, transposable element expansions likely underlie recent genome expansions within the species. Conclusions Taken together, our work establishes a highly complex eukaryotic pangenome providing an unprecedented toolbox to study how pangenome structure impacts crop-pathogen interactions.
-
a 19 isolate reference quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici
BMC Biology, 2020Co-Authors: Thomas Badet, Bruce A Mcdonald, Ursula Oggenfuss, Leen Abraham, Daniel CrollAbstract:The gene content of a species largely governs its ecological interactions and adaptive potential. A species is therefore defined by both core genes shared between all individuals and accessory genes segregating presence-absence variation. There is growing evidence that eukaryotes, similar to bacteria, show intra-specific variability in gene content. However, it remains largely unknown how functionally relevant such a pangenome structure is for eukaryotes and what mechanisms underlie the emergence of highly polymorphic genome structures. Here, we establish a reference-quality pangenome of a fungal pathogen of wheat based on 19 complete genomes from isolates sampled across six continents. Zymoseptoria tritici causes substantial worldwide losses to wheat production due to rapidly evolved tolerance to fungicides and evasion of host resistance. We performed transcriptome-assisted annotations of each genome to construct a global pangenome. Major chromosomal rearrangements are segregating within the species and underlie extensive gene presence-absence variation. Conserved orthogroups account for only ~ 60% of the species pangenome. Investigating gene functions, we find that the accessory genome is enriched for pathogenesis-related functions and encodes genes involved in metabolite production, host tissue degradation and manipulation of the immune system. De novo transposon annotation of the 19 complete genomes shows that the highly diverse chromosomal structure is tightly associated with transposable element content. Furthermore, transposable element expansions likely underlie recent genome expansions within the species. Taken together, our work establishes a highly complex eukaryotic pangenome providing an unprecedented toolbox to study how pangenome structure impacts crop-pathogen interactions.
-
MINI REVIEW ARTICLE Recent advances in the Zymoseptoria tritici -wheat interaction: insights from pathogenomics
2020Co-Authors: Megan C Mcdonald, Bruce A Mcdonald, Peter S Solomon, Adi Avni, Agriculture Guus Bakkeren, Agri-food Canada, Canada David, J StudholmeAbstract:We examine the contribution of next generation sequencing (NGS) to our understanding of the interaction between the fungal pathogen Zymoseptoria tritici and its wheat host. Recent interspecific whole genome comparisons between Z. tritici and its close relatives provide evidence that Z. tritici has undergone strong adaptive evolution, which is attributed to specialization by Z. tritici on wheat. We also assess the contribution of recent RNA sequencing datasets toward identifying pathogen genes and mechanisms critical for disease. While these studies have yet to report a major effector gene, they illustrate that assembling reads to the reference genome is a robust method to identify fungal transcripts from in planta infections. They also highlight the strong influence that the wheat cultivar has on effector gene expression. Lastly, we suggest future directions for NGS-guided approaches to address largely unanswered questions related to cultivar and lifecycle dependent gene expression and propose that future experiments with Z. tritici be conducted on a single wheat cultivar to enable comparisons across experiments
-
quantitative trait locus mapping reveals complex genetic architecture of quantitative virulence in the wheat pathogen Zymoseptoria tritici
Molecular Plant Pathology, 2018Co-Authors: Ethan L Stewart, Daniel Croll, Andrea Sanchezvallet, Javier Palmaguerrero, Fanny E Hartmann, Mark H Lendenmann, Bruce A McdonaldAbstract:Summary We conducted a comprehensive analysis of virulence in the fungal wheat pathogen Zymoseptoria tritici using quantitative trait locus (QTL) mapping. High-throughput phenotyping based on automated image analysis allowed the measurement of pathogen virulence on a scale and with a precision that was not previously possible. Across two mapping populations encompassing more than 520 progeny, 540 710 pycnidia were counted and their sizes and grey values were measured. A significant correlation was found between pycnidia size and both spore size and number. Precise measurements of percentage leaf area covered by lesions provided a quantitative measure of host damage. Combining these large and accurate phenotypic datasets with a dense panel of restriction site-associated DNA sequencing (RADseq) genetic markers enabled us to genetically dissect pathogen virulence into components related to host damage and those related to pathogen reproduction. We showed that different components of virulence can be under separate genetic control. Large- and small-effect QTLs were identified for all traits, with some QTLs specific to mapping populations, cultivars and traits and other QTLs shared among traits within the same mapping population. We associated the presence of four accessory chromosomes with small, but significant, increases in several virulence traits, providing the first evidence for a meaningful function associated with accessory chromosomes in this organism. A large-effect QTL involved in host specialization was identified on chromosome 7, leading to the identification of candidate genes having a large effect on virulence.
Daniel Croll - One of the best experts on this subject based on the ideXlab platform.
-
A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici
BMC Biology, 2020Co-Authors: Thomas Badet, Bruce A Mcdonald, Ursula Oggenfuss, Leen Abraham, Daniel CrollAbstract:Background The gene content of a species largely governs its ecological interactions and adaptive potential. A species is therefore defined by both core genes shared between all individuals and accessory genes segregating presence-absence variation. There is growing evidence that eukaryotes, similar to bacteria, show intra-specific variability in gene content. However, it remains largely unknown how functionally relevant such a pangenome structure is for eukaryotes and what mechanisms underlie the emergence of highly polymorphic genome structures. Results Here, we establish a reference-quality pangenome of a fungal pathogen of wheat based on 19 complete genomes from isolates sampled across six continents. Zymoseptoria tritici causes substantial worldwide losses to wheat production due to rapidly evolved tolerance to fungicides and evasion of host resistance. We performed transcriptome-assisted annotations of each genome to construct a global pangenome. Major chromosomal rearrangements are segregating within the species and underlie extensive gene presence-absence variation. Conserved orthogroups account for only ~ 60% of the species pangenome. Investigating gene functions, we find that the accessory genome is enriched for pathogenesis-related functions and encodes genes involved in metabolite production, host tissue degradation and manipulation of the immune system. De novo transposon annotation of the 19 complete genomes shows that the highly diverse chromosomal structure is tightly associated with transposable element content. Furthermore, transposable element expansions likely underlie recent genome expansions within the species. Conclusions Taken together, our work establishes a highly complex eukaryotic pangenome providing an unprecedented toolbox to study how pangenome structure impacts crop-pathogen interactions.
-
a 19 isolate reference quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici
BMC Biology, 2020Co-Authors: Thomas Badet, Bruce A Mcdonald, Ursula Oggenfuss, Leen Abraham, Daniel CrollAbstract:The gene content of a species largely governs its ecological interactions and adaptive potential. A species is therefore defined by both core genes shared between all individuals and accessory genes segregating presence-absence variation. There is growing evidence that eukaryotes, similar to bacteria, show intra-specific variability in gene content. However, it remains largely unknown how functionally relevant such a pangenome structure is for eukaryotes and what mechanisms underlie the emergence of highly polymorphic genome structures. Here, we establish a reference-quality pangenome of a fungal pathogen of wheat based on 19 complete genomes from isolates sampled across six continents. Zymoseptoria tritici causes substantial worldwide losses to wheat production due to rapidly evolved tolerance to fungicides and evasion of host resistance. We performed transcriptome-assisted annotations of each genome to construct a global pangenome. Major chromosomal rearrangements are segregating within the species and underlie extensive gene presence-absence variation. Conserved orthogroups account for only ~ 60% of the species pangenome. Investigating gene functions, we find that the accessory genome is enriched for pathogenesis-related functions and encodes genes involved in metabolite production, host tissue degradation and manipulation of the immune system. De novo transposon annotation of the 19 complete genomes shows that the highly diverse chromosomal structure is tightly associated with transposable element content. Furthermore, transposable element expansions likely underlie recent genome expansions within the species. Taken together, our work establishes a highly complex eukaryotic pangenome providing an unprecedented toolbox to study how pangenome structure impacts crop-pathogen interactions.
-
rapid parallel evolution of azole fungicide resistance in australian populations of the wheat pathogen Zymoseptoria tritici
Applied and Environmental Microbiology, 2019Co-Authors: Megan C Mcdonald, Daniel Croll, Melanie Renkin, Merrin Spackman, Beverley Orchard, Peter S Solomon, Andrew MilgateAbstract:ABSTRACT Zymoseptoria tritici is a globally distributed fungal pathogen which causes Septoria tritici blotch on wheat. Management of the disease is attempted through the deployment of resistant wheat cultivars and the application of fungicides. However, fungicide resistance is commonly observed in Z. tritici populations, and continuous monitoring is required to detect breakdowns in fungicide efficacy. We recently reported azole-resistant isolates in Australia; however, it remained unknown whether resistance was brought into the continent through gene flow or whether resistance emerged independently. To address this question, we screened 43 isolates across five Australian locations for azole sensitivity and performed whole-genome sequencing on 58 isolates from seven locations to determine the genetic basis of resistance. Population genomic analyses showed extremely strong differentiation between the Australian population recovered after azoles began to be used and both Australian populations recovered before azoles began to be used and populations on different continents. The apparent absence of recent gene flow between Australia and other continents suggests that azole fungicide resistance has evolved de novo and subsequently spread within Tasmania. Despite the isolates being distinct at the whole-genome level, we observed combinations of nonsynonymous substitutions at the CYP51 locus identical to those observed elsewhere in the world. We observed nine previously reported nonsynonymous mutations as well as isolates that carried a combination of the previously reported L50S, S188N, A379G, I381V, Y459DEL, G460DEL, and N513K substitutions. Assays for the 50% effective concentration against a subset of isolates exposed to the tebuconazole and epoxiconazole fungicides showed high levels of azole resistance. The rapid, parallel evolution of a complex CYP51 haplotype that matches a dominant European haplotype demonstrates the enormous potential for de novo resistance emergence in pathogenic fungi. IMPORTANCE Fungicides are essential to control diseases in agriculture because many crops are highly susceptible to pathogens. However, many pathogens rapidly evolve resistance to fungicides. A large body of studies have described specific mutations conferring resistance and have often made inferences about the origins of resistance based on sequencing data from the target gene alone. Here, we show the de novo acquisition of resistance to the ubiquitously used azole fungicides in genetically isolated populations of the wheat pathogen Zymoseptoria tritici in Tasmania, Australia. We confirm evidence for parallel evolution through genome-scale analyses of representative worldwide populations. The emergence of complex resistance haplotypes following a well-documented recent introduction of azoles into Australian farming practices demonstrates how rapidly chemical resistance evolves in agricultural ecosystems.
-
quantitative trait locus mapping reveals complex genetic architecture of quantitative virulence in the wheat pathogen Zymoseptoria tritici
Molecular Plant Pathology, 2018Co-Authors: Ethan L Stewart, Daniel Croll, Andrea Sanchezvallet, Javier Palmaguerrero, Fanny E Hartmann, Mark H Lendenmann, Bruce A McdonaldAbstract:Summary We conducted a comprehensive analysis of virulence in the fungal wheat pathogen Zymoseptoria tritici using quantitative trait locus (QTL) mapping. High-throughput phenotyping based on automated image analysis allowed the measurement of pathogen virulence on a scale and with a precision that was not previously possible. Across two mapping populations encompassing more than 520 progeny, 540 710 pycnidia were counted and their sizes and grey values were measured. A significant correlation was found between pycnidia size and both spore size and number. Precise measurements of percentage leaf area covered by lesions provided a quantitative measure of host damage. Combining these large and accurate phenotypic datasets with a dense panel of restriction site-associated DNA sequencing (RADseq) genetic markers enabled us to genetically dissect pathogen virulence into components related to host damage and those related to pathogen reproduction. We showed that different components of virulence can be under separate genetic control. Large- and small-effect QTLs were identified for all traits, with some QTLs specific to mapping populations, cultivars and traits and other QTLs shared among traits within the same mapping population. We associated the presence of four accessory chromosomes with small, but significant, increases in several virulence traits, providing the first evidence for a meaningful function associated with accessory chromosomes in this organism. A large-effect QTL involved in host specialization was identified on chromosome 7, leading to the identification of candidate genes having a large effect on virulence.
-
comparative transcriptome analyses in Zymoseptoria tritici reveal significant differences in gene expression among strains during plant infection
Molecular Plant-microbe Interactions, 2017Co-Authors: Javier Palmaguerrero, Stefano F F Torriani, Marcello Zala, Daniel Croll, Carolina Sardinha Francisco, Fanny E Hartmann, Bruce A McdonaldAbstract:Zymoseptoria tritici is an ascomycete fungus that causes Septoria tritici blotch, a globally distributed foliar disease on wheat. Z. tritici populations are highly polymorphic and exhibit significant quantitative variation for virulence. Despite its importance, the genes responsible for quantitative virulence in this pathogen remain largely unknown. We investigated the expression profiles of four Z. tritici strains differing in virulence in an experiment conducted under uniform environmental conditions. Transcriptomes were compared at four different infection stages to characterize the regulation of gene families thought to be involved in virulence and to identify new virulence factors. The major components of the fungal infection transcriptome showed consistent expression profiles across strains. However, strain-specific regulation was observed for many genes, including some encoding putative virulence factors. We postulate that strain-specific regulation of virulence factors can determine the outcome of...
Megan C Mcdonald - One of the best experts on this subject based on the ideXlab platform.
-
the identification of a transposon affecting the asexual reproduction of the wheat pathogen Zymoseptoria tritici
Molecular Plant Pathology, 2021Co-Authors: Chen Wang, Megan C Mcdonald, Peter S Solomon, Andrew MilgateAbstract:Zymoseptoria tritici, the causal agent of Septoria tritici blotch, is a fungal wheat pathogen that causes significant global yield losses. Within Z. tritici populations, quantitative differences in virulence among different isolates are commonly observed; however, the genetic components that underpin these differences remain elusive. In this study, intraspecific comparative transcriptomic analysis was used to identify candidate genes that contribute to differences in virulence on the wheat cultivar WW2449. This led to the identification of a multicopy gene that was not expressed in the high-virulence isolate when compared to the medium- and low-virulence isolates. Further investigation suggested this gene resides in a 7.9-kb transposon. Subsequent long-read sequencing of the isolates used in the transcriptomic analysis confirmed that this gene did reside in an active Class II transposon, which is composed of four genes named REP9-1 to -4. Silencing and overexpression of REP9-1 in two distinct genetic backgrounds demonstrated that its expression alone reduces the number of pycnidia produced by Z. tritici during infection. The REP9-1 gene identified within a Class II transposon is the first discovery of a gene in a transposable element that influences the virulence of Z. tritici. This discovery adds further complexity to genetic loci that contribute to quantitative virulence in this important pathogen.
-
MINI REVIEW ARTICLE Recent advances in the Zymoseptoria tritici -wheat interaction: insights from pathogenomics
2020Co-Authors: Megan C Mcdonald, Bruce A Mcdonald, Peter S Solomon, Adi Avni, Agriculture Guus Bakkeren, Agri-food Canada, Canada David, J StudholmeAbstract:We examine the contribution of next generation sequencing (NGS) to our understanding of the interaction between the fungal pathogen Zymoseptoria tritici and its wheat host. Recent interspecific whole genome comparisons between Z. tritici and its close relatives provide evidence that Z. tritici has undergone strong adaptive evolution, which is attributed to specialization by Z. tritici on wheat. We also assess the contribution of recent RNA sequencing datasets toward identifying pathogen genes and mechanisms critical for disease. While these studies have yet to report a major effector gene, they illustrate that assembling reads to the reference genome is a robust method to identify fungal transcripts from in planta infections. They also highlight the strong influence that the wheat cultivar has on effector gene expression. Lastly, we suggest future directions for NGS-guided approaches to address largely unanswered questions related to cultivar and lifecycle dependent gene expression and propose that future experiments with Z. tritici be conducted on a single wheat cultivar to enable comparisons across experiments
-
rapid parallel evolution of azole fungicide resistance in australian populations of the wheat pathogen Zymoseptoria tritici
Applied and Environmental Microbiology, 2019Co-Authors: Megan C Mcdonald, Daniel Croll, Melanie Renkin, Merrin Spackman, Beverley Orchard, Peter S Solomon, Andrew MilgateAbstract:ABSTRACT Zymoseptoria tritici is a globally distributed fungal pathogen which causes Septoria tritici blotch on wheat. Management of the disease is attempted through the deployment of resistant wheat cultivars and the application of fungicides. However, fungicide resistance is commonly observed in Z. tritici populations, and continuous monitoring is required to detect breakdowns in fungicide efficacy. We recently reported azole-resistant isolates in Australia; however, it remained unknown whether resistance was brought into the continent through gene flow or whether resistance emerged independently. To address this question, we screened 43 isolates across five Australian locations for azole sensitivity and performed whole-genome sequencing on 58 isolates from seven locations to determine the genetic basis of resistance. Population genomic analyses showed extremely strong differentiation between the Australian population recovered after azoles began to be used and both Australian populations recovered before azoles began to be used and populations on different continents. The apparent absence of recent gene flow between Australia and other continents suggests that azole fungicide resistance has evolved de novo and subsequently spread within Tasmania. Despite the isolates being distinct at the whole-genome level, we observed combinations of nonsynonymous substitutions at the CYP51 locus identical to those observed elsewhere in the world. We observed nine previously reported nonsynonymous mutations as well as isolates that carried a combination of the previously reported L50S, S188N, A379G, I381V, Y459DEL, G460DEL, and N513K substitutions. Assays for the 50% effective concentration against a subset of isolates exposed to the tebuconazole and epoxiconazole fungicides showed high levels of azole resistance. The rapid, parallel evolution of a complex CYP51 haplotype that matches a dominant European haplotype demonstrates the enormous potential for de novo resistance emergence in pathogenic fungi. IMPORTANCE Fungicides are essential to control diseases in agriculture because many crops are highly susceptible to pathogens. However, many pathogens rapidly evolve resistance to fungicides. A large body of studies have described specific mutations conferring resistance and have often made inferences about the origins of resistance based on sequencing data from the target gene alone. Here, we show the de novo acquisition of resistance to the ubiquitously used azole fungicides in genetically isolated populations of the wheat pathogen Zymoseptoria tritici in Tasmania, Australia. We confirm evidence for parallel evolution through genome-scale analyses of representative worldwide populations. The emergence of complex resistance haplotypes following a well-documented recent introduction of azoles into Australian farming practices demonstrates how rapidly chemical resistance evolves in agricultural ecosystems.
-
genetic mapping of stb19 a new resistance gene to Zymoseptoria tritici in wheat
Theoretical and Applied Genetics, 2018Co-Authors: Nannan Yang, Megan C Mcdonald, Peter S Solomon, Andrew MilgateAbstract:A new and dominant R gene Stb19 is identified from a soft wheat cultivar ‘Lorikeet’ and was mapped on the distal region of chromosome 1DS. Two tightly linked KASP markers were also discovered and validated for molecular-assisted breeding programs. A new R gene, designated as Stb19, provides resistance to Zymoseptoria tritici in wheat. This new dominant gene resides on the short arm of chromosome 1D, exhibiting complete resistance to three Z. tritici isolates, WAI332, WAI251, and WAI161, at the seedling stage. A genetic linkage map, based on an F2:3 population of ‘Lorikeet’ and ‘Summit,’ found the Stb19 gene at a 9.3 cM region on 1DS, closely linked with two Kompetitive Allele-Specific PCR markers, snp_4909967 and snp_1218021. Further, the two markers were tested and validated in another F2:3 population and 266 different wheat accessions, which gave over 95% accuracy of resistance/susceptibility prediction. Combined with the physical location of the identified SNPs and the previous evidence of gene order on chromosome 1DS (centromere–Sr45–Sr33–Lr21–telomere), Stb19 is proposed to be located between Sr33 and Lr21. Thus, the newly discovered Stb19 along with the KASP markers represents an increase in genetic resources available for wheat breeding resistance to Z. tritici.
-
utilizing gene tree variation to identify candidate effector genes in Zymoseptoria tritici
G3: Genes Genomes Genetics, 2016Co-Authors: Megan C Mcdonald, Andrew Milgate, Lachlan Mcginness, James K Hane, Angela H Williams, Peter S SolomonAbstract:Zymoseptoria tritici is a host-specific, necrotrophic pathogen of wheat. Infection by Z. tritici is characterized by its extended latent period, which typically lasts 2 wks, and is followed by extensive host cell death, and rapid proliferation of fungal biomass. This work characterizes the level of genomic variation in 13 isolates, for which we have measured virulence on 11 wheat cultivars with differential resistance genes. Between the reference isolate, IPO323, and the 13 Australian isolates we identified over 800,000 single nucleotide polymorphisms, of which ∼10% had an effect on the coding regions of the genome. Furthermore, we identified over 1700 probable presence/absence polymorphisms in genes across the Australian isolates using de novo assembly. Finally, we developed a gene tree sorting method that quickly identifies groups of isolates within a single gene alignment whose sequence haplotypes correspond with virulence scores on a single wheat cultivar. Using this method, we have identified < 100 candidate effector genes whose gene sequence correlates with virulence toward a wheat cultivar carrying a major resistance gene.
Peter S Solomon - One of the best experts on this subject based on the ideXlab platform.
-
the identification of a transposon affecting the asexual reproduction of the wheat pathogen Zymoseptoria tritici
Molecular Plant Pathology, 2021Co-Authors: Chen Wang, Megan C Mcdonald, Peter S Solomon, Andrew MilgateAbstract:Zymoseptoria tritici, the causal agent of Septoria tritici blotch, is a fungal wheat pathogen that causes significant global yield losses. Within Z. tritici populations, quantitative differences in virulence among different isolates are commonly observed; however, the genetic components that underpin these differences remain elusive. In this study, intraspecific comparative transcriptomic analysis was used to identify candidate genes that contribute to differences in virulence on the wheat cultivar WW2449. This led to the identification of a multicopy gene that was not expressed in the high-virulence isolate when compared to the medium- and low-virulence isolates. Further investigation suggested this gene resides in a 7.9-kb transposon. Subsequent long-read sequencing of the isolates used in the transcriptomic analysis confirmed that this gene did reside in an active Class II transposon, which is composed of four genes named REP9-1 to -4. Silencing and overexpression of REP9-1 in two distinct genetic backgrounds demonstrated that its expression alone reduces the number of pycnidia produced by Z. tritici during infection. The REP9-1 gene identified within a Class II transposon is the first discovery of a gene in a transposable element that influences the virulence of Z. tritici. This discovery adds further complexity to genetic loci that contribute to quantitative virulence in this important pathogen.
-
extracellular vesicles from the apoplastic fungal wheat pathogen Zymoseptoria tritici
Fungal Biology and Biotechnology, 2020Co-Authors: Erin Hill, Peter S SolomonAbstract:The fungal pathogen Zymoseptoria tritici is a significant constraint to wheat production in temperate cropping regions around the world. Despite its agronomic impacts, the mechanisms allowing the pathogen to asymptomatically invade and grow in the apoplast of wheat leaves before causing extensive host cell death remain elusive. Given recent evidence of extracellular vesicles (EVs)—secreted, membrane-bound nanoparticles containing molecular cargo—being implicated in extracellular communication between plants and fungal pathogen, we have initiated an in vitro investigation of EVs from this apoplastic fungal wheat pathogen. We aimed to isolate EVs from Z. tritici broth cultures and examine their protein composition in relation to the soluble protein in the culture filtrate and to existing fungal EV proteomes. Zymoseptoria tritici EVs were isolated from broth culture filtrates using differential ultracentrifugation (DUC) and examined with transmission electron microscopy (TEM) and nanoparticle tracking analysis (NTA). Z. tritici EVs were observed as a heterogeneous population of particles, with most between 50 and 250 nm. These particles were found in abundance in the culture filtrates of viable Z. tritici cultures, but not heat-killed cultures incubated for an equivalent time and of comparable biomass. Bottom-up proteomic analysis using LC–MS/MS, followed by stringent filtering revealed 240 Z. tritici EV proteins. These proteins were distinct from soluble proteins identified in Z. tritici culture filtrates, but were similar to proteins identified in EVs from other fungi, based on sequence similarity analyses. Notably, a putative marker protein recently identified in Candida albicans EVs was also consistently detected in Z. tritici EVs. We have shown EVs can be isolated from the devastating fungal wheat pathogen Z. tritici and are similar to protein composition to previously characterised fungal EVs. EVs from human pathogenic fungi are implicated in virulence, but the role of EVs in the interaction of phytopathogenic fungi and their hosts is unknown. These in vitro analyses provide a basis for expanding investigations of Z. tritici EVs in planta, to examine their involvement in the infection process of this apoplastic wheat pathogen and more broadly, advance understanding of noncanonical secretion in filamentous plant pathogens.
-
MINI REVIEW ARTICLE Recent advances in the Zymoseptoria tritici -wheat interaction: insights from pathogenomics
2020Co-Authors: Megan C Mcdonald, Bruce A Mcdonald, Peter S Solomon, Adi Avni, Agriculture Guus Bakkeren, Agri-food Canada, Canada David, J StudholmeAbstract:We examine the contribution of next generation sequencing (NGS) to our understanding of the interaction between the fungal pathogen Zymoseptoria tritici and its wheat host. Recent interspecific whole genome comparisons between Z. tritici and its close relatives provide evidence that Z. tritici has undergone strong adaptive evolution, which is attributed to specialization by Z. tritici on wheat. We also assess the contribution of recent RNA sequencing datasets toward identifying pathogen genes and mechanisms critical for disease. While these studies have yet to report a major effector gene, they illustrate that assembling reads to the reference genome is a robust method to identify fungal transcripts from in planta infections. They also highlight the strong influence that the wheat cultivar has on effector gene expression. Lastly, we suggest future directions for NGS-guided approaches to address largely unanswered questions related to cultivar and lifecycle dependent gene expression and propose that future experiments with Z. tritici be conducted on a single wheat cultivar to enable comparisons across experiments
-
rapid parallel evolution of azole fungicide resistance in australian populations of the wheat pathogen Zymoseptoria tritici
Applied and Environmental Microbiology, 2019Co-Authors: Megan C Mcdonald, Daniel Croll, Melanie Renkin, Merrin Spackman, Beverley Orchard, Peter S Solomon, Andrew MilgateAbstract:ABSTRACT Zymoseptoria tritici is a globally distributed fungal pathogen which causes Septoria tritici blotch on wheat. Management of the disease is attempted through the deployment of resistant wheat cultivars and the application of fungicides. However, fungicide resistance is commonly observed in Z. tritici populations, and continuous monitoring is required to detect breakdowns in fungicide efficacy. We recently reported azole-resistant isolates in Australia; however, it remained unknown whether resistance was brought into the continent through gene flow or whether resistance emerged independently. To address this question, we screened 43 isolates across five Australian locations for azole sensitivity and performed whole-genome sequencing on 58 isolates from seven locations to determine the genetic basis of resistance. Population genomic analyses showed extremely strong differentiation between the Australian population recovered after azoles began to be used and both Australian populations recovered before azoles began to be used and populations on different continents. The apparent absence of recent gene flow between Australia and other continents suggests that azole fungicide resistance has evolved de novo and subsequently spread within Tasmania. Despite the isolates being distinct at the whole-genome level, we observed combinations of nonsynonymous substitutions at the CYP51 locus identical to those observed elsewhere in the world. We observed nine previously reported nonsynonymous mutations as well as isolates that carried a combination of the previously reported L50S, S188N, A379G, I381V, Y459DEL, G460DEL, and N513K substitutions. Assays for the 50% effective concentration against a subset of isolates exposed to the tebuconazole and epoxiconazole fungicides showed high levels of azole resistance. The rapid, parallel evolution of a complex CYP51 haplotype that matches a dominant European haplotype demonstrates the enormous potential for de novo resistance emergence in pathogenic fungi. IMPORTANCE Fungicides are essential to control diseases in agriculture because many crops are highly susceptible to pathogens. However, many pathogens rapidly evolve resistance to fungicides. A large body of studies have described specific mutations conferring resistance and have often made inferences about the origins of resistance based on sequencing data from the target gene alone. Here, we show the de novo acquisition of resistance to the ubiquitously used azole fungicides in genetically isolated populations of the wheat pathogen Zymoseptoria tritici in Tasmania, Australia. We confirm evidence for parallel evolution through genome-scale analyses of representative worldwide populations. The emergence of complex resistance haplotypes following a well-documented recent introduction of azoles into Australian farming practices demonstrates how rapidly chemical resistance evolves in agricultural ecosystems.
-
genetic mapping of stb19 a new resistance gene to Zymoseptoria tritici in wheat
Theoretical and Applied Genetics, 2018Co-Authors: Nannan Yang, Megan C Mcdonald, Peter S Solomon, Andrew MilgateAbstract:A new and dominant R gene Stb19 is identified from a soft wheat cultivar ‘Lorikeet’ and was mapped on the distal region of chromosome 1DS. Two tightly linked KASP markers were also discovered and validated for molecular-assisted breeding programs. A new R gene, designated as Stb19, provides resistance to Zymoseptoria tritici in wheat. This new dominant gene resides on the short arm of chromosome 1D, exhibiting complete resistance to three Z. tritici isolates, WAI332, WAI251, and WAI161, at the seedling stage. A genetic linkage map, based on an F2:3 population of ‘Lorikeet’ and ‘Summit,’ found the Stb19 gene at a 9.3 cM region on 1DS, closely linked with two Kompetitive Allele-Specific PCR markers, snp_4909967 and snp_1218021. Further, the two markers were tested and validated in another F2:3 population and 266 different wheat accessions, which gave over 95% accuracy of resistance/susceptibility prediction. Combined with the physical location of the identified SNPs and the previous evidence of gene order on chromosome 1DS (centromere–Sr45–Sr33–Lr21–telomere), Stb19 is proposed to be located between Sr33 and Lr21. Thus, the newly discovered Stb19 along with the KASP markers represents an increase in genetic resources available for wheat breeding resistance to Z. tritici.
Ethan L Stewart - One of the best experts on this subject based on the ideXlab platform.
-
quantitative trait locus mapping reveals complex genetic architecture of quantitative virulence in the wheat pathogen Zymoseptoria tritici
Molecular Plant Pathology, 2018Co-Authors: Ethan L Stewart, Daniel Croll, Andrea Sanchezvallet, Javier Palmaguerrero, Fanny E Hartmann, Mark H Lendenmann, Bruce A McdonaldAbstract:Summary We conducted a comprehensive analysis of virulence in the fungal wheat pathogen Zymoseptoria tritici using quantitative trait locus (QTL) mapping. High-throughput phenotyping based on automated image analysis allowed the measurement of pathogen virulence on a scale and with a precision that was not previously possible. Across two mapping populations encompassing more than 520 progeny, 540 710 pycnidia were counted and their sizes and grey values were measured. A significant correlation was found between pycnidia size and both spore size and number. Precise measurements of percentage leaf area covered by lesions provided a quantitative measure of host damage. Combining these large and accurate phenotypic datasets with a dense panel of restriction site-associated DNA sequencing (RADseq) genetic markers enabled us to genetically dissect pathogen virulence into components related to host damage and those related to pathogen reproduction. We showed that different components of virulence can be under separate genetic control. Large- and small-effect QTLs were identified for all traits, with some QTLs specific to mapping populations, cultivars and traits and other QTLs shared among traits within the same mapping population. We associated the presence of four accessory chromosomes with small, but significant, increases in several virulence traits, providing the first evidence for a meaningful function associated with accessory chromosomes in this organism. A large-effect QTL involved in host specialization was identified on chromosome 7, leading to the identification of candidate genes having a large effect on virulence.
-
an improved method for measuring quantitative resistance to the wheat pathogen Zymoseptoria tritici using high throughput automated image analysis
Phytopathology, 2016Co-Authors: Ethan L Stewart, Christopher C Mundt, Ziming Zhong, Christina H Hagerty, Alexey Mikaberidze, Bruce A McdonaldAbstract:Zymoseptoria tritici causes Septoria tritici blotch (STB) on wheat. An improved method of quantifying STB symptoms was developed based on automated analysis of diseased leaf images made using a flatbed scanner. Naturally infected leaves (n = 949) sampled from fungicide-treated field plots comprising 39 wheat cultivars grown in Switzerland and 9 recombinant inbred lines (RIL) grown in Oregon were included in these analyses. Measures of quantitative resistance were percent leaf area covered by lesions, pycnidia size and gray value, and pycnidia density per leaf and lesion. These measures were obtained automatically with a batch-processing macro utilizing the image-processing software ImageJ. All phenotypes in both locations showed a continuous distribution, as expected for a quantitative trait. The trait distributions at both sites were largely overlapping even though the field and host environments were quite different. Cultivars and RILs could be assigned to two or more statistically different groups for each measured phenotype. Traditional visual assessments of field resistance were highly correlated with quantitative resistance measures based on image analysis for the Oregon RILs. These results show that automated image analysis provides a promising tool for assessing quantitative resistance to Z. tritici under field conditions.
-
qtl mapping reveals complex genetic architecture of quantitative virulence in the wheat pathogen Zymoseptoria tritici
bioRxiv, 2016Co-Authors: Ethan L Stewart, Daniel Croll, Andrea Sanchezvallet, Javier Palmaguerrero, Fanny E Hartmann, Mark H Lendenmann, Bruce A McdonaldAbstract:We conducted a comprehensive analysis of virulence in the fungal wheat pathogen Zymoseptoria tritici using QTL mapping. High throughput phenotyping based on automated image analysis allowed measurement of pathogen virulence on a scale and with a precision that was not previously possible. Across two mapping populations encompassing more than 520 progeny, 540,710 pycnidia were counted and their sizes and grey values were measured, yielding over 1.6 million phenotypes associated with pathogen reproduction. Large pycnidia were shown to produce more numerous and larger spores than small pycnidia. Precise measures of percent leaf area covered by lesions provided a quantitative measure of host damage. Combining these large and accurate phenotype datasets with a dense panel of RADseq genetic markers enabled us to genetically dissect pathogen virulence into components related to host damage and components related to pathogen reproduction. We show that different components of virulence can be under separate genetic control. Large- and small-effect QTLs were identified for all traits, with some QTLs specific to mapping populations, cultivars and traits and other QTLs shared among traits within the same mapping population. We associated the presence or absence of accessory chromosomes with several virulence traits, providing the first evidence for an important function associated with accessory chromosomes in this organism. A large-effect QTL involved in host specialization was identified on chromosome 7, leading to identification of candidate genes having a large effect on virulence.
-
quantitative trait locus mapping of melanization in the plant pathogenic fungus Zymoseptoria tritici
G3: Genes Genomes Genetics, 2014Co-Authors: Mark H Lendenmann, Ethan L Stewart, Daniel Croll, Bruce A McdonaldAbstract:Melanin plays an important role in virulence and antimicrobial resistance in several fungal pathogens. The wheat pathogen Zymoseptoria tritici is important worldwide, but little is known about the genetic architecture of pathogenicity, including the production of melanin. Because melanin production can exhibit complex inheritance, we used quantitative trait locus (QTL) mapping in two crosses to identify the underlying genes. Restriction site−associated DNA sequencing was used to genotype 263 (cross 1) and 261 (cross 2) progeny at ~8500 single-nucleotide polymorphisms and construct two dense linkage maps. We measured gray values, representing degrees of melanization, for single-spore colonies growing on Petri dishes by using a novel image-processing approach that enabled high-throughput phenotyping. Because melanin production can be affected by stress, each offspring was grown in two stressful environments and one control environment. We detected six significant QTL in cross 1 and nine in cross 2, with three QTL shared between the crosses. Different QTL were identified in different environments and at different colony ages. By obtaining complete genome sequences for the four parents and analyzing sequence variation in the QTL confidence intervals, we identified 16 candidate genes likely to affect melanization. One of these candidates was PKS1, a polyketide synthase gene known to play a role in the synthesis of dihydroxynaphthalene melanin. Three candidate quantitative trait nucleotides were identified in PKS1. Many of the other candidate genes were not previously associated with melanization.
-
measuring quantitative virulence in the wheat pathogen Zymoseptoria tritici using high throughput automated image analysis
Phytopathology, 2014Co-Authors: Ethan L Stewart, Bruce A McdonaldAbstract:Zymoseptoria tritici, causal agent of Septoria tritici blotch on wheat, produces pycnidia in chlorotic and necrotic lesions on infected leaves. A high-throughput phenotyping method was developed based on automated digital image analysis that accurately measures the percentage of leaf area covered by lesions (PLACL) as well as pycnidia size and number. A seedling inoculation assay was conducted using 361 Z. tritici isolates originating from a controlled cross and two different winter wheat cultivars. Pycnidia size and density were found to be quantitative traits that showed a continuous distribution in the progeny. There was a weak correlation between pycnidia density and size (r = -0.27) and between pycnidia density and PLACL (r = 0.37). There were significant differences in PLACL and pycnidia density on resistant and susceptible cultivars. In all, >20% of the offspring exhibited significantly different pycnidia density on the two cultivars, consistent with host specialization. Automated image analysis provided greater accuracy and precision compared with traditional visual estimates of virulence. These results show that digital image analysis provides a powerful tool for measuring differences in quantitative virulence among strains of Z. tritici.
