Phylogenetic Diversity and Host Specialization of Corynespora cassiicola Responsible for Emerging Target Spot Disease of Cotton and Other Crops in the Southeastern United States

Overexpression of the CcCYP51A and CcCYP51B genes confer Corynespora cassiicola resistance to prochloraz

Cucumber Corynespora leaf spot caused by Corynespora cassiicola is the primary disease responsible for reducing cucumber yield, and prochloraz is the main fungicide used to control C. cassiicola. This study investigated the sensitivity and resistance mechanism of C. cassiicola isolates to prochloraz, and found that C. cassiicola has developed resistance to prochloraz. The prochloraz EC50 values ranged from 0.02 to 2.33 μg/mL, with a mean of 0.436 ± 0.447 μg/mL. In total, 36 of 146 isolates exhibited prochloraz resistance. The resistant isolates had no fitness cost and could not be completely controlled by 50 μg/mL prochloraz on detached leaves. Prochloraz exhibited positive cross-resistance with propiconazole and tebuconazole but not with difenoconazole, carbendazim, trifloxystrobin and pydiflumetofen. The sensitive isolates had significantly lower ergosterol content than the resistant isolates after prochloraz treatment. Compared to sensitive isolates, prochloraz-resistant isolates had no CcCYP51 gene mutation, but the CcCYP51A and CcCYP51B gene expression levels were significantly higher under the treatment of prochloraz. The overexpression of CcCYP51A and CcCYP51B were associated with prochloraz resistance in C. cassiicola.

Deciphering the genetic architecture of resistance to Corynespora cassiicola in soybean (Glycine max L.) by integrating genome-wide association mapping and RNA-Seq analysis

Target spot caused by Corynespora cassiicola is a problematic disease in tropical and subtropical soybean (Glycine max) growing regions. Although resistant soybean genotypes have been identified, the genetic mechanisms underlying target spot resistance has not yet been studied. To address this knowledge gap, this is the first genome-wide association study (GWAS) conducted using the SoySNP50K array on a panel of 246 soybean accessions, aiming to unravel the genetic architecture of resistance. The results revealed significant associations of 14 and 33 loci with resistance to LIM01 and SSTA C. cassiicola isolates, respectively, with six loci demonstrating consistent associations across both isolates. To identify potential candidate genes within GWAS-identified loci, dynamic transcriptome profiling was conducted through RNA-Seq analysis. The analysis involved comparing gene expression patterns between resistant and susceptible genotypes, utilizing leaf tissue collected at different time points after inoculation. Integrating results of GWAS and RNA-Seq analyses identified 238 differentially expressed genes within a 200 kb region encompassing significant quantitative trait loci (QTLs) for disease severity ratings. These genes were involved in defense response to pathogen, innate immune response, chitinase activity, histone H3-K9 methylation, salicylic acid mediated signaling pathway, kinase activity, and biosynthesis of flavonoid, jasmonic acid, phenylpropanoid, and wax. In addition, when combining results from this study with previous GWAS research, 11 colocalized regions associated with disease resistance were identified for biotic and abiotic stress. This finding provides valuable insight into the genetic resources that can be harnessed for future breeding programs aiming to enhance soybean resistance against target spot and other diseases simultaneously.

Defining Fungicide Resistance Mechanisms in the Corynespora cassiicola Population from Mississippi Soybean

Target spot, caused by Corynespora cassiicola, is a common lower canopy soybean disease in the southern United States. Recently, target spot has resurged in importance especially following the identification of resistance to the quinone outside inhibitor (QoI) fungicides. As a result, a survey of C. cassiicola from soybean throughout Mississippi began in 2018. A total of 819 C. cassiicola monoconidial isolates were obtained from 228 fields in 75 counties. The molecular mechanism of QoI resistance was determined, which resulted from an amino acid substitution from glycine (G) to alanine (A) at position 143 using a PCR-RFLP method and comparing nucleotide sequences of the cytochrome b gene. Five previously defined geographic regions were used to present the distribution of the G143A substitution and included the Capital, Coast, Delta, Hills, and Pines. The Capital had the greatest proportion of G143A-containing isolates (95.0%), followed by the Coast (92.9%), Delta (89.8%), Pines (78.8%), and Hills (69.4%). In all, 85.8% of the C. cassiicola isolates carried the G143A substitution. In addition, the effective fungicide concentration (EC50) of randomly selected C. cassiicola isolates to azoxystrobin was used to characterize isolates as resistant (n = 14) (based on the presence of the G143A substitution and EC50 values >52 μg/ml) or sensitive (n = 11) (based on the absence of the G143A substitution and EC50 values <46 μg/ml). The EC50 values varied among isolates (P < 0.0001), with QoI-sensitive isolates exhibiting lower EC50 values than QoI-resistant isolates. The current study revealed that a reduction in sensitivity to QoI fungicides has likely resulted based on the percentage of C. cassiicola isolates containing the G143A substitution identified in Mississippi.

Subcutaneous phaeohyphomycosis caused by plant pathogenic Corynespora cassiicola: A case report

Corynespora cassiicola is a common plant pathogen responsible for leaf-spotting diseases in the tropical and subtropical areas. C. cassiicola seldom causes human infections. Here we describe a case of subcutaneous phaeohyphomycosis caused by C. cassiicola in a 76-year-old Chinese man, who presented to our hospital with a purulent discharge and painful sensation on his right leg. Skin biopsy revealed an abscess, and culture confirmed C. cassiicola to be the causative agent. The result was further identified by sequence analysis of the internal transcribed spacer region. The patient was successfully treated with systemic voriconazole and wound debridement: the lesion disappeared after 20 days.

The necrosis- and ethylene-inducing peptide 1-like protein (NLP) gene family of the plant pathogen Corynespora cassiicola

Effectors are secreted by plant-associated microorganisms to modify the host cell physiology. As effectors, the Necrosis- and Ethylene-inducing peptide 1-like proteins (NLPs) are involded in the early phases of plant infection and may trigger host immune responses. Corynespora cassiicola is a polyphagous plant pathogen that causes target spot on many agriculturally important crops. Using genome assembly, gene prediction, and proteome annotation tools, we retrieved 135 NLP-encoding genes from proteomes of 44 isolates. We explored the evolutionary history of NLPs using Bayesian phylogeny, gene genealogies, and selection analyses. We accessed the expression profiles of the NLP genes during the early phase of C. cassiicola-soybean interaction. Three NLP putative-effector genes (Cc_NLP1.1, Cc_NLP1.2A, and Cc_NLP1.2B) were maintained in the genomes of all isolates tested. An NLP putative-non-effector gene (Cc_NLP1.3) was found in three isolates that had been originally obtained from soybean. Putative-effector NLPs were under different selective constraints: Cc_NLP1.1 was under stronger selective pressure, while Cc_NLP1.2A was under a more relaxed constraint. Meanwhile, Cc_NLP1.2B likely evolved under either positive or balancing selection. Despite highly divergent, the putative-effector NLPs maintain conserved the residues necessary to trigger plant immune responses, suggesting they are potentially functional. Only the Cc_NLP1.1 putative-effector gene was significantly expressed at the early hours of soybean colonization, while Cc_NLP1.2A and Cc_NLP1.2B showed much lower levels of gene expression.

Comparative genomics of host-specialized populations of Corynespora cassiicola causing target spot epidemics in the southeastern United States

Numerous plant-pathogenic fungi secrete necrotrophic effectors (syn. host-selective toxins) that are important determinants of pathogenicity and virulence in species that have a necrotrophic lifestyle. Corynespora cassiicola is a necrotrophic fungus causing emerging target spot epidemics in the southeastern United States (US). Previous studies revealed that populations of C. cassiicola from cotton, soybean, and tomato are clonal, host specialized and genetically distinct. Additionally, cassiicolin - the necrotrophic effector identified in some C. cassiicola isolates - is an important toxin for virulence on rubber. It is encoded by seven Cas gene variants. Our goal was to conduct comparative genomic analyses to identify variation among putative necrotrophic effector genes and to determine if lack of one of the mating-types explained clonal populations in C. cassiicola causing outbreaks in the southeastern US and the apparent absence of sexual reproduction worldwide. A total of 12 C. cassiicola genomes, with four each from isolates from tomato, soybean, and cotton, were sequenced using an Illumina Next Seq platform. Each genome was assembled de novo, compared with the reference genome from rubber, and searched for known Cas, and other gene clusters with homologs of secondary metabolites. Cas2 and/or Cas6 were present in isolates from soybean in the southeastern US, whereas Cas1 and Cas2 were present in isolates from cotton in the southeastern US. In addition, several toxin genes, including the T-toxin biosynthetic genes were present in all C. cassiicola from cotton, soybean, and tomato. The mating-type locus was identified in all of the sequenced genomes, with the MAT1-1 idiomorph present in all cotton isolates and the rubber isolate, whereas the MAT1-2 idiomorph was present in all soybean isolates. We developed a PCR-based marker for mating-type in C. cassiicola. Both mating types were present in isolates from tomato. Thus, C. cassiicola has both mating-types necessary for sexual reproduction, but the absence of both mating-types within soybean and cotton populations could explain clonality in these populations. Variation in necrotrophic effectors may underlie host specialization and disease emergence of target spot on cotton, soybean, and tomato in the southeastern US.

Unraveling the Host-Selective Toxic Interaction of Cassiicolin with Lipid Membranes and Its Cytotoxicity

Cassiicolin (Cas), a toxin produced by Corynespora cassiicola, is responsible for Corynespora leaf fall disease in susceptible rubber trees. Currently, the molecular mechanisms of the cytotoxicity of Cas and its host selectivity have not been fully elucidated. Here, we analyzed the binding of Cas1 and Cas2 to membranes consisting of different plant lipids and their membrane disruption activities. Using high-speed atomic force microscopy and confocal microscopy, we reveal that the binding and disruption activities of Cas1 and Cas2 on lipid membranes are strongly dependent on the specific plant lipids. The negative phospholipids, glycerolipids, and sterols are more sensitive to membrane damage caused by Cas1 and Cas2 than neutral phospholipids and betaine lipids. Mature Cas1 and Cas2 play an essential role in causing membrane disruption. Cytotoxicity tests on rubber leaves of Rubber Research Institute of Vietnam (RRIV) 1, RRIV 4, and Prang Besar (PB) 255 clones suggest that the toxins cause necrosis of rubber leaves, except for the strong resistance of PB 255 against Cas2. Cryogenic scanning electron microscopy analyses of necrotic leaf tissues treated with Cas1 confirm that cytoplasmic membranes are vulnerable to the toxin. Thus, the host selectivity of Cas toxin is attained by the lipid-dependent binding activity of Cas to the membrane, and the cytotoxicity of Cas arises from its ability to form biofilm-like structures and to disrupt specific membranes.

Mitogenome-wide comparison and phylogeny reveal group I intron dynamics and intraspecific diversification within the phytopathogen Corynespora cassiicola

Corynespora cassiicola, the causal agent of an extensive range of plant diseases worldwide, is a momentous fungus with diverse lifestyles and rich in intraspecies variations. In the present study, a total of 56 mitochondrial genomes of C. cassiicola were assembled (except two available online) and analyzed, of which 16 mitogenomes were newly sequenced here. All these circular mitochondrial DNA (mtDNA) molecules, ranging from 39,223 bp to 45,786 bp in length, comprised the same set of 13 core protein-coding genes (PCGs), two rRNAs and 27 tRNAs arranged in identical order. Across the above conserved genes, nad3 had the largest genetic distance between different isolates and was possibly subjected to positive selection pressure. Comparative mitogenomic analysis indicated that seven group I (IB, IC1, and IC2) introns with a length range of 1013-1876 bp were differentially inserted in three core PCGs (cox1, nad1, and nad5), resulting in the varied mitogenome sizes among C. cassiicola isolates. In combination with dynamic distribution of the introns, a well-supported mitogenome-wide phylogeny of the 56 C. cassiicola isolates revealed eight phylogenetic groups, which only had weak correlations with host range and toxin class. Different groups of isolates exhibited obvious differences in length and GC content of some genes, while a degree of variance in codon usage and tRNA structure was also observed. This research served as the first report on mitogenomic comparisons within C. cassiicola, and could provide new insights into its intraspecific microevolution and genetic diversity.

Retrotransposons and multilocus sequence analysis reveals diversity and genetic variability in endophytic fungi-associated with Serjania laruotteana Cambess

The composition of endophytic communities is dynamic and demonstrates host specificity; besides, they have great intra- and interspecific genetic variability. In this work, we isolated leaf endophytic fungi from Serjania laruotteana, identify them using multilocus analysis, and evaluate the genetic variability using IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microssatellite amplified polymorphism). A total of 261 fungi were isolated and 58 were identified. Multilocus phylogenetic analysis using the partial sequences from the ITS1-5.8S-ITS2 regions, elongation factor 1-alpha, β-tubulin, actin, glyceraldehyde-3-phosphate dehydrogenase, and calmodulin genes identify that most strains belonged to the Colletotrichum and Diaporthe genera, other isolated genera were Xylaria, Phyllosticta, Muyocopron, Fusarium, Nemania, Plectosphaerella, Corynespora, Bipolaris, and Curvularia. The IRAP and REMAP analyzes were performed with Colletotrichum and Diaporthe genera and showed 100% of polymorphism and high intra- and interspecific variability. This is the first report of the diversity of endophytic fungi from S. laruotteana. In addition, it demonstrated that the IRAP and REMAP can be used to distinguish morphologically similar lineages, revealing differences even strains of the same species.

Developing a Greenhouse Protocol for Evaluating Resistance to Corynespora cassiicola in Cotton (Gossypium hirsutum)

Target spot, caused by Corynespora cassiicola, has reemerged as a disease of economic importance in cotton (Gossypium hirsutum L.) in the southeastern United States. Although this pathogen affects other economically important crops, relatively little is known about C. cassiicola on cotton, especially with regard to conditions conducive for disease development and sources of genetic resistance. Therefore, to more efficiently screen cotton genotypes for resistance, a greenhouse protocol is needed. Optimum temperature and conducive leaf wetness duration were determined in growth chamber trials. Temperature range for disease onset and greatest lesion counts occurred between 20 and 28°C. Generally, with ≥24 h of leaf wetness at these temperatures, disease onset was noted as rapidly as 1 day after inoculation on a cultivar that was previously determined to be susceptible to target spot. A mist irrigation system was used to maintain prolonged periods of leaf wetness in the greenhouse. In greenhouse trials, inoculation of cotyledons with 4 × 10⁴ conidia/ml allowed differentiation of five selected genotypes with disease reactions that reflected their field rankings. The current protocol will be useful for evaluating cotton breeding lines for resistance to target spot.

Genome sequences and in silico effector mining of Corynespora cassiicola CC_29 and Corynespora olivacea CBS 114450

The placement of Corynespora olivacea within the large genus Corynespora (Pleosporales) is controversial, because the species is distantly related to other congeners, including the type species C. cassiicola. Corynespora cassiicola is a polyphagous, cosmopolitan plant pathogen. Successful colonization of plant tissues requires the pathogen's effector repertoire to modulate host cell physiology and facilitate the infection process. We sequenced and performed functional annotations on the genomes of C. cassiicola CC_29 (genome size about 44.8 Mb; isolated from soybean leaves) and C. olivacea CBS 114450 (32.3 Mb). Our phylogenomic approach showed that C. cassiicola is distantly related to C. olivacea, which clustered among the Massarinaceae family members, supporting a hypothesis that C. olivacea was originally misclassified. The predicted sizes for the proteome and secretome of C. cassiicola (18,487 and 1327, respectively) were larger than those of C. olivacea (13,501 and 920; respectively). Corynespora cassiicola had a richer repertoire of effector proteins (CAZymes, proteases, lipases, and effectors) and genes associated with secondary metabolism than did C. olivacea.

First Report of Leaf Spot Caused by Corynespora cassiicola on Acanthus ilicifolius in China

Acanthus ilicifolius, also referred to as holly mangrove, usually grows in the coastal areas in southern China. It is not only a pioneer species of mangroves but also an important medicinal mangrove plant. In June 2019, leaf spots on A. ilicifolius with disease incidence of about 30 to 40% were observed in about 150 plants in a field located in Zhanjiang City, Guangdong Province, China. The disease mainly occurred on the leaf margins or tips. Initial symptoms of the disease were dark brown spots (5 to 9 mm) surrounded by a yellow halo, that expanded irregularly or semicircularly, until finally the leaves turned chlorotic and defoliated. Six samples of symptomatic leaves were excised, surface sterilized with 75% ethanol 30 s, 0.1% HgCl2 30 s, and rinsed three times with sterile water, and cut into small pieces (5 mm × 5 mm), placed on potato dextrose agar (PDA) at 25°C and darkness, and two isolates with different morphological characteristics were obtained after 3 days. For pathogenicity tests of the isolates, wounded and non-wounded leaves were inoculated. Fresh wounds were made with a sterile needle. Mycelial plugs from 8-day-old cultures of two isolates, ALY1 and ALY2, on PDA were inoculated on adaxial surface of wounded and non-wounded healthy young leaves of the A. ilicifolius seedlings (2 years old, 4 leaves per plant, 2 replicate plants per isolate), covered with wet cotton and kept in moist chambers at 25 ± 1°C, 80% relative humidity. Leaves inoculated with sterile PDA plugs were used as the control. After 3-5 days, the wounded and non-wounded leaves inoculated with ALY1 showed symptoms of leaf spots, similar to those observed in the field, while leaves inoculated with ALY2 and the control leaves remained symptomless. The pathogenicity tests were repeated three times under the same conditions and similar results were observed. ALY1 was confirmed as the pathogen causing the leaf spot. On PDA, ALY1 produced a gray to grayish brown colony. The conidia were obclavate to cylindrical, straight to slightly curved, pale brown, with 6 to 18 pseudosepta, 62.5 to 225.0×3.8 to 14.8 μm (n=17). According to the morphological characteristics, ALY1 was preliminarily identified as Corynespora cassiicola (Zhang et al.2018). For molecular identification, the internal transcribed spacer (ITS), the actin gene (ACT), the β-tubulin gene (TUB2) and translation elongation factor 1-alpha gene (TEF1-α) of the three single-spore isolates from ALY1 (ALY1-1 to ALY1-3) were amplified and sequenced with primers ITS4/ITS5 (White et al.1990), ACT512F/ACT783R(Carbone and Kohn 1999), T1/T2 (Glass and Donaldson 1995), and EF1-728F/EF1-986R (O'Donnell et al.1998) respectively. The ITS region of ALY1 (-1, -2, -3) (GenBank accession number MN860006, -07, -08) was 99-100% identical (579/585, 586/586, 581/584 base pairs) to a corresponding ITS (MH255527) of C. cassiicola. Similarly, the ACT (MN887504, -05, -06), TUB2 (MN887507, -08, -09) and TEF1-α (MN887501, -02, -03) were 100% (342/342, 342/342, 342/342 base pairs), 100% (664/664, 662/662, 664/664 base pairs) and 100% (290/290, 290/290, 290/290 base pairs) to corresponding genes FJ853033, MH763700, and MK589886 sequences of C. cassiicola in GenBank, respectively. Phylogenetic tree generated with MEGA7 by the neighbor-joining analysis revealed that the isolate's ITS, ACT, TUB2 and TEF1-α sequences were grouped in the same clade to C. cassiicola. Based on both the morphological characteristics and sequences analyses, the pathogen causing leaf spot of A. ilicifolius was identified as C. cassiicola. This species had been reported on the A. ilicifolius in Guam America and Hong Kong China (Lu et al. 2000; Zhuang 2001; Dixon et al. 2009; Sumabat et al. 2018). The best of our knowledge, it is the first report of C. cassiicola causing leaf spot of A. ilicifolius in China. This disease may a potential threat to A. ilicifolius along the coastal regions of southern China.

Gene Genealogies Reveal High Nucleotide Diversity and Admixture Haplotypes Within Three Alternaria Species Associated with Tomato and Potato

Early blight (EB) and leaf blight are two destructive diseases of tomato in North Carolina (NC), caused by Alternaria linariae and A. alternata, respectively. During the last decade, EB caused by A. solani has increased in potato-producing areas in Wisconsin (WI). We collected 152 isolates of three Alternaria spp. associated with tomato and potato in NC and WI and used the gene genealogical approach to compare the genetic relationships among them. Two nuclear genes: the glyceraldehyde-3-phosphate dehydrogenase (GPDH), RNA polymerase second largest subunit (RPB2), and the rDNA internal transcribed spacer (ITS) region of these isolates were sequenced. Besides, sequences of the GPDH locus from international isolates described in previous studies were included for comparison purposes. A set of single nucleotide polymorphisms was assembled to identify locus-specific and species-specific haplotypes. Nucleotide diversity varied among gene sequences and species analyzed. For example, the estimates of nucleotide diversity and Watterson's theta were higher in A. alternata than in A. linariae and A. solani. There was little or no polymorphisms in the ITS sequences and thus restricted haplotype placement. The RPB2 sequences were less informative to detect haplotype diversity in A. linariae and A. solani, yet six haplotypes were detected in A. alternata. The GPDH sequences enabled strongly supported phylogenetic inferences with the highest haplotype diversity and belonged to five haplotypes (AaH1 to AaH5), which consisted of only A. alternata from NC. However, 13 haplotypes were identified within and among A. linariae and A. solani sequences. Among them, six (AsAlH1 to AsAlH6) were identical to previously reported haplotypes in global samples and the remaining were new haplotypes. The most divergent haplotypes were AaH1, AsAlH2/AsAlH3, and AsAlH4 and consisted exclusively of A. alternata, A. linariae, and A. solani, respectively. Neutrality tests suggested an excess of mutations and population expansion, and selection may play an important role in nucleotide diversity of Alternaria spp.

Genome sequence and spore germination-associated transcriptome analysis of Corynespora cassiicola from cucumber

BACKGROUND

Corynespora cassiicola, as a necrotrophic phytopathogenic ascomycetous fungus, can infect hundreds of species of plants and rarely causes human diseases. This pathogen infects cucumber species and causes cucumber target spot, which has recently caused large cucumber yield losses in China. Genome sequence and spore germination-associated transcriptome analysis will contribute to the understanding of the molecular mechanism of pathogenicity and spore germination of C. cassiicola.

RESULTS

First, we reported the draft genome sequences of the cucumber-sampled C. cassiicola isolate HGCC with high virulence. Although conspecific, HGCC exhibited distinct genome sequence differences from a rubber tree-sampled isolate (CCP) and a human-sampled isolate (UM591). The proportion of secreted proteins was 7.2% in HGCC. A total of 28.9% (4232) of HGCC genes, 29.5% (4298) of CCP genes and 28.6% (4214) of UM591 genes were highly homologous to experimentally proven virulence-associated genes, respectively, which were not significantly different (P = 0.866) from the average (29.7%) of 10 other phytopathogenic fungi. Thousands of putative virulence-associated genes in various pathways or families were identified in C. cassiicola. Second, a global view of the transcriptome of C. cassiicola spores during germination was evaluated using RNA sequencing (RNA-Seq). A total of 3288 differentially expressed genes (DEGs) were identified. The majority of KEGG-annotated DEGs were involved in metabolism, genetic information processing, cellular processes, the organismal system, human diseases and environmental information processing.

CONCLUSIONS

These results facilitate the exploration of the molecular pathogenic mechanism of C. cassiicola in cucumbers and the understanding of molecular and cellular processes during spore germination.

Widespread QoI Fungicide Resistance Revealed Among Corynespora cassiicola Tomato Isolates in Florida

Target spot of tomato caused by Corynespora cassiicola is one of the most economically destructive diseases of tomato in Florida. A collection of 123 isolates from eight counties in Florida were evaluated for sensitivity to azoxystrobin and fenamidone based on mycelial growth inhibition (MGI), spore germination (SG), detached leaflet assays (DLAs), and sequence-based analysis of the cytochrome b gene (cytb). Cleavage of cytb by restriction enzyme (Fnu4HI) revealed the presence of a mutation conferring a glycine (G) to alanine (A) mutation at amino acid position 143 (G143A) in approximately 90% of the population, correlating with quinone outside inhibitor (QoI) resistance based on MGI (<40% at 5 μg/ml), SG (<50% at 1 and 10 μg/ml), and DLA (<10% severity reduction). The mutation conferring a phenylalanine (F) to leucine (L) substitution at position 129 (F129L) was confirmed in moderately resistant isolates (#9, #19, and #74) based on MGI (40 to 50% at 5 μg/ml), SG (<50% at 1 μg/ml and >50% at 10 μg/ml), and DLA (>10% and <43% severity reduction) for both QoI fungicides, whereas sensitive isolates (#1, #4, #7, #28, #29, #46, #61, #74, #75, #76, #91, #95, and #118) based on MGI (>50% at 5 μg/ml), SG (>50% at 1 μg/ml and 10 μg/ml), and DLA (>50% severity reduction) correlated to non-mutation-containing isolates or those with a silent mutation. This study indicates that QoI resistance among C. cassiicola isolates from tomato is widespread in Florida and validates rapid screening methods using MGI or molecular assays to identify resistant isolates in future studies.

Multiyear Regional Evaluation of Foliar Fungicide Applications for Cotton Target Spot Management in the Southeastern United States

Fungicide programs for managing target spot of cotton caused by Corynespora cassiicola were evaluated over 15 site-years in the southeastern United States between 2014 and 2016. Two cultivars, hypothesized to vary in target spot susceptibility, PhytoGen 499WRF (PHY499) and Deltapine 1137B2RF (DPL1137), and four fungicides (azoxystrobin, flutriafol, pyraclostrobin, pyraclostrobin + fluxapyroxad) plus nontreated control, were compared. Fungicide programs consisted of 1) a single application at first flower or disease onset and 2) the first application followed by a second 14 days later. Treatments were applied in a factorial, randomized complete block design. Target spot onset and severity varied among site-years. Except when severity was low, target spot-associated defoliation was greater on PHY499 than on DP1137. Fungicides delayed disease development and defoliation, but application number had little impact. Based on a meta-analysis of 15 site-years, pyraclostrobin-based applications resulted in a 4 to 6% yield preservation, and yield preservation was greater at site-years with early disease onset and >40% target spot associated defoliation. Results suggest a single well-timed application of a pyraclostrobin-based fungicide reduces defoliation and protects cotton yield at locations with high target spot severity. Additional research is needed to identify risk factors for target spot-associated yield losses in cotton production systems.

An updated phylogenetic classification of Corynespora cassiicola isolates and a practical approach to their identification based on the nucleotide polymorphisms at the ga4 and caa5 loci

Corynespora cassiicola (Burk. & M.A. Curtis) C.T. Wei. is an anamorphic fungus that affects more than 530 plant species, including economically important crops. Several lineages of this pathogen have been recognized, but the classification of isolates into clades is time-consuming and still sometimes leads to unclear results. In this work, eight major phylogenetic clades (PhL1-PhL8) including 245 isolates of C. cassiicola from 44 plant species were established based on a Bayesian inference analysis of four combined C. cassiicola genomic loci retrieved from GenBank, i.e., rDNA internal transcribed spacer (ITS), actin-1,ga4, and caa5. The existence of PhL1-PhL5 and PhL7 as clonal lineages was further confirmed through the analysis of full-genome single-nucleotide polymorphisms of 39 isolates. Haplotypes of the caa5 locus were PhL specific and encode isoforms of the LDB19 domain of a putative α-arrestin N-terminal-like protein. Evolution of the Caa5 arrestin is in correspondence with the PhLs. ga4 and caa5 PhL consensus sequences and a cleaved amplified polymorphic sequence (CAPS) procedure were generated based on the conserved nucleotide sequences and enzyme restriction patterns observed among isolates from the same lineage, respectively. The CAPS method was validated in silico, and its practical use allowed us to differentiate between tomato and papaya isolates, as well as to reveal the prevalence of PhL1 among isolates infecting soybean in Brazil. This novel approach could be useful in the efforts to control the diseases associated with C. cassiicola.

Endophytes from Wild Rubber Trees as Antagonists of the Pathogen Corynespora cassiicola

The Corynespora leaf fall disease of rubber trees, caused by the necrotrophic fungus Corynespora cassiicola, is responsible for important yield losses in Asian and African plantations, whereas its impact is negligible in South America. The objective of this study was to identify potential antagonists of C. cassiicola among fungal endophytes (i.e., Pestalotiopsis, Colletotrichum, and Trichoderma spp.) isolated from wild and cultivated rubber trees distributed in the Peruvian Amazon. We first tested the endophytes in dual in vitro confrontation assays against a virulent C. cassiicola isolate (CCP) obtained from diseased rubber trees in the Philippines. All Trichoderma isolates overran the CCP colony, suggesting some antagonistic mechanism, while species from the other genera behaved as mutual antagonists. Trichoderma isolates were then tested through antibiosis assays for their capacity to produce growth-inhibiting molecules. One isolate (LA279), recovered as an endophyte from a wild Hevea guianensis specimen and identified as Trichoderma koningiopsis, showed significant antibiosis capacity. We demonstrated that LA279 was also able to endophytically colonize the cultivated rubber tree species (H. brasiliensis). Under controlled laboratory conditions, rubber plants were inoculated with three Trichoderma strains, including LA279, in combination with the pathogenic CCP. Results showed that 1 week preinoculation with the endophytes differentially reduced CCP mycelial development and symptoms. In conclusion, this study suggests that T. koningiopsis isolate LA279-and derivate compounds-could be a promising candidate for the biological control of the important rubber tree pathogen C. cassiicola.

Clonality and geographic structure of host-specialized populations of Corynespora cassiicola causing emerging target spot epidemics in the southeastern United States

Corynespora cassiicola is a destructive plant-pathogenic fungus causing widespread target spot epidemics, including outbreaks on cotton, soybean, and tomato in the southeastern United States. Previous studies revealed that populations from the three hosts are genetically distinct and host specialized. Although variation in aggressiveness to cotton and tomato were observed, no genetic diversity was detected within populations sampled from each of these hosts. We aimed to gain a better understanding of the emerging target spot epidemics by developing microsatellite markers for C. cassiicola to assess genetic variation, population structure, and to infer modes of reproduction and mechanisms of dispersal. Two hundred sixty-five isolates from cotton, soybean, tomato, and other host plants were genotyped with 13 microsatellite markers. Genotypic diversity revealed genetic variation within each of the populations collected from different hosts, with the population from cotton dominated by clonal genotypes and showing the least genetic diversity. In addition, C. cassiicola populations on different host species were genetically distinct and structured based on host species. No association between genetic and geographic distances was identified in the tomato populations, and the association in cotton populations was low. However, significant regional geographic structure was detected in the soybean populations of C. cassiicola. These results further support previous findings of introduced host specialized isolates or the evolution of more aggressive strains on each host. The lack of geographic structure suggests that the clones on cotton and tomato spread rapidly, or similar founder populations were established by human-mediated dispersal, and that dispersal is not limited. However, regional geographic structure of populations on soybean suggests limited dispersal among more established populations of C. cassiicola, or genetic differences in founder populations that colonized different geographic areas.