The Colletotrichum acutatum species complex

Fungicide resistance in Colletotrichum fructicola and Colletotrichum siamense causing peach anthracnose in China

Peach is one of the popular and economically important fruit crops in China. Peach cultivation is hampered due to attacks of anthracnose disease, causing significant economic losses. Colletotrichum fructicola and Colletotrichum siamense belong to the Colletotrichum gloeosporioides species complex and are considered major pathogens of peach anthracnose. Application of different groups of fungicides is a routine approach for controlling this disease. However, fungicide resistance is a significant drawback in managing peach anthracnose nowadays. In this study, 39 isolates of C. fructicola and 41 isolates of C. siamense were collected from different locations in various provinces in China. The sensitivity of C. fructicola and C. siamense to some commonly used fungicides, i.e., carbendazim, iprodione, fluopyram, and propiconazole, was determined. All the isolates of C. fructicola collected from Guangdong province showed high resistance to carbendazim, whereas isolates collected from Guizhou province were sensitive. In C. siamense, isolates collected from Hebei province showed moderate resistance, while those from Shandong province were sensitive to carbendazim. On the other hand, all the isolates of C. fructicola and C. siamense showed high resistance to the dicarboximide (DCF) fungicide iprodione and succinate dehydrogenase inhibitor (SDHI) fungicide fluopyram. However, they are all sensitive to the demethylation inhibitor (DMI) fungicide propiconazole. Positive cross-resistance was observed between carbendazim and benomyl as they are members of the same methyl benzimidazole carbamate (MBC) group. While no correlation of sensitivity was observed between different groups of fungicides. No significant differences were found in each fitness parameter between carbendazim-resistant and sensitive isolates in both species. Molecular characterization of the β-tubulin 2 (TUB2) gene revealed that in C. fructicola, the E198A point mutation was the determinant for the high resistance to carbendazim, while the F200Y point mutation was linked with the moderate resistance to carbendazim in C. siamense. Based on the results of this study, DMI fungicides, e.g., propiconazole or prochloraz could be used to control peach anthracnose, especially at locations where the pathogens have already developed the resistance to carbendazim and other fungicides.

Fungal community and toxigenic taxa in chestnut fruits in postharvest conditioning process and storage

BACKGROUND

Chestnut fruit quality is affected by fungal contamination. The study of the patterns of contamination in the postharvest is crucial to individuate the critical phases and propose solutions. To understand how fungal colonization varies on fruits, the composition of mycobiota was investigated in postharvest handling and in between tissues (shell and kernel).

RESULTS

Fungal sequences were clustered into 308 operational taxonomic units (OTUs). Biodiversity was higher in shell than kernel tissues. Results evidenced the risk of new contamination in specific phases such as the 'cold bath' and storage. Genera known as mycotoxin producers were detected in all phases. Specifically, 47 OTUs belonging to Penicillium, eight to Fusarium and two to Aspergillus genera were identified. While Fusarium spp. was sensitive to 'warm bath' phase, Penicillium spp. was largely insensitive and accumulated in storage conditions. Surprisingly, Aspergillus spp. was poorly represented. Aflatoxin, ochratoxin A, fumonisins and T-2/HT-2 detection was performed for shell and kernel, and process phases. Higher contamination was observed on shell than in kernel samples. While aflatoxins were within the European Union (EU) limits for dry fruits, Ochratoxin exceeded the EU limits. The present study represents the first report of fumonisins and T-2/HT-2 detection in chestnuts.

CONCLUSION

Fungal contamination taxa is high in chestnut fruits following postharvest handling and storage. A parametrization of process phases such as the 'warm bath' is functional to reduce the risk for some taxa. For other spoilage and mycotoxigenic genera strict sanitation procedures of equipment and water must be individuated and implemented to reduce their impact. © 2024 The Author(s). Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

What are the 100 most cited fungal genera?

The global diversity of fungi has been estimated between 2 to 11 million species, of which only about 155 000 have been named. Most fungi are invisible to the unaided eye, but they represent a major component of biodiversity on our planet, and play essential ecological roles, supporting life as we know it. Although approximately 20 000 fungal genera are presently recognised, the ecology of most remains undetermined. Despite all this diversity, the mycological community actively researches some fungal genera more commonly than others. This poses an interesting question: why have some fungal genera impacted mycology and related fields more than others? To address this issue, we conducted a bibliometric analysis to identify the top 100 most cited fungal genera. A thorough database search of the Web of Science, Google Scholar, and PubMed was performed to establish which genera are most cited. The most cited 10 genera are Saccharomyces, Candida, Aspergillus, Fusarium, Penicillium, Trichoderma, Botrytis, Pichia, Cryptococcus and Alternaria. Case studies are presented for the 100 most cited genera with general background, notes on their ecology and economic significance and important research advances. This paper provides a historic overview of scientific research of these genera and the prospect for further research. Citation: Bhunjun CS, Chen YJ, Phukhamsakda C, Boekhout T, Groenewald JZ, McKenzie EHC, Francisco EC, Frisvad JC, Groenewald M, Hurdeal VG, Luangsa-ard J, Perrone G, Visagie CM, Bai FY, Błaszkowski J, Braun U, de Souza FA, de Queiroz MB, Dutta AK, Gonkhom D, Goto BT, Guarnaccia V, Hagen F, Houbraken J, Lachance MA, Li JJ, Luo KY, Magurno F, Mongkolsamrit S, Robert V, Roy N, Tibpromma S, Wanasinghe DN, Wang DQ, Wei DP, Zhao CL, Aiphuk W, Ajayi-Oyetunde O, Arantes TD, Araujo JC, Begerow D, Bakhshi M, Barbosa RN, Behrens FH, Bensch K, Bezerra JDP, Bilański P, Bradley CA, Bubner B, Burgess TI, Buyck B, Čadež N, Cai L, Calaça FJS, Campbell LJ, Chaverri P, Chen YY, Chethana KWT, Coetzee B, Costa MM, Chen Q, Custódio FA, Dai YC, Damm U, de Azevedo Santiago ALCM, De Miccolis Angelini RM, Dijksterhuis J, Dissanayake AJ, Doilom M, Dong W, Alvarez-Duarte E, Fischer M, Gajanayake AJ, Gené J, Gomdola D, Gomes AAM, Hausner G, He MQ, Hou L, Iturrieta-González I, Jami F, Jankowiak R, Jayawardena RS, Kandemir H, Kiss L, Kobmoo N, Kowalski T, Landi L, Lin CG, Liu JK, Liu XB, Loizides M, Luangharn T, Maharachchikumbura SSN, Makhathini Mkhwanazi GJ, Manawasinghe IS, Marin-Felix Y, McTaggart AR, Moreau PA, Morozova OV, Mostert L, Osiewacz HD, Pem D, Phookamsak R, Pollastro S, Pordel A, Poyntner C, Phillips AJL, Phonemany M, Promputtha I, Rathnayaka AR, Rodrigues AM, Romanazzi G, Rothmann L, Salgado-Salazar C, Sandoval-Denis M, Saupe SJ, Scholler M, Scott P, Shivas RG, Silar P, Souza-Motta CM, Silva-Filho AGS, Spies CFJ, Stchigel AM, Sterflinger K, Summerbell RC, Svetasheva TY, Takamatsu S, Theelen B, Theodoro RC, Thines M, Thongklang N, Torres R, Turchetti B, van den Brule T, Wang XW, Wartchow F, Welti S, Wijesinghe SN, Wu F, Xu R, Yang ZL, Yilmaz N, Yurkov A, Zhao L, Zhao RL, Zhou N, Hyde KD, Crous PW (2024). What are the 100 most cited fungal genera? Studies in Mycology 108: 1-411. doi: 10.3114/sim.2024.108.01.

Quantitative Trait Loci Analysis and Marker Development for Fruit Rot Resistance in Cranberry Shows Potential Genetic Association with Epicuticular Wax

Fruit rot is a fungal disease complex that threatens cranberry yields in North American growing operations. Management of fruit rot is especially difficult because of the diversity of the infecting fungal species, and although infections take place early in the season, the pathogens usually remain latent in the ovary until the fruit ripen. Control methods heavily rely on fungicide applications, a practice that may be limited in viability long term. Breeding for fruit rot resistance (FRR) is essential for sustainable production. It is likely that field resistance is multifaceted and involves a myriad of traits that fortify cranberry plants against the biotic and abiotic stresses contributing to fruit rot. In this study, we identified quantitative trait loci (QTL) for FRR in a segregating population. Interestingly, a QTL associated with resistance was found to overlap with one associated with fruit epicuticular wax (ECW). A single-nucleotide polymorphism genotyping assay successfully identified accessions that exhibit the desired phenotypes (i.e., less rot and more ECW), thus making it a useful tool for marker-assisted selection. Candidate genes that may contribute to FRR and ECW were also identified. This work will expedite breeding for improved cranberry fruit quality.

Mitigating Emerging and Reemerging Diseases of Fruit and Vegetable Crops in a Changing Climate

Fruit and vegetable crops are important sources of nutrition and income globally. Producing these high-value crops requires significant investment of often scarce resources, and, therefore, the risks associated with climate change and accompanying disease pressures are especially important. Climate change influences the occurrence and pressure of plant diseases, enabling new pathogens to emerge and old enemies to reemerge. Specific environmental changes attributed to climate change, particularly temperature fluctuations and intense rainfall events, greatly alter fruit and vegetable disease incidence and severity. In turn, fruit and vegetable microbiomes, and subsequently overall plant health, are also affected by climate change. Changing disease pressures cause growers and researchers to reassess disease management and climate change adaptation strategies. Approaches such as climate smart integrated pest management, smart sprayer technology, protected culture cultivation, advanced diagnostics, and new soilborne disease management strategies are providing new tools for specialty crops growers. Researchers and educators need to work closely with growers to establish fruit and vegetable production systems that are resilient and responsive to changing climates. This review explores the effects of climate change on specialty food crops, pathogens, insect vectors, and pathosystems, as well as adaptations needed to ensure optimal plant health and environmental and economic sustainability.

New Species-Specific Real-Time PCR Assays for Colletotrichum Species Causing Bitter Rot of Apple

Bitter rot of apple is an economically important worldwide disease caused by different Colletotrichum species, depending on many factors such as climate, geography, other hosts, and crop management practices. Culture, morphology, and single-locus sequencing-based methods for identifying the Colletotrichum species are severely limited in effectiveness, while the multilocus sequence typing methods available for delineating species are costly, time-intensive, and require high expertise. We developed species-specific hydrolysis probe real-time PCR assays for the following nine Colletotrichum species causing bitter rot in the Mid-Atlantic U.S.A.: C. fructicola, C. chrysophilum, C. noveboracense, C. gloeosporioides s.s., C. henanense, C. siamense and C. theobromicola from the C. gloeosporioides species complex, and C. fioriniae and C. nymphaeae from the C. acutatum species complex. After searching 14 gene regions, we designed primers and probes in 5 of them for the nine target species. Four primer-probe set pairs were able to be duplexed. Sensitivity tests showed as little as 0.5 pg DNA were detectable. These real-time PCR assays will provide rapid and reliable identification of these key Colletotrichum species and will be critically important for studies aiming to elucidate their biology, epidemiology, and management on apples as the number one produced and consumed tree fruit in the U.S.A.

Complete genome sequence of a novel alternavirus isolated from the phytopathogenic fungus Colletotrichum fioriniae

A novel double-strand RNA (dsRNA) mycovirus, named "Colletotrichum fioriniae alternavirus1" (CfAV1), was isolated from the strain CX7 of Colletotrichum fioriniae, the causal agent of walnut anthracnose. The complete genome of CfAV1 is composed of three dsRNA segments: dsRNA1 (3528 bp), dsRNA2 (2485 bp), and dsRNA3 (2481 bp). The RNA-dependent RNA polymerase (RdRp) is encoded by dsRNA1, while both dsRNA2 and dsRNA3 encode hypothetical proteins. Based on multiple sequence alignments and phylogenetic analysis, CfAV1 is identified as a new member of the family Alternaviridae. This is the first report of an alternavirus that infects the phytopathogenic fungus C. fioriniae.

Diversity of Leaf Fungal Endophytes from Two Coffea arabica Varieties and Antagonism towards Coffee Leaf Rust

Coffee has immense value as a worldwide-appreciated commodity. However, its production faces the effects of climate change and the spread of severe diseases such as coffee leaf rust (CLR). The exploration of fungal endophytes associated with Coffea sp. has already found the existence of nearly 600 fungal species, but their role in the plants remains practically unknown. We have researched the diversity of leaf fungal endophytes in two Coffea arabica varieties: one susceptible and one resistant to CLR. Then, we conducted cross-infection essays with four common endophyte species (three Colletotrichum sp. and Xylaria sp. 1) and Hemileia vastatrix (CLR) in leaf discs, to investigate the interaction of the endophytes on CLR colonisation success and severity of infection. Two Colletotrichum sp., when inoculated 72 h before H. vastatrix, prevented the colonisation of the leaf disc by the latter. Moreover, the presence of endophytes prior to the arrival of H. vastatrix ameliorated the severity of CLR. Our work highlights both the importance of characterising the hidden biodiversity of endophytes and investigating their potential roles in the plant-endophyte interaction.

Identification and Genetic Diversity Analysis of the Pathogen of Anthracnose of Pepper in Guizhou

Anthracnose of pepper is a significant disease caused by Colletotrichum spp. In 2017 and 2021, 296 isolates were obtained from 69 disease samples. Through morphological analysis, pathogenicity detection, and polygenic phylogenetic analysis, the above strains were attributed to 10 species: C. scovillei, C. fructicola, C. karstii, C. truncatum, C. gloeosporioides, C. kahawae, C. boninense, C. nymphaeae, C. plurivorum, and C. nigrum. C. scovillei had the most strains (150), accounting for 51.02% of the total isolates; C. fructicola came in second (72 isolates), accounting for 24.49%. Regarding regional distribution, Zunyi City has the highest concentration of strains-92 strains total, or 34.18%-across seven species. Notably, this investigation showed that C. nymphaeae infected pepper fruit for the first time in China. Genetic diversity analysis showed that C. fructicola could be divided into seven haplotypes, and the population in each region had apparent genetic differentiation. However, the genetic distance between each population was not significantly related to geographical distance. Neutral detection and nucleotide mismatch analysis showed that C. fructicola might have undergone population expansion.

Identification and Fungicide Screening of Fungal Species Associated with Walnut Anthracnose in Shaanxi and Liaoning Provinces, China

Walnut is cultivated around the world for its precious woody nut and edible oil. Recently, walnut infected by Colletotrichum spp. resulted in a great yield and quality loss. In August and September 2014, walnut fruits with anthracnose were sampled from two commercial orchards in Shaanxi and Liaoning provinces, and five representative isolates were used in this study. To identify the pathogen properly, four genes per region (internal transcribed spacer, glyceraldehyde-3-phosphate dehydrogenase, actin, and chitin synthase) were sequenced and used in phylogenetic studies. Based on multilocus phylogenetic analysis, five isolates clustered with Colletotrichum fioriniae, including its ex-type, with 100% bootstrap support. The results of multilocus phylogenetic analyses, morphology, and pathogenicity confirmed that C. fioriniae was one of the walnut anthracnose pathogens in China. All 13 fungicides tested inhibited mycelial growth and spore germination. Flusilazole, fluazinam, prochloraz, and pyraclostrobin showed the strongest suppressive effects on the mycelial growth than the others, the average EC50 values ranged from 0.09 to 0.40 μg/ml, and there was not any significant difference (P < 0.05). Pyraclostrobin, thiram, and azoxystrobin were the most effective fungicides on spore germination (P < 0.05), and the EC50 values ranged from 0.01 to 0.44 μg/ml. Pyraclostrobin, azoxystrobin, fluazinam, flusilazole, mancozeb, thiram, and prochloraz exhibited a good control effect on walnut anthracnose caused by C. fioriniae, and preventive activities were greater than curative activities. Pyraclostrobin at 250 a.i. μg/ml and fluazinam at 500 a.i. μg/ml provided the highest preventive and curative efficacy, and the values ranged from 81.3 to 82.2% and from 72.9 to 73.6%, respectively. As a consequence, mancozeb and thiram could be used at the preinfection stage, and pyraclostrobin, azoxystrobin, flusilazole, fluazinam, and prochloraz could be used at the early stage for effective prevention and control of walnut anthracnose caused by C. fioriniae. The results will provide more significant instructions for controlling the disease effectively in northern China.

What's in my Pot? Six Colletotrichum Species Causing Anthracnose in Brazilian Pecan Orchards

Pecan (Carya illinoinensis) is one important exotic forest crop cultivated in South America, specifically in Brazil, Uruguay, and Argentina. However, diseases such as anthracnose, favored by high humidity conditions and high summer temperatures, make its cultivation difficult, causing important loss to pecan farmers. This study used morphological and molecular approaches to identify the Colletotrichum species causing anthracnose in pecan plantations in Southern Brazil. The isolates obtained from pecan fruits with anthracnose symptoms were grouped through quantitative morphological characteristics into three distinct morphotypes. Molecular analysis of nuclear genes allowed the identification of six species of Colletotrichum causing anthracnose in pecan: C. nymphaeae, C. fioriniae, C. gloeosporioides, C. siamense, C. kahawae, and C. karsti. Three of these species are reported for the first time as causal agents of anthracnose in pecan. Therefore, these results provide an important basis for the adoption and/or development of anthracnose management strategies in pecan orchards cultivated in southern Brazil and neighboring countries.

Fungal Endophytes: Discovering What Lies within Some of Canada's Oldest and Most Resilient Grapevines

Plant diseases and pests reduce crop yields, accounting for global crop losses of 30% to 50%. In conventional agricultural production systems, these losses are typically controlled by applying chemical pesticides. However, public pressure is mounting to curtail agrochemical use. In this context, employing beneficial endophytic microorganisms is an increasingly attractive alternative to the use of conventional chemical pesticides in agriculture. A multitude of fungal endophytes are naturally present in plants, producing enzymes, small peptides, and secondary metabolites due to their bioactivity, which can protect hosts from pathogens, pests, and abiotic stresses. The use of beneficial endophytic microorganisms in agriculture is an increasingly attractive alternative to conventional pesticides. The aim of this study was to characterize fungal endophytes isolated from apparently healthy, feral wine grapes in eastern Canada that have grown without agrochemical inputs for decades. Host plants ranged from unknown seedlings to long-lost cultivars not widely propagated since the 1800s. HPLC-MS was used to identify unique endophyte-derived chemical compounds in the host plants, while dual-culture competition assays showed a range in endophytes' ability to suppress the mycelial growth of Botrytis, which is typically controlled in viticulture with pesticides. Twelve of the most promising fungal endophytes isolated were identified using multilocus sequencing and morphology, while DNA barcoding was employed to identify some of their host vines. These fungal endophyte isolates, which consisted of both known and putative novel strains, belonged to seven genera in six families and five orders of Ascomycota. Exploring the fungal endophytes in these specimens may yield clues to the vines' survival and lead to the discovery of novel biocontrol agents.

Genome evolution and transcriptome plasticity is associated with adaptation to monocot and dicot plants in Colletotrichum fungi

BACKGROUND

Colletotrichum fungi infect a wide diversity of monocot and dicot hosts, causing diseases on almost all economically important plants worldwide. Colletotrichum is also a suitable model for studying gene family evolution on a fine scale to uncover events in the genome associated with biological changes.

RESULTS

Here we present the genome sequences of 30 Colletotrichum species covering the diversity within the genus. Evolutionary analyses revealed that the Colletotrichum ancestor diverged in the late Cretaceous in parallel with the diversification of flowering plants. We provide evidence of independent host jumps from dicots to monocots during the evolution of Colletotrichum, coinciding with a progressive shrinking of the plant cell wall degradative arsenal and expansions in lineage-specific gene families. Comparative transcriptomics of 4 species adapted to different hosts revealed similarity in gene content but high diversity in the modulation of their transcription profiles on different plant substrates. Combining genomics and transcriptomics, we identified a set of core genes such as specific transcription factors, putatively involved in plant cell wall degradation.

CONCLUSIONS

These results indicate that the ancestral Colletotrichum were associated with dicot plants and certain branches progressively adapted to different monocot hosts, reshaping the gene content and its regulation.

Blueberry floral probiotics: nectar microbes inhibit the growth of Colletotrichum pathogens

AIMS

To identify whether microorganisms isolated from blueberry flowers can inhibit the growth of Colletotrichum, an opportunistic plant pathogen that infects flowers and threatens yields, and to assess the impacts of floral microbes and Colletotrichum pathogens on artificial nectar sugars and honey bee consumption.

METHODS AND RESULTS

The growth inhibition of Colletotrichum (Colletotrichum acutatum, Colletotrichum fioriniae, and Colletotrichum gloeosporioides) was screened using both artificial nectar co-culture and dual culture plate assays. All candidate nectar microbes were screened for antagonism against a single C. acutatum isolate. Then, the top four candidate nectar microbes showing the strongest inhibition of C. acutatum (Neokomagataea thailandica, Neokomagataea tanensis, Metschnikowia rancensis, and Symmetrospora symmetrica) were evaluated for antagonism against three additional C. acutatum isolates, and single isolates of both C. fioriniae and C. gloeosporioides. In artificial nectar assays, single and three-species cultures inhibited the growth of two of four C. acutatum isolates by ca. 60%, but growth of other Colletotrichum species was not affected. In dual culture plate assays, inhibition was observed for all Colletotrichum species for at least three of four selected microbial antagonists (13%‒53%). Neither honey bee consumption of nectar nor nectar sugar concentrations were affected by any microbe or pathogen tested.

CONCLUSIONS

Selected floral microbes inhibited growth of all Colletotrichum species in vitro, although the degree of inhibition was specific to the assay and pathogen examined. In all microbial treatments, nectar sugars were preserved, and honey bee preference was not affected.

Blueberries infected with the fungal pathogen Colletotrichum fioriniae release odors that repel Drosophila suzukii

BACKGROUND

Spotted-wing drosophila, Drosophila suzukii, is a serious pest of thin-skinned fruits. Alternative methods to control this pest are needed to reduce insecticide use, including new repellents. Previous research demonstrated that D. suzukii adults use odor cues to avoid blueberries infected with the fungal pathogen Colletotrichum fioriniae, which causes the disease anthracnose. To identify novel D. suzukii repellents, we investigated the volatile emission from experimentally-infected fruit, which were inoculated with C. fioriniae isolates in the laboratory, and from field-collected fruit, which were naturally infected and harvested from a field. We then tested the pathogen-induced volatiles on D. suzukii adult behavior.

RESULTS

Volatile emission was similar between all five C. fioriniae strains, with good agreement between experimentally-infected and field-collected berries. In total, 14 volatiles were found to be more abundant in infected versus uninfected fruit headspace. In multiple-choice bioassays, nine of the 14 volatiles elicited repellency responses from adult D. suzukii. These nine volatiles were further evaluated in dual choice assays, where all nine reduced fly capture by 43-96% compared to the control. The most repellent compounds tested were the esters ethyl butanoate and ethyl (E)-but-2-enoate, which were more or equally repellent to the known D. suzukii repellents 1-octen-3-ol, geosmin, and 2-pentylfuran. Dose-response assays identified concentration-dependent effects on D. suzukii repellency and oviposition when applied individually and consistent aversion observed across doses of a 1:1 blend.

CONCLUSION

We report two repellents from C. fioriniae-infected blueberries that could be useful semiochemicals for the behavioral manipulation of D. suzukii in the field. © 2023 Society of Chemical Industry. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.

Epidemiological Relevance of Colletotrichum Species Isolated from Glomerella Leaf Spot Causing Symptoms in Apple Fruit

Colletotrichum isolates from apple leaves with symptoms of Glomerella leaf spot (GLS) can cause fruit rot and several small lesion spots, here called Colletotrichum fruit spot (CFS). This work investigated the epidemiological relevance of Colletotrichum species obtained from leaves with GLS in causing diseases in immature apple fruit by comparing different fruit sizes (phenological stages) for symptom development. In the first experiment, five Colletotrichum species were inoculated in 'Gala' (Ø = 5.5 cm) and 'Eva' (Ø = 4.8 cm) fruit in the field (2016/17 season). Subsequently, C. chrysophilum and C. nymphaeae were inoculated in fruit of different sizes (Ø = 2.4 to 6.3 cm) in the field (2017/18 and 2021/22 seasons) and in the laboratory according to the phenological stages of growing fruit. At harvest of the immature inoculated fruit in the field, only CFS symptoms were observed in both cultivars. For Gala, the CFS incidence reached 50% regardless of season, pathogen species, and fruit size. For Eva, CFS symptoms were observed after inoculation with C. melonis in the 2016/17 season and in smaller fruit inoculated with C. chrysophilum and C. nymphaeae in 2021/22. During postharvest, bitter rot symptoms developed, but did not seem to come from CFS symptoms. It can be concluded that the Gala cultivar has a high susceptibility to CFS caused by the two Colletotrichum species of the greatest epidemiological importance for GLS in Brazil in all fruit sizes tested.

New Insights in the Detection and Management of Anthracnose Diseases in Strawberries

Anthracnose diseases, caused by Colletotrichum spp., are considered to be among the most destructive diseases that have a significant impact on the global production of strawberries. These diseases alone can cause up to 70% yield loss in North America. Colletotrichum spp. causes several disease symptoms on strawberry plants, including root, fruit, and crown rot, lesions on petioles and runners, and irregular black spots on the leaf. In many cases, a lower level of infection on foliage remains non-symptomatic (quiescent), posing a challenge to growers as these plants can be a significant source of inoculum for the fruiting field. Reliable detection methods for quiescent infection should play an important role in preventing infected plants' entry into the production system or guiding growers to take appropriate preventative measures to control the disease. This review aims to examine both conventional and emerging approaches for detecting anthracnose disease in the early stages of the disease cycle, with a focus on newly emerging techniques such as remote sensing, especially using unmanned aerial vehicles (UAV) equipped with multispectral sensors. Further, we focused on the acutatum species complex, including the latest taxonomy, the complex life cycle, and the epidemiology of the disease. Additionally, we highlighted the extensive spectrum of management techniques against anthracnose diseases on strawberries and their challenges, with a special focus on new emerging sustainable management techniques that can be utilized in organic strawberry systems.

A Bitter, Complex Problem: Causal Colletotrichum Species in Virginia Orchards and Apple Fruit Susceptibility

Bitter rot, caused by Colletotrichum species, is one of the most devastating summer rot diseases affecting apple production in the Eastern United States. Given the differences in virulence and fungicide sensitivity levels between organisms belonging to the acutatum species complex (CASC) and the gloeosporioides species complex (CGSC), monitoring their diversity, geographic distribution, and frequency are essential for successful bitter rot management. In a 662-isolate collection from apple orchards in Virginia, isolates from CGSC were dominant (65.5%) in comparison to the CASC (34.5%). In a subsample of 82 representative isolates, using morphological and multilocus phylogenetic analyses, we identified C. fructicola (26.2%), C. chrysophilum (15.6%), C. siamense (0.8%), and C. theobromicola (0.8%) from CGSC and C. fioriniae (22.1%) and C. nymphaeae (1.6%) from CASC. The dominant species were C. fructicola, followed by C. fioriniae and C. chrysophilum. C. siamense followed by C. theobromicola developed the largest and deepest rot lesions on Honeycrisp fruit in our virulence tests. Detached fruit of nine apple cultivars and one wild accession (Malus sylvestris) were harvested early and late season and tested in controlled conditions for their susceptibility to C. fioriniae and C. chrysophilum. All cultivars were susceptible to both representative bitter rot species, with Honeycrisp fruit being the most susceptible and M. sylvestris, accession PI 369855, being the most resistant. We demonstrate that the frequency and prevalence of species in Colletotrichum complexes are highly variable in the Mid-Atlantic and provide region-specific data on apple cultivar susceptibility. Our findings are necessary for the successful management of bitter rot as an emerging and persistent problem in apple production both pre- and postharvest.

Characterization of Colletotrichum Causing Anthracnose on Rubber Trees in Yunnan: Two New Records and Two New Species from China

Among the most damaging diseases of rubber trees is anthracnose caused by the genus Colletotrichum, which leads to significant economic losses. Nonetheless, the specific Colletotrichum spp. that infect rubber trees in Yunnan Province, an important natural rubber base in China, have not been extensively investigated. Here, we isolated 118 Colletotrichum strains from rubber tree leaves exhibiting anthracnose symptoms in multiple plantations in Yunnan. Based on comparisons of their phenotypic characteristics and internal transcribed spacer ribosomal DNA sequences, 80 representative strains were chosen for additional phylogenetic analysis based on eight loci (act, ApMat, cal, CHS-1, GAPDH, GS, his3, and tub2), and nine species were identified. Colletotrichum fructicola, C. siamense, and C. wanningense were found to be the dominant pathogens causing rubber tree anthracnose in Yunnan. C. karstii was common, whereas C. bannaense, C. brevisporum, C. jinpingense, C. mengdingense, and C. plurivorum were rare. Among these nine species, C. brevisporum and C. plurivorum are reported for the first time in China, and two species are new to the world: C. mengdingense sp. nov. in the C. acutatum species complex and C. jinpingense sp. nov. in the C. gloeosporioides species complex. Their pathogenicity was confirmed with Koch's postulates by inoculating each species in vivo on rubber tree leaves. This study clarifies the geographic distribution of Colletotrichum spp. associated with anthracnose on rubber trees in representative locations of Yunnan, which is crucial for the implementation of quarantine measures.

The Role of Fatty Acids from Plant Surfaces in the Infectivity of Colletotrichum fioriniae

Aqueous extracts derived from flowers stimulate germination, secondary conidiation, and appressorial formation of various latent fruit rotting fungi. Even raindrops passing over flowers accumulate sufficient activity to influence the infectivity of fruit rotting fungi. Using a spore germination bioassay, high levels of bioactivity were found in chloroform extracts from plant tissues, implicating the nonpolar components of the cuticle. The fatty acid (FA) and fatty acid methyl ester (FAME) composition (C9-C20) of blueberry and cranberry tissues as well as aqueous flower extracts were characterized using a gas chromatography-mass spectrometry (GC-MS) method. The FAs and FAMEs found in the plant extracts were then tested for bioactivity using a spore germination bioassay. The C16:0 and C18:2 FAs and FAMEs, as well as the C18:0 FAME and the C20:0 FA, all stimulated appressorial formation while the C10:0 FA stimulated secondary conidiation. The C10:0 and C16:0 FAs were the only two bioactive components also identified from the aqueous floral extracts of both blueberry and cranberry and are therefore considered as contributors to the bioactivity observed in these extracts. The aqueous extracts from surfaces other than flowers showed little or no activity, and it is speculated that the movement of FAs may be related to the level of polymerization and cutin polyester development in flowers versus other plant organs. This study highlights the importance of the bloom period for infection and that the apparent effects on host susceptibility may therefore depend on the availability of specific FAs or combinations thereof.

Two new species of Colletotrichum (Glomerellaceae, Glomerellales) causing walnut anthracnose in Beijing

Colletotrichum species are plant pathogens, saprobes and endophytes on various plant hosts. It is regarded as one of the 10 most important genera of plant pathogens in the world. Walnut anthracnose is one of the most severe diseases affecting walnut productivity and quality in China. In this study, 162 isolates were obtained from 30 fruits and 65 leaf samples of walnut collected in Beijing, China. Based on morphological characteristics and DNA sequence analyses of the concatenated loci, namely internal transcribed spacer (ITS), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin (ACT), chitin synthase 1 (CHS-1) and beta-tubulin (TUB2), these isolates were identified as two novel species of Colletotrichum, i.e. C.juglandicola and C.peakense. Koch's postulates indicated that both C.juglandicola and C.peakense could cause anthracnose in walnut.

The evolution of mini-chromosomes in the fungal genus Colletotrichum

Anthracnose diseases caused by Colletotrichum species are among the most common fungal diseases. These symptoms typically manifest as dark, sunken lesions on leaves, stems, and fruit. In China, mango anthracnose seriously affects fruit yield and quality. Genome sequencing of several species shows the presence of mini-chromosomes. These are thought to contribute to virulence, but their formation and activity remain to be fully elucidated. Here, we assembled 17 Colletotrichum genomes (16 isolated from mango plus one from persimmon) through PacBio long-read sequencing. Half of the assembled scaffolds had telomeric repeats at both ends indicating full-length chromosomes. Based on comparative genomics analysis at interspecies and intraspecies levels, we identified extensive chromosomal rearrangements events. We analyzed mini-chromosomes of Colletotrichum spp. and found large variation among close relatives. In C. fructicola, homology between core chromosomes and mini-chromosomes suggested that some mini-chromosomes were generated by recombination of core chromosomes. In C. musae GZ23-3, we found 26 horizontally transferred genes arranged in clusters on mini-chromosomes. In C. asianum FJ11-1, several potential pathogenesis-related genes on mini-chromosomes were upregulated, especially in strains with highly pathogenic phenotypes. Mutants of these upregulated genes showed obvious defects in virulence. Our findings provide insights into the evolution and potential relationships to virulence associated with mini-chromosomes. IMPORTANCE Colletotrichum is a cosmopolitan fungal genus that seriously affects fruit yield and quality of many plant species. Mini-chromosomes have been found to be related to virulence in Colletotrichum. Further examination of mini-chromosomes can help us elucidate some pathogenic mechanisms of Colletotrichum. In this study, we generated novel assemblies of several Colletotrichum strains. Comparative genomic analyses within and between Colletotrichum species were conducted. We then identified mini-chromosomes in our sequenced strains systematically. The characteristics and generation of mini-chromosomes were investigated. Transcriptome analysis and gene knockout revealed pathogenesis-related genes located on mini-chromosomes of C. asianum FJ11-1. This study represents the most comprehensive investigation of chromosome evolution and potential pathogenicity of mini-chromosomes in the Colletotrichum genus.

Mango anthracnose disease: the current situation and direction for future research

Mango anthracnose disease (MAD) is a destructive disease of mangoes, with estimated yield losses of up to 100% in unmanaged plantations. Several strains that constitute Colletotrichum complexes are implicated in MAD worldwide. All mangoes grown for commercial purposes are susceptible, and a resistant cultivar for all strains is not presently available on the market. The infection can widely spread before being detected since the disease is invincible until after a protracted latent period. The detection of multiple strains of the pathogen in Mexico, Brazil, and China has prompted a significant increase in research on the disease. Synthetic pesticide application is the primary management technique used to manage the disease. However, newly observed declines in anthracnose susceptibility to many fungicides highlight the need for more environmentally friendly approaches. Recent progress in understanding the host range, molecular and phenotypic characterization, and susceptibility of the disease in several mango cultivars is discussed in this review. It provides updates on the mode of transmission, infection biology and contemporary management strategies. We suggest an integrated and ecologically sound approach to managing MAD.

Identification of Colletotrichum aenigma as the new causal agent of leaf blight disease on Aucuba japonica Thunb., and screenings of effective fungicides for its sustainable management

Aucuba japonica Thunb is an evergreen woody ornamental plant with significant economic and ecological values. It also produces aucubin, showing a variety of biological activities. It is widely planted in the southwest region of China, including karst landscape areas in Guizhou Province. In January 2022, a serious leaf blight disease was observed on the leaves of A. japonica in the outdoor gardens of Guizhou University, Guiyang, Guizhou, China. The causal agent was identified as Colletotrichum aenigma through amplification and sequencing of the internal transcribed spacer (ITS) region, translation of the chitin synthase (CHS) and actin (ACT) genes, and morphological characterizations. Koch's postulates were confirmed by its pathogenicity on healthy leaves, including re-isolation and identification. To our knowledge, this is the first report of C. aenigma causing leaf blight on A. japonica worldwide. To identify pathogen characteristics that could be utilized for future disease management, the effects of temperature and light on mycelial growth, conidia production, and conidial germination, and the effects of humidity on conidial germination were studied. Optimal temperatures for mycelial growth of C. aenigma BY827 were 25-30°C, while 15°C and 35°C were favorable for conidia production. Concurrently, alternating 10-h light and 14-h dark, proved to be beneficial for mycelial growth and conidial germination. Additionally, conidial germination was enhanced at 90% humidity. In vitro screenings of ten chemical pesticides to assess their efficacy in suppressing C. aenigma representative strain BY827. Among them, difenoconazole showed the best inhibition rate, with an EC50 (concentration for 50% of maximal effect) value of 0.0148 μg/ml. Subsequently, field experiment results showed that difenoconazole had the highest control efficiency on A. japonica leaf blight (the decreasing rate of disease incidence and decreasing rate of disease index were 44.60 and 47.75%, respectively). Interestingly, we discovered that C. aenigma BY827 may develop resistance to mancozeb, which is not reported yet among Colletotrichum spp. strains. In conclusion, our study provided new insights into the causal agent of A. japonica leaf blight, and the effective fungicides evaluated provided an important basis and potential resource for the sustainable control of A. japonica leaf blight caused by C. aenigma in the field.

Genome-wide association study of resistance to anthracnose in pepper (Capsicum chinense) germplasm

BACKGROUND

Anthracnose is a fungal disease caused by Colletotrichum spp. that has a significant impact on worldwide pepper production. Colletotrichum scovillei is the most common pathogenic anthracnose-causing species in the Republic of Korea.

RESULTS

The resistances of 197 pepper (Capsicum chinense) accessions deposited in Korea's National Agrobiodiversity Center were evaluated for their response against the virulent pathogens Colletotrichum acutatum isolate 'KSCa-1' and C. scovillei isolate 'Hana') in the field and in vitro methods for three consecutive years (2018 to 2020). The severity of the disease was recorded and compared between inoculation methods. Six phenotypically resistant pepper accessions were selected based on three years of disease data. All of the selected resistant pepper accessions outperformed the control resistant pepper in terms of resistance (PI 594,137). A genome-wide association study (GWAS) was carried out to identify single nucleotide polymorphisms (SNPs) associated with anthracnose resistance. An association analysis was performed using 53,518 SNPs and the disease score of the 2020 field and in vitro experiment results. Both field and in vitro experiments revealed 25 and 32 significantly associated SNPs, respectively. These SNPs were found on all chromosomes except Ch06 and Ch07 in the field experiment, whereas in the in vitro experiment they were found on all chromosomes except Ch04 and Ch11.

CONCLUSION

In this study, six resistant C. chinense accessions were selected. Additionally, in this study, significantly associated SNPs were found in a gene that codes for a protein kinase receptor, such as serine/threonine-protein kinase, and other genes that are known to be involved in disease resistance. This may strengthen the role of these genes in the development of anthracnose resistance in Capsicum spp. As a result, the SNPs discovered to be strongly linked in this study can be used to identify a potential marker for selecting pepper material resistant to anthracnose, which will assist in the development of resistant varieties.

Insights into Grape Ripe Rot: A Focus on the Colletotrichum gloeosporioides Species Complex and Its Management Strategies

Grape ripe rot, which is predominantly caused by the Colletotrichum species, presents a growing threat to global grape cultivation. This threat is amplified by the increasing populations of the Colletotrichum species in response to warmer climates. In this review, we investigate the wide-ranging spectrum of grape ripe rot, specifically highlighting the role and characteristics of the C. gloeosporioides species complex (CGSC). We incorporate this understanding as we explore the diverse symptoms that lead to infected grapevines, their intricate life cycle and epidemiology, and the escalating prevalence of C. viniferum in Asia and globally. Furthermore, we delve into numerous disease management strategies, both conventional and emerging, such as prevention and mitigation measures. These strategies include the examination of host resistances, beneficial cultivation practices, sanitation measures, microbiome health maintenance, fungicide choice and resistance, as well as integrated management approaches. This review seeks to enhance our understanding of this globally significant disease, aspiring to assist in the development and improvement of effective prevention and control strategies.

Re-identification of Colletotrichum acutatum Species Complex in Korea and Their Host Plants

Colletotrichum acutatum species complex is one of the most important groups in the genus Colletotrichum with a high species diversity and a wide range of host plants. C. acutatum and related species have been collected from different plants and locations in Korea and deposited into the Korean Agricultural Culture Collection (KACC), National Institute of Agricultural Sciences since the 1990s. These fungal isolates were previously identified based mainly on morphological characteristics, and a limitation of molecular data was provided. To confirm the identification of species, 64 C. acutatum species complex isolates in KACC were used in this study for DNA sequence analyses of six loci: nuclear ribosomal internal transcribed spacers (ITS), betatubulin 2 (TUB2), histone-3 (HIS3), glyceraldehyde3-phosphate dehydrogenase (GAPDH), chitin synthase 1 (CHS-1), and actin (ACT). The molecular analysis revealed that they were identified in six different species of C. fioriniae (24 isolates), C. nymphaeae (21 isolates), C. scovillei (12 isolates), C. chrysanthemi (three isolates), C. lupini (two isolates), and C. godetiae (one isolate), and a novel species candidate. We compared the hosts of KACC isolates with "The List of Plant Diseases in Korea", previous reports in Korea and global reports and found that 23 combinations between hosts and pathogens could be newly reported in Korea after pathogenicity tests, and 12 of these have not been recorded in the world.

Spore Dispersal Patterns of Colletotrichum fioriniae in Orchards and the Timing of Apple Bitter Rot Infection Periods

Bitter rot is a major disease of apple fruit in warm and humid regions. It is caused by various species in the Colletotrichum gloeosporioides and C. acutatum species complexes, of which C. fioriniae of the C. acutatum species complex is most common in the Mid-Atlantic region of the United States. While bitter rot management begins with good cultural practices, fungicides are generally used for consistent control. Fungicides should be applied before or during infection periods, but the timing of infection is unclear due to the hemibiotrophic lifestyle of the causal species. To determine when infection periods occur, we quantified C. fioriniae spore dispersal throughout three growing seasons and compared the temporal susceptibility of apples in two seasons of field trials. Spores were detected in rainwater from bud break to leaf drop, with the highest spore quantities in the summer and early fall correlating with optimal temperatures for C. fioriniae. Late-season-inoculated fruit had more bitter rot than early-season-inoculated fruit, but this was also positively correlated with periods of optimal temperatures and moisture for infection. In the context of previous experiments, these results suggest that infection periods are primarily determined by temperature and moisture rather than apple fruit phenology. Based on the relative numbers of spores and biotrophic and necrotrophic infections, only a tiny proportion of spores establish viable biotrophic infections, but a relatively high proportion of biotrophic infections switch to necrotrophy. We suggest bitter rot management should focus on preventing initial biotrophic infections by protecting apples during weather conditions that favor infection.

Profiling Walnut Fungal Pathobiome Associated with Walnut Dieback Using Community-Targeted DNA Metabarcoding

Walnut dieback can be caused by several fungal pathogenic species, which are associated with symptoms ranging from branch dieback to fruit necrosis and blight, challenging the one pathogen-one disease concept. Therefore, an accurate and extensive description of the walnut fungal pathobiome is crucial. To this end, DNA metabarcoding represents a powerful approach provided that bioinformatic pipelines are evaluated to avoid misinterpretation. In this context, this study aimed to determine (i) the performance of five primer pairs targeting the ITS region in amplifying genera of interest and estimating their relative abundance based on mock communities and (ii) the degree of taxonomic resolution using phylogenetic trees. Furthermore, our pipelines were also applied to DNA sequences from symptomatic walnut husks and twigs. Overall, our results showed that the ITS2 region was a better barcode than ITS1 and ITS, resulting in significantly higher sensitivity and/or similarity of composition values. The ITS3/ITS4_KYO1 primer set allowed to cover a wider range of fungal diversity, compared to the other primer sets also targeting the ITS2 region, namely, GTAA and GTAAm. Adding an extraction step to the ITS2 sequence influenced both positively and negatively the taxonomic resolution at the genus and species level, depending on the primer pair considered. Taken together, these results suggested that Kyo set without ITS2 extraction was the best pipeline to assess the broadest fungal diversity, with a more accurate taxonomic assignment, in walnut organs with dieback symptoms.

Whole genome resequencing reveal patterns of genetic variation within Colletotrichum acutatum species complex from rubber trees in China

The Colletotrichum acutatum species complex possesses a diverse number of important traits, such as a wide host range and host preference, different modes of reproduction, and different strategies of host infection. Research using comparative genomics has attempted to find correlations between these traits. Here, we used multi-locus techniques and gene genealogical concordance analysis to investigate the phylogenetic relationships and taxonomic status of the Colletotrichum acutatum species complex using field isolates obtained from rubber trees. The results revealed that the dominant species was C. australisinense, followed by C. bannaense, while strain YNJH17109 was identified as C. laticiphilum. The taxonomic status of strains YNLC510 and YNLC511 was undetermined. Using whole-genome single nucleotide polymorphism data to analyze population structure, 18 strains of C. australisinense were subsequently divided into four populations, one of which was derived from an admixture of two populations. In addition, the strains LD1687, GD1628, and YNLC516, did not belong to any populations, and were considered to be admixtures of two or more populations. A split decomposition network analysis also provided evidence for genetic recombination within Colletotrichum acutatum species complex from rubber trees in China. Overall, a weak phylogeographic sub-structure was observed. Analysis also revealed significant differences in morphological characters and levels of virulence between populations.

First report of Colletotrichum fioriniae infections in brown marmorated stink bugs, Halyomorpha halys

An epizootic caused by fungal pathogens occurred among Halyomorpha halys, brown marmorated stink bugs, while they were overwintering, with infections also occurring after overwintering. We report that one of the two pathogens responsible was Collectotrichum fioriniae (Marcelino & Gouli), Pennycook; a species well known as a plant pathogen and endophyte and which has only previously been reported naturally infecting elongate hemlock scales, Fiorinia externa. To prove pathogenicity, H. halys adults challenged with conidia died from infections and the fungus subsequently produced conidia externally on cadavers.

Diagnosis of Soybean Diseases Caused by Fungal and Oomycete Pathogens: Existing Methods and New Developments

Soybean (Glycine max) acreage is increasing dramatically, together with the use of soybean as a source of vegetable protein and oil. However, soybean production is affected by several diseases, especially diseases caused by fungal seed-borne pathogens. As infected seeds often appear symptomless, diagnosis by applying accurate detection techniques is essential to prevent propagation of pathogens. Seed incubation on culture media is the traditional method to detect such pathogens. This method is simple, but fungi have to develop axenically and expert mycologists are required for species identification. Even experts may not be able to provide reliable type level identification because of close similarities between species. Other pathogens are soil-borne. Here, traditional methods for detection and identification pose even greater problems. Recently, molecular methods, based on analyzing DNA, have been developed for sensitive and specific identification. Here, we provide an overview of available molecular assays to identify species of the genera Diaporthe, Sclerotinia, Colletotrichum, Fusarium, Cercospora, Septoria, Macrophomina, Phialophora, Rhizoctonia, Phakopsora, Phytophthora, and Pythium, causing soybean diseases. We also describe the basic steps in establishing PCR-based detection methods, and we discuss potentials and challenges in using such assays.

Entomopathogens infecting brown marmorated stink bugs before, during, and after overwintering

The microsporidian, Nosema maddoxi Becnel, Solter, Hajek, Huang, Sanscrainte & Estep, infects brown marmorated stink bug, Halyomorpha halys (Stål) (Hemiptera: Pentatomidae), populations in North America and Asia and causes decreased fitness in infected insects. This host overwinters as adults, often in aggregations in sheltered locations, and variable levels of mortality occur over the winter. We investigated pathogen prevalence in H. halys adults before, during, and after overwintering. Population level studies resulted in detection of N. maddoxi in H. halys in 6 new US states, but no difference in levels of infection by N. maddoxi in autumn versus the following spring. Halyomorpha halys that self-aggregated for overwintering in shelters deployed in the field were maintained under simulated winter conditions (4°C) for 5 months during the 2021-2022 winter and early spring, resulting in 34.6 ± 4.8% mortality. Over the 2020-2021 and 2021-2022 winters, 13.4 ± 3.5% of surviving H. halys in shelters were infected with N. maddoxi, while N. maddoxi infections were found in 33.4 ± 10.8% of moribund and dead H. halys that accumulated in shelters. A second pathogen, Colletotrichum fioriniae Marcelino & Gouli, not previously reported from H. halys, was found among 46.7 ± 7.8% of the H. halys that died while overwintering, but levels of infection decreased after overwintering. These 2 pathogens occurred as co-infections in 11.1 ± 5.9% of the fungal-infected insects that died while overwintering. Increasing levels of N. maddoxi infection caused epizootics among H. halys reared in greenhouse cages after overwintering.

Attack of the clones: Population genetics reveals clonality of Colletotrichum lupini, the causal agent of lupin anthracnose

Colletotrichum lupini, the causative agent of lupin anthracnose, affects lupin cultivation worldwide. Understanding its population structure and evolutionary potential is crucial to design successful disease management strategies. The objective of this study was to employ population genetics to investigate the diversity, evolutionary dynamics, and molecular basis of the interaction of this notorious lupin pathogen with its host. A collection of globally representative C. lupini isolates was genotyped through triple digest restriction site-associated DNA sequencing, resulting in a data set of unparalleled resolution. Phylogenetic and structural analysis could distinguish four independent lineages (I-IV). The strong population structure and high overall standardized index of association (r̅_d ) indicates that C. lupini reproduces clonally. Different morphologies and virulence patterns on white lupin (Lupinus albus) and Andean lupin (Lupinus mutabilis) were observed between and within clonal lineages. Isolates belonging to lineage II were shown to have a minichromosome that was also partly present in lineage III and IV, but not in lineage I isolates. Variation in the presence of this minichromosome could imply a role in host-pathogen interaction. All four lineages were present in the South American Andes region, which is suggested to be the centre of origin of this species. Only members of lineage II have been found outside South America since the 1990s, indicating it as the current pandemic population. As a seedborne pathogen, C. lupini has mainly spread through infected but symptomless seeds, stressing the importance of phytosanitary measures to prevent future outbreaks of strains that are yet confined to South America.

Colletotrichum Species Associated with Anthracnose in Salix babylonica in China

Salix babylonica L. is a popular ornamental tree species in China and widely cultivated in Asia, Europe, and North America. Anthracnose in S. babylonica poses a serious threat to its growth and reduces its medicinal properties. In 2021, a total of 55 Colletotrichum isolates were isolated from symptomatic leaves in three provinces in China. Phylogenetic analyses using six loci (ITS, ACT, CHS-1, TUB2, CAL, and GAPDH) and a morphological characterization of the 55 isolates showed that they belonged to four species of Colletotrichum, including C. aenigma, C. fructicola, C. gloeosporioides s.s., and C. siamense. Among them, C. siamense was the dominant species, and C. gloeosporioides s.s. was occasionally discovered from the host tissues. Pathogenicity tests revealed that all the isolates of the aforementioned species were pathogenic to the host, and there were significant differences in pathogenicity or virulence among these isolates. The information on the diversity of Colletotrichum spp. that causes S. babylonica anthracnose in China is new.

Colletotrichum siamense Strain LVY 9 Causing Spot Anthracnose on Winterberry Holly in China

Winterberry holly (Ilex verticillata) is an economically valuable landscaping ornamental plant. Serious outbreaks have been reported, in its leaf tips curl upward, irregular black brown spots appear on leaves, and extensive defoliation is commonly observed. The incidence in Hangzhou was estimated at 50% and resulted in large economic losses for growers in 2018. Samples were collected from the main cultivation area in Zhejiang Province. In total, 11 fungal isolates were obtained from diseased leaves through a single-spore purification method, and isolate LVY 9 exhibited strong pathogenicity. Based on morphology and molecular phylogenetic analyses based on multilocus sequence typing of the glyceraldehyde-3-phosphate dehydrogenase (GAPDH), internal transcribed spacer (ITS) regions, actin (ACT), calmodulin (CAL), and chitin synthase (CHS-1) genes, we identified the pathogen as Colletotrichum siamense, causative agent of anthracnose of winterberry holly.

Development of a model for Colletotrichum diseases with calibration for phylogenetic clades on different host plants

Fungi in the genus Colletotrichum cause serious pre- and post-harvest losses to several agricultural crops worldwide. Through a systematic literature review, we retrieved the published information on Colletotrichum anthracnose diseases on different host plants and developed a mechanistic model incorporating the main stages of the pathogen's life cycle and the effect of weather. The model predicts anthracnose progress during the growing season on the aerial organs of different crops, and was parameterized for seven Colletotrichum clades (acutatum, dematium, destructivum, gloeosporioides, graminicola, and orbiculare) and the singleton species, C. coccodes. The model was evaluated for the anthracnose diseases caused by fungi belonging to five clades on six hosts by using data from 17 epidemics that occurred in Italy, the USA, Canada, and Japan. A comparison of observed versus predicted data showed a concordance correlation coefficient of 0.928 and an average distance between real data and the fitted line of 0.044. After further validation, the model could be used to support decision-making for crop protection.

First Report of Colletotrichum godetiae Causing Anthracnose on Walnut (Juglans regia and Juglans sigillata) in China

In August 2020, anthracnose lesions were observed on fruits of Juglans regia and J. sigillata in walnut orchards, in Yijun (Shaanxi Province) and Nanhua (Yunnan Province) counties, China. Symptoms on walnut fruits first appeared as small necrotic spots that rapidly enlarged into subcircular or irregular sunken black lesions (Fig. 1a, b). Sixty diseased walnut fruits (30 fruits of J. regia and J. sigillata, respectively) were randomly sampled from six orchards (10-15 ha each orchard, three orchards were selected in each county) with severe anthracnose (incidence rate of fruit anthracnose is over 60% in the orchard.) in two counties. Twenty-six single spore isolates were obtained from diseased fruits as described by Cai et al. (2009). After seven days, isolates formed grey to milky white colony with abundant aerial hyphae on the upper surface of colony, and milky white to light olive on the back of PDA (Fig. 1c). Conidiogenous cells were hyaline, smooth-walled, and cylindrical to clavate (Fig. 1d). Conidia were smooth-walled, aseptate, cylindrical to fusiform, with both ends acute or one end round and one end slightly acute (Fig. 1e), and ranged in size from 15.5-24.3×4.9-8.1 µm (n=30). Appressoria were brown to medium brown, clavate to elliptical, with the edge entire or undulate (Fig. 1f), and ranged in size from 8.0-27.6×4.7-13.7μm (n=30). The morphological characteristics of 26 isolates were similar to those of the species complex Colletotrichum acutatum (Damm et al. 2012). Six representative isolates were randomly selected (three isolates for each province) for molecular analysis. The ribosomal internal transcribed spacers (ITS) (White et al. 1990), beta-tubulin (TUB2) (Glass and Donaldson 1995), glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (Templeton et al.1992) and chitin synthase 1 (CHS-1) (Carbone and Kohn 1999) genes were amplified and sequenced. Sequences of 6 of 26 isolates were submitted to GenBank (Accession Nos: ITS: MT799938-MT799943, TUB: MT816321-MT816326, GAPDH:MT816327-MT816332, CHS-1: MT816333-816338). Multi-locus phylogenetic analyses revealed that six isolates clustered together with Colletotrichum godetiae ex-type culture isolates CBS133.44 and CBS130251, and the bootstrap support value was 100% (Fig.2). The pathogenicity of two representative isolates (CFCC54247 and CFCC54244) was tested using healthy fruits of the " J. regia cv. Xiangling" and " J. sigillata cv. Yangbi" varieties. Forty sterilized fruits (20 fruits were inoculated with CFCC54247, and 20 fruits with CFCC54244) were wounded by puncturing with a sterile needle through walnut pericarp and inoculated in the wound site with 10 μl of conidial suspension (106 conidia/ml) from seven day old colonies grown on PDA at 25℃. Twenty wounded fruits were inoculated with sterile water as control. Inoculated and control fruits were incubated in containers at 25℃ in a 12/12h light/dark cycle. The experiment was repeated three times. Anthracnose symptoms (Fig. 1g-h) were observed in all inoculated fruits after 12 days, whereas controls showed no symptoms. Fungal isolates from inoculated diseased fruits showed the same morphological and molecular characteristics as the isolates obtained in this study, confirming Koch's postulates. To our knowledge, this is the first report of C. godetiae causing anthracnose on the two walnut species in China. The result will be helpful for providing a basis for further research on the control of the disease.

Two Newly Identified Colletotrichum Species Associated with Mango Anthracnose in Central Thailand

Anthracnose caused by Colletotrichum spp. is one of the major problems in mango production worldwide, including Thailand. All mango cultivars are susceptible, but Nam Dok Mai See Thong (NDMST) is the most vulnerable. Through a single spore isolation method, a total of 37 isolates of Colletotrichum spp. were obtained from NDMST showing anthracnose symptoms. Identification was performed using a combination of morphology characteristics, Koch's postulates, and phylogenetic analysis. The pathogenicity assay and Koch's postulates on leaves and fruit confirmed that all Colletotrichum spp. tested were causal agents of mango anthracnose. Multilocus analysis using DNA sequences of internal transcribed spacer (ITS) regions, β-tubulin (TUB2), actin (ACT), and chitin synthase (CHS-1) was performed for molecular identification. Two concatenated phylogenetic trees were constructed using either two-loci of ITS and TUB2, or four-loci of ITS, TUB2, ACT, and CHS-1. Both phylogenetic trees were indistinguishable and showed that these 37 isolates belong to C. acutatum, C. asianum, C. gloeosporioides, and C. siamense. Our results indicated that using at least two loci of ITS and TUB2, were sufficient to infer Colletotrichum species complexes. Of 37 isolates, C. gloeosporioides was the most dominant species (19 isolates), followed by C. asianum (10 isolates), C. acutatum (5 isolates), and C. siamense (3 isolates). In Thailand, C. gloeosporioides and C. acutatum have been reported to cause anthracnose in mango, however, this is the first report of C. asianum and C. siamense associated with mango anthracnose in central Thailand.

Molecular Characterization and Fungicide Sensitivity of Jujube Pathogens Colletotrichum gloeosporioides Sensu Stricto and Colletotrichum nymphaeae in South Korea

Jujube (Ziziphus jujuba) is cultivated across South Korea because of its medicinal and economic value. It is used as a sweetener in jam, tea, and snacks and a garnish in many cuisines. Anthracnose caused by Colletotrichum spp. accounts for huge economic losses for jujube growers. In 2019 and 2020, severe anthracnose was observed in the jujube-growing areas of South Korea. The infected fruit displayed small, water-soaked, sunken, circular spots. Infected fruit were collected from different commercial orchards of Boeungun and Gyeongsan regions of South Korea, and putative causal agents were isolated on potato dextrose agar. Based on the morphological and molecular characteristics, the fungal isolates were identified as Colletotrichum gloeosporioides sensu stricto and C. nymphaeae. The pathogenicity of these isolates was confirmed by inoculating a conidial suspension (1 × 10⁶ conidia ml^-1) on healthy fruit. The in vitro sensitivity of the fungal isolates to tebuconazole, carbendazim, and azoxystrobin was also tested. All isolates showed high sensitivity to azoxystrobin in terms of mycelial growth inhibition (half maximal effective concentration value of 0.01 to 0.6 µg/ml). To the best of our knowledge, this is also the first report of jujube anthracnose caused by C. nymphaeae in South Korea.

Endophytic Colletotrichum (Sordariomycetes, Glomerellaceae) species associated with Citrus grandis cv. “Tomentosa” in China

Colletotrichum species are well-known plant pathogens, saprobes, endophytes, human pathogens and entomopathogens. However, little is known about Colletotrichum as endophytes of plants and cultivars including Citrus grandis cv. “Tomentosa”. In the present study, 12 endophytic Colletotrichum isolates were obtained from this host in Huazhou, Guangdong Province (China) in 2019. Based on morphology and combined multigene phylogeny [nuclear ribosomal internal transcribed spacer (ITS), glyceraldehyde-3-phosphate dehydrogenase (gapdh), chitin synthase 1 (chs-1), histone H3 (his3) actin (act), beta-tubulin (β-tubulin) and glutamine synthetase (gs)], six Colletotrichum species were identified, including two new species, namely Colletotrichum guangdongense and C. tomentosae. Colletotrichum asianum, C. plurivorum, C. siamense and C. tainanense are identified as being the first reports on C. grandis cv. “Tomentosa” worldwide. This study is the first comprehensive study on endophytic Colletotrichum species on C. grandis cv. “Tomentosa” in China.

Molecular Approaches for Detection of Trichoderma Green Mold Disease in Edible Mushroom Production

Due to the evident aggressive nature of green mold and the consequently huge economic damage it causes for producers of edible mushrooms, there is an urgent need for prevention and infection control measures, which should be based on the early detection of various Trichoderma spp. as green mold causative agents. The most promising current diagnostic tools are based on molecular methods, although additional optimization for real-time, in-field detection is still required. In the first part of this review, we briefly discuss cultivation-based methods and continue with the secondary metabolite-based methods. Furthermore, we present an overview of the commonly used molecular methods for Trichoderma species/strain detection. Additionally, we also comment on the potential of genomic approaches for green mold detection. In the last part, we discuss fast screening molecular methods for the early detection of Trichoderma infestation with the potential for in-field, point-of-need (PON) application, focusing on isothermal amplification methods. Finally, current challenges and future perspectives in Trichoderma diagnostics are summarized in the conclusions.

First report of tobacco anthracnose caused by Colletotrichum nymphaeae in China

Tobacco (Nicotiana tabacum L.) is one of the most widely cultivated economic crops in approximately 120 countries (Peedin 2011). In July 2020 and 2021, typical symptoms of tobacco anthracnose were widely found in the flue-cured tobacco-planted areas of Wufeng, Xuan'en, and Xianfeng, Hubei Province, China. The disease incidence reached up to 60% in some fields at that time, with estimated 10,000 ha of the cultivated area affected. On tobacco leaves, lesions were initially water soaked and yellow green, and these enlarged to produce dark-brown necrosis which became cracked after drying, extending until the leaves withered. After surface-sterilization with 75% ethanol for 45 s and 5% sodium hypochlorite for 60 s, diseased leaf tissues were washed with sterilized water for 60 s three times and then cultured on potato dextrose agar (PDA) plates for seven days at 25°C in the dark. Isolates of Colletotrichum sp. were consistently recovered with isolation rate of 71%, and the five isolates BB005ES1, BB005ES2, BB005ES3, BB005ES4 and BB005ES5 were used to further evaluate characteristics of the pathogen. On PDA medium for seven days, the aerial hyphae of cultures were dense and blanket-like. The aerial surface of the colony was dark gray to white, and the center of the basal surface of the colony was orange-red. Conidia were transparent, aseptate, smooth-walled, straight, cylindrical with one end obtuse and the other end funnel-shaped, and the size was 11.8-12.0 μm×2.7-2.9 μm (n=100). Appressoria were single, smooth, black, oval or irregular shapes with size of 4.6-4.9 μm×8.5-8.7 μm (n=100). The most typical feature of Colletotrichum acutatum species complex is the shape of conidia which have at least one acute end (Damm et al., 2012). Thus, the five strains were identified as part of the Acutatum complex. The sequences of ACT, TUB2, CHS-1, GAPDH and ITS were then amplified from the five strains (Damm et al., 2012), and all the five strains had the similar sequence for each gene (Accession numbers in GeneBank: ON637946, ON637947, ON637945, ON637948 and ON394623). The combined sequences ACT-TUB2-CHS-1-GAPDH-ITS of the five strains were used for constructing multigene phylogenetic tree using Maximum Parsimony method (Prihastuti et al. 2009), and C. gloeosporioides (IMI356878) was selected as an outgroup. The five strains were found to be closely related to the type strains of C. nymphaeae. Hence, the five isolated strains were identified as C. nymphaeae. Pathogenicity of the five strains was determined by placing seven-day-old fungal plugs on attached leaves of 20-day-old tobacco plants in lab. After inoculation, plants were incubated in a 28°C and 95% RH incubator in the dark for five days. The five strains caused the typical dark brown lesions on all inoculated tobacco leaves, whereas no disease symptoms were found on the healthy tobacco leaves for agar-plug inoculation controls. Koch's postulates were fulfilled by re-isolating C. nymphaeae from diseased leaves. Previously, only C. fructicola, C. nicotiance, C. orbiculare and C. cliviicola were documented as causal agents of tobacco anthracnose (Wang et al. 2016；Wang et al. 2022). To our knowledge, this is the first report of C. nymphaeae causing tobacco anthracnose worldwide.

Functional characterization of MANNOSE-BINDING LECTIN 1, a G-type lectin gene family member, in response to fungal pathogens of strawberry

The mannose-binding lectin gene MANNOSE-BINDING LECTIN 1 (MBL1) is a member of the G-type lectin family and is involved in defense in strawberry (Fragaria × ananassa). Genome-wide identification of the G-type lectin family was carried out in woodland strawberry, F. vesca, and 133 G-lectin genes were found. Their expression profiles were retrieved from available databases and indicated that many are actively expressed during plant development or interaction with pathogens. We selected MBL1 for further investigation and generated stable transgenic FaMBL1-overexpressing plants of F. ×ananassa to examine the role of this gene in defense. Plants were selected and evaluated for their contents of disease-related phytohormones and their reaction to biotic stresses, and this revealed that jasmonic acid decreased in the overexpressing lines compared with the wild-type (WT). Petioles of the overexpressing lines inoculated with Colletotrichum fioriniae had lower disease incidence than the WT, and leaves of these lines challenged by Botrytis cinerea showed significantly smaller lesion diameters than the WT and higher expression of CLASS II CHITINASE 2-1. Our results indicate that FaMBL1 plays important roles in strawberry response to fungal diseases caused by C. fioriniae and B. cinerea.

Concurrent waterlogging and anthracnose-twister disease in rainy-season onions (Allium cepa): Impact and management

Waterlogging and anthracnose-twister disease are significant obstacles in rainy-season onion cultivation. As a shallow-rooted crop, onions are highly sensitive to waterlogging. Wherever rainy-season onion cultivation has been undertaken, the anthracnose-twister disease complex is also widespread across the world in addition to waterlogging. Waterlogging is the major predisposing factor for anthracnose and other fungal diseases. However, studies on the combined stress impact on onions have been ignored. In the present review, we have presented an overview of the anthracnose-twister disease, the waterlogging effect on host physiology, host-pathogen interaction under waterlogging stress, and appropriate management strategies to mitigate the combined stress effects. Crucial soil and crop management strategies can help cope with the negative impact of concurrent stresses. Raised bed planting with drip irrigation, the use of plant bio-regulators along with nutrient management, and need-based fungicide sprays would be the most reliable and feasible management options. The most comprehensive solution to withstand combined stress impacts would be a genetic improvement of commercial onion cultivars.

Cytochrome b Gene-Based Assay for Monitoring the Resistance of Colletotrichum spp. to Pyraclostrobin

Resistance to pyraclostrobin due to a single nucleotide polymorphism at 143rd amino acid position on the cytochrome b gene has been a major source of concern in red pepper field infected by anthracnose in Korea. Therefore, this study investigated the response of 24 isolates of C. acutatum and C. gloeosporioides isolated from anthracnose infected red pepper fruits using agar dilution method and other molecular techniques such as cytochrome b gene sequencing, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), and allele-specific polymerase chain reaction (PCR). The result showed that four isolates were resistant to pyraclostrobin on agar dilution method and possessed GCT (alanine) codon at 143rd amino acid position, whereas the sensitive isolates possessed GGT (glycine). Furthermore, this study illustrated the difference in the cytochrome b gene structure of C. acutatum and C. gloeosporioides. The use of cDNA in this study suggested that the primer Cacytb-P2 can amplify the cytochrome b gene of both C. acutatum and C. gloeosporioides despite the presence of various introns in the cytochrome b gene structure of C. gloeosporioides. The use of allele-specific PCR and PCR-RFLP provided clear difference between the resistant and sensitive isolates. The application of molecular technique in the evaluation of the resistance status of anthracnose pathogen in red pepper provided rapid, reliable, and accurate results that can be helpful in the early adoption of fungicide-resistant management strategies for the strobilurins in the field.

Detection of Anthracnose in Strawberry and Methods of Etiological Diagnosis

Anthracnose of strawberry caused by Colletotrichum fungi is a dangerous disease associated with serious damage in berry plantations. Colletotrichum nymphaeae, C. lineola, and C. godetiae have been found in Russian and international planting material of strawberry plants. The cultural and morphological characteristics are described for the isolates and nucleotide ITS1-5.8S-ITS2 sequences of fragments received are identified. It is shown that the fragments of glyceraldehyde 3-phosphate dehydrogenase and actin genes can be used to efficiently differentiate the C. lineola species from the closely related С. dematium. Two diagnostic test systems for acutatum complex identification are compared. The studied test systems do not demonstrate any false-positive results; the prepared set of С. acutatum complex-RT (ZAO Sintol) shows specificity only for the C. nymphaeae and C. fioriniae species and turned out to be nonspecific to the C. godetiae species included in the acutatum complex. The test system elaborated by Garrido et al. is found to be highly sensitive and specific to the target species of the acutatum complex.

Detection of Colletotrichum spp. Resistant to Benomyl by Using Molecular Techniques

Colletotrichum species is known as the major causal pathogen of red pepper anthracnose in Korea and various groups of fungicides are registered for the management of the disease. However, the consistent use of fungicides has resulted in the development of resistance in many red pepper-growing areas of Korea. Effective management of the occurrence of fungicide resistance depends on constant monitoring and early detection. Thus, in this study, various methods such as agar dilution method (ADM), gene sequencing, allele-specific polymerase chain reaction (PCR), and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) were applied for the detection of benzimidazole resistance among 24 isolates of Colletotrichum acutatum s. lat. and Colletotrichum gloeosporioides s. lat. The result of the ADM showed that C. gloeosporioides s. lat. was classified into sensitive and resistant isolates to benomyl while C. acutatum s. lat. was insensitive at ≥1 µg/ml of benomyl. The sequence analysis of the β-tubulin gene showed the presence of a single nucleotide mutation at the 198th amino acid position of five isolates (16CACY14, 16CAYY19, 15HN5, 15KJ1, and 16CAYY7) of C. gloeosporioides s. lat. Allele-specific PCR and PCR-RFLP were used to detect point mutation at 198th amino acid position and this was done within a day unlike ADM which usually takes more than one week and thus saving time and resources that are essential in the fungicide resistance management in the field. Therefore, the molecular techniques established in this study can warrant early detection of benzimidazole fungicide resistance for the adoption of management strategies that can prevent yield losses among farmers.

Identification and characterization of Colletotrichum fioriniae and C. fructicola that cause anthracnose in pecan

Pecan (Carya illinoinensis Wang. K. Koch) is a deciduous tree of the Juglandaceae family with important economic value worldwide. Anthracnose of the pecan leaves and shuck is a devastating disease faced by pecan-growing areas in China. However, the causal species occurring on pecan remain largely unidentified. we collected samples of diseased pecan from the provinces of China, Leaves and fruits affected by anthracnose were sampled and subjected to fungus isolation, The morphological characters of all strains were observed and compared; Multi-locus phylogenetic analyses [Internally transcribed spacer (ITS), Actin (ACT), Calmodulin (CAL), Chitin synthase (CHS1), Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and b-tubulin (TUB2)] were performed on selected representative strains; examine their pathogenicity on leaves of pecan.The results showed that: (1) resulting in a total of 11 Colletotrichum isolates, Two Colletotrichum species were identifified to be C. fioriniae and C. fructicola; (2) Pathogenicity tests revealed that both species caused black spots on pecan leaves and fruit, The virulence of the different isolates varied substantially, with C. fioriniae PCJD179 being the most virulent; (3) The susceptibility levels of pecan tree varieties, 'Mahan' and 'Kanza', were determined, No significant differences were observed in the lesion sizes produced by the various isolates in 'Kanza', while there were signifificant differences in 'Mahan'. This study is thefifirst to determine that C. fructicola and C. fioriniaecan cause anthracnose in pecan in China. It improves the understanding of the species that cause anthracnose in pecan and provides useful information for the effective control of this disease in China.

Sensitivity of Colletotrichum gloeosporioides species complex (CGSC) isolated from strawberry in Taiwan to benzimidazole and strobilurin

Colletotrichum gloeosporioides species complex (CGSC) is the major pathogen causing strawberry anthracnose in Taiwan. Benzimidazoles and strobilurins are common fungicides used to control strawberry anthracnose. A total of 108 CGSC isolates were collected from five major strawberry-producing areas in Taiwan. The half-maximal effective concentration (EC₅₀) values of most CGSC isolates for benomyl (59 isolates), carbendazim (70 isolates), and thiabendazole (63 isolates) were higher than 500 µg a.i./mL. Strobilurin tests showed that the EC₅₀ values of most CGSC isolates for azoxystrobin (66 isolates), kresoxim-methyl (42 isolates), and trifloxystrobin (56 isolates) were higher than 500 µg a.i./mL. However, most CGSC isolates were sensitive to pyraclostrobin at 100 µg a.i./mL. Fungicide tests indicated that CGSC isolates show multi-resistance to benzimidazoles and strobilurins. Benzimidazole-resistant isolates were associated with a point mutation in codon 198 of the β-tubulin gene, and strobilurin-resistant isolates did not correspond with mutation in the cyt b gene or alternative oxidase activity.