Draft Genome Sequences of the Turfgrass Pathogen Sclerotinia homoeocarpa

A one-step multiplex PCR assay for the detection and differentiation of four species of Clarireedia causing dollar spot on turfgrass

BACKGROUND

Dollar spot (DS) is one of the most destructive and economically important diseases of cool- and warm-season turfgrasses worldwide. A total of six species causing DS disease in the genus Clarireedia have been described, and four of them have been reported to be distributed countrywide in China. Identification of different species of Clarireedia is a prerequisite for the effective management of DS disease.

RESULTS

Here we report a novel polymerase chain reaction (PCR)-based method for the detection and differentiation of the four species of Clarireedia associated with DS on turfgrass in China: C. jacksonii, C. paspali, C. monteithiana and C. hainanense. Species-specific genes were identified for each species by comparative genomics analysis. Four primer pairs were designed and mixed to amplify species-specific PCR fragments with differential sizes for the four species of Clarireedia in a single multiplex PCR assay. No PCR products were generated from the DNA templates of other common fungal pathogens associated with multiple turfgrass diseases. The multiplex PCR method developed can be used for the rapid and accurate detection and differentiation of the four species of Clarireedia from pure cultures as well as from infected turfgrass blades with DS symptoms.

CONCLUSION

The study developed a one-step multiplex PCR assay for the detection and differentiation of four species of Clarireedia causing DS on turfgrass in China, which will have important implications for DS management in China and worldwide. © 2022 Society of Chemical Industry.

Genome Resources for Four Clarireedia Species Causing Dollar Spot on Diverse Turfgrasses

Dollar spot (DS) is a destructive fungal disease impacting almost all warm- and cool-season turfgrasses worldwide. Multiple fungal species in the genus Clarireedia are causal agents of DS. Here, we present whole-genome assemblies of nine fungal isolates in the genus Clarireedia, including four species (C. paspali, C. hainanense, C. jacksonii, and C. monteithiana) causing DS on seashore paspalum (Paspalum vaginatum Sw.), creeping bentgrass (Agrostis stolonifera L.), and Kentucky bluegrass (Poa pratensis L.) in China. This work provides valuable baseline genomic data to support further research and management of DS pathogens on turfgrasses.

Whole genome sequencing of Clarireedia aff. paspali reveals potential pathogenesis factors in Clarireedia species, causal agents of dollar spot in turfgrass

Dollar spot is one of the most damaging diseases in turfgrass, reducing its quality and playability. Two species, Clarireedia monteithiana and C. jacksonii (formerly Sclerotinia homoeocarpa) have been reported so far in the United States To study the Clarireedia genome, two isolates H2 and H3, sampled from seashore paspalum in Hawaii in 2019 were sequenced via Illumina paired-end sequencing by synthesis technology and PacBio SMRT sequencing. Both isolates were identified as C. aff. paspali, a novel species in the United States Using short and long reads, C. aff. paspali H3 contained 193 contigs with 48.6 Mbp and presented the most completed assembly and annotation among Clarireedia species. Out of the 13,428 protein models from AUGUSTUS, 349 cytoplasmic effectors and 13 apoplastic effectors were identified by EffectorP. To further decipher Clarireedia pathogenicity, C. aff. paspali genomes (H2 and H3), as well as available C. jacksonii (LWC-10 and HRI11), C. monteithiana (DRR09 and RB-19) genomes were screened for fifty-four pathogenesis determinants, previously identified in S. sclerotiorum. Seventeen orthologs of pathogenicity genes have been identified in Clarireedia species involved in oxalic acid production (pac1, nox1), mitogen-activated protein kinase cascade (pka1, smk3, ste12), appressorium formation (caf1, pks13, ams2, rgb1, rhs1) and glycolytic pathway (gpd). Within these genes, 366 species-specific SNPs were recorded between Clarireedia species; twenty-eight were non-synonymous and non-conservative. The predicted protein structure of six of these genes showed superimposition of the models among Clarireedia spp. The genomic variations revealed here could potentially lead to differences in pathogenesis and other physiological functions among Clarireedia species.

New Approaches to an Old Problem: Dollar Spot of Turfgrass

Dollar spot, caused by fungal pathogens Clarireedia spp. (formerly Sclerotinia homoeocarpa), is the most common and widely distributed disease of turfgrass worldwide. It can drastically reduce the quality of turfgrass species and affect their aesthetic value and playability. Management of dollar spot typically includes a costly program of multiple application of fungicides within a growing season. Consequently, there have been reported cases of fungicide resistance in populations of Clarireedia spp. Host resistance could be an important component of dollar spot management; however, this approach has been hampered by the lack of sources of resistance because nearly all known warm- and cool-season turfgrass species are susceptible. With the recent advancement in genome sequencing technologies, studies on pathogen genomics and host-pathogen interactions are emerging with the hope of revealing candidate resistance genes in turfgrass and genes for virulence and pathogenicity in Clarireedia spp. Large-scale screening of turfgrass germplasm and quantitative trait locus (QTL) analysis for dollar spot resistance are important for resistance breeding, but only a handful of such studies have been conducted to date. This review summarizes currently available information on the dollar spot pathosystem, taxonomy, pathogen genomics, host-pathogen interaction, genetics of resistance, and QTL mapping and also provides some thoughts for future research prospects to better manage this disease.

Genome Resources for Seven Fungal Isolates That Cause Dollar Spot Disease in Turfgrass, Including Clarireedia jacksonii and C. monteithiana

Fungi in the genus Clarireedia are widespread and destructive pathogens of grasses worldwide, and are best known as the causal agents of dollar spot disease in turfgrass. Here, we report genome assemblies of seven Clarireedia isolates, including ex-types of the two most widespread species, Clarireedia jacksonii and C. monteithiana. These datasets provide a valuable resource for ongoing studies of the dollar spot pathogens that include population diversity, host-pathogen interactions, marker development, and disease control.

Prediction of pathogenicity genes involved in adaptation to a lupin host in the fungal pathogens Botrytis cinerea and Sclerotinia sclerotiorum via comparative genomics

Background

Narrow-leafed lupin is an emerging crop of significance in agriculture, livestock feed and human health food. However, its susceptibility to various diseases is a major obstacle towards increased adoption. Sclerotinia sclerotiorum and Botrytis cinerea – both necrotrophs with broad host-ranges - are reported among the top 10 lupin pathogens. Whole-genome sequencing and comparative genomics are useful tools to discover genes responsible for interactions between pathogens and their hosts.

Results

Genomes were assembled for one isolate of B. cinerea and two isolates of S. sclerotiorum, which were isolated from either narrow-leafed or pearl lupin species. Comparative genomics analysis between lupin-derived isolates and others isolated from alternate hosts was used to predict between 94 to 98 effector gene candidates from among their respective non-conserved gene contents.

Conclusions

Detection of minor differences between relatively recently-diverged isolates, originating from distinct regions and with hosts, may highlight novel or recent gene mutations and losses resulting from host adaptation in broad host-range fungal pathogens.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5774-2) contains supplementary material, which is available to authorized users.

Resistance of Sclerotinia homoeocarpa Field Isolates to Succinate Dehydrogenase Inhibitor Fungicides

Sclerotinia homoeocarpa isolates were collected from golf courses in Japan and the United States (2016-2017). Japan isolates were collected during a monitoring study and the U.S. isolates were collected due to field failure. Five succinate dehydrogenase inhibitor (SDHI) active ingredients (boscalid, fluopyram, fluxapyroxad, isofetamid, and penthiopyrad) were examined using in vitro sensitivity assays to determine cross-resistance. Sequence analysis revealed a point mutation leading to an amino acid substitution (H267Y) and a silent mutation (CTT to CTC) at codon 181 in the SdhB subunit gene. Isolates with the B-H267Y (n = 10) mutation were resistant to boscalid and penthiopyrad and had increased sensitivity to fluopyram. SdhB silent mutation 181C>T isolates (n = 2) were resistant to boscalid, isofetamid, and penthiopyrad. Sequence analysis revealed 3 mutations leading to an amino acid substitution (G91R, n = 5; G150R, n = 1; G159W, n = 1) in the SdhC subunit gene. Isolates harboring the SdhC (G91R or G150R) mutations were resistant to boscalid, fluxapyroxad, isofetamid, and penthiopyrad. A genetic transformation system was used to generate mutants from a SDHI sensitive isolate to confirm the B-H267Y and C-G91R mutations were direct determinants of SDHI resistance and associated with in vitro sensitivity assay results.

Thiophanate-methyl resistance in Sclerotinia homoeocarpa from golf courses in China

Sclerotinia homoeocarpa causes dollar spot disease on many turfgrass species and is a significant problem worldwide. Thiophanate-methyl (TM), a methyl benzimidazole carbamate (MBC) fungicide, has been used for over forty years to manage dollar spot. Here we describe genetic mutations linked to three distinct TM fungicide resistance phenotypes: sensitive (S), moderately resistant (MR) and highly resistant (HR). These were established using multiple doses of TM, compared to previous studies using single discriminatory doses. In total, 19 S, 3 MR and 22 HR isolates were detected. Analysis of the β-tubulin gene revealed the MR isolates had a point mutation from T to A at codon 200 changing phenylalanine (TTC) to tyrosine (TAC). Twenty HR isolates had a mutation at codon 198 changing glutamic acid (GAG) to alanine (GCG) and two HR isolates had a mutation at codon 198 changing glutamic acid (GAG) to lysine (AAG). Allele-specific PCR assays were developed for rapid detection of these mutations in isolates of S. homoeocarpa. In addition, our results suggest a two-dose system for in vitro screening provides useful information for monitoring the development of resistance.

A Xenobiotic Detoxification Pathway through Transcriptional Regulation in Filamentous Fungi

Fungi are known to utilize transcriptional regulation of genes that encode efflux transporters to detoxify xenobiotics; however, to date it is unknown how fungi transcriptionally regulate and coordinate different phases of detoxification system (phase I, modification; phase II, conjugation; and phase III, secretion). Here we present evidence of an evolutionary convergence between the fungal and mammalian lineages, whereby xenobiotic detoxification genes (phase I coding for cytochrome P450 monooxygenases [CYP450s] and phase III coding for ATP-binding cassette [ABC] efflux transporters) are transcriptionally regulated by structurally unrelated proteins. Following next-generation RNA sequencing (RNA-seq) analyses of a filamentous fungus, Sclerotinia homoeocarpa, the causal agent of dollar spot on turfgrasses, a multidrug resistant (MDR) field strain was found to overexpress phase I and III genes, coding for CYP450s and ABC transporters for xenobiotic detoxification. Furthermore, there was confirmation of a gain-of-function mutation of the fungus-specific transcription factor S. homoeocarpa XDR1 (ShXDR1), which is responsible for constitutive and induced overexpression of the phase I and III genes, resulting in resistance to multiple classes of fungicidal chemicals. This fungal pathogen detoxifies xenobiotics through coordinated transcriptional control of CYP450s, biotransforming xenobiotics with different substrate specificities and ABC transporters, excreting a broad spectrum of xenobiotics or biotransformed metabolites. A Botrytis cinerea strain harboring the mutated ShXDR1 showed increased expression of phase I (BcCYP65) and III (BcatrD) genes, resulting in resistance to fungicides. This indicates the regulatory system is conserved in filamentous fungi. This molecular genetic mechanism for xenobiotic detoxification in fungi holds potential for facilitating discovery of new antifungal drugs and further studies of convergent and divergent evolution of xenobiotic detoxification in eukaryote lineages.IMPORTANCE Emerging multidrug resistance (MDR) in pathogenic filamentous fungi is a significant threat to human health and agricultural production. Understanding mechanisms of MDR is essential to combating fungal pathogens; however, there is still limited information on MDR mechanisms conferred by xenobiotic detoxification. Here, we report for the first time that overexpression of phase I drug-metabolizing monooxygenases (cytochrome P450s) and phase III ATP-binding cassette efflux transporters is regulated by a gain-of-function mutation in the fungus-specific transcription factor in the MDR strains of the filamentous plant-pathogenic fungus Sclerotinia homoeocarpa This study establishes a novel molecular mechanism of MDR through the xenobiotic detoxification pathway in filamentous fungi, which may facilitate the discovery of new antifungal drugs to control pathogenic fungi.

Clarireedia: A new fungal genus comprising four pathogenic species responsible for dollar spot disease of turfgrass

Dollar spot is one of the most destructive and economically important fungal diseases of amenity turfgrasses. The causal agent was first described in 1937 as the ascomycete Sclerotinia homoeocarpa. However, the genus-level taxonomic placement of this fungus has been the subject of an ongoing debate for over 75 y. Existing morphological and rDNA sequence evidence indicates that this organism is more appropriately placed in the family Rutstroemiaceae rather than the Sclerotiniaceae. Here we use DNA sequence data from samples of the dollar spot fungus and other members of the Rutstroemiaceae (e.g. Rutstroemia, Lanzia, Lambertella) collected throughout the world to determine the generic identity of the turfgrass dollar spot pathogen. Phylogenetic evidence from three nucleotide sequence markers (CaM, ITS and Mcm7; 1810-bp) confirmed that S. homoeocarpa is not a species of Sclerotinia; nor is it a member of any known genus in the Rutstroemiaceae. These data support the establishment of a new genus, which we describe here as Clarireedia gen. nov. The type species for the genus, Clarireedia homoeocarpa comb. nov., is described to accommodate the dollar spot fungus, and a neotype is designated. Three new species in this clade, Clarireedia bennettii sp. nov., Clarireedia jacksonii sp. nov., and Clarireedia monteithiana sp. nov. that also cause dollar spot disease are described. Clarireedia homoeocarpa and C. bennettii occur primarily on Festuca rubra (C3 grass) hosts and appear to be restricted to the United Kingdom. Clarireedia jacksonii and C. monteithiana occur on a variety of C3 and C4 grass hosts, respectively, and appear to be globally distributed. This resolved taxonomy puts to rest a major controversy amongst plant pathologists and provides a foundation for better understanding the nature and biology of these destructive pathogens.

Antifungal mechanisms of ZnO and Ag nanoparticles to Sclerotinia homoeocarpa

Fungicides have extensively been used to effectively combat fungal diseases on a range of plant species, but resistance to multiple active ingredients has developed in pathogens such as Sclerotinia homoeocarpa, the causal agent of dollar spot on cool-season turfgrasses. Recently, ZnO and Ag nanoparticles (NPs) have received increased attention due to their antimicrobial activities. In this study, the NPs' toxicity and mechanisms of action were investigated as alternative antifungal agents against S. homoeocarpa isolates that varied in their resistance to demethylation inhibitor (DMI) fungicides. S. homoeocarpa isolates were treated with ZnO NPs and ZnCl₂ (25-400 μg ml^-1) and Ag NPs and AgNO₃ (5-100 μg ml^-1) to test antifungal activity of the NPs and ions. The mycelial growth of S. homoeocarpa isolates regardless of their DMI sensitivity was significantly inhibited on ZnO NPs (≥200 μg ml^-1), Ag NPs (≥25 μg ml^-1), Zn²⁺ ions (≥200 μg ml^-1), and Ag⁺ ions (≥10 μg ml^-1) amended media. Expression of stress response genes, glutathione S-transferase (Shgst1) and superoxide dismutase 2 (ShSOD2), was significantly induced in the isolates by exposure to the NPs and ions. In addition, a significant increase in the nucleic acid contents of fungal hyphae, which may be due to stress response, was observed upon treatment with Ag NPs using Raman spectroscopy. We further observed that a zinc transporter (Shzrt1) might play an important role in accumulating ZnO and Ag NPs into the cells of S. homoeocarpa due to overexpression of Shzrt1 significantly induced by ZnO or Ag NPs within 3 h of exposure. Yeast mutants complemented with Shzrt1 became more sensitive to ZnO and Ag NPs as well as Zn²⁺ and Ag⁺ ions than the control strain and resulted in increased Zn or Ag content after exposure. This is the first report of involvement of the zinc transporter in the accumulation of Zn and Ag from NP exposure in filamentous plant pathogenic fungi. Understanding the molecular mechanisms of NPs' antifungal activities will be useful in developing effective management strategies to control important pathogenic fungal diseases.

Molecular Mechanisms Involved in Qualitative and Quantitative Resistance to the Dicarboximide Fungicide Iprodione in Sclerotinia homoeocarpa Field Isolates

The dicarboximide fungicide class is commonly used to control Sclerotinia homoeocarpa, the causal agent of dollar spot on turfgrass. Despite frequent occurrences of S. homoeocarpa field resistance to iprodione (dicarboximide active ingredient), the genetic mechanisms of iprodione resistance have not been elucidated. In this study, 15 field isolates (seven suspected dicarboximide resistant, three multidrug resistance (MDR)-like, and five dicarboximide sensitive) were used for sequence comparison of a histidine kinase gene, Shos1, of S. homoeocarpa. The suspected dicarboximide-resistant isolates displayed nonsynonymous polymorphisms in codon 366 (isoleucine to asparagine) in Shos1, while the MDR-like and sensitive isolates did not. Further elucidation of the Shos1 function, using polyethylene glycol-mediated protoplast transformation indicated that S. homoeocarpa mutants (Shos1^I366N) from a sensitive isolate gained resistance to dicarboximides but not phenylpyrrole and polyols. The deletion of Shos1 resulted in higher resistance to dicarboximide and phenylpyrrole and higher sensitivity to polyols than Shos1^I366N. Levels of dicarboximide sensitivity in the sensitive isolate, Shos1^I366N, and Shos1 deletion mutants were negatively correlated to values of iprodione-induced expression of ShHog1, the last kinase in the high-osmolarity glycerol pathway. Increased constitutive and induced expression of the ATP-binding cassette multidrug efflux transporter ShPDR1 was observed in six of seven dicarboximide-resistant isolates. In conclusion, S. homoeocarpa field isolates gained dicarboximide resistance through the polymorphism in Shos1 and the overexpression of ShPDR1.