The Colletotrichum dracaenophilum, C. magnum and C. orchidearum species complexes

Multilocus Phylogenetic Analyses of Colletotrichum gloeosporioides Species Complex Causing Crown Rot on Strawberry in Florida

Colletotrichum gloeosporioides is the causal agent of Colletotrichum crown rot of strawberry in the southern United States. Recent multigene studies defined C. gloeosporioides as a complex species comprised of 37 species. In our study, we phylogenetically characterized C. gloeosporioides isolates from strawberry and other noncultivated plants around strawberry fields. One hundred fifteen strawberry isolates and 38 isolates from noncultivated hosts were sequenced for five genomic regions: internal transcribed spacer, actin, calmodulin, chitin synthase, and glyceraldehyde-3-phosphate dehydrogenase. Phylogenetic analysis using the maximum likelihood and Bayesian inference methods, based on partition-specific models, revealed that most of the isolates in Florida (86%) were closely related to C. siamense, whereas 14 isolates were closely related to C. theobromicola (syn. C. fragariae), four isolates were C. fructicola, and three isolates were C. clidemiae. However, only the first three species were pathogenic to strawberry. Morphological characteristics evaluated show that mycelial growth of all species is approximately 5 mm/day, but colony morphology varies by species and incubation conditions. In vitro mating of the isolates demonstrated that C. fructicola is homothallic whereas C. siamense and C. theobromicola isolates are heterothallic. The biological importance of these different Colletotrichum species is currently being investigated to determine whether different management strategies are needed in strawberry production fields.

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.

Comparative Genomics of Three Colletotrichum scovillei Strains and Genetic Analysis Revealed Genes Involved in Fungal Growth and Virulence on Chili Pepper

Colletotrichum scovillei causes anthracnose of chili pepper in many countries. Three strains of this pathogen, Coll-524, Coll-153, and Coll-365, show varied virulence on chili pepper. Among the three strains, Coll-365 showed significant defects in growth and virulence. To decipher the genetic variations among these strains and identify genes contributing to growth and virulence, comparative genomic analysis and gene transformation to show gene function were applied in this study. Compared to Coll-524, Coll-153, and Coll-365 had numerous gene losses including 32 candidate effector genes that are mainly exist in acutatum species complex. A cluster of 14 genes in a 34-kb genomic fragment was lost in Coll-365. Through gene transformation, three genes in the 34-kb fragment were identified to have functions in growth and/or virulence of C. scovillei. CsPLAA encoding a phospholipase A2-activating protein enhanced the growth of Coll-365. A combination of CsPLAA with one transcription factor CsBZTF and one C6 zinc finger domain-containing protein CsCZCP was found to enhance the pathogenicity of Coll-365. Introduction of CsGIP, which encodes a hypothetical protein, into Coll-365 caused a reduction in the germination rate of Coll-365. In conclusion, the highest virulent strain Coll-524 had more genes and encoded more pathogenicity related proteins and transposable elements than the other two strains, which may contribute to the high virulence of Coll-524. In addition, the absence of the 34-kb fragment plays a critical role in the defects of growth and virulence of strain Coll-365.

An account of Colletotrichum species associated with anthracnose of Atractylodes ovata in South Korea based on morphology and molecular data

Ovate-leaf atractylodes (OLA) (Atractylodes ovata) is a well-known medicinal plant in Korea; its dried rhizome and root extracts are used in herbal medicine. However, anthracnose is a great challenge to the OLA cultivation in South Korea. Colletotrichum spp. is a major group of plant pathogens responsible for anthracnose on a range of economically important hosts. Its occurrence on OLA remains unresolved. To investigate the diversity, morphology, phylogeny, and biology of Colletotrichum spp., 32 fungal isolates were obtained from 30 OLA-affected leaves collected from five different farms, in two regions in South Korea, Mungyeong and Sangju. The phylogenetic analysis with four or five gene loci (ITS, TUB2, ACT, GAPDH, and CHS-1) along with morphology of 26 representative isolates delineated six previously known Colletotrichum species including C. fructicola, C. gloeosporioides sensu stricto (s.s), C. cigarro, C. plurivorum, C. siamense and C. sojae, and one new species, described here as C. ovataense. Amongst these species, C. gloeosporioides s.s. and C. plurivorum were the most prevalent species. A pathogenicity test on the detached leaves revealed that different Colletotrichum species presented a distinct degree of virulence, confirming Koch's postulates. In this study, C. fructicola, C. cigarro, C. plurivorum, C. siamense, and C. sojae were reported from A. ovata for the first time, as the causal agent of ovate-leaf atractylodes anthracnose. Understanding the diversity and biology of the Colletotrichum species population will help in managing this disease.

Evaluation of Streptomyces saraciticas as Soil Amendments for Controlling Soil-Borne Plant Pathogens

Soil-borne diseases are the major problems in mono cropping. A mixture (designated LTM-m) composed of agricultural wastes and a beneficial microorganism Streptomyces saraceticus SS31 was used as soil amendments to evaluate its efficacy for managing Rhizoctonia solani and root knot nematode (Meloidogyne incognita). In vitro antagonistic assays revealed that SS31 spore suspensions and culture broths effectively suppressed the growth of R. solani, reduced nematode egg hatching, and increased juvenile mortality. Assays using two Petri dishes revealed that LTM-m produced volatile compounds to inhibit the growth of R. solani and cause mortality to the root knot nematode eggs and juveniles. Pot and greenhouse tests showed that application of 0.08% LTM-m could achieve a great reduction of both diseases and significantly increase plant fresh weight. Greenhouse trials revealed that application of LTM-m could change soil properties, including soil pH value, electric conductivity, and soil organic matter. Our results indicate that application of LTM-m bio-organic amendments could effectively manage soil-borne pathogens.

Identification and Comparison of Colletotrichum Secreted Effector Candidates Reveal Two Independent Lineages Pathogenic to Soybean

Colletotrichum is one of the most important plant pathogenic genus of fungi due to its scientific and economic impact. A wide range of hosts can be infected by Colletotrichum spp., which causes losses in crops of major importance worldwide, such as soybean. Soybean anthracnose is mainly caused by C. truncatum, but other species have been identified at an increasing rate during the last decade, becoming one of the most important limiting factors to soybean production in several regions. To gain a better understanding of the evolutionary origin of soybean anthracnose, we compared the repertoire of effector candidates of four Colletotrichum species pathogenic to soybean and eight species not pathogenic. Our results show that the four species infecting soybean belong to two lineages and do not share any effector candidates. These results strongly suggest that two Colletotrichum lineages have acquired the capability to infect soybean independently. This study also provides, for each lineage, a set of candidate effectors encoding genes that may have important roles in pathogenicity towards soybean offering a new resource useful for further research on soybean anthracnose management.

Pest categorisation of Colletotrichum plurivorum

The EFSA Plant Health Panel performed a pest categorisation of Colletotrichum plurivorum Damm, Alizadeh & Toy. Sato, a well-defined fungus of the C. orchidearum species complex which has been reported from Africa, Asia and America to cause anthracnose and pre- and post-harvest fruit rots on more than 30 plant genera. The pathogen has not been reported from the EU territory and is not included in EU Commission Implementing Regulation 2019/2072. Because of the very wide host range, this pest categorisation focused on Abelmoschus esculentus, Capsicum spp., Carica papaya, Glycine max, Manihot esculenta, Phaseolus lunatus, Pyrus bretschneideri and Vitis spp. for which there was robust evidence that C. plurivorum was formally identified by morphology and multilocus gene sequencing analysis. Host plants for planting and fresh fruits are the main pathways for the entry of the pathogen into the EU. The host availability and climate suitability factors occurring in some parts of the EU are favourable for the establishment of the pathogen. Economic impact on the production of the main hosts is expected if establishment occurs. Phytosanitary measures are available to prevent the introduction of the pathogen into the EU. Colletotrichum plurivorum satisfies the criteria that are within the remit of EFSA to assess for this species to be regarded as a potential Union quarantine pest. However, there is a high uncertainty on the status of C. plurivorum in the EU territory because of the lack of specific surveys following the re-evaluation of the taxonomy of the genus Colletotrichum.

Identification of Fungal Pathogens to Control Postharvest Passion Fruit (Passiflora edulis) Decays and Multi-Omics Comparative Pathway Analysis Reveals Purple Is More Resistant to Pathogens than a Yellow Cultivar

Production of passion fruit (Passiflora edulis) is restricted by postharvest decay, which limits the storage period. We isolated, identified, and characterized fungal pathogens causing decay in two passion fruit cultivars during two fruit seasons in China. Morphological characteristics and nucleotide sequences of ITS-rDNA regions identified eighteen isolates, which were pathogenic on yellow and purple fruit. Fusarium kyushuense, Fusarium concentricum, Colletotrichum truncatum, and Alternaria alternata were the most aggressive species. Visible inspections and comparative analysis of the disease incidences demonstrated that wounded and non-wounded yellow fruit were more susceptible to the pathogens than the purple fruit. Purple cultivar showed higher expression levels of defense-related genes through expression and metabolic profiling, as well as significantly higher levels of their biosynthesis pathways. We also found fungi with potential beneficial features for the quality of fruits. Our transcriptomic and metabolomics data provide a basis to identify potential targets to improve the pathogen resistance of the susceptible yellow cultivar. The identified fungi and affected features of the fruit of both cultivars provide important information for the control of pathogens in passion fruit industry and postharvest storage.

Unique patterns of mating pheromone presence and absence could result in the ambiguous sexual behaviors of Colletotrichum species

Colletotrichum species are known to engage in unique sexual behaviors that differ significantly from the mating strategies of other filamentous ascomycete species. For example, most ascomycete fungi require the expression of both the MAT1-1-1 and MAT1-2-1 genes to induce sexual reproduction. In contrast, all isolates of Colletotrichum harbor only the MAT1-2-1 gene and yet, are capable of recognizing suitable mating partners and producing sexual progeny. The molecular mechanisms contributing to mating types and behaviors in Colletotrichum are, however, unknown. A comparative genomics approach analyzing 35 genomes, representing 31 Colletotrichum species and two Verticillium species, was used to elucidate a putative molecular mechanism underlying the unique sexual behaviors observed in Colletotrichum species. The existence of only the MAT1-2 idiomorph was confirmed across all species included in this study. Comparisons of the loci harboring the two mating pheromones and their cognate receptors revealed interesting patterns of gene presence and absence. The results showed that these genes have been lost multiple, independent times over the evolutionary history of this genus. These losses indicate that the pheromone pathway no longer plays an active role in mating type determination, suggesting an undiscovered mechanism by which mating partner recognition is controlled in these species. This further suggests that there has been a redirection of the underlying genetic mechanisms that regulate sexual development in Colletotrichum species. This research thus provides a foundation from which further interrogation of this topic can take place.

Field-Relevant New Sources of Resistance to Anthracnose Caused by Colletotrichum truncatum in a Mungbean Mini-Core Collection

Anthracnose is a prevalent disease of mungbean in Asian countries and Sub-Saharan Africa. It is caused by multiple Colletotrichum species. The high levels of anthracnose resistance in mungbean have not been studied in depth in India, but genetic resistance is desired. In this study, we identified the causal agent of mungbean anthracnose in two regions of India as Colletotrichum truncatum through morphological and molecular methods. A set of 296 mungbean mini-core accessions developed by WorldVeg was screened under a natural disease pressure from July to September (kharif season) in 2016, 2017, and 2018 in Hyderabad (a hot spot for anthracnose) to identify anthracnose resistance. Based on disease severity scores, 22 accessions were consistently anthracnose resistant under the categories of immune, highly resistant, and resistant with scores ranging from ≥1.0 to ≤3.0 during the period of study. Furthermore, based on the agronomic performance, anthracnose resistance in Hyderabad, and other desirable traits, a subset of 74 mungbean accessions was selected from 296 mini-core accessions. These accessions were evaluated under natural disease pressure from July to September in 2018 and 2019 in Palampur (another hot spot for anthracnose) to determine the variation in anthracnose resistance. Out of the 74 accessions, two accessions were resistant in 2018; in 2019, one was immune, nine were highly resistant, and 15 were resistant. Combined analysis of variance of 65 accessions common in Hyderabad and Palampur revealed highly significant effects of environment, genotype (accessions), and genotype × environment interaction on the disease severity. The combined GGE biplot analysis of data across years and locations confirmed that the seven accessions MC-24, MC-51, MC-75, MC-127, MC-207, MC-208, and MC-292 were resistant during 2016 to 2018 in Hyderabad, and only in 2019 in Palampur, and the same accessions were moderately resistant in 2018 in Palampur. The seven resistant accessions identified from both test locations could be used as potential donors in the anthracnose resistance breeding program.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Identification of Colletotrichum liriopes as the Causative Agent of Anthracnose in Buckwheat (Fagopyrum esculentum) in China

Buckwheat (Fagopyrum esculentum), belonging to the Polygonaceae family, is one of the most important "functional food" crops in China. In fall 2020, buckwheat plants grown in field exhibiting stem canker symptoms were found in Tongxin county, Ningxia province, China. Symptoms included stem canker, dieback and extensive vascular discoloration. Cankers were bleached, silvery-white to dark gray, slightly sunken, oval to linear with slightly tapered tips, pycnidia formation was also observed within the cankers. Disease incidence was approximately 30% and moderate to high severity across the field. Symptomatic tissues were cut into 1-2 cm pieces, surface sterilized (75% ethanol for 30 s and 0.1% NaClO for 2 min) and washed four times with sterile distilled water, dried in sterile filter paper for 3 times, and placed on potato dextrose agar (PDA) at 25 ℃. Fluffy mycelium was visible for all isolates after 48 h of incubation. Twenty-five single isolates were hyphal-tip purified on PDA. Six representative isolates were used for further study. The fungal colonies on PDA were flat with an entire margin, gray aerial hyphae, light brown pigmentation, appressed slimy mycelium within which numerous brown-black perithecia formed. Colonies on oatmeal agar (OA) were flat, with flocculent mycelium, conidiomata and conidia and the reverse side was black to smoke-grey. Sparse brown-black perithecia were observed within the mycelium. Conidia were hyaline, one-celled, smooth-walled, rarely finely verruculose, aseptate, slightly curved, both sides gradually tapering towards the round to slightly acute apex and truncate base, measured (15.7-23.7) µm (length) × (2.8-5.7) µm (width), (avg. 20.2 µm×4.2 µm, n=100). Genomic DNA was extracted from the same six isolates, the internal transcribed spacer (ITS) region and the genes encoding beta-tubulin (TUB), chitin synthase (CHS), glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and histone H3 (HIS3) were independently amplified with primers V9G/ITS4, T1/Bt-2b, CHS-354R/CHS-79F, GDF1/GDR1 and CYLH3F/CYLH3R, respectively (Damm et al., 2019). Sequences for all six isolates were identical. The sequences of the representative isolate 9J1 were deposited in GenBank (accession nos. MW819604, MW836580, MW836577, MW836578 and MW836579). The results of BLASTn showed that the ITS, TUB, CHS, GAPDH and HIS3 sequences of 9J1 were greater than 98% (555/557bp, 477/486bp, 258/259bp, 242/248bp and 339/345bp, respectively) identical to those of Colletotrichum liriopes (GenBank: MT645674 (ITS), GU228098 (TUB), MT663546 (CHS), MH291255 (GAPDH) and MH292811 (HIS3)). MrBayes phylogenetic analysis using concatenated sequences of ITS, TUB, CHS, GAPDH and HIS3 showed that the isolate clustered monophyletically with strains of C. liriopes. Based on morphological and molecular characteristics, the isolate was identified as C. liriopes. To fulfill Koch's postulates, spores of the isolate 9J1 grown on OA for 14 days were harvested in 0.01% Tween 20, and the suspension were adjusted to 104 spores/ml. Six one-month-old potted plants of buckwheat were inoculated by spraying the spore suspension until run-off. Plants were kept inside a plastic bag for 3 d to maintain high relative humidity and maintained in the greenhouse. Six control plants were sprayed with sterile deionized water and kept under the same conditions. Two weeks after inoculation, all inoculated plants showed stem canker symptoms as described above, whereas control plants remained healthy. The pathogen was successfully reisolated from leaf and stem symptomatic tissue, and identified as C. liriopes based on morphological features and DNA sequence analysis, thereby fulfilling Koch's postulates. C. liriopes has been reported causing anthracnose on Eria coronaria (Yang et al., 2011), Liriope spicata (Chen et al., 2019) in China, Liriope muscari in Mexico (Damm et al., 2009), Rohdea japonica in Korea (Kwon and Kim, 2013) and in the United States (Trigiano et al., 2018). To our knowledge, this is the first report of C. liriopes causing anthracnose on buckwheat worldwide. Occurrence of this disease may represent a significant impact for buckwheat production because this crop is the major agricultural commodity in some parts of China. More studies are needed to understand the epidemiology of this disease and foster disease management programs in China.

New and Interesting Fungi. 4

An order, family and genus are validated, seven new genera, 35 new species, two new combinations, two epitypes, two lectotypes, and 17 interesting new host and / or geographical records are introduced in this study. Validated order, family and genus: Superstratomycetales and Superstratomycetaceae (based on Superstratomyces ). New genera: Haudseptoria (based on Haudseptoria typhae); Hogelandia (based on Hogelandia lambearum); Neoscirrhia (based on Neoscirrhia osmundae); Nothoanungitopsis (based on Nothoanungitopsis urophyllae); Nothomicrosphaeropsis (based on Nothomicrosphaeropsis welwitschiae); Populomyces (based on Populomyces zwinianus); Pseudoacrospermum (based on Pseudoacrospermum goniomae). New species: Apiospora sasae on dead culms of Sasa veitchii (Netherlands); Apiospora stipae on dead culms of Stipa gigantea (Spain); Bagadiella eucalyptorum on leaves of Eucalyptus sp. (Australia); Calonectria singaporensis from submerged leaf litter (Singapore); Castanediella neomalaysiana on leaves of Eucalyptus sp. (Malaysia); Colletotrichum pleopeltidis on leaves of Pleopeltis sp. (South Africa); Coniochaeta deborreae from soil (Netherlands); Diaporthe durionigena on branches of Durio zibethinus (Vietnam); Floricola juncicola on dead culm of Juncus sp. (France); Haudseptoria typhae on leaf sheath of Typha sp. (Germany); Hogelandia lambearum from soil (Netherlands); Lomentospora valparaisensis from soil (Chile); Neofusicoccum mystacidii on dead stems of Mystacidium capense (South Africa); Neomycosphaerella guibourtiae on leaves of Guibourtia sp. (Angola); Niesslia neoexosporioides on dead leaves of Carex paniculata (Germany); Nothoanungitopsis urophyllae on seed capsules of Eucalyptus urophylla (South Africa); Nothomicrosphaeropsis welwitschiae on dead leaves of Welwitschia mirabilis (Namibia); Paracremonium bendijkiorum from soil (Netherlands); Paraphoma ledniceana on dead wood of Buxus sempervirens (Czech Republic); Paraphoma salicis on leaves of Salix cf. alba (Ukraine); Parasarocladium wereldwijsianum from soil (Netherlands); Peziza ligni on masonry and plastering (France); Phyllosticta phoenicis on leaves of Phoenix reclinata (South Africa); Plectosphaerella slobbergiarum from soil (Netherlands); Populomyces zwinianus from soil (Netherlands); Pseudoacrospermum goniomae on leaves of Gonioma kamassi (South Africa); Pseudopyricularia festucae on leaves of Festuca californica (USA); Sarocladium sasijaorum from soil (Netherlands); Sporothrix hypoxyli in sporocarp of Hypoxylon petriniae on Fraxinus wood (Netherlands); Superstratomyces albomucosus on Pycnanthus angolensis (Netherlands); Superstratomyces atroviridis on Pinus sylvestris (Netherlands); Superstratomyces flavomucosus on leaf of Hakea multilinearis (Australia); Superstratomyces tardicrescens from human eye specimen (USA); Taeniolella platani on twig of Platanus hispanica (Germany), and Tympanis pini on twigs of Pinus sylvestris (Spain). Citation: Crous PW, Hernández-Restrepo M, Schumacher RK, Cowan DA, Maggs-Kölling G, Marais E, Wingfield MJ, Yilmaz N, Adan OCG, Akulov A, Álvarez Duarte E, Berraf-Tebbal A, Bulgakov TS, Carnegie AJ, de Beer ZW, Decock C, Dijksterhuis J, Duong TA, Eichmeier A, Hien LT, Houbraken JAMP, Khanh TN, Liem NV, Lombard L, Lutzoni FM, Miadlikowska JM, Nel WJ, Pascoe IG, Roets F, Roux J, Samson RA, Shen M, Spetik M, Thangavel R, Thanh HM, Thao LD, van Nieuwenhuijzen EJ, Zhang JQ, Zhang Y, Zhao LL, Groenewald JZ (2021). New and Interesting Fungi. 4. Fungal Systematics and Evolution 7: 255-343. doi: 10.3114/fuse.2021.07.13.

Colletotrichum spp. from Soybean Cause Disease on Lupin and Can Induce Plant Growth-Promoting Effects

Protein crop plants such as soybean and lupin are attracting increasing attention because of their potential use as forage, green manure, or for the production of oil and protein for human consumption. Whereas soybean production only recently gained more importance in Germany and within the whole EU in frame of protein strategies, lupin production is already well-established in Germany. The cultivation of lupins is impeded by the hemibiotrophic ascomycete Colletotrichum lupini, the causal agent of anthracnose disease. Worldwide, soybean is also a host for a variety of Colletotrichum species, but so far, this seems to not be the case in Germany. Cross-virulence between lupin- and soybean-infecting isolates is a potential threat, especially considering the overlap of possible soybean and lupin growing areas in Germany. To address this question, we systematically investigated the interaction of different Colletotrichum species isolated from soybean in Brazil on German soybean and lupin plant cultivars. Conversely, we tested the interaction of a German field isolate of C. lupini with soybean. Under controlled conditions, Colletotrichum species from soybean and lupin were able to cross-infect the other host plant with varying degrees of virulence, thus underpinning the potential risk of increased anthracnose diseases in the future. Interestingly, we observed a pronounced plant growth-promoting effect for some host–pathogen combinations, which might open the route to the use of beneficial biological agents in lupin and soybean production.

First Report of Anthracnose of American Ginseng caused by Colletotrichum sojae in Northeast China

American ginseng (Panax quinquefolium) is a medicinal plant that is commercially cultivated in China. Anthracnose is a devastating disease of American ginseng, with annual production losses exceeding 20%. In July 2019, anthracnose of American ginseng was observed on 3-year-old plants in Fusong County, Jilin Province, China, the most important region of American ginseng. Round or irregular-shaped, brown, sunken and necrotic lesions (5 to 11 mm in diameter), occasionally with a concentric ring or surrounded by brown halos, were detected on leaves (Fig. 1). Multiple lesions gradually coalesced, eventually causing yellowing and wilting. More than 36% of plants in a 30-ha field were infected. Symptomatic leaves (n=16) were collected and the diseased tissue was cut into small pieces, immersed in 1% NaOCl for 2 min, rinsed three times with sterile water, and placed on acidified potato dextrose agar (PDA) in Petri dishes. After incubation in darkness at 25°C for 4 days, 15 suspected Colletotrichum single-spore isolates purified in water agar were obtained. The isolate XTJ2 was randomly selected for identification. On PDA, colonies were white to gray, occasionally mixed with gray-black strips, and the reverse was similar to the surface. Colonies on nutrient-poor agar (SNA) were flat, thin, floccose, with an entire margin, whitish to pale gray with the same colors on the reverse. The conidia were hyaline, smooth-walled, straight with a rounded base and apex, ranging from 11.1 to 21.2 × 4.0 to 5.5 μm (n=100), with length/width =3.5. Conidia were initially aseptate, but became septate with age. Setae were dark brown with a slightly acute tip, 2 to 3-septa, and 31.5 to 81.6 μm long. Appressoria were rarely observed, brown, smooth-walled, oval, bullet-shaped or irregular. Chlamydospores were not observed. The isolate was initially identified as Colletotrichum sp. (Damm et al. 2019). Initial BLAST searches of XTJ2 sequences of the rDNA internal transcribed spacer region (GenBank accession no. MW048745), a partial glyceraldehyde-3-phosphate dehydrogenase (MW053381), chitin synthase 1 (MW053382), histone H3 (MW053383), actin (MW053384) and beta-tubulin (MW053385) in GenBank showed that the sequences were respectively 100% similar to Colletotrichum sojae sequences: NR_158358, MG600810, MG600860, MG600899, MG600954 and MG601016 (Carbone and Kohn 1999; Crous et al. 2004;Guerber et al. 2003). The identity of XTJ2 was confirmed by constructing a phylogenetic tree combining all loci, which grouped the isolate and the type strain of C. sojae into one clade (Fig. 2). The sequences of all isolates were genetically identical to the XTJ2 sequences. For pathogenicity tests, 15 healthy 3-year-old plants grown in five pots were spray-inoculated with the XTJ2 conidial suspension (1×105 spores/mL), and the same number of plants were sprayed with water as the control. This experiment was repeated twice. Plants were kept in a greenhouse (28°C, natural light, and 85% relative humidity) under clear plastic bags. After 10 days, inoculated leaves exhibited symptoms that were similar to those observed in the field, whereas the controls were symptomless. The same fungus was recovered and sequenced, and its identity was confirmed by a phylogenetic analysis. This is the first report of C. sojae causing anthracnose of American ginseng in China, being a potential threat to the production of this culture. More studies on the epidemiology of this disease are needed to improve disease management.

Conyza bonariensis as an alternative host for Colletotrichum species in Argentina

AIMS

This study investigated the diversity of Colletotrichum isolates recovered from Conyza bonariensis leaves through the use of morphological characteristics, growth rate, carbon sources utilization and phylogenetic analysis.

METHODS AND RESULTS

In all, 30 Colletotrichum isolates recovered from C. bonariensis leaves showing symptoms of disease were included in the present study. Based on the analysis of morphology and sequences, the isolates were distributed into six Colletotrichum species complexes. The concatenated alignment of GAPDH and ITS sequences showed that 20 out of 30 isolates were included in four species complexes which comprise the most important pathogens causing anthracnose in soybean or anthracnose and stalk rot in maize: C. truncatum, C. orchidearum, C. gloeosporioides and C. graminicola. The remaining 10 isolates were included in the C. boninense and C. destructivum species complexes or could not be assigned to any complex with the available information.

CONCLUSION

Weeds belonging to genus Conyza are host to soybean and maize potential pathogenic species of Colletotrichum and could have a role as inoculum reservoir for cross contamination in the agroecosystem.

SIGNIFICANCE AND IMPACT OF THE STUDY

The combined use of morphological, kinetics and physiological parameters of growth and phylogenetic analysis in Colletotrichum isolates from Conyza leaves allowed the detection of species complexes previously not identified in Argentina.

Soybean anthracnose caused by Colletotrichum species: Current status and future prospects

Soybean (Glycine max) is one of the most important cultivated plants worldwide as a source of protein-rich foods and animal feeds. Anthracnose, caused by different lineages of the hemibiotrophic fungus Colletotrichum, is one of the main limiting factors to soybean production. Losses due to anthracnose have been neglected, but their impact may threaten up to 50% of the grain production.

TAXONOMY

While C. truncatum is considered the main species associated with soybean anthracnose, recently other species have been reported as pathogenic on this host. Until now, it has not been clear whether the association of new Colletotrichum species with the disease is related to emerging species or whether it is due to the undergoing changes in the taxonomy of the genus.

DISEASE SYMPTOMS

Typical anthracnose symptoms are pre- and postemergence damping-off; dark, depressed, and irregular spots on cotyledons, stems, petioles, and pods; and necrotic laminar veins on leaves that can result in premature defoliation. Symptoms may evolve to pod rot, immature opening of pods, and premature germination of grains.

CHALLENGES

As accurate species identification of the causal agent is decisive for disease control and prevention, in this work we review the taxonomic designation of Colletotrichum isolated from soybean to understand which lineages are pathogenic on this host. We also present a comprehensive literature review of soybean anthracnose, focusing on distribution, symptomatology, epidemiology, disease management, identification, and diagnosis. We consider the knowledge emerging from population studies and comparative genomics of Colletotrichum spp. associated with soybean providing future perspectives in the identification of molecular factors involved in the pathogenicity process.

USEFUL WEBSITE

Updates on Colletotrichum can be found at http://www.colletotrichum.org/. All available Colletotrichum genomes on GenBank can be viewed at http://www.colletotrichum.org/genomics/.

First report of Colletotrichum fructicola causing anthracnose on water hyacinth in China

Water hyacinth (Eichhornia crassipes), a worst invasive aquatic weed has been caused the widespread problems for the water bodies and water resources, particularly the case in China. Plant pathogens are a promising alternative as biocontrol agents (Dagno et al. 2011), but success in this strategy will require the selection of some highly virulent pathogen strains. In September 2020, irregular necrotic lesions on leaves, stems, as well as crown and petiole rots symptoms, occurred on water hyacinth, in Minjiang and Xiyuanjiang watershed, in Fuzhou, China. Fragments from symptomatic leaf tissue (5x5mm) were superficially disinfected in 0.1% MgCl2 solution for 30 s, followed by rinsing three times in sterile water, placed on potato dextrose agar (PDA), and then incubated in darkness at 28°C for 5 days. Two fungal isolates (F3 and F11) were recovered and obtained pure cultures from the affected leaves and deposited in the Institute of Oceanography, Minjiang University. The colonies were stale, with felted, dense, pale grey aerial mycelium, scattered dark based acervuli with orange conidial masses near centre; in reverse side pinkish orange with patches of grey pigment near centre. The hyphae were septate, branched, and 2 to 6 µm in width. Appressoria were not observed. Conidiogenous cells were 20-24 × 3.5-4.5 µm, cylindric to flask-shaped, towards margin the conidiophores with a much looser structure, conidiogenous loci at apex and often also at septa. Asci were 60-80 × 15-20 µm, cylindric to subfusoid, 8-spored. Ascospores were 17-23 × 4-6 µm, gently curved, tapering to quite narrow, rounded ends. Perithecia mature after about 15 days, and were dark brown, subglobose, and 50-150 μm in diameter, and with scattered, dark brown setae about 50-80 µm long. Conidia were 15-25 × 4.5-6 μm, unicellular, colorless, and cylindrical to fusiform. Genomic DNA from two isolates was extracted with a modified DNA Midi Kit (TIANGEN, Inc., Beijing, China), and amplified using ITS4/ITS1F, CL1/CL2A, CHS-79F/CHS-345R, T1/T2 and GDF/GDR primers by PCR (Weir et al. 2012; White et al. 1990). Sequences of F3 and F11 were submitted to GenBank (accession no. ITS, MW307302, MW307303; CAL, MW303427, MW303429; CHS-1, MW303428, MW303430; TUB, MW531006, MW531007; GADPH, MW531008, MW531009). A phylogenetic tree using the maximum likelihood methods and including ITS-CHS-CAL-TUB-GADPH concatenated sequences from Colletotrichum gloeosporioides complex was obtained (Cai et al. 2009; Damm et al. 2018; Weir et al. 2012). Phylogenetic analyses revealed that isolate F3 and F11 were grouped into the clade C. fructicola. To test Koch's postulates, conidial suspensions (107 CFU/ml) of the isolate F3 and F11 were micro-injected into 20 water hyacinth seedlings per isolate. Another 20 seedlings were injected with water without conidia as control. Inoculated plants were kept in 50-liter plastic tanks, and maintained in a greenhouse at room temperature (19-24ºC) for two weeks. The Koch's test was conducted twice. After 10 days, typical anthracnose symptoms similar to the field appeared on the inoculated leaves, while the control leaves remained asymptomatic. The C. fructicola was re-isolated and identified by microscopy, PCR and sequencing, but not on non-inoculated controls. Anthracnose disease caused by C. fructicola has been reported affecting numerous plants worldwide, including cotton, coffea, grape, citrus, ect (Guarnaccia et al. 2017). However, to our knowledge, this is the first report of C. fructicola causing anthracnose on water hyacinth in China. Further studies for the efficacy of C. fructicola and/or of the genus Colletotrichum as biocontrol agent for water hyacinth or another aquatic plant are required (Ding et al. 2007; Dagno et al. 2012).

First Report of Anthracnose on Jerusalem Cherry Caused by Colletotrichum liaoningense in Shandong, China

Jerusalem cherry (Solanum pseudocapsicum), which belongs to the genus Solanum and the family Solanaceae, possesses high ornamental value and is widely cultivated as an indoor ornament due to its bright red berries at maturity (Xu et al., 2018). In September 2019, leaf spot was detected on jerusalem cherry plants in Yuxiu Park, Shizhong district, Jinan, Shandong Province. Field surveys were done in a 1/15 ha park. Disease incidence was estimated at approximately 18% across the survey area. Foliar symptoms began as small white spots. As the disease progressed, lesions expanded and merged, and developed into large irregular white spots, with pale grey edge. At last, lesions were densely distributed throughout the leaves. To isolate the pathogen, twenty leaf tissues (5 × 5 mm) were cut from the border between diseased and healthy tissue, surface disinfected in 75% alcohol for 15 s, soaked in 0.1% mercuric chloride for 1 min, washed with sterile distilled water three times, and cultured on potato dextrose agar (PDA) at 25°C. Nineteen fungal isolates were obtained and were single-spored to obtain pure cultures. The colony of LCL7, a representative isolate, on PDA was initially white to orange, but turned black after 3 to 4 days incubation with black conidial masses. Conidia were single-celled, hyaline, straight, cylindrical, apex obtuse, and ranged from 13.4 to 18.3 × 3.2 to 4.9 μm (n = 50) （Diao et al., 2017）. To validate the species identification, rDNA internal transcribed spacer (ITS) region (White et al., 1990), and the partial sequences of glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin (ACT), β-tubulin (TUB2), and chitin synthase (CHS-1) (Damm et al., 2019; He et al., 2019), were amplified and sequenced. The ITS, GAPDH, ACT, TUB2, and CHS-1 sequences of isolate LCL7 were submitted to GenBank (MW221320, MW227217, MW227218, MW227219, and MW266988, respectively). ITS, ACT, TUB2, and CHS-1 BLAST showed 99-100% homology with sequences of Colletotrichum liaoningense (ITS, 100% to MH636504; ACT, 100% to MH622582; TUB2, 99.56% to MH622714, CHS-1, 99.33% to MH622446, respectively), although GAPDH showed 93.98% homology with sequence MH681383 (234/249bp). Neighbor-joining tree based on concatenated sequences of the five genes was constructed using MEGA7.0. The results showed the isolate was closely related to C. liaoningense. Based on morphological and molecular characteristics, the isolate LCL7 was identified as C. liaoningense. Pathogenicity tests were performed by spraying a conidial suspension (1 × 105 conidia/mL) on ten two-year-old healthy jerusalem cherry plants. Ten other plants with sterile water served as controls. All samples were incubated in a growth chamber at 25±2°C and transparent plastic bags to keep relative humidity high for 2 days. All inoculated plants showed symptoms similar to those observed in the field after 21 days, but no disease occurred on control plants. The same fungus was successfully reisolated from inoculated leaves and reidentified based on morphology and molecular characteristics, and the fungus was not isolated from the control plants, thus confirming Koch's postulates. Pathogenicity tests were repeated twice. C. liaoningense can cause anthracnose in chili and mango in China (Diao et al., 2017; Li et al., 2019).To our knowledge, this is the first report of anthracnose on jerusalem cherry caused by C. liaoningense in China, which influences ornamental value and reduces market value. Identification of the causes of the disease will help develop effective strategies for managing this disease.

Changes in global Orchidaceae disease geographical research trends: recent incidences, distributions, treatment, and challenges

Many of the Orchidaceae species are threatened due to environmental changes and over exploitation for full fill global demands. The main objective of this article was critically analyzed the recent global distribution of Orchidaceae diversity, its disease patterns, microbial disease identification, detection, along with prevention and challenges. Critical analysis findings revealed that Orchidaceae growth and developments were affected indirectly or directly as a result of complex microbial ecological interactions. Studies have identified many species associated with orchids, some are pathogenic and cause symptoms such as soft rot, brown rot, brown spot, black rot, wilt, foliar, root rot, anthracnose, leaf spot. The review was provided the comprehensive data to evaluate the identification and detection of microbial disease, which is the most important challenge for sustainable cultivation of Orchidaceae diversity. Furthermore, this article is the foremost of disease triggering microbes, orchid relations, and assimilates various consequences that both promoted the considerate and facts of such disease multipart, and will permit the development of best operative disease management practices.

First Report of Colletotrichum brevisporum Causing Soybean Anthracnose in China

In March 2020, widespread anthracnose was observed on soybean (Glycine max) in southeastern Jiangsu (Nantong municipality; 120.53° E, 31.58° N) in China. Plants exhibited irregular brown necrotic lesions in stem and leaves, and pronounced wilting. The symptoms were detected in one soybean field, 0.42 ha, surrounded by healthy wheat fields. Approximately 65% of the soybean plants showed the disease symptoms, and crop yield was reduced by 28-35% with respect the yield achieved in previous years, when no symptoms were observed. The symptoms were consistent with those previously reported for anthracnose on soybean caused by Colletotrichum chlorophyti, C. cliviae and C. gloeosporioides (Barbieri et al. 2017; Mahmodi et al. 2013; Yang et al. 2012). Diseased, 3-week old plants were collected. Small pieces, approximately 1 cm2 in size, of symptomatic tissue were surface sterilized in 1.5% NaOCl for 1 min, and washed twice with sterile ddH2O. The pathogen was isolated and cultured on potato dextrose agar (Song et al. 2020), containing chloramphenicol (50 µg/mL), under darkness at 28 °C for 3 days. Sequence of internal transcribed spacer (ITS), actin (ACT), β-tubulin (TUB2) and glyceraldehyde 3-phosphate dehydrogenase (GAP/span>DH) genes was performed as reported by Yang et al. (2015). Sequences were submitted to GenBank under accession numbers MT361074 (ITS) and MT415548-MT415550 (ACT, TUB2 and GAPDH). Blast search revealed that the amplified sequences had 100% (ITS; C. brevisporum TCHD, MH883805), 97.66% (ACT; C. brevisporum S38, KY986905), 99.06% (TUB2; C. brevisporum PF-2, KY705061) and 100% (GAPDH; C. brevisporum LJTJ27, KP823797) matches to multiple C. brevisporum strains, whereas all reported C. chlorophyti, C. cliviae and C. gloeosporioides strains showed no similarity to at least 2 of the studied genes. Molecular phylogenetic tree constructed using MEGA7 confirmed the identity of the pathogen. ACT and ITS sequences were blasted separately in Muscle (https://www.ebi.ac.uk/Tools/msa/muscle/) and then combined together to make the phylogenetic tree. The evolutionary history was inferred by using the Maximum Likelihood method based on the Tamura 3-parameter model, and the tree with the highest log likelihood (-1749.2186) is shown in Figure 1. The Colletotrichum strains previously found causing anthracnoseon soybean, and other relevant strains used in taxonomic analyses were included in the phylogenetic tree. Microscope observations showed the presence of 15-µm-long cylindrical conidia and septate mycelium, and agree with those reported for the morphology of C. brevisporum by Damm et al. (2019). To confirm pathogenicity, the mycelia from a 2 day-old culture on PDA was collected and suspended in sterile ddH2O (≈ 106 cells/mL) to prepare the inoculum. The pathogen was sprayed-inoculated on stem and leaves of healthy soybean plants. In control plants, sterile ddH2O was used. Inoculated plants were maintained in growth chamber at 28 °C and 50% relative humidity. Typical anthracnose symptoms were obsered 20 days after inoculation (Figure 2). C. brevisporum was reported to produce anthracnose on pumpkin, papaya, mulberry, coffee, passion fruit and pepper in China (Liu et al. 2017; Liu et al. 2019; Xue et al. 2019). Here, we report for the first time C. brevisporum causing anthracnose on soybean, an economically-relevant crop in China.

Characterization and Pathogenicity of Colletotrichum Species on Philodendron tatei cv. Congo in Gansu Province, China

In recent years in China, leaf spot caused by Colletotrichum species has been an emerging disease of Philodendron tatei cv. Congo. From 2016 to 2019, typical symptoms, appearing as circular or ovoid, sunken, and brown lesions with a yellow halo, were commonly observed on P. tatei cv. Congo in and around Lanzhou, Gansu Province, China. Conidiomata were often visible on infected leaf surfaces. Leaf disease incidence was approximately 5 to 20%. A total of 126 single-spored Colletotrichum isolates were obtained from leaf lesions. Multilocus phylogenetic relationships were analyzed based on seven genomic loci (ITS, ACT, GAPDH, HIS3, CAL, CHS-1, and TUB2) and the morphological characters of the isolates determined. These isolates were identified as three Colletotrichum species in this study. A further 93 isolates, accounting for 74% of all Colletotrichum isolates, were described as new species and named as Colletotrichum philodendricola sp. nov. after the host plant genus name, Philodendron; another two isolates were named as C. pseudoboninense sp. nov. based on phylogenetic and morphological relativeness to C. boninense; the other 31 isolates, belonging to the C. orchidearum species complex, were identified as a known species-C. orchidearum. Both novel species C. philodendricola and C. pseudoboninense belong to the C. boninense species complex. Pathogenicity tests by both spray and point inoculations confirmed that all three species could infect leaves of P. tatei cv. Congo. For spray inoculation, the mean infection rate of leaves on the three species was only 4.7% (0 to 12%), and the size on lesions was mostly 1 to 2 mm in length. For point inoculation, 30 days after nonwounding inoculation, the infection rate on leaves was 0 to 35%; in wounding inoculation, the infection rate of leaves was 35 to 65%; wounding in healthy leaves greatly enhanced the pathogenicity of these three species to P. tatei cv. Congo; however, the sizes of lesions among the three species were not significantly different. To our knowledge, this is the first report of Colletotrichum species associated with anthracnose diseases on P. tatei cv. Congo. Results obtained in this study will assist the disease prevention and appropriate management strategies.

One stop shop IV: taxonomic update with molecular phylogeny for important phytopathogenic genera: 76–100 (2020)

This is a continuation of a series focused on providing a stable platform for the taxonomy of phytopathogenic fungi and fungus-like organisms. This paper focuses on one family: Erysiphaceae and 24 phytopathogenic genera: Armillaria, Barriopsis, Cercospora, Cladosporium, Clinoconidium, Colletotrichum, Cylindrocladiella, Dothidotthia,, Fomitopsis, Ganoderma, Golovinomyces, Heterobasidium, Meliola, Mucor, Neoerysiphe, Nothophoma, Phellinus, Phytophthora, Pseudoseptoria, Pythium, Rhizopus, Stemphylium, Thyrostroma and Wojnowiciella. Each genus is provided with a taxonomic background, distribution, hosts, disease symptoms, and updated backbone trees. Species confirmed with pathogenicity studies are denoted when data are available. Six of the genera are updated from previous entries as many new species have been described.

Genome Sequence Resources of Colletotrichum truncatum, C. plurivorum, C. musicola, and C. sojae: Four Species Pathogenic to Soybean (Glycine max)

Colletotrichum is a large genus of plant pathogenic fungi comprising more than 200 species. In this work, we present the genome sequences of four Colletotrichum species pathogenic to soybean: C. truncatum, C. plurivorum, C. musicola, and C. sojae. While C. truncatum is globally considered the most important pathogen, the other three species have been described and associated with soybean only recently. The genome sequences will provide insights into factors that contribute to pathogenicity toward soybean and will be useful for further research into the evolution of Colletotrichum.

Pathogenic Adaptations Revealed by Comparative Genome Analyses of Two Colletotrichum spp., the Causal Agent of Anthracnose in Rubber Tree

Colletotrichum siamense and Colletotrichum australisinense cause Colletotrichum leaf disease that differ in their symptoms in rubber tree (Hevea brasiliensis), and pathogenicity of these two fungal species is also not identical on different cultivars of rubber tree. This divergence is often attributed to pathogen virulence factors, namely carbohydrate-active enzymes (CAZymes), secondary metabolites (SM), and small-secreted protein (SSP) effectors. The draft genome assembly and functional annotation of potential pathogenicity genes of both species obtained here provide an important and timely genomic resource for better understanding the biology and lifestyle of Colletotrichum spp. This should pave the way for designing more efficient disease control strategies in plantations of rubber tree. In this study, the genes associated with these categories were manually annotated in the genomes of C. australisinense GX1655 and C. siamense HBCG01. Comparative genomic analyses were performed to address the evolutionary relationships among these gene families in the two species. First, the size of genome assembly, number of predicted genes, and some of the functional categories differed significantly between the two congeners. Second, from the comparative genomic analyses, we identified some specific genes, certain higher abundance of gene families associated with CAZymes, CYP450, and SM in the genome of C. siamense, and Nep1-like proteins (NLP) in the genome of C. australisinense.

Prunus trees in Germany—a hideout of unknown fungi?

Prunus belongs to the economically most important genera of fruit crops in Germany. Although wood pathogens possess the capability to damage the host substantially, the knowledge of the fungal pathogenic community and the mycobiome of Prunus wood in general is low. During a survey in important fruit production areas in Germany, branches with symptoms of fungal infection were sampled in Prunus avium, P. cerasus and P. domestica orchards, and 1018 fungal isolates were obtained primarily from the transition zone of symptomatic to non-symptomatic wood. By a combination of blastn searches and phylogenetic analyses based on ITS and LSU sequences with a strong focus on reliable reference data, a diversity of 172 fungal taxa belonging to Ascomycota, Basidiomycota and Mucoromycota were differentiated. The majority of the strains belonged to three classes of Ascomycota, namely Sordariomycetes, Leotiomycetes and Dothideomycetes. The dominant species were Aposphaeria corallinolutea (Dothideomycetes) and Pallidophorina paarla (Leotiomycetes) that were isolated more than a hundred times each, while all other taxa were isolated ≤ 30 times. Only part of them could be identified to species level. Because of the high plasticity of species boundaries, the identification certainty was divided into categories based on nucleotide differences to reference sequences. In total, 82 species were identified with high and 20 species with low (cf.) certainty. Moreover, about 70 species could not be assigned to a known species, which reveals Prunus wood to represent a habitat harbouring high numbers of potentially new species, even in a well-explored region like Germany.

Colletotrichum cymbidiicola Causing Anthracnose on Cymbidium Orchids in Korea

A Colletotrichum species was isolated from leaves of Cymbidium exhibiting symptoms of anthracnose. In this study, the isolates obtained were identified based on recent taxonomic approaches for the genus Colletotrichum. The identity of the causal pathogen was confirmed using morphological data and phylogenetic analysis of combined multi-gene dataset (internal transcribed spacer, glyceraldehyde 3-phosphate dehydrogenase, chitin synthase-1, actin, histone3, beta-tubulin, and calmodulin). Pathogenicity testing revealed that the isolates were pathogenic to Cymbidium. Based on these results, the fungal pathogen occurring on Cymbidium orchids was identified as Colletotrichum cymbidiicola, which is a newly recorded species in Korea.

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.

The Many Questions about Mini Chromosomes in Colletotrichum spp

Many fungal pathogens carry accessory regions in their genome, which are not required for vegetative fitness. Often, although not always, these regions occur as relatively small chromosomes in different species. Such mini chromosomes appear to be a typical feature of many filamentous plant pathogens. Since these regions often carry genes coding for effectors or toxin-producing enzymes, they may be directly related to virulence of the respective pathogen. In this review, we outline the situation of small accessory chromosomes in the genus Colletotrichum, which accounts for ecologically important plant diseases. We summarize which species carry accessory chromosomes, their gene content, and chromosomal makeup. We discuss the large variation in size and number even between different isolates of the same species, their potential roles in host range, and possible mechanisms for intra- and interspecies exchange of these interesting genetic elements.

Fungal diversity notes 1151–1276: taxonomic and phylogenetic contributions on genera and species of fungal taxa

Fungal diversity notes is one of the important journal series of fungal taxonomy that provide detailed descriptions and illustrations of new fungal taxa, as well as providing new information of fungal taxa worldwide. This article is the 11th contribution to the fungal diversity notes series, in which 126 taxa distributed in two phyla, six classes, 24 orders and 55 families are described and illustrated. Taxa in this study were mainly collected from Italy by Erio Camporesi and also collected from China, India and Thailand, as well as in some other European, North American and South American countries. Taxa described in the present study include two new families, 12 new genera, 82 new species, five new combinations and 25 new records on new hosts and new geographical distributions as well as sexual-asexual reports. The two new families are Eriomycetaceae (Dothideomycetes, family incertae sedis) and Fasciatisporaceae (Xylariales, Sordariomycetes). The twelve new genera comprise Bhagirathimyces (Phaeosphaeriaceae), Camporesiomyces (Tubeufiaceae), Eriocamporesia (Cryphonectriaceae), Eriomyces (Eriomycetaceae), Neomonodictys (Pleurotheciaceae), Paraloratospora (Phaeosphaeriaceae), Paramonodictys (Parabambusicolaceae), Pseudoconlarium (Diaporthomycetidae, genus incertae sedis), Pseudomurilentithecium (Lentitheciaceae), Setoapiospora (Muyocopronaceae), Srinivasanomyces (Vibrisseaceae) and Xenoanthostomella (Xylariales, genera incertae sedis). The 82 new species comprise Acremonium chiangraiense, Adustochaete nivea, Angustimassarina camporesii, Bhagirathimyces himalayensis, Brunneoclavispora camporesii, Camarosporidiella camporesii, Camporesiomyces mali, Camposporium appendiculatum, Camposporium multiseptatum, Camposporium septatum, Canalisporium aquaticium, Clonostachys eriocamporesiana, Clonostachys eriocamporesii, Colletotrichum hederiicola, Coniochaeta vineae, Conioscypha verrucosa, Cortinarius ainsworthii, Cortinarius aurae, Cortinarius britannicus, Cortinarius heatherae, Cortinarius scoticus, Cortinarius subsaniosus, Cytospora fusispora, Cytospora rosigena, Diaporthe camporesii, Diaporthe nigra, Diatrypella yunnanensis, Dictyosporium muriformis, Didymella camporesii, Diutina bernali, Diutina sipiczkii, Eriocamporesia aurantia, Eriomyces heveae, Ernakulamia tanakae, Falciformispora uttaraditensis, Fasciatispora cocoes, Foliophoma camporesii, Fuscostagonospora camporesii, Helvella subtinta, Kalmusia erioi, Keissleriella camporesiana, Keissleriella camporesii, Lanspora cylindrospora, Loratospora arezzoensis, Mariannaea atlantica, Melanographium phoenicis, Montagnula camporesii, Neodidymelliopsis camporesii, Neokalmusia kunmingensis, Neoleptosporella camporesiana, Neomonodictys muriformis, Neomyrmecridium guizhouense, Neosetophoma camporesii, Paraloratospora camporesii, Paramonodictys solitarius, Periconia palmicola, Plenodomus triseptatus, Pseudocamarosporium camporesii, Pseudocercospora maetaengensis, Pseudochaetosphaeronema kunmingense, Pseudoconlarium punctiforme, Pseudodactylaria camporesiana, Pseudomurilentithecium camporesii, Pseudotetraploa rajmachiensis, Pseudotruncatella camporesii, Rhexocercosporidium senecionis, Rhytidhysteron camporesii, Rhytidhysteron erioi, Septoriella camporesii, Setoapiospora thailandica, Srinivasanomyces kangrensis, Tetraploa dwibahubeeja, Tetraploa pseudoaristata, Tetraploa thrayabahubeeja, Torula camporesii, Tremateia camporesii, Tremateia lamiacearum, Uzbekistanica pruni, Verruconis mangrovei, Wilcoxina verruculosa, Xenoanthostomella chromolaenae and Xenodidymella camporesii. The five new combinations are Camporesiomyces patagoniensis, Camporesiomyces vaccinia, Camposporium lycopodiellae, Paraloratospora gahniae and Rhexocercosporidium microsporum. The 22 new records on host and geographical distribution comprise Arthrinium marii, Ascochyta medicaginicola, Ascochyta pisi, Astrocystis bambusicola, Camposporium pellucidum, Dendryphiella phitsanulokensis, Diaporthe foeniculina, Didymella macrostoma, Diplodia mutila, Diplodia seriata, Heterosphaeria patella, Hysterobrevium constrictum, Neodidymelliopsis ranunculi, Neovaginatispora fuckelii, Nothophoma quercina, Occultibambusa bambusae, Phaeosphaeria chinensis, Pseudopestalotiopsis theae, Pyxine berteriana, Tetraploa sasicola, Torula gaodangensis and Wojnowiciella dactylidis. In addition, the sexual morphs of Dissoconium eucalypti and Phaeosphaeriopsis pseudoagavacearum are reported from Laurus nobilis and Yucca gloriosa in Italy, respectively. The holomorph of Diaporthe cynaroidis is also reported for the first time.

Multi-locus phylogeny and taxonomy of an unresolved, heterogeneous species complex within the genus Golovinomyces (Ascomycota, Erysiphales), including G. ambrosiae, G. circumfusus and G. spadiceus

Background

Previous phylogenetic analyses of species within the genus Golovinomyces (Ascomycota, Erysiphales), based on ITS and 28S rDNA sequence data, revealed a co-evolutionary relationship between powdery mildew species and hosts of certain tribes of the plant family Asteraceae. Golovinomyces growing on host plants belonging to the Heliantheae formed a single lineage, comprised of a morphologically differentiated complex of species, which included G. ambrosiae, G. circumfusus, and G. spadiceus. However, the lineage also encompassed sequences retrieved from Golovinomyces specimens on other Asteraceae tribes as well as other plant families, suggesting the involvement of a plurivorous species. A multilocus phylogenetic examination of this complex, using ITS, 28S, IGS (intergenic spacer), TUB2 (beta-tubulin), and CHS1 (chitin synthase I) sequence data was carried out to clarify the discrepancies between ITS and 28S rDNA sequence data and morphological differences. Furthermore, the circumscription of species and their host ranges were emended.

Results

The phylogenetic and morphological analyses conducted in this study revealed three distinct species named, viz., (1) G. ambrosiae emend. (including G. spadiceus), a plurivorous species that occurs on a multitude of hosts including, Ambrosia spp., multiple species of the Heliantheae and plant species of other tribes of Asteraceae including the Asian species of Eupatorium; (2) G. latisporus comb. nov. (≡ Oidium latisporum), the closely related, but morphologically distinct species confined to hosts of the Heliantheae genera Helianthus, Zinnia, and most likely Rudbeckia; and (3) G. circumfusus confined to Eupatorium cannabinum in Europe.

Conclusions

The present results provide strong evidence that the combination of multi-locus phylogeny and morphological analysis is an effective way to identify species in the genus Golovinomyces.

Arboricolonus simplex gen. et sp. nov. and novelties in Cadophora, Minutiella and Proliferodiscus from Prunus wood in Germany

During a survey on fungi associated with wood necroses of Prunus trees in Germany, strains belonging to the Leotiomycetes and Eurotiomycetes were detected by preliminary analyses of ITS sequences. Multi-locus phylogenetic analyses (LSU, ITS, TUB, EF-1α, depending on genus) of 31 of the 45 strains from Prunus and reference strains revealed several new taxa, including Arboricolonus gen. nov., a new genus in the Helotiales (Leotiomycetes) with a collophorina-like asexual morph. Seven Cadophora species (Helotiales, Leotiomycetes) were treated. The 29 strains from Prunus belonged to five species, of which C. luteo-olivacea and C. novi-eboraci were dominating; C. africana sp. nov., C. prunicola sp. nov. and C. ramosa sp. nov. were revealed as new species. The genus Cadophora was reported from Prunus for the first time. Phialophora bubakii was combined in Cadophora and differentiated from C. obscura, which was resurrected. Asexual morphs of two Proliferodiscus species (Helotiales, Leotiomycetes) were described, including one new species, Pr. ingens sp. nov. Two Minutiella species (Phaeomoniellales, Eurotiomycetes) were detected, including the new species M. pruni-avium sp. nov. Prunus avium and P. domestica are reported as host plants of Minutiella.

Colletotrichum: species complexes, lifestyle, and peculiarities of some sources of genetic variability

The genus Colletotrichum comprises species with different lifestyles but is mainly known for phytopathogenic species that infect crops of agronomic relevance causing considerable losses. The fungi of the genus Colletotrichum are distributed in species complexes and within each complex some species have particularities regarding their lifestyle. The most commonly found and described lifestyles in Colletotrichum are endophytic and hemibiotrophic phytopathogenic. Several of these phytopathogenic species show wide genetic variability, which makes long-term maintenance of resistance in plants difficult. Different mechanisms may play an important role in the emergence of genetic variants but are not yet fully understood in this genus. These mechanisms include heterokaryosis, a parasexual cycle, sexual cycle, transposable element activity, and repeat-induced point mutations. This review provides an overview of the genus Colletotrichum, the species complexes described so far and the most common lifestyles in the genus, with a special emphasis on the mechanisms that may be responsible, at least in part, for the emergence of new genotypes under field conditions.

Distribution and Pathogenicity of Colletotrichum Species Associated With Mango Anthracnose in Mexico

Mango anthracnose, caused by Colletotrichum spp., is the most significant disease of mango (Mangifera indica L.) in almost all production areas around the world. In Mexico, mango anthracnose has only been attributed to C. asianum and C. gloeosporioides. The aims of this study were to identify the Colletotrichum species associated with mango anthracnose symptoms in Mexico by phylogenetic inference using the ApMat marker, to determine the distribution of these species, and to test their pathogenicity and virulence on mango fruits. Surveys were carried out from 2010 to 2012 in 59 commercial orchards in the major mango growing states of Mexico, and a total of 118 isolates were obtained from leaves, twigs, and fruits with typical anthracnose symptoms. All isolates were tentatively identified in the C. gloeosporioides species complex based on morphological and cultural characteristics. The Bayesian inference phylogenetic tree generated with Apn2/MAT intergenic spacer sequences of 59 isolates (one per orchard) revealed that C. alienum, C. asianum, C. fructicola, C. siamense, and C. tropicale were associated with symptoms of mango anthracnose. In this study, C. alienum, C. fructicola, C. siamense, and C. tropicale are reported for the first time in association with mango tissues in Mexico. This study represents the first report of C. alienum causing mango anthracnose worldwide. The distribution of Colletotrichum species varied among the mango growing states from Mexico. Chiapas was the only state in which all five species were found. Pathogenicity tests on mango fruit cultivar Manila showed that all Colletotrichum species from this study could induce anthracnose lesions. However, differences in virulence were evident among species. C. siamense and C. asianum were the most virulent, whereas C. alienum and C. fructicola were considered the least virulent species.

Etiology of Cyclocarya paliurus Anthracnose in Jiangsu Province, China

Cyclocarya paliurus is an extremely valuable and multifunctional tree species whose leaves have traditionally been used in used in medicine or as a medicinal tea in China. In recent years, anthracnose has been frequently observed on young leaves of C. paliurus in several nurseries located in Jiangsu Province, resulting in great yield and quality losses. To date, no information is available about the prevalence of C. paliurus anthracnose in China. The main purpose of the present study was to characterize the etiology of C. paliurus anthracnose. Phylogenetic analysis of the eight-loci concatenated dataset revealed that all 44 single-spore Colletotrichum isolates belonged to three species in the Colletotrichum gloeosporioides species complex, namely, Colletotrichum aenigma, Colletotrichum fructicola, and C. gloeosporioides sensu stricto. Phenotypic features, including the colony appearance and the morphology of conidia, appressoria, and ascospores, were consistent with the phylogenetic grouping. Virulence tests validated that the three Colletotrichum species could cause typical symptoms of anthracnose on C. paliurus leaves, similar to those observed in the field. The optimum mycelial growth temperature ranged from 25 to 30°C for all representative isolates, while C. gloeosporioides s. s. isolates exhibited greater tolerance to high temperature (40°C). Fungicide sensitivity assays indicated that all three Colletotrichum species were sensitive to tetramycin, which may be a potential alternative for the management of C. paliurus anthracnose. To our knowledge, this study provides the first report of C. aenigma, C. fructicola, and C. gloeosporioides s. s. causing C. paliurus anthracnose in China as well as in the world.

Colletotrichum species associated with mango in southern China

Mango (Mangifera indica L.) is an economically significant fruit crop in provinces of southern China including Hainan, Yunnan, Sichuan, Guizhou, Guangdong and Fujian. The objective of this study was to examine the diversity of Colletotrichum species infecting mango cultivars in major growing areas in China, using morphological and molecular techniques together with pathogenicity tests on detached leaves and fruits. Over 200 Colletotrichum isolates were obtained across all mango orchards investigated, and 128 of them were selected for sequencing and analyses of actin (ACT), chitin synthase (CHS-1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), the internal transcribed spacer (ITS) region, β-tubulin (TUB2) genomic regions. Our results showed that the most common fungal isolates associated with mango in southern China involved 13 species: Colletotrichum asianum, C. cliviicola, C. cordylinicola, C. endophytica, C. fructicola, C. gigasporum, C. gloeosporioides, C. karstii, C. liaoningense, C. musae, C. scovillei, C. siamense and C. tropicale. The dominant species were C. asianum and C. siamense each accounting for 30%, and C. fructicola for 25%. Only C. asianum, C. fructicola, C. scovillei and C. siamense have previously been reported on mango, while the other nine Colletotrichum species listed above were first reports associated with mango in China. From this study, five Colletotrichum species, namely C. cordylinicola, C. endophytica, C. gigasporum, C. liaoningense and C. musae were the first report on mango worldwide. Pathogenicity tests revealed that all 13 species caused symptoms on artificially wounded mango fruit and leaves (cv. Tainong). There was no obvious relationship between aggressiveness and the geographic origin of the isolates. These findings will help in mango disease management and future disease resistance breeding.

Optimal markers for the identification of Colletotrichum species

Colletotrichum is among the most important genera of fungal plant pathogens. Molecular phylogenetic studies over the last decade have resulted in a much better understanding of the evolutionary relationships and species boundaries within the genus. There are now approximately 200 species accepted, most of which are distributed among 13 species complexes. Given their prominence on agricultural crops around the world, rapid identification of a large collection of Colletotrichum isolates is routinely needed by plant pathologists, regulatory officials, and fungal biologists. However, there is no agreement on the best molecular markers to discriminate species in each species complex. Here we calculate the barcode gap distance and intra/inter-specific distance overlap to evaluate each of the most commonly applied molecular markers for their utility as a barcode for species identification. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone-3 (HIS3), DNA lyase (APN2), intergenic spacer between DNA lyase and the mating-type locus MAT1-2-1 (APN2/MAT-IGS), and intergenic spacer between GAPDH and a hypothetical protein (GAP2-IGS) have the properties of good barcodes, whereas sequences of actin (ACT), chitin synthase (CHS-1) and nuclear rDNA internal transcribed spacers (nrITS) are not able to distinguish most species. Finally, we assessed the utility of these markers for phylogenetic studies using phylogenetic informativeness profiling, the genealogical sorting index (GSI), and Bayesian concordance analyses (BCA). Although GAPDH, HIS3 and β-tubulin (TUB2) were frequently among the best markers, there was not a single set of markers that were best for all species complexes. Eliminating markers with low phylogenetic signal tends to decrease uncertainty in the topology, regardless of species complex, and leads to a larger proportion of markers that support each lineage in the Bayesian concordance analyses. Finally, we reconstruct the phylogeny of each species complex using a minimal set of phylogenetic markers with the strongest phylogenetic signal and find the majority of species are strongly supported as monophyletic.

Current Status of Soybean Anthracnose Associated with Colletotrichum truncatum in Brazil and Argentina

Brazil and Argentina have a combined soybean area of 53.6 million hectares, which accounts for over half of the total global production. The soybean crop in South America extends from latitude 8–10° S to 32–36° S. Such a vast, almost contiguous area imposes a serious sanitary risk to the crop. Currently, the prevalence of anthracnose is increasing, with recurring reports of severe epidemics and expressive yield losses. Soybean anthracnose is mainly associated with Colletotrichum truncatum, although other Colletotrichum species have also been reported as causal agents of this disease. Knowledge about the morphological, cultural, and molecular variability of C. truncatum in South America is crucial for disease management. Here, we present data on the molecular, morphological, biological, cultural, and pathogenicity of C. truncatum isolates collected in Brazil and Argentina. Light microscopy and randomly-amplified polymorphic DNA (RAPD) analysis were used for estimating the variability of isolates. Colletotrichum truncatum displayed three types of conidiogenesis, viz. conidial formation from conidiogenous cells on hyphal extremities, in conidiomas in acervuli, and directly from fertile setae (a mechanism yet-unreported for C. truncatum). RAPD profiling was effective in revealing the genetic diversity among C. truncatum isolates. The intra-group similarity was greater among the Argentinian isolates when compared to the Brazilian group. Furthermore, the results indicated a strong correlation between geographical origin and molecular grouping, with the exclusive or semi-exclusive assembling of Brazilian and Argentinian isolates in distinct clades. Finally, a preliminary account of the reaction of soybean accessions to C. truncatum is also included.

Angioinvasive, cutaneous infection due to Colletotrichum siamense in a stem cell transplant recipient: Report and review of prior cases

Colletotrichum is an important fungal plant pathogen, yet an uncommon cause of human disease. Herein we report a case of invasive, cutaneous infection in a stem cell transplant recipient due to Colletotrichum species, with accompanying review of the literature. The infection was successfully treated with a combination of liposomal amphotericin B and voriconazole. Multilocus phylogenetic analysis revealed that the distinct isolate belongs to Colletotrichum siamense, a member of the Colletotrichum gloeosporioides species complex not previously described as a human pathogen. Colletotrichum infection remains in the differential for skin lesions in the immune compromised host.

Molecular Detection of the Seed-Borne Pathogen Colletotrichum lupini Targeting the Hyper-Variable IGS Region of the Ribosomal Cluster

Lupins anthracnose is a destructive seed and airborne disease caused by Colletotrichum lupini, affecting stems and pods. Primary seed infections as low as 0.01-0.1% can cause very severe yield losses. One of the most effective management strategies is the development of a robust and sensitive seed detection assay to screen seed lots before planting. PCR-based detection systems exhibit higher levels of sensitivity than conventional techniques, but when applied to seed tests they require the extraction of PCR-quality DNA from target organisms in backgrounds of saprophytic organisms and inhibitory seed-derived compounds. To overcome these limitations, a new detection protocol for C. lupini based on a biological enrichment step followed by a PCR assay was developed. Several enrichment protocols were compared with Yeast Malt Broth amended with ampicillin, streptomycin, and lactic acid were the most efficient. A species-specific C. lupini primer pair was developed based on rDNA IGS sequences. The specificity was evaluated against 17 strains of C. lupini, 23 different Colletotrichum species, and 21 different organisms isolated from seeds of Lupinus albus cv. Multitalia, L. luteus cv. Mister, and L. angustifolius cv. Tango. The protocol described here enabled the detection of C. lupini in samples artificially infected with less than 1/10,000 infected seed.