Global genotype flow in Cercospora beticola populations confirmed through genotyping-by-sequencing

Genome-wide Evidence of Host Specialization in Wild and Farmland Populations of the Fungal Leaf Spot Pathogen, Cercospora beticola

One of the most recent crop species to be domesticated is sugar beet (Beta vulgaris L. ssp. vulgaris Doell.), which was bred for high sucrose content within the last few centuries in Europe. Crop domestication can also lead to the evolution of novel pathogens, which may spread across large geographical distances with their crop host. In this study, we addressed the recent evolution of the fungal pathogen causing the disease Cercospora leaf spot, Cercospora beticola. This pathogen has become increasingly important in sugar beet and table beet production worldwide. We used genome sequences of 326 C. beticola isolates collected from 4 continents from 4 closely related Beta subspecies (3 domesticated and 1 wild). We applied population genomic analyses to identify signatures of population differentiation and host specialization in C. beticola populations derived from the cultivated and wild hosts. We found evidence that C. beticola populations in agro-ecosystems likely originate from sea beet-infecting isolates. Intriguingly, host jumps from wild to cultivated beet occurred in at least 2 independent events as evidenced by our population data of C. beticola from wild beet collected in the Mediterranean and the UK. We explore the occurrence of genetic variants associated with fungicide resistance and virulence and show that standing genetic variation in C. beticola populations from both wild and domesticated plants may serve as a reservoir of functionally important alleles. Overall, our results highlight the ability of C. beticola to invade the agro-ecosystem and establish new populations, demonstrating the rapid adaptation potential of the species.

Identification of Cercospora spp. on Corn in North America and Baseline Flutriafol Fungicide Sensitivity

Gray leaf spot (GLS) is an important corn disease reportedly caused by Cercospora zeae-maydis and C. zeina. Recently, flutriafol, a demethylation inhibitor (azole) fungicide, received Environmental Protection Agency registration as Xyway LFR, a product that is applied at planting for management of fungal diseases in corn, including suppression of GLS. In this study, 448 Cercospora spp. isolates were collected in 2020 and 2021 from symptomatic corn leaf samples submitted from the United States and Ontario, Canada. The Cercospora spp. were identified using multilocus genotyping of the internal transcribed spacer, elongation factor 1-α, calmodulin, histone H3, and actin genes. Based on the multilocus phylogenetic analyses, six species were identified; C. cf. flagellaris (n = 77), C. kikuchii (n = 4), C. zeae-maydis (n = 361), Cercospora sp. M (n = 2), Cercospora sp. Q (n = 1), and Cercospora sp. T (n = 3). In subsequent pathogenicity tests using selected isolates from each of these species, only C. zeae-maydis resulted in symptoms on corn, with no disease symptoms observed after inoculation with C. cf. flagellaris, C. kikuchii, Cercospora sp. M, Cercospora sp. Q, and Cercospora sp. T. Disease symptoms were observed on soybean following inoculation with C. cf. flagellaris, C. kikuchii, and Cercospora sp. Q, but not the other three species. Fungicide sensitivity of Cercospora spp. to flutriafol was assessed using a subset of 340 isolates. The minimum inhibitory concentration (MIC) to inhibit the growth of Cercospora spp. completely was determined based on growth of each species on flutriafol-amended clarified V8 agar at nine concentrations. The effective concentration of fungicide required for 50% growth inhibition (EC50) was also calculated from the same trial by measuring relative growth as compared with the nonamended control. Cercospora zeae-maydis was sensitive to flutriafol, with mean MIC values of 2.5 μg/ml and EC50 values ranging from 0.016 to 1.020 μg/ml with a mean of 0.346 μg/ml. Cercospora cf. flagellaris, C. kikuchii, Cercospora sp. M, Cercospora sp. Q, and Cercospora sp. T had mean EC50 values of 1.25, 7.14, 2.48, 1.81, and 2.24 μg/ml, respectively. These findings will assist in monitoring the sensitivity to the flutriafol fungicide in Cercospora spp. populations.

Population-level whole-genome sequencing of Ascochyta rabiei identifies genomic loci associated with isolate aggressiveness

Ascochyta blight caused by the ascomycete Ascochyta rabiei poses a major biotic threat to chickpea (Cicer arietinum) industries worldwide and incurs substantial costs to the Australian multimillion-dollar chickpea industry in both disease control and yield loss. The fungus was introduced to Australia in the 1970s from an unknown source population and, within a few decades, successfully established in all Australian agroecological chickpea-growing regions. Although genetically highly clonal, a broad range of phenotypic variation in terms of aggressiveness exists among the Australian A. rabiei isolates. More recently, highly aggressive isolates capable of causing severe disease symptoms on moderate to highly resistant chickpea cultivars have increased in frequency. To identify genetic loci potentially associated with A. rabiei aggressiveness on Australian chickpea cultivars, we performed deep genome sequencing of 230 isolates collected from a range of agroecological chickpea-growing regions between 2013 and 2020. Population genetic analyses using genome-wide SNP data identified three main clusters of genetically closely related isolates in Australia. Phylogenetic analyses showed that highly aggressive phenotypes developed multiple times independently throughout the phylogeny. The results point to a minor contribution of multiple genetic regions and most likely epigenomic variations to aggressiveness of A. rabiei isolates on Australian chickpea cultivars.

Nighttime Applications of Germicidal UV Light to Suppress Cercospora Leaf Spot in Table Beet

Cercospora leaf spot (CLS), caused by the hemibiotrophic fungus Cercospora beticola, is a destructive disease affecting table beet. Multiple applications of fungicides are needed to reduce epidemic progress to maintain foliar health and enable mechanized harvest. The sustainability of CLS control is threatened by the rapid development of fungicide resistance, the need to grow commercially acceptable yet CLS-susceptible cultivars, and the inability to manipulate agronomic conditions to mitigate disease risk. Nighttime applications of germicidal UV light (UV-C) have recently been used to suppress several plant diseases, notably those caused by ectoparasitic biotrophs such as powdery mildews. We evaluated the efficacy of nighttime applications of UV-C for suppression of CLS in table beet. In vitro lethality of UV-C to germinating conidia increased with increasing dose, with complete suppression at 1,000 J/m2. Greenhouse-grown table beet tolerated relatively high doses of UV-C without lethal effects despite some bronzing on the leaf blade. A UV-C dose >1,500 J/m2 resulted in phytotoxicity severities greater than 50%. UV-C exposure to ≤750 J/m2 resulted in negligible phytotoxicity. Older (6-week-old) greenhouse-grown plants were more susceptible to UV-C damage than younger (2- and 4-week-old) plants. Suppression of CLS by UV-C was greater when applied within 6 days of C. beticola inoculation than if delayed until 13 days after infection in greenhouse-grown plants. In field trials, there were significant linear relationships between UV-C dose and CLS control and phytotoxicity severity, and a significant negative linear relationship between phytotoxicity and CLS severity at the final assessment. Significant differences between UV-C doses on the severity of CLS and phytotoxicity indicated an efficacious dose near 800 J/m2. Collectively, these findings illustrate significant and substantial suppression by nighttime applications of UV-C for CLS control on table beet, with potential for incorporation in both conventional and organic table beet broadacre production systems.

GWAS reveals a rapidly evolving candidate avirulence effector in the Cercospora leaf spot pathogen

The major resistance gene BvCR4 recently bred into sugar beet hybrids provides a high level of resistance to Cercospora leaf spot caused by the fungal pathogen Cercospora beticola. The occurrence of pathogen strains that overcome BvCR4 was studied using field trials in Switzerland conducted under natural disease pressure. Virulence of a subset of these strains was evaluated in a field trial conducted under elevated artificial disease pressure. We created a new C. beticola reference genome and mapped whole genome sequences of 256 isolates collected in Switzerland and Germany. These were combined with virulence phenotypes to conduct three separate genome-wide association studies (GWAS) to identify candidate avirulence genes. We identified a locus associated with avirulence containing a putative avirulence effector gene named AvrCR4. All virulent isolates either lacked AvrCR4 or had nonsynonymous mutations within the gene. AvrCR4 was present in all 74 isolates from non-BvCR4 hybrids, whereas 33 of 89 isolates from BvCR4 hybrids carried a deletion. We also mapped genomic data from 190 publicly available US isolates to our new reference genome. The AvrCR4 deletion was found in only one of 95 unique isolates from non-BvCR4 hybrids in the United States. AvrCR4 presents a unique example of an avirulence effector in which virulent alleles have only recently emerged. Most likely these were selected out of standing genetic variation after deployment of BvCR4. Identification of AvrCR4 will enable real-time screening of C. beticola populations for the emergence and spread of virulent isolates.

Cercospora leaf spot disease of sugar beet

Leaf spot disease caused by Cercospora beticola Sacc. is the most damaging foliar disease threatening sugar beet production worldwide. The wide spread of disease incurs a reduction of yield and economic losses. The in-depth knowledge of disease epidemiology and virulence factor of pathogen is crucial and basic for preventing fungal disease. The integrated control strategies are needed for an efficient and sustainable disease management. The rotation of fungicides and crop could reduce the initial inoculum and delay the emergence of resistant pathogens. Spraying fungicides under the guide of forecasting models and molecular detecting techniques may hinder the onset of disease prevalence. The resistant varieties of sugar beet to cercospora leaf spot could be obtained by combining classical and molecular breeding methods. More effective approaches are supposed to develop for prevention and control for fungal disease of sugar beet.

An in-field heat treatment to reduce Cercospora beticola survival in plant residue and improve Cercospora leaf spot management in sugarbeet

Introduction

Sugarbeets account for 55 to 60% of U.S. sugar production. Cercospora leaf spot (CLS), primarily caused by the fungal pathogen Cercospora beticola, is a major foliar disease of sugarbeet. Since leaf tissue is a primary site of pathogen survival between growing seasons, this study evaluated management strategies to reduce this source of inoculum.

Methods

Fall- and spring-applied treatments were evaluated over three years at two study sites. Treatments included standard plowing or tilling immediately post-harvest, as well as the following alternatives to tillage: a propane-fueled heat treatment either in the fall immediately pre-harvest or in the spring prior to planting, and a desiccant (saflufenacil) application seven days pre-harvest. After fall treatments, leaf samples were evaluated to determine C. beticola viability. The following season, inoculum pressure was measured by monitoring CLS severity in a susceptible beet variety planted into the same plots and by counting lesions on highly susceptible sentinel beets placed into the field at weekly intervals (fall treatments only).

Results

No significant reductions in C. beticola survival or CLS were observed following fall-applied desiccant. The fall heat treatment, however, significantly reduced lesion sporulation (2019-20 and 2020-21, P < 0.0001; 2021-22, P < 0.05) and C. beticola isolation (2019-20, P < 0.05) in at-harvest samples. Fall heat treatments also significantly reduced detectable sporulation for up to 70- (2021-22, P < 0.01) or 90-days post-harvest (2020-21, P < 0.05). Reduced numbers of CLS lesions were observed on sentinel beets in heat-treated plots from May 26-June 2 (P < 0.05) and June 2-9 (P < 0.01) in 2019, as well as June 15-22 (P < 0.01) in 2020. Both fall- and spring-applied heat treatments also reduced the area under the disease progress curve for CLS assessed the season after treatments were applied (Michigan 2020 and 2021, P < 0.05; Minnesota 2019, P < 0.05; 2021, P < 0.0001).

Discussion

Overall, heat treatments resulted in CLS reductions at levels comparable to standard tillage, with more consistent reductions across year and location. Based on these results, heat treatment of fresh or overwintered leaf tissue could be used as an integrated tillage-alternative practice to aid in CLS management.

Seedborne Cercospora beticola Can Initiate Cercospora Leaf Spot from Sugar Beet (Beta vulgaris) Fruit Tissue

Cercospora leaf spot (CLS) is a globally important disease of sugar beet (Beta vulgaris) caused by the fungus Cercospora beticola. Long-distance movement of C. beticola has been indirectly evidenced in recent population genetic studies, suggesting potential dispersal via seed. Commercial sugar beet "seed" consists of the reproductive fruit (true seed surrounded by maternal pericarp tissue) coated in artificial pellet material. In this study, we confirmed the presence of viable C. beticola in sugar beet fruit for 10 of 37 tested seed lots. All isolates harbored the G143A mutation associated with quinone outside inhibitor resistance, and 32 of 38 isolates had reduced demethylation inhibitor sensitivity (EC₅₀ > 1 µg/ml). Planting of commercial sugar beet seed demonstrated the ability of seedborne inoculum to initiate CLS in sugar beet. C. beticola DNA was detected in DNA isolated from xylem sap, suggesting the vascular system is used to systemically colonize the host. We established nuclear ribosomal internal transcribed spacer region amplicon sequencing using the MinION platform to detect fungi in sugar beet fruit. Fungal sequences from 19 different genera were identified from 11 different sugar beet seed lots, but Fusarium, Alternaria, and Cercospora were consistently the three most dominant taxa, comprising an average of 93% relative read abundance over 11 seed lots. We also present evidence that C. beticola resides in the pericarp of sugar beet fruit rather than the true seed. The presence of seedborne inoculum should be considered when implementing integrated disease management strategies for CLS of sugar beet in the future.

Population Structure of Pyrenophora teres f. teres Barley Pathogens from Different Continents

Net form net blotch disease, caused by Pyrenophora teres f. teres, results in significant yield losses to barley industries. Up-to-date knowledge of the genetic diversity and structure of pathogen populations is critical for elucidating the disease epidemiology and unraveling pathogen survival and dispersal mechanisms. Thus, this study investigated long-distance dispersal and adaptation by analyzing the genetic structure of 250 P. teres f. teres isolates collected from Australia, Canada, Hungary, and Republic of South Africa (RSA), and historical isolates from Canada, Denmark, Japan, and Sweden. The population genetic structure detected by discriminant analysis of principal components, with the use of 5,890 Diversity Arrays Technology markers, revealed the presence of four clusters. Two of these contained isolates from all regions, and all isolates from RSA were grouped in these two. Australia and Hungary showed three clusters each. One of the Australian clusters contained only Australian isolates. One of the Hungarian clusters contained only Hungarian isolates and one Danish isolate. STRUCTURE analysis indicated that some isolates from Australia and Hungary shared recent ancestry with RSA, Canada, and historical isolates and were thus admixed. Subdivisions of the neighbor joining network indicated that isolates from distinct countries were closely related, suggesting that multiple introduction events conferred genetic heterogeneity in these countries. Through a neighbor joining analysis and amplification with form-specific DNA markers, we detected two hybrid isolates, CBS 281.31 from Japan and H-919 from Hungary, collected in 1931 and 2018, respectively. These results provide a foundation for exploring improved management of disease incursions and pathogen control through strategic deployment of resistance.

Cercospora beticola: The intoxicating lifestyle of the leaf spot pathogen of sugar beet

Cercospora leaf spot, caused by the fungal pathogen Cercospora beticola, is the most destructive foliar disease of sugar beet worldwide. This review discusses C. beticola genetics, genomics, and biology and summarizes our current understanding of the molecular interactions that occur between C. beticola and its sugar beet host. We highlight the known virulence arsenal of C. beticola as well as its ability to overcome currently used disease management strategies. Finally, we discuss future prospects for the study and management of C. beticola infections in the context of newly employed molecular tools to uncover additional information regarding the biology of this pathogen.

TAXONOMY

Cercospora beticola Sacc.; Kingdom Fungi, Phylum Ascomycota, Class Dothideomycetes, Order Capnodiales, Family Mycosphaerellaceae, Genus Cercospora.

HOST RANGE

Well-known pathogen of sugar beet (Beta vulgaris subsp. vulgaris) and most species of the Beta genus. Reported as pathogenic on other members of the Chenopodiaceae (e.g., lamb's quarters, spinach) as well as members of the Acanthaceae (e.g., bear's breeches), Apiaceae (e.g., Apium), Asteraceae (e.g., chrysanthemum, lettuce, safflower), Brassicaceae (e.g., wild mustard), Malvaceae (e.g., Malva), Plumbaginaceae (e.g., Limonium), and Polygonaceae (e.g., broad-leaved dock) families.

DISEASE SYMPTOMS

Leaves infected with C. beticola exhibit circular lesions that are coloured tan to grey in the centre and are often delimited by tan-brown to reddish-purple rings. As disease progresses, spots can coalesce to form larger necrotic areas, causing severely infected leaves to wither and die. At the centre of these spots are black spore-bearing structures (pseudostromata). Older leaves often show symptoms first and younger leaves become infected as the disease progresses.

MANAGEMENT

Application of a mixture of fungicides with different modes of action is currently performed although elevated resistance has been documented in most employed fungicide classes. Breeding for high-yielding cultivars with improved host resistance is an ongoing effort and prudent cultural practices, such as crop rotation, weed host management, and cultivation to reduce infested residue levels, are widely used to manage disease. USEFUL WEBSITE: https://www.ncbi.nlm.nih.gov/genome/11237?genome_assembly_id=352037.

Detection of Cercospora beticola and Phoma betae on Table Beet Seed using Quantitative PCR

Cercospora beticola and Phoma betae are important pathogens of table beet, sugar beet, and Swiss chard (Beta vulgaris subsp. vulgaris), causing Cercospora leaf spot (CLS) and Phoma leaf spot, root rot, and damping-off, respectively. Both pathogens may be seedborne; however, limited evidence is available for seed infestation by C. beticola. Due to the limitations of culture-based seed assessment methods, detection of these pathogens was investigated using PCR. A P. betae-specific quantitative PCR assay was developed and used in conjunction with a C. beticola-specific assay to assess the presence of pathogen DNA in 12 table beet seed lots. DNA of C. beticola and P. betae was detected in four and eight seed lots, respectively. Plate tests and BIO-PCR confirmed the viability of each pathogen; however, competitive growth of other microbes and low incidence limited the frequency and sensitivity of detection in some seed lots. The results for P. betae support previously described infestation of seed. Further investigation of C. beticola-infested seed lots indicated the ability of seedborne C. beticola to cause CLS on plants grown from infested seed. Detection of viable C. beticola on table beet seed demonstrates the potential for pathogen dispersal and disease initiation via infested seed, and provides valuable insight into the epidemiology of CLS. Surveys of commercial table beet seed are required to determine the frequency and source of C. beticola seed infestation and its role as primary inoculum for epidemics, and to evaluate the effectiveness of seed treatments.

Genetic Diversity and Structure in Regional Cercospora beticola Populations from Beta vulgaris subsp. vulgaris Suggest Two Clusters of Separate Origin

Cercospora leaf spot, caused by Cercospora beticola, is a highly destructive disease of Beta vulgaris subsp. vulgaris worldwide. C. beticola populations are usually characterized by high genetic diversity, but little is known of the relationships among populations from different production regions around the world. This information would be informative of population origin and potential pathways for pathogen movement. For the current study, the genetic diversity, differentiation, and relationships among 948 C. beticola isolates in 28 populations across eight geographic regions were investigated using 12 microsatellite markers. Genotypic diversity, as measured by Simpson's complement index, ranged from 0.18 to 1.00, while pairwise index of differentiation values ranged from 0.02 to 0.42, with the greatest differentiation detected between two New York populations. In these populations, evidence for recent expansion was detected. Assessment of population structure identified two major clusters: the first associated with New York, and the second with Canada, Chile, Eurasia, Hawaii, Michigan, North Dakota, and one population from New York. Inferences of gene flow among these regions suggested that the source for one cluster likely is Eurasia, whereas the source for the other cluster is not known. These results suggest a shared origin of C. beticola populations across regions, except for part of New York, where population divergence has occurred. These findings support the hypothesis that dispersal of C. beticola occurs over long distances.

Temporal Genetic Differentiation of Cercospora beticola Populations in New York Table Beet Fields

Annual epidemics of Cercospora leaf spot (CLS), caused by the fungus Cercospora beticola, can result in substantial defoliation in table beet fields in New York. High allelic and genotypic diversity have been described within C. beticola populations; however, information on the temporal stability of populations is lacking. C. beticola isolates were obtained from symptomatic leaves in three table beet fields in successive years. Two of the fields were organic mixed-cropping farms and the third was managed conventionally in a broad-acre cropping system. C. beticola isolates (n = 304) were genotyped using 12 microsatellite markers. Genotypic diversity (Simpson's complement index = 0.178 to 0.990), allele frequencies, and indices of differentiation between years varied. Pairwise index of differentiation values ranged from 0.02 to 0.25 for clone-corrected data, and indicated significant genetic differentiation at Farm 2. No multilocus genotype was shared between years. The shift in multilocus genotypes between years questions the role of clonally reproducing primary inoculum. Collectively, these results suggest that a dominant inoculum source for initiating annual CLS epidemics is external to the field of interest. These findings have implications for CLS disease management in conventional and organic table beet production.

IMA Genome-F 9: Draft genome sequence of Annulohypoxylon stygium, Aspergillus mulundensis, Berkeleyomyces basicola (syn. Thielaviopsis basicola), Ceratocystis smalleyi, two Cercospora beticola strains, Coleophoma cylindrospora, Fusarium fracticaudum, Phialophora cf. hyalina, and Morchella septimelata

Draft genomes of the species Annulohypoxylon stygium, Aspergillus mulundensis, Berkeleyomyces basicola (syn. Thielaviopsis basicola), Ceratocystis smalleyi, two Cercospora beticola strains, Coleophoma cylindrospora, Fusarium fracticaudum, Phialophora cf. hyalina and Morchella septimelata are presented. Both mating types (MAT1-1 and MAT1-2) of Cercospora beticola are included. Two strains of Coleophoma cylindrospora that produce sulfated homotyrosine echinocandin variants, FR209602, FR220897 and FR220899 are presented. The sequencing of Aspergillus mulundensis, Coleophoma cylindrospora and Phialophora cf. hyalina has enabled mapping of the gene clusters encoding the chemical diversity from the echinocandin pathways, providing data that reveals the complexity of secondary metabolism in these different species. Overall these genomes provide a valuable resource for understanding the molecular processes underlying pathogenicity (in some cases), biology and toxin production of these economically important fungi.

Cryptic diversity, pathogenicity, and evolutionary species boundaries in Cercospora populations associated with Cercospora leaf spot of Beta vulgaris

The taxonomy and evolutionary species boundaries in a global collection of Cercospora isolates from Beta vulgaris was investigated based on sequences of six loci. Species boundaries were assessed using concatenated multi-locus phylogenies, Generalized Mixed Yule Coalescent (GMYC), Poisson Tree Processes (PTP), and Bayes factor delimitation (BFD) framework. Cercospora beticola was confirmed as the primary cause of Cercospora leaf spot (CLS) on B. vulgaris. Cercospora apii, C. cf. flagellaris, Cercospora sp. G, and C. zebrina were also identified in association with CLS on B. vulgaris. Cercospora apii and C. cf. flagellaris were pathogenic to table beet but Cercospora sp. G and C. zebrina did not cause disease. Genealogical concordance phylogenetic species recognition, GMYC and PTP methods failed to differentiate C. apii and C. beticola as separate species. On the other hand, multi-species coalescent analysis based on BFD supported separation of C. apii and C. beticola into distinct species; and provided evidence of evolutionary independent lineages within C. beticola. Extensive intra- and intergenic recombination, incomplete lineage sorting and dominance of clonal reproduction complicate evolutionary species recognition in the genus Cercospora. The results warrant morphological and phylogenetic studies to disentangle cryptic speciation within C. beticola.