Unraveling evolutionary relationships among the divergent lineages of colletotrichum causing anthracnose disease in turfgrass and corn

Two Previously Unrecorded Fungal Species Isolated from Muui Island in Korea

Fungi are cosmopolitan and they occupy diverse niches as consumers, producers, and decomposers. They play critical roles in the environment by enabling nutrient cycling and generating a plethora of secondary metabolites. This study aimed to identify and characterize fungal strains isolated from diverse sources on Muui Island, Republic of Korea. In 2023, a total of 86 fungal strains were collected and examined. Investigation of the morphological features and phylogenetic analyses of multiple barcode loci identified one putative novel species and two species previously unrecorded in the Republic of Korea: Colletotrichum sp., Colletotrichum guizhouense, and Fusarium brachygibbosum. This study provides a comprehensive description of their molecular phylogenies and morphological characteristics. These findings will contribute to the existing knowledge about fungal species in the Republic of Korea and future research on the fungal diversity on Muui Island.

Population Genomics Provide Insights into the Global Genetic Structure of Colletotrichum graminicola, the Causal Agent of Maize Anthracnose

Understanding the genetic diversity and mechanisms underlying genetic variation in pathogen populations is crucial to the development of effective control strategies. We investigated the genetic diversity and reproductive biology of Colletotrichum graminicola isolates which infect maize by sequencing the genomes of 108 isolates collected from 14 countries using restriction site-associated DNA sequencing (RAD-seq) and whole-genome sequencing (WGS). Clustering analyses based on single-nucleotide polymorphisms revealed three genetic groups delimited by continental origin, compatible with short-dispersal of the pathogen and geographic subdivision. Intra- and intercontinental migration was observed between Europe and South America, likely associated with the movement of contaminated germplasm. Low clonality, evidence of genetic recombination, and high phenotypic diversity were detected. We show evidence that, although it is rare (possibly due to losses of sexual reproduction- and meiosis-associated genes) C. graminicola can undergo sexual recombination. Our results support the hypotheses that intra- and intercontinental pathogen migration and genetic recombination have great impacts on the C. graminicola population structure. IMPORTANCE Plant pathogens cause significant reductions in yield and crop quality and cause enormous economic losses worldwide. Reducing these losses provides an obvious strategy to increase food production without further degrading natural ecosystems; however, this requires knowledge of the biology and evolution of the pathogens in agroecosystems. We employed a population genomics approach to investigate the genetic diversity and reproductive biology of the maize anthracnose pathogen (Colletotrichum graminicola) in 14 countries. We found that the populations are correlated with their geographical origin and that migration between countries is ongoing, possibly caused by the movement of infected plant material. This result has direct implications for disease management because migration can cause the movement of more virulent and/or fungicide-resistant genotypes. We conclude that genetic recombination is frequent (in contrast to the traditional view of C. graminicola being mainly asexual), which strongly impacts control measures and breeding programs aimed at controlling this disease.

Cultural and morphological characteristics of Colletotrichum sublineolum isolates infecting sorghum in eastern Ethiopia

Colletotrichum sublineolum is the most destructive pathogen causing sorghum anthracnose worldwide. The fungus is known to have highly variable pathotypes. A characteristic study of pathogen is important to document the change occurring in population as variability in morphology indicates the existence of different pathotypes. Controlled condition experiment was conducted to examine cultural and morphological characteristics of C. sublineolum isolates infecting sorghum in eastern Ethiopia. Sorghum leaves showing symptoms of anthracnose were collected from five districts through survey. To study the characteristics of C. sublineolum, single-spore isolates representing isolate collection districts were selected from the stock cultures and cultivated on potato dextrose agar. Culture growth, colony color, elevations, texture and margin, conidial diameter and shape were used to characterize isolates. The isolates were varied significantly in many aspects. Colony colors were differed from light-gray to gray, purple-gray to cottony-gray, white to salmon-whit, plum-pink to beige and rosy brown on upper side of the petri dishes. The mean culture growth of C. sublineolum isolates showed highly significant (P < 0.01) variations among each other and ranged from 15 to 44 mm eight-days after incubation. Most of the isolates were produced hyaline, smooth walled, falcate conidia but without septa. Conidial diameter of C. sublineolum isolates showed variations with width and length ranged from 2.97 to 6.01 μm and 10.01-27.75 μm, respectively. Most isolates had smooth colony margin and few had undulated margin. This finding revealed that substantial variations were observed among C. sublineolum isolates and the existence of variable characteristic showed the presence of several sub-species of the pathogen infecting sorghum in different agro-ecologies of eastern Ethiopia.

Maize Anthracnose Stalk Rot in the Genomic Era

Anthracnose stalk rot (ASR) of maize results in millions of dollars in losses annually in the United States. ASR, together with anthracnose leaf blight and anthracnose top dieback, is caused by the fungus Colletotrichum graminicola. Current ASR management recommendations emphasize host resistance and reduction of plant stressors (e.g., drought, heat, low fertility, or soil acidity). Stress reduction may be more difficult to achieve in the future due to more high-intensity production protocols and climate change. Moreover, cultural and chemical management practices may conflict with other important goals, including environmental sustainability and maximization of yield potential. Thus, future ASR management may rely more heavily on host resistance, for which there are relatively few highly effective sources. The last comprehensive review of C. graminicola and maize anthracnose was written over two decades ago. The genomic age has brought important new insights into mechanisms governing the host-pathogen interaction from the application of molecular and cytological technologies. This review provides a summary of our current model of maize anthracnose etiology, including how increased knowledge of molecular and cellular events could contribute to better ASR management. Improved understanding of C. graminicola taxonomy has confirmed that the fungus is specific to Zea mays, and that it colonizes living maize tissues via a critical biotrophic phase. Successful biotrophic establishment relies on an array of secreted protein effectors and secondary metabolites produced at different stages of infection and dispersed to multiple locations. These molecules could provide therapeutic targets for the next generation of transgenic or gene-edited ASR-resistant hybrids.

Colletotrichum Species Associated with Anthracnose Disease of Watermelon (Citrullus lanatus) in China

Colletotrichum species are important plant pathogens, causing anthracnose in virtually every crop grown throughout the world. However, little is known about the species that infect watermelon. A total of 526 strains were isolated from diseased watermelon samples of eight major watermelon growing provinces in China. Phylogenetic analyses using seven loci (ITS, gadph, chs-1, his3, act, tub2, and gs) coupled with morphology of 146 representative isolates showed that they belonged to 12 known species of Colletotrichum, including C. aenigma, C. chlorophyti, C. fructicola, C. jiangxiense, C. karstii, C. magnum, C. nymphaeae, C. nigrum, C. orbiculare, C. plurivorum, C. sojae, and C. truncatum and three new species, here described as C. citrulli, C. kaifengense, and C. qilinense. Colletotrichum orbiculare was the dominant species. Pathogenicity tests revealed that all isolates of the species described above were pathogenic, with C. magnum and C. kaifengense being the most aggressive to leaves and fruits, respectively. This is the first report of C. aenigma, C. chlorophyti, C. fructicola, C. jiangxiense, C. nymphaeae, C. nigrum, C. plurivorum, and C. sojae on watermelon. These findings shed light on the Colletotrichum spp. involved in watermelon anthracnose and provide useful information for implementing effective control of watermelon anthracnose in China.

Temperature requirements of Colletotrichum spp. belonging to different clades

The fungal genus Colletotrichum includes plant pathogens that cause substantial economic damage to horticultural, ornamental, and fruit tree crops worldwide. Here, we conducted a systematic literature review to retrieve and analyze the metadata on the influence of temperature on four biological processes: (i) mycelial growth, (ii) conidial germination, (iii) infection by conidia, and (iv) sporulation. The literature review considered 118 papers (selected from a total of 1,641 papers found with the literature search), 19 Colletotrichum species belonging to eight clades (acutatum, graminicola, destructivum, coccodes, dematium, gloeosporioides, and orbiculare), and 27 host plants (alfalfa, almond, apple, azalea, banana, barley, bathurst burr, blueberry, celery, chilli, coffee, corn, cotton, cowpea, grape, guava, jointvetch, lentil, lupin, olive, onion, snap bean, spinach, strawberry, tomato, watermelon, and white bean). We used the metadata to develop temperature-dependent equations representing the effect of temperature on the biological processes for the different clades and species. Inter- and intra-clades similarities and differences are analyzed and discussed. A multi-factor cluster analysis identified four groups of clades with similar temperature dependencies. The results should facilitate further research on the biology and epidemiology of Colletotrichum species and should also contribute to the development of models for the management of anthracnose diseases.

Trichothecene Genotype Profiling of Wheat Fusarium graminearum Species Complex in Paraguay

Paraguay is a non-traditional wheat-producing country in one of the warmest regions in South America. Fusarium Head Blight (FHB) is a critical disease affecting this crop, caused by the Fusarium graminearum species complex (FGSC). A variety of these species produce trichothecenes, including deoxynivalenol (DON) and its acetylated forms (3-ADON and 15-ADON) or nivalenol (NIV). This study characterized the phylogenetic relationships, and chemotype diversity of 28 strains within FGSC collected from wheat fields across different country regions. Phylogenetic analysis based on the sequence of elongation factor-1α gene (EF-1α) from 28 strains revealed the presence of four species in the FGSC: F. graminearum sensu stricto, F. asiaticum, F. meridionale and F. cortaderiae. Ten strains selected for further analysis revealed that all F. graminearum strains were 15-ADON chemotype, while the two strains of F. meridionale and one strain of F. asiaticum were NIV chemotype. Thus, the 15-ADON chemotype of F. graminearum sensu stricto was predominant within the Fusarium strains isolated in the country. This work is the first report of phylogenetic relationships and chemotype diversity among Fusarium strains which will help understand the population diversity of this pathogen in Paraguay.

New species of Colletotrichum from wild Poaceae and Cyperaceae plants in Iran

Twenty-two Colletotrichum strains were isolated from anthracnose symptoms or leaf spots on leaves of various wild Poaceae and Cyperaceae plants collected in three provinces of Iran and tentatively identified as belonging to the Graminicola species complex based on morphology. All strains were studied via a polyphasic approach combining colony characteristics, morphology and phylogeny inferred from multi-locus sequences, including the nuc rDNA ITS1-5.8S-ITS2 (ITS), partial sequences of the β-tubulin (tub2), actin (act), manganese superoxide dismutase 2 (sod2), DNA lyase 2 (apn2) genes, a 200-bp intron of the glyceraldehyde-3-phosphate dehydrogenase (gapdh), and the intergenic spacer between the apn2 gene and the mat1 idiomorph (apn2/mat1). Six species were distinguished, including three new species, namely C. caspicum, C. persicum, and C. sacchari, and three previously described species, C. cereale, C. nicholsonii and C. sublineola. Comprehensive morphological descriptions and illustrations are provided for all species. Furthermore, this study provided new insights into the distribution and host range of known species.

Anthracnose Disease of Carpetgrass (Axonopus compressus) Caused by Colletotrichum hainanense sp. nov

Carpetgrass (Axonopus compressus) is a creeping, stoloniferous, perennial warm-season grass that is adapted to humid tropical and subtropical climates. Recently, outbreaks of anthracnose disease of A. compressus caused by an unidentified Colletotrichum sp. were observed in the Hainan and Guangdong provinces in southern China. In late winter and early spring, the disease incidence reached 100% in some badly infected lawns. Under high-moisture conditions, the crowns and oldest leaf sheaths of the majority of the plants became necrotic, which led to whole lawns turning reddish brown. Pathogenicity was confirmed by inoculating uninfected A. compressus plants with a conidial suspension of the Colletotrichum sp. isolated from diseased Axonopus plants. Phylogenetic analyses of the combined internal transcribed spacer, Sod2, Apn2, and Apn2/Mat1 sequences revealed the pathogen to be a novel species of the Colletotrichum graminicola species complex. Microscopic examination showed that the species was also morphologically distinct from related Colletotrichum species. As a result of the phylogenetic, morphological, and pathogenicity analyses, we propose the name Colletotrichum hainanense for this pathogen of A. compressus in southern China.

Phylogenetically Diverse Fusarium Species Associated with Sorghum (Sorghum Bicolor L. Moench) and Finger Millet (Eleusine Coracana L. Garten) Grains from Ethiopia

Fusarium is one of the most diverse fungal genera affecting several crops around the world. This study describes the phylogeny of Fusarium species associated with grains of sorghum and finger millet from different parts of Ethiopia. Forty-two sorghum and 34 finger millet grain samples were mycologically analysed. All of the sorghum and more than 40% of the finger millet grain samples were contaminated by the Fusarium species. The Fusarium load was higher in sorghum grains than that in finger millet grains. In addition, 67 test isolates were phylogenetically analysed using EF-1α and β-tubulin gene primers. Results revealed the presence of eight phylogenetic placements within the genus Fusarium, where 22 of the isolates showed a close phylogenetic relation to the F. incarnatum–equiseti species complex. Nevertheless, they possess a distinct shape of apical cells of macroconidia, justifying the presence of new species within the Fusarium genus. The new species was the most dominant, represented by 33% of the test isolates. The current work can be seen as an important addition to the knowledge of the biodiversity of fungal species that exists within the Fusarium genus. It also reports a previously unknown Fusarium species that needs to be investigated further for toxin production potential.

A new leaf blight disease of turfgrasses caused by Microdochium poae, sp. nov

A novel species of Microdochium was identified as the causal agent of a leaf blight of Poa pratensis (Kentucky blue grass) and Agrostis stolonifera (Creeping bentgrasses), two cold-season turfgrasses widely grown on golf courses in northern China. This disease first appears as small, water-soaked, and scattered leaf spots. Under conditions of high temperatures and successive days of rain, the infected leaves rapidly lose their integrity and large diseased patches appear. Fungal strains were isolated from blighted leaf spots. A phylogenetic analysis based on the nuc rDNA internal transcribed spacer regions and 5.8S rRNA gene (ITS1-5.8S-ITS2 = ITS) and parts of the β-tubulin (TUB2) and RNA polymerase II second largest subunit (RPB2) genes strongly supported that these isolates are a distinct evolutionary lineage in Microdochium (Microdochiaceae, Xylariales) that represents a new taxonomic species, herein named as M. poae. Microscopic characters confirmed that these strains were morphologically distinct from known Microdochium species. The pathogenicity of M. poae was confirmed by inoculating spore suspension on both grasses and reisolation of the pathogen from symptomatic tissues. The optimal growth temperature suggests that the occurrence of the new leaf blight disease caused by M. poae was significantly different from the microdochium patch disease caused by M. nivale.

Characterization and Fungicide Sensitivity of Colletotrichum spp. from Different Hosts in Shandong, China

Anthracnose, caused by Colletotrichum species, can severely infect the fruits and leaves of more than 30 plants and thus results in great yield and quality losses. To identify the major Colletotrichum species infecting walnut fruits, strawberry leaves, grape fruits, and tea leaves in Shandong Province, China, 101 strains were collected and isolated. The morphological characteristics of all isolates were observed, and multilocus phylogenetic analyses (ITS, GAPDH, ACT, TUB2, CAL, CHS-1, and HIS3) were conducted on the representative isolates. The strains were identified as five Colletotrichum species, namely, C. gloeosporioides sensu stricto, C. fructicola, C. camelliae, C. acutatum sensu stricto, and C. viniferum. Among them, C. viniferum was reported for the first time from walnut fruits and strawberry leaves in Shandong Province, China. Corresponding leaves or fruits were used as a model to clarify the pathogenicity of these isolates. The results showed that C. fructicola obtained from strawberry leaves was more aggressive than C. viniferum. All of the isolates obtained from various hosts were highly sensitive to pyraclostrobin, difenoconazole, fludioxonil, tebuconazole, pyrisoxazole, and tetramycin in terms of mycelial growth inhibition (EC₅₀ values of 0.07 to 1.63 mg/liter). The fastest mycelial growth was observed in the temperature range of 25-28°C for all isolates. In addition, anthracnose symptoms occur frequently under these conditions. Overall, this study can improve the understanding of Colletotrichum species causing anthracnose in walnut fruits, strawberry leaves, grape fruits, and tea leaves and can provide a solid foundation for the effective control of this disease in different hosts.

Why species delimitation matters for fungal ecology: Colletotrichum diversity on wild and cultivated cashew in Brazil

Anthracnose is one of the most important plant diseases globally, occurring on a wide range of cultivated and wild host species. This study aimed to identify the Colletotrichum species associated with cashew anthracnose in Brazil, determine their phylogenetic relationships and geographical distribution, and provide some insight into the factors that may be influencing community composition. Colletotrichum isolates collected from symptomatic leaves, stems, inflorescences, and fruit of cultivated and wild cashew, across four Brazilian biomes, were identified as Colletotrichum chrysophilum, Colletotrichum fragariae, Colletotrichum fructicola, Colletotrichum gloeosporioides sensu stricto, Colletotrichum queenslandicum, Colletotrichum siamense and Colletotrichum tropicale. Colletotrichum siamense was the most dominant species. The greatest species richness was associated with cultivated cashew; leaves harbored more species than the other organs; the Atlantic Forest encompassed more species than the other biomes; and Pernambuco was the most species-rich location. However, accounting for the relative abundance of Colletotrichum species and differences in sample size across strata, the interpretation of which community is most diverse depends on how species are delimited. The present study provides valuable information about the Colletotrichum/cashew pathosystem, sheds light on the causal agents identification,and highlights the impact that species delimitation can have on ecological studies of fungi.

The virome of Drosophila suzukii, an invasive pest of soft fruit

Drosophila suzukii (Matsumura) is one of the most damaging and costly pests to invade temperate horticultural regions in recent history. Conventional control of this pest is challenging, and an environmentally benign microbial biopesticide is highly desirable. A thorough exploration of the pathogens infecting this pest is not only the first step on the road to the development of an effective biopesticide, but also provides a valuable comparative dataset for the study of viruses in the model family Drosophilidae. Here we use a metatransciptomic approach to identify viruses infecting this fly in both its native (Japanese) and invasive (British and French) ranges. We describe eighteen new RNA viruses, including members of the Picornavirales, Mononegavirales, Bunyavirales, Chuviruses, Nodaviridae, Tombusviridae, Reoviridae, and Nidovirales, and discuss their phylogenetic relationships with previously known viruses. We also detect 18 previously described viruses of other Drosophila species that appear to be associated with D. suzukii in the wild.

Genera of phytopathogenic fungi: GOPHY 1

Genera of Phytopathogenic Fungi (GOPHY) is introduced as a new series of publications in order to provide a stable platform for the taxonomy of phytopathogenic fungi. This first paper focuses on 21 genera of phytopathogenic fungi: Bipolaris, Boeremia, Calonectria, Ceratocystis, Cladosporium, Colletotrichum, Coniella, Curvularia, Monilinia, Neofabraea, Neofusicoccum, Pilidium, Pleiochaeta, Plenodomus, Protostegia, Pseudopyricularia, Puccinia, Saccharata, Thyrostroma, Venturia and Wilsonomyces. For each genus, a morphological description and information about its pathology, distribution, hosts and disease symptoms are provided. In addition, this information is linked to primary and secondary DNA barcodes of the presently accepted species, and relevant literature. Moreover, several novelties are introduced, i.e. new genera, species and combinations, and neo-, lecto- and epitypes designated to provide a stable taxonomy. This first paper includes one new genus, 26 new species, ten new combinations, and four typifications of older names.

A comparative genomic analysis of putative pathogenicity genes in the host-specific sibling species Colletotrichum graminicola and Colletotrichum sublineola

Background

Colletotrichum graminicola and C. sublineola cause anthracnose leaf and stalk diseases of maize and sorghum, respectively. In spite of their close evolutionary relationship, the two species are completely host-specific. Host specificity is often attributed to pathogen virulence factors, including specialized secondary metabolites (SSM), and small-secreted protein (SSP) effectors. Genes relevant to these categories were manually annotated in two co-occurring, contemporaneous strains of C. graminicola and C. sublineola. A comparative genomic and phylogenetic analysis was performed to address the evolutionary relationships among these and other divergent gene families in the two strains.

Results

Inoculation of maize with C. sublineola, or of sorghum with C. graminicola, resulted in rapid plant cell death at, or just after, the point of penetration. The two fungal genomes were very similar. More than 50% of the assemblies could be directly aligned, and more than 80% of the gene models were syntenous. More than 90% of the predicted proteins had orthologs in both species. Genes lacking orthologs in the other species (non-conserved genes) included many predicted to encode SSM-associated proteins and SSPs. Other common groups of non-conserved proteins included transporters, transcription factors, and CAZymes. Only 32 SSP genes appeared to be specific to C. graminicola, and 21 to C. sublineola. None of the SSM-associated genes were lineage-specific. Two different strains of C. graminicola, and three strains of C. sublineola, differed in no more than 1% percent of gene sequences from one another.

Conclusions

Efficient non-host recognition of C. sublineola by maize, and of C. graminicola by sorghum, was observed in epidermal cells as a rapid deployment of visible resistance responses and plant cell death. Numerous non-conserved SSP and SSM-associated predicted proteins that could play a role in this non-host recognition were identified. Additional categories of genes that were also highly divergent suggested an important role for co-evolutionary adaptation to specific host environmental factors, in addition to aspects of initial recognition, in host specificity. This work provides a foundation for future functional studies aimed at clarifying the roles of these proteins, and the possibility of manipulating them to improve management of these two economically important diseases.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3457-9) contains supplementary material, which is available to authorized users.

Development of a greenhouse-based inoculation protocol for the fungus Colletotrichum cereale pathogenic to annual bluegrass (Poa annua)

The fungus Colletotrichum cereale incites anthracnose disease on Poa annua (annual bluegrass) turfgrass. Anthracnose disease is geographically widespread throughout the world and highly destructive to cool-season turfgrasses, with infections by C. cereale resulting in extensive turf loss. Comprehensive research aimed at controlling turfgrass anthracnose has been performed in the field, but knowledge of the causal organism and its basic biology is still needed. In particular, the lack of a reliable greenhouse-based inoculation protocol performed under controlled environmental conditions is an obstacle to the study of C. cereale and anthracnose disease. Our objective was to develop a consistent and reproducible inoculation protocol for the two major genetic lineages of C. cereale. By adapting previously successful field-based protocols and combining with components of existing inoculation procedures, the method we developed consistently produced C. cereale infection on two susceptible P. annua biotypes. Approximately 7 to 10 days post-inoculation, plants exhibited chlorosis and thinning consistent with anthracnose disease symptomology. Morphological inspection of inoculated plants revealed visual signs of the fungus (appressoria and acervuli), although acervuli were not always present. After stringent surface sterilization of inoculated host tissue, C. cereale was consistently re-isolated from symptomatic tissue. Real-time PCR detection analysis based on the Apn2 marker confirmed the presence of the pathogen in host tissue, with both lineages of C. cereale detected from all inoculated plants. When a humidifier was not used, no infection developed for any biotypes or fungal isolates tested. The inoculation protocol described here marks significant progress for in planta studies of C. cereale, and will enable scientifically reproducible investigations of the biology, infectivity and lifestyle of this important grass pathogen.

Anthracnose Disease on Annual Bluegrass as Affected by Foot Traffic and Sand Topdressing

Sand topdressing is applied to maintain or enhance playability of the turf surface of putting greens. Anthracnose is a devastating disease of annual bluegrass (ABG; Poa annua) putting green turf, caused by Colletotrichum cereale. The disease is more severe on weakened turf and reputed to be exacerbated by management practices that wound turf. A 2-year field study was initiated in 2007 to evaluate the effects of foot traffic (0 versus 327 footsteps m^-2, equivalent to 200 rounds day^-1) and sand topdressing (0 and 0.3 liter m^-2 every week) on anthracnose severity of ABG mowed at 3.2 mm. Surprisingly, foot traffic reduced anthracnose severity as much as 28%, regardless of sand topdressing, during both years. Although sand topdressing initially increased disease severity (up to 7%) in 2007, continued applications decreased severity by 9% later in August 2007 and again in 2008. The treatment combination of foot traffic 5 days week^-1 and weekly sand topdressing resulted in the best turf quality by the end of both seasons. Results indicate that the practice of sand topdressing can be continued even under conditions of intense foot traffic and anthracnose disease development on ABG putting greens.

Colletotrichum caudatum s.l. is a species complex

Colletotrichum caudatum sensu lato is a widespread fungal pathogen of warm-season grasses. The fungus is easily differentiated from other Colletotrichum species through the presence of a unique filiform appendage at the apex of the conidium. Multi-locus phylogenetic analysis of four DNA sequence markers from 21 isolates of C. caudatum s.l. from six grass hosts recovered the morphospecies as a well-supported monophyletic group. Although closely related to other Colletotrichum species pathogenic to warm-season grasses (e.g. C. sublineola, C. falcatum, C. navitas, C. graminicola), the sister taxon placement of C. caudatum remained unclear. Four major subgroups and three monotypic lineages were identified from the C. caudatum s.l. isolates. Despite the presence of localized, taxon-specific incongruence between gene trees and evidence for recombination in the dataset, application of genealogical concordance species recognition criteria diagnosed the four subgroups as phylogenetic species. Traditional morphology-based species concept defines C. caudatum as one species with a broad host range; however, multi-locus phylogenetic analyses refuted this model. Instead, isolates from different hosts were mainly segregated into different lineages. In particular, isolates from the type locale and host (USA, Sorghastrum nutans) collected within a 400 km radius were divided into three distinct species that corresponded with the three sampling sites. These data established that traditional morphological and ecological features are not informative for recognition of taxa within C. caudatum s.l., although there is some evidence that some species may be host specific. To stabilize the application of the name C. caudatum, DNA sequence data from the lectotype was generated, an epitype strain consistent with the type was designated and illustrated, and an emended description of C. caudatum sensu stricto is provided. Colletotrichum alcornii, C. baltimorense, C. somersetense, and C. zoysiae are described as new morphologically cryptic species related to C. caudatum s.s.

Influence of host and geographic locale on the distribution of Colletotrichum cereale lineages

Colletotrichum cereale is an ascomycete inhabitant of cool-season Pooideae grasses. The fungus has increased in frequency over the past decade as a destructive pathogen of Poa annua and Agrostis stolonifera turfgrass. Colletotrichum cereale exists as two lineages, designated clades A and B, but little is known about the distribution of these clades in natural environments, or what role these subdivisions may play in the trajectory of disease outbreaks. In this study, our objective was to determine the frequency of C. cereale clades A and B. To rapidly discriminate between the two C. cereale clades, a real-time PCR assay was developed based on the Apn2 gene. A collection of 700 C. cereale pathogens and endophytes from twenty Pooideae grass genera were genotyped. 87% of the collection was identifed as part of clade A, 11.7% as part of clade B, and 1.3% was a mixture. Colletotrichum cereale from turfgrass hosts in North America were most commonly members of clade A (78%). The overabundance of clade A in turfgrass isolates was directly attributable to the dominance of this lineage from southern sampling sites, irrespective of host. In contrast, 111 C. cereale turfgrass isolates collected from northern sampling sites were evenly distributed between clades A and B. Only 28% of C. cereale from A. stolonifera at northern sampling sites were part of clade A. These data show that environmental factors such as geographic location and host identity likely played a role in the distribution of the major C. cereale clades in North American turfgrass.

Identification and molecular mapping of a wheat gene for resistance to an unadapted isolate of Colletotrichum cereale

To elucidate genetic mechanisms of host species specificity between graminicolous anthracnose fungi and gramineous plants, infection assays were performed with a Sorghum isolate (Colletotrichum sublineolum), a Digitaria isolate (C. hanaui), a Polypogon isolate (C. cereale), and an Avena isolate (C. cereale). They were specifically virulent on the plants from which they were isolated. When 72 wheat lines were inoculated with an unadapted isolate from Asia Minor bluegrass (Cgp29), however, some exceptional cultivars were recognized. Although most cultivars were resistant to Cgp29, 'Hope' was susceptible. In F2 populations derived from crosses between three resistant cultivars-'Norin 4' (N4), 'Chinese Spring' (CS), and 'Shin-chunaga' (Sch)-and the susceptible Hope, resistant and susceptible seedlings segregated in a 3:1 ratio, suggesting that a major gene is involved in the resistance of each cultivar to Cgp29. In F2 populations derived from crosses between the three resistant cultivars, all seedlings were resistant, suggesting that these three cultivars carry the same gene. This resistance gene was designated as "resistance to Colletotrichum cereale 1" (Rcc1). Analysis with the CS-Hope chromosome substitution lines and molecular mapping revealed that Rcc1 was located on the long arm of chromosome 5A. Cytologically, Rcc1 was mainly associated with hypersensitive reaction. These results suggest that major genes similar to those controlling cultivar specificity are involved in the resistance of wheat against the unadapted isolate of C. cereale.

Habitat and host indicate lineage identity in Colletotrichum gloeosporioides s.l. from wild and agricultural landscapes in North America

Understanding the factors that drive the evolution of pathogenic fungi is central to revealing the mechanisms of virulence and host preference, as well as developing effective disease control measures. Prerequisite to these pursuits is the accurate delimitation of species boundaries. Colletotrichum gloeosporioides s.l. is a species complex of plant pathogens and endophytic fungi for which reliable species recognition has only recently become possible through a multi-locus phylogenetic approach. By adopting an intensive regional sampling strategy encompassing multiple hosts within and beyond agricultural zones associated with cranberry (Vaccinium macrocarpon Aiton), we have integrated North America strains of Colletotrichum gloeosporioides s.l. from these habitats into a broader phylogenetic framework. We delimit species on the basis of genealogical concordance phylogenetic species recognition (GCPSR) and quantitatively assess the monophyly of delimited species at each of four nuclear loci and in the combined data set with the genealogical sorting index (gsi). Our analysis resolved two principal lineages within the species complex. Strains isolated from cranberry and sympatric host plants are distributed across both of these lineages and belong to seven distinct species or terminal clades. Strains isolated from V. macrocarpon in commercial cranberry beds belong to four species, three of which are described here as new. Another species, C. rhexiae Ellis & Everh., is epitypified. Intensive regional sampling has revealed a combination of factors, including the host species from which a strain has been isolated, the host organ of origin, and the habitat of the host species, as useful indicators of species identity in the sampled regions. We have identified three broadly distributed temperate species, C. fructivorum, C. rhexiae, and C. nupharicola, that could be useful for understanding the microevolutionary forces that may lead to species divergence in this important complex of endophytes and plant pathogens.

Colletotrichum - current status and future directions

A review is provided of the current state of understanding of Colletotrichum systematics, focusing on species-level data and the major clades. The taxonomic placement of the genus is discussed, and the evolution of our approach to species concepts and anamorph-teleomorph relationships is described. The application of multilocus technologies to phylogenetic analysis of Colletotrichum is reviewed, and selection of potential genes/loci for barcoding purposes is discussed. Host specificity and its relation to speciation and taxonomy is briefly addressed. A short review is presented of the current status of classification of the species clusters that are currently without comprehensive multilocus analyses, emphasising the orbiculare and destructivum aggregates. The future for Colletotrichum biology will be reliant on consensus classification and robust identification tools. In support of these goals, a Subcommission on Colletotrichum has been formed under the auspices of the International Commission on Taxonomy of Fungi, which will administer a carefully curated barcode database for sequence-based identification of species within the BioloMICS web environment.

The Colletotrichum gloeosporioides species complex

The limit of the Colletotrichum gloeosporioides species complex is defined genetically, based on a strongly supported clade within the Colletotrichum ITS gene tree. All taxa accepted within this clade are morphologically more or less typical of the broadly defined C. gloeosporioides, as it has been applied in the literature for the past 50 years. We accept 22 species plus one subspecies within the C. gloeosporioides complex. These include C. asianum, C. cordylinicola, C. fructicola, C. gloeosporioides, C. horii, C. kahawae subsp. kahawae, C. musae, C. nupharicola, C. psidii, C. siamense, C. theobromicola, C. tropicale, and C. xanthorrhoeae, along with the taxa described here as new, C. aenigma, C. aeschynomenes, C. alatae, C. alienum, C. aotearoa, C. clidemiae, C. kahawae subsp. ciggaro, C. salsolae, and C. ti, plus the nom. nov. C. queenslandicum (for C. gloeosporioides var. minus). All of the taxa are defined genetically on the basis of multi-gene phylogenies. Brief morphological descriptions are provided for species where no modern description is available. Many of the species are unable to be reliably distinguished using ITS, the official barcoding gene for fungi. Particularly problematic are a set of species genetically close to C. musae and another set of species genetically close to C. kahawae, referred to here as the Musae clade and the Kahawae clade, respectively. Each clade contains several species that are phylogenetically well supported in multi-gene analyses, but within the clades branch lengths are short because of the small number of phylogenetically informative characters, and in a few cases individual gene trees are incongruent. Some single genes or combinations of genes, such as glyceraldehyde-3-phosphate dehydrogenase and glutamine synthetase, can be used to reliably distinguish most taxa and will need to be developed as secondary barcodes for species level identification, which is important because many of these fungi are of biosecurity significance. In addition to the accepted species, notes are provided for names where a possible close relationship with C. gloeosporioides sensu lato has been suggested in the recent literature, along with all subspecific taxa and formae speciales within C. gloeosporioides and its putative teleomorph Glomerella cingulata.

TAXONOMIC NOVELTIES

Name replacement - C. queenslandicum B. Weir & P.R. Johnst. New species - C. aenigma B. Weir & P.R. Johnst., C. aeschynomenes B. Weir & P.R. Johnst., C. alatae B. Weir & P.R. Johnst., C. alienum B. Weir & P.R. Johnst, C. aotearoa B. Weir & P.R. Johnst., C. clidemiae B. Weir & P.R. Johnst., C. salsolae B. Weir & P.R. Johnst., C. ti B. Weir & P.R. Johnst. New subspecies - C. kahawae subsp. ciggaro B. Weir & P.R. Johnst. Typification: Epitypification - C. queenslandicum B. Weir & P.R. Johnst.

Glomerella truncata: another Glomerella species with an atypical mating system

In the genus Glomerella all species studied to date do not fit the usual mating system of heterothallic ascomycetes. This study investigated the mating system of G. truncata (anamorph Colletotrichum truncatum), a pathogen responsible for lentil anthracnose. Twenty-two field isolates from the Canadian prairies were crossed in all possible combinations, including selfings. All isolates also were screened for the presence of the MAT1-1 and MAT1-2 idiomorphs by targeting small conserved areas of the MAT genes (the alpha domain and the high mobility group HMG box) with degenerate primers, and a pair of G. truncata-specific HMG primers (CT21HMG) were designed. The results of the classical mating study suggested that G. truncata is heterothallic. Isolates fell into two incompatibility groups, which is consistent with a bipolar mating system but different from what has been described in other Glomerella species. Molecular screening showed that the HMG box used as a marker for the MAT1-2 idiomorph was present in both partners of fertile crosses in G. truncata, unlike in the typical ascomycete system, but as previously described for two other Glomerella species. G. truncata therefore appears to share unusual mating system characteristics with the other Glomerella species studied to date.

Molecular Analysis of Turfgrass Rusts Reveals the Widespread Distribution of Puccinia coronata as a Pathogen of Kentucky Bluegrass in the United States

Over the past 10 years, rust diseases have become increasingly prevalent on certain cultivars of Kentucky bluegrass. This pattern suggests that new races or new species of rust fungi may have emerged. To test this hypothesis, 66 samples of turfgrass rust fungi collected from across the United States were evaluated based on sequences of the internal transcribed spacer (ITS)-5.8S rDNA region. Phylogenetic analysis revealed three species: Puccinia coronata, P. graminis, and P. striiformis, comprising 67, 28, and 5% of the samples, respectively. P. coronata was frequently found in association with Kentucky bluegrass, a host-pathogen relationship that has not been previously reported. Comparison of molecular analyses with the use of standard field identification techniques-host association and pustule pigmentation-showed that 58% of the Kentucky bluegrass samples would have been incorrectly diagnosed using nonmolecular criteria. To avoid such misidentifications, a real-time polymerase chain reaction diagnostic protocol was developed for turfgrass-associated P. graminis, P. coronata, and P. striiformis using ITS sequences. Accurate, reproducible, species-specific identifications were made using as few as 50 to 150 urediniospores, even in mixed infections. This study represents the first DNA-based evaluation of turfgrass rust fungi and provides a quick and reliable sequence-based protocol as an alternative to less reliable field-based identification techniques.

Application of the Apn2/MAT locus to improve the systematics of the Colletotrichum gloeosporioides complex: an example from coffee (Coffea spp.) hosts

To improve phylogenetic resolution of the Colletotrichum gloeosporioides species complex we developed and tested the performance of a new set of primers for the Apn2/MAT locus with a case study of 22 isolates. These were isolated mainly from coffee plants and represent six divergent and well characterized species within the C. gloeosporioides complex. Following previous studies on this locus, we have generated sequence data from an expanded region (> 4600 bp), revealing increased phylogenetic informativeness when compared to other commonly used markers such as ITS, β-tub2 and GS. Within the Apn2/MAT locus the ApMAT marker alone was almost as informative in terms of phylogenetic resolution as a seven-gene concatenated dataset. Our results further revealed that gene-tree discordance may come to be a common issue in resolving evolutionary relationships in the C. gloeosporioides complex, highlighting the importance of multilocus approaches. The use of state-of-the-art data analysis techniques and a highly informative dataset as employed here may abate this issue and hopefully assist in disentangling the C. gloeosporioides complex.

Occurrence and Molecular Identification of Azoxystrobin-Resistant Colletotrichum cereale Isolates from Golf Course Putting Greens in the Southern United States

Turfgrass anthracnose, caused by Colletotrichum cereale (≡C. graminicola), has become a common disease of creeping bentgrass and annual bluegrass putting greens throughout the southern United States. Strobilurin (QoI) fungicides such as azoxystrobin are single-site mode-of-action fungicides applied to control C. cereale. In vitro bioassays with azoxystrobin at 0.031 and 8 μg/ml incorporated into agar were performed to evaluate the sensitivity of 175 isolates collected from symptomatic turfgrasses in Alabama, Mississippi, North Carolina, Tennessee, and Virginia. Three sensitivity levels were identified among C. cereale isolates. Resistant, intermediately resistant, and sensitive isolates were characterized by percent relative growth based on the controls with means of 81, 23, and 4%, respectively, on media containing azoxystrobin at 8 μg/ml. The molecular mechanism of resistance was determined by comparing amino acid sequences of the cytochrome b protein. Compared with sensitive isolates, C. cereale isolates exhibiting QoI resistance had a G143A substitution, whereas isolates expressing intermediate resistance had a F129L substitution. C. cereale isolates displaying azoxystrobin resistance in vitro were not controlled by QoI fungicides in a field evaluation. The dominance of QoI-resistant C. cereale isolates identified in this study indicates a shift to resistant populations on highly managed golf course putting greens.

Two Mutations in β-Tubulin 2 Gene Associated with Thiophanate-Methyl Resistance in Colletotrichum cereale Isolates from Creeping Bentgrass in Mississippi and Alabama

Turfgrass anthracnose, caused by Colletotrichum cereale (≡C. graminicola), has become a common disease of creeping bentgrass putting greens during the summer in Mississippi and Alabama over the last 15 years. Thiophanate-methyl is a single-site mode-of-action fungicide applied to control C. cereale. In vitro bioassays were performed to evaluate the sensitivity of 103 isolates to thiophanate-methyl concentrations ranging from 0.039 to 10 μg/ml. Eighty-three isolates were collected from creeping bentgrass in Mississippi and Alabama that had been exposed to thiophanate-methyl. An additional 20 isolates were included from nonexposed turfgrasses. Radial colony growth in amended media was relative to nonamended media for all in vitro bioassays. With thiophanate-methyl at 10 μg/ml, relative growth of exposed isolates ranged from 77.5 to 130.7% with a mean of 99.3% compared with nonexposed, baseline isolates that ranged from 0.0 to 48.7% with a mean of 20.4%. A representative sample of thiophanate-methyl-exposed and nonexposed isolates was used to determine the mechanism of resistance by comparing amino acid sequences of the β-tubulin 2 protein. All of the thiophanate-methyl-exposed isolates that were sequenced had a point mutation resulting in substitutions from glutamic acid to alanine at position 198 or from phenylalanine to tyrosine at position 200 of the β-tubulin 2 protein. These amino acid substitutions in C. cereale isolates from Mississippi and Alabama appear to confer resistance to thiophanate-methyl and differ from those reported previously for this pathogen.

What is the value of ITS sequence data in Colletotrichum systematics and species diagnosis? A case study using the falcate-spored graminicolous Colletotrichum group

Because the genus Colletotrichum is among the most important groups of plant pathogenic fungi worldwide, the ability to accurately diagnose species is vital for the implementation of effective disease control and quarantine measures. Although the long-standing, unresolved taxonomic issues in the genus have recently begun to be addressed through multi-locus phylogenetic research, the tools most commonly used for Colletotrichum species identification are either insufficiently variable (e.g. morphology), or homoplasic (e.g. morphology and host range criteria). In this study, using the systematically well-defined falcate-spored, grass-associated group (FG) of Colletotrichum as a model, we test the utility of ITS sequence data to diagnose species affiliations through similarity-based searches of the NCBI GenBank database or by means of gene trees constructed using phylogenetic methods. 43% of all Colletotrichum sequences accessioned by GenBank are from the ITS region, making it the single most common sequence curated by the community; however, 34% of the ITS accessions existed only as sequence data in the database, with no associated publication. Using Colletotrichum ITS sequence data from 53 FG defined isolates and 16 falcate-spored, non-graminicolous isolates to perform GenBank BLASTN searches, we found that erroneous identifications occurred for 86% of the 14 species tested. In contrast, the phylogenetic tree generated by the ITS sequence data, although poorly supported by bootstrap values, correctly grouped most of the species, but 10% of the individual isolates were incorrectly placed. From this study, we conclude that the currently available infrastructure of Colletotrichum ITS sequence data may yield unreliable species diagnoses, particularly if sequence similarity alone is the only criterion applied.

Anthracnose disease of switchgrass caused by the novel fungal species Colletotrichum navitas

In recent years perennial grasses such as the native tallgrass prairie plant Panicum virgatum (switchgrass) have taken on a new role in the North American landscape as a plant-based source of renewable energy. Because switchgrass is a native plant, it has been suggested that disease problems will be minimal, but little research in this area has been conducted. Recently, outbreaks of switchgrass anthracnose disease have been reported from the northeastern United States. Incidences of switchgrass anthracnose are known in North America since 1886 through herbarium specimens and disease reports, but the causal agent of this disease has never been experimentally determined or taxonomically evaluated. In the present work, we evaluate the causal agent of switchgrass anthracnose, a new species we describe as Colletotrichum navitas (navitas=Latin for energy). Multilocus molecular phylogenetics and morphological characters show C. navitas is a novel species in the falcate-spored graminicolous group of the genus Colletotrichum; it is most closely related to the corn anthracnose pathogen Colletotrichum graminicola. We present a formal description and illustrations for C. navitas and provide experimental confirmation that this organism is responsible for switchgrass anthracnose disease.

Positively selected disease response orthologous gene sets in the cereals identified using Sorghum bicolor L. Moench expression profiles and comparative genomics

Disease response genes (DRGs) diverge under recurrent positive selection as a result of a molecular arms race between hosts and pathogens. Most of these studies were conducted in animals, and few defense genes have been shown to evolve adaptively in plants. To test for adaptation in the molecules mediating disease resistance in the cereals, we first combined information from the expression pattern of Sorghum bicolor genes and from divergence to the full genome of rice to identify candidate DRGs. We then used evolutionary analyses of orthologous gene sets from several grass species, to determine whether the DRGs show signals of positive selection and the residues targeted. We found 140 divergent genes upregulated under biotic stress in S. bicolor by evaluating the relative abundance of expressed sequence tags in different libraries and comparing them with rice genes. For 10 of these genes, we found sets of orthologs including sequences from rice and three other cereals; six genes showed a pattern of substitution that was consistent with positive selection. Three of these genes, a thaumatin, a peroxidase, and a barley mlo homolog, are known antifungal proteins. The other three genes with evidence of positive selection were a MCM-1 agamous deficiens SRF- (MADS) box transcription factor, an eIF5 translation initiation factor, and a gene of unknown function but with evidence of expression during stress. Permutation analyses, using different ortholog and paralog sequences, consistently identified five positively selected codons in the peroxidase, a member of a cluster of genes and a large gene family. We mapped the positively selected residues onto the structure of the peroxidase and thaumatin and found that all sites are on the surface of these proteins and several are close to biochemically determined active sites. Identifying new positively selected plant disease resistance genes and the critical amino acid sites provides a basis for functional studies that may increase our understanding of their underlying molecular mechanisms of action. Additionally, it may lead to the identification of individuals having variation at functionally important sites, as well as eventually using this information in the rational design and engineering of proteins involved in plant disease resistance.

Host plant associations of an entomopathogenic variety of the fungus, Colletotrichum acutatum, recovered from the elongate hemlock scale, Fiorinia externa

A fungal epizootic has been detected in populations of the scale Fiorinia externa Ferris (Hemiptera: Diaspididae) in the eastern hemlock, Tsuga canadensis (L.) Carrière (Pinales: Pinaceae), of several northeastern states. Colletotrichum acutatum Simmonds var. fioriniae Marcelino and Gouli var. nov. inedit (Phyllachorales: Phyllachoraceae), a well-known plant pathogen, was the most commonly recovered fungus from these infected scales. This is the second report of a Colletotrichum sp. infecting scale insects. In Brazil C. gloeosporioides f. sp. ortheziidae recovered from Orthezia praelonga is under development as a biopesticide for citrus production. C. acutatum was detected growing endophytically in 28 species of plants within the epizootic areas. DNA sequences of the High Mobility Box at the MAT 1-2, mating type gene indicate that Colletotrichum sp. isolates recovered from scale insects and plants within epizootic areas were identical. Results from plant bioassays showed that this entomopathogenic Colletotrichum variety grew endophytically in all of the plants tested without causing external symptoms or signs of infection, with the exception of strawberry plants where mild symptoms of infection were observed. The implications of these findings with respect to the use of this fungus as a biological control agent are discussed.

Phylogenetic and population genetic divergence correspond with habitat for the pathogen Colletotrichum cereale and allied taxa across diverse grass communities

Over the past decade, the emergence of anthracnose disease has newly challenged the health of turfgrasses on North American golf courses, resulting in considerable economic loss. The fungus responsible for the outbreaks, Colletotrichum cereale, has also been identified from numerous natural grasses and cereal crops, although disease symptoms are generally absent. Here we utilize phylogenetic and population genetic analyses to determine the role of ecosystem in the advancement of turfgrass anthracnose and assess whether natural grass and/or cereal inhabitants are implicated in the epidemics. Using a four-gene nucleotide data set to diagnose the limits of phylogenetic species and population boundaries, we find that the graminicolous Colletotrichum diverged from a common ancestor into distinct lineages correspondent with host physiology (C3 or C4 photosynthetic pathways). In the C4 lineage, which includes the important cereal pathogens Colletotrichum graminicola, C. sublineolum, C. falcatum, C. eleusines, C. caudatum and several novel species, host specialization predominates, with host-associated lineages corresponding to isolated sibling species. Although the C3 lineage--C. cereale--is comprised of one wide host-range species, it is divided into 10 highly specialized populations corresponding to ecosystem and/or host plant, along with a single generalist population spread across multiple habitat types. Extreme differentiation between the specialized C. cereale populations suggests that asymptomatic nonturfgrass hosts are unlikely reservoirs of infectious disease propagules, but gene flow between the generalist population and the specialized genotypes provides an indirect mechanism for genetic exchange between otherwise isolated populations and ecosystems.

Inferences on the phylogeography of the fungal pathogen Heterobasidion annosum, including evidence of interspecific horizontal genetic transfer and of human-mediated, long-range dispersal

Fungi in the basidiomycete species complex Heterobasidion annosum are significant root-rot pathogens of conifers throughout the northern hemisphere. We utilize a multilocus phylogenetic approach to examine hypotheses regarding the evolution and divergence of two Heterobasidion taxa associated with pines: the Eurasian H. annosum sensu stricto and the North American H. annosum P intersterility group (ISG). Using DNA sequence information from portions of two nuclear and two mitochondrial loci, we infer phylogenetic relationships via parsimony, Bayesian and median-joining network analysis. Analysis of isolates representative of the entire known geographic range of the two taxa results in monophyletic sister Eurasian and North American lineages, with North America further subdivided into eastern and western clades. Genetically anomalous isolates from the Italian presidential estate of Castelporziano are always part of a North American clade and group with eastern North America, upholding the hypothesis of recent, anthropogenically mediated dispersal. P ISG isolates from Mexico have phylogenetic affinity with both eastern and western North America. Results for an insertion in the mitochondrial rDNA suggest this molecule was obtained from the Heterobasidion S ISG, a taxon sympatric with the P ISG in western North America. These data are compatible with an eastern Eurasian origin of the species, followed by dispersal of two sister taxa into western Eurasia and into eastern North America over a Beringean land bridge, a pattern echoed in the phylogeography of other conifer-associated basidiomycetes.

Detection and Characterization of Benzimidazole Resistance in California Populations of Colletotrichum cereale

Colletotrichum cereale is the causal agent of turfgrass anthracnose, which has become a serious problem on annual bluegrass (Poa annua) and creeping bentgrass (Agrostis palustris) golf course putting greens. Thiophanate-methyl is a benzimidazole (methyl benzimidazole carbamate [MBC]) fungicide used for the management of anthracnose. In this study, we examined 481 isolates from 10 California populations to determine the presence and frequency of MBC resistance. An in vitro methodology was developed to construct a baseline sensitivity distribution using 60 isolates from an unexposed population (TCGC). The 50% effective dose (ED₅₀) values for the baseline sensitivity distribution for thiophanate-methyl ranged from 0.14 to 2.3 μg/ml with a mean of 0.75 μg/ml. For 60 isolates assayed from an exposed population (AHCC), 57 isolates were not responsive to in vitro concentrations of thiophanate-methyl of up to 30 μg/ml. Isolates nonresponsive to thiophanate-methyl were not responsive to benomyl in vitro. Two isolates nonresponsive in vitro to thiophanate-methyl or benomyl were not controlled in vivo on annual bluegrass plants treated preventively with either fungicide at 11 mg/ml, confirming the results of the in vitro testing. The remaining 361 isolates from eight populations were tested using the single discriminatory dose of thiophanate-methyl at 10 μg/ml. A high proportion (>90%) of isolates from six of the populations were resistant to thiophanate-methyl, indicating the presence of practical resistance at these locations. To determine the molecular mechanism of MBC resistance, the two β-tubulin genes, TUB1 and TUB2, of 12 resistant and 6 sensitive isolates were amplified and sequenced, revealing a glutamic acid to lysine substitution at position 198 of TUB2 that was present in all resistant isolates. This work confirms the presence of MBC resistance in C. cereale populations from California and presents methods and information that can be used to manage resistance to the MBC fungicides and improve anthracnose management programs.

Sensitivity Distributions of California Populations of Colletotrichum cereale to the DMI Fungicides Propiconazole, Myclobutanil, Tebuconazole, and Triadimefon

The baseline sensitivity of a California population of Colletotrichum cereale (turfgrass anthracnose) to the sterol demethylation inhibitor (DMI) fungicide propiconazole was determined using an in vitro assay with known reproducibility. The 50% effective dose (ED₅₀) values for propiconazole for a nonexposed, baseline population ranged from 0.025 to 0.35 μg/ml with a mean of 0.14 μg/ml. Examination of two DMI-exposed populations indicated an approximate increase of 6.5× in mean ED₅₀ values. In vivo testing of two isolates with ED₅₀ values of propiconazole at 0.15 and 0.90 μg/ml indicated reduced control for the less sensitive isolate by propiconazole at rates ≤38 μg/ml. It was determined that single discriminatory dose testing in vitro with propiconazole at 0.50 μg/ml could differentiate sensitive and resistant isolates. Using this dose, six additional populations were tested and DMI-exposed populations were found to be three to nine times less sensitive compared with the baseline population. Two populations were assayed for sensitivity to myclobutanil, tebuconazole, and triadimefon. Mean ED₅₀ values for a nonexposed population were 0.72, 0.082, and 5.6 μg/ml, respectively; for a DMI-exposed population, mean ED₅₀ values were 3.8, 0.35, and 18 μg/ml, respectively. This work provides information on the development of DMI resistance in populations of C. cereale in California and methodologies for future resistance monitoring for this pathogen.

Occurrence and Distribution of QoI-Resistant Isolates of Colletotrichum cereale from Annual Bluegrass in California

Turfgrass anthracnose, caused by Colletotrichum cereale (ex. Colletotrichum graminicola), is an important disease of turf used on golf course putting greens. Recent management of the disease has become increasingly difficult, partly due to the possible development of practical resistance to the QoI fungicides. In all, 558 single-conidia isolates of C. cereale were collected from 10 California golf courses, 8 of which had been exposed to QoI fungicides and 2 where no fungicides had been used. Isolates were tested using a mycelial expansion assay on azoxystrobinamended media. For the two nonexposed populations, in vitro 50% effective dose (ED₅₀) values ranged from 0.0060 to 0.089 μg/ml. All isolates from the exposed populations could not be fully inhibited by doses of azoxystrobin as high as 8.0 μg/ml. A subset of these isolates were tested in vitro with the QoI fungicides pyraclostrobin and trifloxystrobin and found to be similar in response, indicating that these isolates were fully cross-resistant to all three fungicides. In greenhouse pot experiments, three isolates nonresponsive to QoI fungicides in vitro were not controlled by label rates of the fungicides. Spore germination assays also were examined; for 10 isolates identified as sensitive by mycelial expansion assays, ED₅₀ values for axoystrobin ranged from 0.0040 to 0.0047 μg/ml; for 25 isolates identified as QoI-resistant, 93 to 100% of the conidia germinated at azoxystrobin concentrations as high as 8.0 μg/ml relative to the nonamended check treatments. Mitochondrial cytochrome b genes from a subset of 15 isolates (12 resistant and 3 sensitive) were partially cloned and sequenced; all resistant isolates had an alanine substitution that corresponded to position 143 of the gene product. These results indicate that QoI resistance is present in California populations of C. cereale and is contributing to the difficulty in controlling this disease.

Comparison of Colletotrichum orbiculare and Several Allied Colletotrichum spp. for mtDNA RFLPs, Intron RFLP and Sequence Variation, Vegetative Compatibility, and Host Specificity

ABSTRACT Based on spore morphology, appressorium development, sequence similarities of the rDNA, and similarities in amplified restriction fragment length polymorphism (AFLP), it has been proposed that Colletotrichum orbiculare, C. trifolii, C. lindemuthianum, and C. malvarum represent a single phylogenetic species, C. orbiculare. In the current study, the phylogenetic relationship among isolates in the C. orbiculare species complex was reassessed. In all, 72 isolates of C. orbiculare from cultivated cucurbit or weed hosts, C. trifolii from alfalfa, C. lindemuthianum from green bean, and C. malvarum from prickly sida (Sida spinosa) were examined for mitochondrial DNA (mtDNA) restriction fragment length polymorphisms (RFLPs), RFLPs and sequence variation of a 900-bp intron of the glutamine synthetase gene and a 200-bp intron of the glyceraldehyde-3-phosphate dehydrogenase gene, and vegetative compatibility. In addition, host specificity was examined in foliar inoculations on cucurbit, bean, and alfalfa hosts. Inoculations also were conducted on cucumber fruit. Genetically distinct isolates, based on vegetative compatibility, within the species complex (C. orbiculare, C. trifolii, and C. malvarum) had an identical mtDNA haplotype (haplotype A) when examined with each of three different restriction enzymes. Isolates of C. lindemuthianum had a very similar mtDNA haplotype to haplotype A, with a single polymorphism detected with the enzyme HaeIII. The four species represent a phylogenetically closely related group based on a statistical analysis of the 900- and 200-bp intron sequences. However, distinct RFLPs in the 900-bp intron were consistently associated with each species and could be used to qualitatively and quantitatively distinguish each species. Furthermore, each of the species showed distinct host specificity, with isolates of C. orbiculare (from cucurbits), C. lindemuthianum, and C. trifolii being pathogenic only on cucurbits, green bean, and alfalfa, respectively. Consequently, distinct and fixed nucleotide, or genotypic (intron sequences and RFLPs) and phenotypic (host specificity) characteristics can be used to distinguish C. orbiculare, C. lindemuthianum, and C. trifolii from one another; therefore, they should be recognized as distinct species. This species delineation is consistent with the most current species concepts in fungi. More isolates and further characterization is needed to determine whether C. orbiculare from cocklebur and C. malvarum represent distinct species. RFLPs of the 900-bp intron may represent a relatively inexpensive, reliable, and useful diagnostic tool for general species differentiation in the genus Colletotrichum.