The Colletotrichum acutatum species complex

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.

Morphological, Pathological and Genetic Diversity of the Colletotrichum Species, Pathogenic on Solanaceous Vegetable Crops in Bulgaria

Colletotrichum species are among the most devastating plant pathogens in a wide range of hosts. Their accurate identification requires a polyphasic approach, including geographical, ecological, morphological, and genetic data. Solanaceous crops are of significant economic importance for Bulgarian agriculture. Colletotrichum-associated diseases pose a serious threat to the yield and quality of production but are still largely unexplored. The aim of this study was to identify and characterize 26 pathogenic Colletotrichum isolates that threaten solanaceous crops based on morphological, pathogenic, and molecular data. DNA barcodes enabled the discrimination of three main taxonomic groups: C. acutatum, C. gloeosporioides, and C. coccodes. Three different species of acutatum complex (C. nymphaeae, C. godetiae, and C. salicis) and C. cigarro of the gloeosporioides complex were associated with fruit anthracnose in peppers and tomatoes. The C. coccodes group was divided in two clades: C. nigrum, isolated predominantly from fruits, and C. coccodes, isolated mainly from roots. Only C. salicis and C. cigarro produced sexual morphs. The species C. godetiae, C. salicis, and C. cigarro have not previously been reported in Bulgaria. Our results enrich the knowledge of the biodiversity and specific features of Colletotrichum species, which are pathogenic to solanaceous hosts, and may serve as a scientific platform for efficient disease control and resistance breeding.

First report of ring spot disease on sugarcane caused by Curvularia ischaemi in China

Sugarcane (Saccharum spp. hybrids) is an economically important crop widely cultivated in the south of China, such as Guangxi, Yunnan, and Guangdong for use as the main raw material of the sugar and alcohol industry (Li and Yang et al. 2015). In July 2021, the sugarcane cultivar GT94-119 planted in Guangzhou (113° 22' E, 23° 09' N), Guangdong province, China showed red to brown ring lesions on the older leaves (Fig.1A). Multiple disease spots gradually merged, eventually leading to leaf wilting and necrosis was observed. Symptoms were present on 11% and 18% of plants in the two observation areas, respectively; however, since symptoms were primarily noted on older leaves, the yield effect was limited. Symptomatic leaf pieces (0.5 × 0.5 cm) were collected and surface-sterilized for 10s in 75% ethanol, followed by 10% NaClO for 30s, washed 3 times with distilled sterile water, blotted dry with sterile tissue, and plated on potato dextrose agar (PDA). The dishes were placed in an incubator at 28 ℃ for 72 h, and the resulting mycelia were transferred to new PDA to obtain pure cultures. The fungal colonies were brownish green, with concentric rings and radial edges (Fig.1B). The hyphae were transparent, separated, and apical hypertrophy (Fig.1C). Conidia were produced within 14 days, ranging in size from 20.0 to 25.5 × 2.5 to 4.5 µm (n=50), upright or curved spindle shaped, clustered or isolated at the end of the conidia stem, with a diaphragm (Fig.1D and E). Eleven isolates purified on PDA were obtained. Morphological identification showed that six of the 11 isolates were similar in morphology and preliminarily identified as Curvularia ischaemi (Mckenzie et al., 1981). One of the above six isolates, named GZ01, was selected for molecular identification. Following the CTAB method for extracting total DNA, the internal transcribed spacer (ITS) region and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) region were amplified and sequenced by using ITS4/ITS5 primer (White et al. 1990) and GDF/GDR primer (Damm et al. 2012), respectively. The amplified sequence was compared to nucleotide sequence reported in GenBank using BLAST search, with 98.49% similarity to Curvularia ischaemi strain CBS 630.82 (GenBank MH861533.1) and 99.81% similarity to the GAPDH sequence of Curvularia ischaemi (GenBank LT715790.1). The phylogenetic tree based on sequence data for the two genes mentioned above and other reference sequences indicated that our isolate (GZ01) was closely identified as Curvularia ischaemi (Fig.2). To obtain a spore suspension of GZ01 for pathogenicity test, spores were cultured (28℃) in PDA for 14 days, washed with sterilized distilled water, and filtered with cheese cloth. The pathogenicity test was carried out in a greenhouse at 28℃ using a spore suspension (1×104 mL-1) and distilled water as inoculation sources. Healthy seedlings of the susceptible sugarcane cultivar LC05-136 were inoculated at the 5 to 6 leaf stage. The spore suspension was evenly sprayed on nine seedlings until the leaves were fully wet, additional nine seedlings were evenly sprayed with the same volume of sterile water to serve as the control. At 14 days after inoculation, all inoculated plants with suspension showed the same symptoms as observed in the greenhouse (Fig.1F), while all plants inoculated with sterile water showed no symptoms. Curvularia ischaemi was again isolated from the infected leaves with symptoms. The results confirm Koch's postulates. Curvularia ischaemi has been previously reported to cause disease on Batiki blusgrass (Ischaemum indicum) (Mckenzie et al. 1981). To our knowledge, this is the first report of C. ischaemi causing ring spot disease on sugarcane in China. For different ecological types of sugarcane areas, whether this disease will occur in the early stage of sugarcane growth and have an impact on sugarcane yield is worth further investigation.

First Report of Post-Harvest Anthracnose of Kiwifruit Caused by Colleotrichum fioriniae in Liaoning and Sichuan Province, China

Kiwifruit (Actinidia spp.) is one of the most important fruit crops in China. Post-harvest anthracnose symptoms were observed on kiwifruit in October 2021. Kiwifruits 'Longcheng 2' (n=200) were obtained from an orchard in Kuandian city of Liaoning province, China (124°32'E, 40°20'N). And cultivar 'Cuiyu' (n=100) were harvested from orchards in Mianzhu city, Sichuan Province, China (104°03'E, 31°15'N). After storage at 24 °C and 80% relative humidity (RH) for 8 days, the disease incidence of 'Longcheng 2' and 'Cuiyu' was 30% and 15%, respectively. Symptoms of diseased fruits appeared as water-soaked, irregular and light brown lesions. Orangish conidial masses were observed on some fruits. Ten lesion margins (5×5 mm) from 'Longcheng2' or 'Cuiyu' were respectively excised, surface sterilized by 70% ethanol (1 min), 1% NaOCl (5 min), washed, dried, plated on potato dextrose agar (PDA), and incubated at 25 °C for 5 days. Eight isolates were obtained from 'Longcheng 2' (LC1-3 to LC1-10) and nine strains from 'Cuiyu' (CY1-2 to CY1-10). The representative isolates LC1-3 and CY1-2 were put on PDA, and appeared white to pale gray on the upper side. However, isolate LC1-3 secreted red pigments after 7 days of culture. Conidia of LC1-3 were hyaline, smooth-walled, single-celled, cylindrical (3.0 to 4.9×7.2 to 14.7 µm, n=50). Ellipsoidal single cell conidia of CY1-2 were hyaline, and ranged in size from 3.2 to 5.0×8.5 to 13.9 µm (n=50) born on conidiophores. Appressorium of isolates LC1-3 and CY1-2 were globose to ellipsoid with 4.2 to 7.4×7.3 to 10.8 µm and 3.0 to 4.9×6.3 to 10.3 µm in size, respectively (n=50) (Fu et al. 2019 ). Four genes (ACT, CHS, GAPDH, TUB2) and the ITS region were successfully amplified and sequenced from all isolates (Weir et al. 2012). Based on sequence alignment, the isolates from 'Longcheng 2' or 'Cuiyu' were identical. BLAST analysis of the ACT, CHS, GAPDH, ITS and TUB2 sequences of LC1-3 (ON018724, ON018722, ON018720, OM980324, ON018718) or CY1-2 (ON018725, ON018723, ON018721, OM980325, ON018719) showed high similarity with C. fioriniae (CBS 128517; JQ949613, JQ948953, JQ948622, MH865005, JQ949943) were 97.1% to 99.7% or 98.1% to 99.7%, respectively. Phylogenetic analysis using concatenated sequences (maximum likelihood method) with MEGA 11 showed LC1-3 and CY1-2 were located within the same clade with C. fioriniae. Previous studies showed that C. fioriniae was classified into three subclades (Damm et al. 2012; Fu et al. 2019). However, LC1-3 and CY1-2 were located within a new subclade, namely the subclade IV. To test pathogenicity, healthy and mature kiwifruits 'Donghong', 'Cuiyu', 'Xuxiang', 'Hayward' and 'Jinyan' were surface sterilized. Each un-wounded fruit was dropped with 10 μl conidial suspension (105 conidia/ml) on the fruit surface. All fruits were placed into a plastic box and stored at 24 °C under 80% RH. Each treatment consisted of 10 fruits and were repeated three times. After 8 days, typical anthracnose lesions were observed on all inoculated fruits. Whereas, the controls treated with sterile distilled water remained asymptomatic. The pathogens re-isolated from diseased fruits were similar morphological and identical to the original isolates, fulfilling Koch's postulates. Anthracnose caused by C. fioriniae has been reported on many fruits (Ling et al. 2020; Waller et al. 2021), but to our knowledge, this is the first report of anthracnose on kiwifruit caused by C. fioriniae. The results will provide valuable information for avoiding post-harvest anthracnose on kiwifruit.

Characterization and fungicide sensitivity of Colletotrichum godetiae causing sweet cherry fruit anthracnose in Guizhou, China

Sweet cherry is an important fruit crop with high economic and ornamental value in China. However, cherry fruit anthracnose, caused by Colletotrichum species, greatly impacts cherry yield and quality. Here, we surveyed cherry anthracnose in Guizhou, China from 2019–2020. Necrotic sweet cherry fruits were collected from different areas in Guizhou and examined. A total of 116 Colletotrichum strains were isolated from these symptomatic fruits. Based on the morphological characteristics of the isolates and phylogenetic analyses of concatenate internal transcribed spacer (ITS) region and ACT, CHS-1, GAPDH, TUB2, and HIS3 genes, the pathogen responsible for causing sweet cherry anthracnose was identified as Colletotrichum godetiae. Pathogenicity tests were conducted by inoculating healthy sweet cherry fruits with spore suspensions of the fungal pathogen, and Koch’s postulates were confirmed by pathogen re-isolation and identification. The Q-1 isolate showed different sensitivities to 13 fungicides, exhibiting seven different modes of action, and its EC₅₀ values ranged from 0.04 to 91.26 μg ml⁻¹. According to that, the sensitivity of 20 isolates from different samples to ten fungicides with better performance, were measured. The results showed that 6 of the 10 fungicides (difenoconazole, propiconazole, prochloraz-manganese, pyraclostrobin, trifloxystrobin-tebuconazole, and difenoconazole-azoxystrobin) all showed higher sensitive to the 20\u00B0C. godetiae isolates, and no resistance groups appeared. Its EC50 values ranged from 0.013 to 1.563 μg ml⁻¹. In summary, this is the first report demonstrating that C. godetiae causes sweet cherry anthracnose and the results of this study provide insights into how sweet cherry anthracnose could be effectively controlled in China.

Fusarium oxysporum and Colletotrichum musae Associated with Wilt Disease of Coffea arabica in Coffee Gardens in Saudi Arabia

This study aimed to identify if Fusarium and Colletotrichum species are linked to coffee leaf wilt symptoms (Coffea arabica L.) gardens in Jazan region, Kingdom Saudi Arabia. The symptomatic wilted leaves and shoots were collected from Jazan Mountain Region Development Authority (JMRDA) farm in jabal Fifa. Samples of roots and leaves tissues were plated on Dox' Agar medium and incubated for one week at 24^oC. Two morphologically different fungus colonies grew on the medium. A PCR-based method was used for the molecular amplification and characterization of the fungi using a 18SrRNA specific primer. 1323 and 1501 bp PCR products were obtained by using the 1% agarose gel electrophoresis. The sequence analysis and genbank homology revealed that the present fungi were Fusarium oxysporum and Colletotrichum musae with 99 and 98% similarity, respectively. Both fungi sequences were submitted to the genebank under accession numbers OP010081 and OP010082, respectively. This is the first report of these two genera of fungi infecting the roots and leaves of coffee trees in Jazan Region of Saudi Arabia and suggests that other fungus species may play a significant role as diseases in other coffee-producing areas.

Characterization of Colletotrichum Isolates from Strawberry and Other Hosts with Reference to Cross-Inoculation Potential

Colletotrichum is an important phytopathogenic fungus that causes anthracnose disease in diverse agronomically important tropical food crops. Accurate pathogen identification is critical for early diagnosis and efficient management of anthracnose. ITS is not a reliable marker for this fungal genus due to its failure to phylogenetically resolve cryptic species. In this study, 36 Colletotrichum isolates belonging to the Acutatum, Boninense and Gloeosporioides species complexes were characterized using multigene phylogenetic analyses, morphology and pathogenicity assays. Additionally, the cross-inoculation potential of a representative subset of isolates was evaluated revealing that cross-infection potential is possible among the isolates belonging to the same species complex.

First report of Colletotrichum fioriniae causing anthracnose fruit rot on Vaccinium corymbosum in Chile

Vaccinium corymbosum L. is the most cultivated blueberry species in Chile. Chilean fruits typically take up to 50 days to reach oversea markets; therefore, controlling post-harvest pathogens is of outmost importance to maintain international food safety and quality standards. In February 2019, the Microbial Genetic Resources Bank at INIA received fruits of V. corymbosum cv. 'Brigitta Blue' from Mariquina (-39.567869, -72.992461), located in the southern Chilean blueberry production zone, for post-harvest disease diagnosis. Asymptomatic fruits were incubated in moist-chambers at 25 °C with light/darkness cycles of 12 h. After 5 d, some fruits showed sunken areas and small surface wounds that exudated orange masses of conidia; under the epidermis, gray acervuli were also detected. After 15d, these fruits became dehydrated, mummified, and covered by mycelia, all characteristic symptoms of anthracnose (Wharton and Schilder 2008). In Chile, Colletotrichum gloeosporioides has, thus far, been the only causal agent of anthracnose reported in blueberry (Lara et al. 2003). Conidia exudated from the diseased fruit were inoculated on potato-dextrose agar (PDA) and incubated at 25 °C for 7 d. The resulting colony was predominantly cottony with gray aerial mycelium, displaying masses of pale orange conidia; on the reverse side, the colony was a pink-reddish color. Under a microscope, conidia were hyaline, fusiform to elliptic in shape, and displaying guttulate of 12.2±1.2 × 4.17±0.3 μm (n=30), characteristics coinciding with those described for Colletotrichum fioriniae (Pennycook 2017; Shivas and Tan 2009) (Supplementary Figure 1). The isolate was deposited in the Chilean Collection of Microbial Genetic Resources (CChRGM) as RGM 3330. Genomic DNA extraction of RGM 3330 and phylogenetic analyses were carried out according to Cisterna-Oyarce et al. (2022). A multi-locus sequencing analysis was carried out using five genetic markers. The internal transcribed spacer (ITS), glyceraldehyde 3-phosphate dehydrogenase (gapdh), actin (act), and chitin synthase 1 (chs-1) were PCR-amplified following Damm et al. (2012) and -tubulin (tub) following Glass and Donaldson (1995). Sequences were deposited in GenBank (ON364141 for ITS and ON369167-70 for tub, act, chs-1, and gapdh, respectively) (Sayers et al. 2021). A BLAST analysis carried out in SequenceServer (Priyam et al. 2019), using a custom database of sequences retrieved from Damm et al. (2012) and Liu et al. (2020), showed that all genetic markers were 100% identical to those of C. fioriniae CBS 128517T (ITS (540/540 identities), gapdh (249/249), act (245/245), and chs-1 (274/274)), except for tub, which shared 99.8% of its identities (416/417) with this species. Maximum likelihood phylogenetic estimation clustered RGM 3330 with C. fioriniae strains CBS 128517T and CBS 126526 with 100% bootstrap support (Supplementary Figure 1). Koch's postulates were carried out with asymptomatic fruits of V. corymbosum cv. 'Brigitta Blue'. Prior to inoculation, fruits were surface-sterilized for 10 s in 70% ethanol, 3 s in 1% NaOCl, 10 s in 70% ethanol, rinsed three times with sterile distilled water, and subsequently placed in moist-chambers. Two groups of three repetitions of 20 fruits each were sprayed with 9 × 106 conidia/mL of RGM 3330 for the first group and with sterile distilled water for the control. After 5 d at 25 °C with light/darkness cycles of 12 h, only fruits sprayed with the conidial solution developed symptoms of anthracnose and the re-isolated fungi were identical in morphology to RGM 3330. This is the first report of C. fioriniae in blueberry in Chile. References Cisterna-Oyarce, V., Carrasco-Fernández, J., Castro, J. F., Santelices, C., Muñoz-Reyes, V., Millas, P., Buddie, A. G., and France, A. 2022. Gnomoniopsis smithogilvyi: identification, characterization and incidence of the main pathogen causing brown rot in postharvest sweet chestnut fruits (Castanea sativa) in Chile. Australasian Plant Disease Notes 17:2. Damm, U., Cannon, P. F., Woudenberg, J. H., and Crous, P. W. 2012. The Colletotrichum acutatum species complex. Stud. Mycol. 73:37-113. Glass, N. L., and Donaldson, G. C. 1995. Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous ascomycetes. Appl. Environ. Microbiol. 61:1323-1330. Lara, O., Velazquez, C. G., and Ascencio, C. 2003. Colletotrichum gloeosporiodes in blueberry fruit. in: XIII Congreso de Fitopatología. Liu, X., Zheng, X., Khaskheli, M. I., Sun, X., Chang, X., and Gong, G. 2020. Identification of Colletotrichum species associated with blueberry anthracnose in Sichuan, China. Pathogens 9:718. Pennycook, S. 2017. Colletotrichum fioriniae comb. & stat. nov., resolving a nomenclatural muddle. Mycotaxon 132:149-152. Priyam, A., Woodcroft, B. J., Rai, V., Moghul, I., Munagala, A., Ter, F., Chowdhary, H., Pieniak, I., Maynard, L. J., Gibbins, M. A., Moon, H., Davis-Richardson, A., Uludag, M., Watson-Haigh, N. S., Challis, R., Nakamura, H., Favreau, E., Gómez, E. A., Pluskal, T., Leonard, G., Rumpf, W., and Wurm, Y. 2019. Sequenceserver: a modern graphical user interface for custom BLAST databases. Mol. Biol. Evol. 36:2922-2924. Sayers, E. W., Cavanaugh, M., Clark, K., Pruitt, K. D., Schoch, C. L., Sherry, S. T., and Karsch-Mizrachi, I. 2021. GenBank. Nucleic Acids Res. 49:D92-D96. Shivas, R. G., and Tan, Y. P. 2009. A taxonomic re-assessment of Colletotrichum acutatum, introducing C. fioriniae comb. et stat. nov. and C. simmondsii sp. nov. Fungal Divers. 39:111-122. Wharton, P., and Schilder, A. 2008. Novel infection strategies of Colletotrichum acutatum on ripe blueberry fruit. Plant Pathol. 57:122-134. Supplementary material Supplementary Figure 1: Isolation and identification of Colletotrichum fioriniae RGM 3330 from blueberry fruits cv. 'Brigitta Blue' from Chile. (A) A fruit showing anthracnose; (B) colony of Colletotrichum fioriniae RGM 3330 growing on PDA; (C) microscopic observation of the conidia (100x magnification; bar=10 µm); (D) phylogenetic tree resulting from a maximum likelihood analysis of combined sequence data from ITS, act, chs-1, gapdh, and tub regions for Colletotrichum acutatum species complex, number in the nodes represent ultrafast bootstrap values.

First report of Colletotrichum godetiae causing anthracnose fruit rot on Prunus pseudocerasus in Zhejiang province, China

Prunus pseudocerasus (L.) G. Don is an economically important crop, with 8,420 hm2 of harvested area and 35,000 tons in 2020 (https://www.fao.org/faostat/zh/#data/QCL), and is one of the favorite fruits among consumers. A severe fruit rot disease of P. pseudocerasus cultivar "HeiZhenZhu" was observed in an orchard in Pujiang county (119°42'E, 29°21'N), Zhejiang province in April 2022. Sixty-three plants from a survey of about 200 plants showed anthracnose symptoms, with a disease incidence of more than 30%. Ten diseased fruits were collected from eight different trees. The naturally affected fruits during color changing stage showed initial light brown necrotic lesions, later, the lesions were depressed, and dark brown, the fruits were rotten, and pink conidial masses were produced (Fig. 1 A-F). Conidia were transferred using a sterilized needle into sterile water, diluted to approx. 10 conidia/µL, and spread onto potato dextrose agar (PDA) (Thermo Scientific™) (containing cephalosporin 50 µg/mL). After 24 h, single colonies were transferred, and six single-spore isolates were obtained from different plants. When the strains were grown at 26°C for 7 days, the colonies on PDA were flat with entire margin, surface medium gray-green to white, reverse salmon, light gray-green to white (Fig. 1 G). The conidia of the representative strain YTTJ-JHGS5 were unicellular, hyaline, smooth-walled, cylindrical to fusiform with one end round and one end acute, or both acute ends, 14.4 to 18.9 µm (mean = 16.4 ± 0.9 µm, n = 30) × 4.4 to 5.8 µm (mean = 5.1 ± 0.3 µm, n = 30) (Fig. 1 I). Conidiogenous cells were hyaline, smooth-walled, cylindrical to clavate, 6.5-16.8 µm × 2.6-5.3 µm (n = 30), opening 1.1-2.0 µm (Fig. 1 H). Appressoria were single, light brown to medium brown, elliptical or irregular in shape, the outline entire or undulate, 9.2 to 12.1 µm (mean = 9.2 ± 1.1 µm, n = 30) × 4.6 to 6.7 µm (mean = 5.6 ± 0.4 µm, n = 30) (Fig. 1 J). The morphological characteristics of YTTJ-JHGS5 were consistent with the Colletotrichum acutatum species complex (Damm et al. 2012). To further identify the species, the internal transcribed spacer (ITS), actin (ACT), beta-tubulin (TUB), chitin synthase (CHS-1), calmodulin (CAL) and glyceraldehyde-3-phosphate dehydrogenase (GPD) genes were sequenced (Weir et al. 2012; O'Donnell et al. 2000). The thirty-six sequences had been deposited in GenBank (ITS: ON155427-ON155432; ACT: ON191542-ON191547; CAL: ON191548-ON191553; CHS-1: ON167522-ON167527; GPD: ON191554-ON191559; TUB2: ON191560-ON191565, respectively). A BLAST search of these sequences (ITS, ACT, CHS-1, GPD, and TUB2) showed 99% identity with the sequences of ex-holotype C. godetiae CBS133.44 (ITS: JQ948402; ACT: JQ949723; CHS-1: JQ949063; GPD: JQ948733; TUB2: JQ950053) (Damm et al. 2012); the sequences of CAL genes of these strains showed 99% identity with the sequence of C. godetiae VV-087 (CAL: MK416001) (Varjas et al. 2020). The Bayes phylogenesis showed that six strains and C. godetiae CBS133.44 were clustered in a robust branch (Bayesian posterior probability = 1). Based on the morphological characteristics and phylogenesis, these strains were identified as C. godetiae. To fulfill Koch's postulates, in April 2022, live plant pathogenicity tests were performed in the field, and color-changing-stage fruits of five-year-old trees were disinfected with 75% alcohol and air-dried for 10 min to volatilize excess alcohol. A conidial suspension (50 mL of 1 × 106 conidia/mL) was sprayed on fifteen fruits for each plant, fifteen fruits sprayed with sterilized water served as control. The experiment was repeated four times, each repeat contained ten trees. The daily average temperature and daily average RH in the orchard were 22°C and 67%, respectively. After 6 days, the fruit surfaces were depressed, dark brown, later, the lesions were expanded, and pink conidial masses were observed (Fig. 1, L). Control fruits remain healthy (Fig. 1, K). C. godetiae was re-isolated from the lesions of inoculated fruits. C. godetiae has been reported on Ceanothus sp., Fragaria × ananassa and so on worldwide (Farr and Rossman 2022), in addition, C. fructicola infected cherry (Zhao et al. 2022). To our knowledge, this is the first report of C. godetiae causing anthracnose fruit rot on Prunus pseudocerasus in China. This disease occurs mainly on immature fruits and leads to yield loss in the field, therefore it is necessary to take preventive measures in advance.

Sensitivity of Colletotrichum acutatum Species Complex from Strawberry to Fungicide Alternatives to Quinone-Outside Inhibitors

Colletotrichum acutatum is a species complex that causes anthracnose fruit rot and root necrosis on strawberry. The major and minor species within the complex that affect strawberry production are C. nymphaeae and C. fioriniae, respectively. The disease can significantly reduce yield under conducive weather, and its management has greatly relied on quinone-outside inhibitor fungicides (QoI). However, due to the emergence of resistant isolates, such products are no longer effective. Therefore, alternative fungicides were investigated. C. nymphaeae and C. fioriniae isolates were collected from multiple strawberry fields in the United States from 1995 to 2017. The sensitivity of benzovindiflupyr, penthiopyrad, pydiflumetofen, fluazinam, fludioxonil, and cyprodinil was assessed by in vitro and in vivo assays. Both Colletotrichum species were sensitive to benzovindiflupyr, penthiopyrad, fluazinam, and fludioxonil based on mycelial growth assays. Interestingly, of these products, only penthiopyrad did not inhibit conidial germination at 100 µg/ml. For cyprodinil, C. nymphaeae was sensitive based on the mycelial growth, whereas C. fioriniae was not inhibited. Neither species was inhibited by pydiflumetofen in mycelial growth, conidial germination, nor detached fruit assays. The prepackaged mixtures fludioxonil + cyprodinil and fludioxonil + pydiflumetofen were effective in a field trial; however, their use should be carefully considered because of the lack of efficacy of one of the compounds in the mixture. This study sheds light on the potential registration of products alternative to QoIs, such as benzovindiflupyr and fluazinam, which could improve the management of strawberry anthracnose.

Phylogeny and pathogenicity of Colletotrichum lindemuthianum causing anthracnose of Phaseolus vulgaris cv. Bhaderwah-Rajmash from northern Himalayas, India

With an annual loss of up to 100%, anthracnose caused by Colletotrichum is one of the most devastating diseases of common beans (Phaseolus vulgaris L.). Due to few distinctive morphological characters, Colletotrichum species are frequently misidentified. In India, several Colletotrichum species have been reported as pathogens of Phaseolus species, but none had previously been validated by means of molecular tools. In this study, we studied Colletotrichum strains from common beans cv. Bhaderwah-Rajmash from the northern Himalayas of India based on both morphological and DNA sequence data of six loci, namely ITS, gapdh, chs-1, his3, act, tub2. The strains were identified as C. lindemuthianum that belongs to the C. orbiculare species complex. Representative C. lindemuthianum strains tested on Phaseolus vulgaris cv. Bhaderwah-Rajmash were pathogenic and exhibited variation in symptomology and disease progression. By identifying the causal agent, we provided substantial information to develop the best control strategies for anthracnose of Phaseolus vulgaris from the northern Himalayas of India.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03216-0.

Identification of Two Fungal Pathogens Responsible for Liriodendron chinense × tulipifera Black Spot and Screening of Trichoderma sp. for Disease Control

Liriodendron chinense × tulipifera black spot is a newly discovered disease that causes yellowing and early shedding of leaves, affecting the growth of Liriodendron trees, and significantly reducing their ornamental value as a garden species. The pathogen responsible for this disease, and how it can be prevented and controlled, are not clear. In this study, the occurrence of this disease was first investigated according to Koch's postulates, and the primary pathogens causing Liriodendron black spot were determined to be Colletotrichum gloeosporioides and Alternaria alternata. Biocontrol strains antagonistic to these two pathogens were then screened from the leaf microorganisms of L. chinense × tulipifera, and a preliminary investigation of the biological control of Liriodendron black spot was performed. Through the screening of antagonistic microorganisms on the leaf surface of L. chinense × tulipifera, the strain Trichoderma koningiopsis T2, which displayed strong antagonism against C. gloeosporioides and A. alternata, was obtained. The T2 strain could inhibit the growth of the two pathogens via three mechanisms: hyperparasitism, volatile and nonvolatile metabolite production, and environmental acidification. The biocontrol experiments in the greenhouse and field showed that initial spraying with a T. koningiopsis T2 spore suspension followed by the two pathogens resulted in the lowest disease incidence. These results confirmed the black spot pathogens of L. chinense × tulipifera, clarified the antagonistic mechanism of T. koningiopsis T2 against the two pathogens, and provided a theoretical basis and technical support for the biological control of the disease.

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

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

Temperature requirements of Colletotrichum spp. belonging to different clades

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

Diversity of Colletotrichum Species Causing Apple Bitter Rot and Glomerella Leaf Spot in China

Bitter rot and Glomerella leaf spot (GLS) of apples, caused by Colletotrichum species, are major diseases of apples around the world. A total of 98 isolates were obtained from apple fruits with bitter rot, and 53 isolates were obtained from leaves with leaf spot in the primary apple production regions in China. These isolates were characterized morphologically, and five gene regions (ITS, ACT, GAPDH, CHS-1 and TUB2) were sequenced for each isolate. A phylogenetic analysis, combined with a comparison of the morphological, cultural and pathogenic characters, sorted bitter rot isolates into six species: C. alienum, C. fructicola, C. gloeosporioides sensu stricto, C. nymphaeae, C. siamense and one new species, C. orientalis Dandan Fu & G.Y. Sun. Among these, C. siamense was the predominant pathogen associated with bitter rot. Isolates from leaf spot were identified as two species, C. aenigma and C. fructicola. This is the first report of C. orientalis as an apple bitter rot pathogen worldwide, and the results provide important insights into the diversity of Colletotrichum species in China.

New-Generation Sequencing Technology in Diagnosis of Fungal Plant Pathogens: A Dream Comes True?

The fast and continued progress of high-throughput sequencing (HTS) and the drastic reduction of its costs have boosted new and unpredictable developments in the field of plant pathology. The cost of whole-genome sequencing, which, until few years ago, was prohibitive for many projects, is now so affordable that a new branch, phylogenomics, is being developed. Fungal taxonomy is being deeply influenced by genome comparison, too. It is now easier to discover new genes as potential targets for an accurate diagnosis of new or emerging pathogens, notably those of quarantine concern. Similarly, with the development of metabarcoding and metagenomics techniques, it is now possible to unravel complex diseases or answer crucial questions, such as "What's in my soil?", to a good approximation, including fungi, bacteria, nematodes, etc. The new technologies allow to redraw the approach for disease control strategies considering the pathogens within their environment and deciphering the complex interactions between microorganisms and the cultivated crops. This kind of analysis usually generates big data that need sophisticated bioinformatic tools (machine learning, artificial intelligence) for their management. Herein, examples of the use of new technologies for research in fungal diversity and diagnosis of some fungal pathogens are reported.

First report of leaf anthracnose on the Whorled Sunflower, Helianthus verticillatus, caused by Colletotrichum fioriniae in the United States

Whorled sunflower, Helianthus verticillatus Small, is an endangered (U.S. Fish and Wildlife Service 2014) perennial sunflower species indigenous to the southern United States (Matthews et al. 2002; Ellis et al. 2008). Helianthus verticillatus has a showy yellow floral display in the Fall that attracts a diversity of insect visitors (Strange et al. 2020). Its hardiness in the landscape and late-season blooming makes it a potential ornamental (Trigiano et al. 2021). In June 2021, anthracnose-like lesions were observed on mature leaves collected from potted H. verticillatus plants grown in the nursery compound at the University of Tennessee, Knoxville, TN, USA. Irregularly shaped leaf spots with 1‒2 mm tan centers were observed on mature leaves, which later expanded to 3‒5 mm, and became dark brown- to- black surrounded by chlorotic halos (Fig.1). Lesions from three infected leaves were excised from a single potted plant, trimmed to 1.5-cm squares with green borders, and surface-sterilized (Trigiano et al. 2018). Tissues were placed onto potato dextrose agar (PDA), amended with 100 mg/ml of each streptomycin sulfate and chlorotetracycline, and incubated at 21 °C in the dark until axenic cultures were obtained. Initially, appressed white- to- pale gray mycelia were formed that turned light pinkish-orange with age (Fig. 2A). Conidia (Fig. 2B-C) were single-celled, hyaline, and cylindrical- to- fusiform with acute ends, and were similar to Colletotrichum fioriniae (Damm et al. 2012). Conidia measured 8.9 ± 1.3 μm long and 3.3 ± 0.6 μm wide (N=40). Genomic DNA was isolated with a Phire Direct Plant PCR kit (Thermo FisherScientific, Waltham, MA). The partial beta-tubulin (TUB2) gene, chitin synthase 1 (CHS-1) gene, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene, and the internal transcribed spacer (ITS) region of ribosomal DNA were amplified with primers T1/BT2B, CHS-354R/CHS-79F, GDF1/GDR1, and ITS1/ITS4, respectively and sequenced (Damm et al. 2012). The resulting sequences were submitted to GenBank (TUB2, ON036471; CHS-1, ON036472; GAPDH, ON036470; and ITS, ON008206). Consensus sequences had 100% identity with C. fioriniae type culture CBS 128517 accessions JQ949943 (TUB2), JQ948953 (CHS-1), JQ948622 (GAPDH), and MH865005 (ITS rDNA). Because H. verticillatus is endangered, and the scarcity of available plant material, Koch's postulates were performed using a detached leaf assay (Boggess et al. 2022). Six healthy leaves were surface-sterilized using the previously described protocol, longitudinally bisected, and placed on 1.5% water agar in three 15 × 100 mm petri dishes. Three half leaves were inoculated with sterile, 5 mm-diameter PDA plugs (controls). The remaining three leaves were inoculated with 5 mm-diameter PDA plugs of C. fioriniae and incubated as described previously. After ten days, necrotic lesions developed on leaves inoculated with C. fioriniae and were similar to the initially observed lesions on plants. Lesions did not develop on control leaves. Colletotrichum fioriniae was re-isolated from lesions using the previously described protocol. The disease does not appear to cause mortality of H. verticillatus and does not require control measures but does reduce the aesthetic value of the plant. To the best of our knowledge, this is the first report of C. fioriniae infecting H. verticillatus in the United States.

First report of Colletotrichum fioriniae causing anthracnose on pear fruit in Serbia

European pear (Pyrus communis L.) is one of the most important fruits in Serbia, with a total production of 55,938 tonnes in 2021 (Statistical Office of the Republic of Serbia). In November 2021, pear fruits (cv. Santa Maria) with typical anthracnose symptoms were collected in one storage facility in the area of Smederevo, Serbia. The disease incidence was about 2%. A total of nine infected fruits had dark, circular, sunken necrotic lesions with concentric rings of orange conidial masses produced in black acervuli. The tissue pieces from the edges of lesions (3 to 5 mm2) were surface-sterilized in 1% sodium hypochlorite for 1 min, rinsed twice in sterilized distilled water, air-dried, and incubated on potato dextrose agar (PDA) at 25°C. One isolate/diseased fruit was obtained (nine in total). Colony morphology of all isolates on PDA was light gray to pinkish on the upper side, and pink to vinaceous on reverse after 7 days of incubation at 25°C in the dark. Average growth rate was 64 ± 2 mm. The conidia were hyaline, fusiform, aseptate, smooth-walled, with both ends acute, and measured 12.8 to 16.6 µm × 3.5 to 4.5 µm (n =100). Appressoria were single, smooth-walled, dark brown, clavate to irregular outline, 5.5 to 9.6 × 4.8 to 7.2 μm (n =20). These morphological characterstics are consistent with the description of Damm et al. (2012) for Colletotrichum fioriniae. To confirm this identification, genomic DNA of representative isolate SZ-21-36 was extracted and the ITS region of the rDNA, partial beta-tubulin gene (BenA), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and partial actin gene (ACT) were amplified using the primers ITS1/ITS4, Bt2a/Bt2b, GDF1/GDR1, and ACT512F/ACT783R, respectively (Hassan et al. 2019). The nucleotide sequence of each locus has been deposited in GenBank under Accession Nos. ON171625 (ITS), ON186696 (BenA), ON186697 (GAPDH), and ON186698 (ACT). Multilocus phylogenetic analysis based on the above mentioned molecular markers placed Serbian isolate of C. fioriniae with other isolates of this species deposited in GenBank (bootstrap support of 100%). Pathogenicity test was conducted on symptomless, detached pear fruits (cv. Santa Maria). Five surface-sterilized fruits were wound-inoculated with 50 μl of a conidial suspension (1 × 106 conidia/ml). After 10 days of incubation in a plastic chamber (25°C, 90% relative humidity, and 12-h photoperiod), typical anthracnose lesions developed on inoculated fruits. Five control fruits inoculated with sterile distilled water remained asymptomatic. The experiment was repeated once. Fungal colonies reisolated from the lesions showed the same morphological features as the original isolate. Pathogen was not reisolated from the control fruits. C. fioriniae was previously reported on European pear fruits in Croatia (Ivić et al. 2013), France (Da Lio et al. 2017), China (Fu et el. 2019), and in the USA (Pavlović et al. 2019). To our knowledge, this is the first report of anthracnose of pear fruit caused by C. fioriniae in Serbia. Currently, the economic impact of anthracnose caused by this pathogen is minimal, but its presence decreases commercial value and quality of pear fruits, and can be a risk to the further spread of C. fioriniae to other plant species.

Characterization of Colletotrichum Isolates Causing Colletotrichum Dieback of Citrus in California

Dieback caused by Colletotrichum spp. is an emerging disease in California citrus groves. A large-scale survey with emphasis on seasonal variations of latent infections was conducted throughout citrus orchards in Fresno, Kern, and Tulare counties in 2019 and 2020. Latent infections on citrus leaves and twigs varied markedly between years. Isolates of Colletotrichum spp. were obtained from asymptomatic tissue, and two groups were formed based on colony and spore morphology. The morphological groups were further identified based on multigene sequence analysis using the DNA regions ITS1-5.8S-ITS2, TUB2, and GAPDH. Results revealed that isolates belong to two phylogenetic species, C. gloeosporioides and C. karstii, being C. karstii more frequently isolated. Representative isolates of each species were further selected and characterized based on the response of physiological variables to temperature. Both species had similar optimum growth temperatures but differed in maximum growth rates, with C. gloeosporioides exhibiting a greater growth rate than that of C. karstii on media. Pathogenicity tests on citrus trees demonstrated the ability of C. gloeosporioides and C. karstii to cause lesions on twigs and no differences in aggressiveness. A fungicide screening performed in this study determined that the DMI fungicides were the most effective in reducing the mycelial growth of C. gloeosporioides and C. karstii. The QoI fungicides showed a remarkably inhibitory impact on spore germination of both species. On average, C. karstii was more sensitive to the DMI fungicides than C. gloeosporioides. The findings of this study provide new information to understand the Colletotrichum dieback of citrus.

First Report of Colletotrichum fioriniae Causing Grapevine Anthracnose in New York

Grapevine is one of the most widely-planted fruit crops in the world, and is the most economically important fruit crop in the state of New York, USA. Symptoms of anthracnose on grapevine are similarly widely-reported on grapevine fruit and foliage, and such symptoms are commonly attributed to Elsinöe ampelina (Wilcox et al., 2015). However, similar symptoms, if not identical, to those associated with E. ampelina have been sporadically attributed to various species in the genus Colletotrichum. In September 2021, a survey was conducted in three research vineyards at Cornell AgriTech in Geneva, NY. Symptoms of anthracnose werebserved on four Vitis interspecific hybrid breeding lines in a 1 ha vineyard. Leaves, fruit, and petioles showing symptoms of anthracnose, i.e., sunken necrotic lesions with grayish centers and brownish margins, were collected. Symptomatic and healthy portions of surface-sterilized tissues were placed on PDA medium and incubated at 23oC for 7 days. Several petiole samples yielded colonies of white to greyish mycelium, with some red to orange pigmentation (Fig. 1A and 1B), similar to those described by Chowdappa et al. (2009) for Colletotrichum species isolated from grapevine in India. Cultures were allowed to sporulate. Slides from cultures were prepared and examined at 400X magnification. Conidia from cultures were cylindrical with rounded ends, 13.5-15.2 μm in length and 7.6-9.0 μm in width (Fig. 1C). Koch's postulates were fulfilled by inoculating detached healthy leaves of V. vinifera 'Chardonnay' that had been surface sterilized in 10% sodium hypochlorite and triple-rinsed in sterile distilled water. Drop inoculation was used from a suspension of 105 conidia/ml from the foregoing pure cultures as five 2 µL droplets per leaf. Inoculated detached leaves were maintained on water agar in a Petri dish at 23oC. Four days after inoculation, symptoms were observed and compared with the originally collected samples. Inoculated leaves displayed symptoms typically found on the collected tissues, and the original pathogen, as confirmed by colony morphology and conidial characteristics and dimensions, was reisolated from inoculated leaves, and not from non-inoculated controls. For molecular characterization, fungal DNA was isolated by using Qiagen DNeasy kit and amplified using the following primer pairs: ITS1/ITS4, TEF (Hyun et al., 2009), E. ampelina F/R (Santos et al. 2018), TUB2, ACT, HIS3, GAPDH and CHS1 (Damm et al., 2001). PCR products were purified using ExoSAP-IT, and samples were Sanger sequenced. Sequences were analyzed using Geneious Prime software, and the resulting sequences (NCBI accessions OL720215, OL720216, OL720217, OL720218, OL853836, OM982612, OM982613, OM982614, OM982615 and OM982616) had 94 to 100% identity to Colletotrichum fioriniae NCBI accessions MN944922.1, MK646015.1, MN944922.1, MN856415.1, KU847413.1, MN520490.1, MN544294.1, KY695259.1, MN535117.1 and MN544295.1. Symptoms of grapevine anthracnose caused by Colletotrichum species have been reported from India (Chowdappa et al., 2009) and Korea (Kim et al., 2021). To our knowledge this is the first report of grapevine anthracnose caused by C. fioriniae Anthracnose and ripe rot are diseases of increasing importance, particularly as new grapevine cultivars with resistance to powdery mildew or downy mildew are adopted. Taxonomy of the causal agents (E. ampelina and Colletotrichum spp.) has undergone considerable revision. Consequently, distribution and relative prevalence of the various taxa will require further study.

Development of a nested PCR assay for detecting Colletotrichum siamense and Colletotrichum fructicola on symptomless strawberry plants

Anthracnose is a major disease of strawberry that seriously impacts the strawberry industry. To prevent the spread of anthracnose through symptomless plants, it is important to detect pathogenic Colletotrichum spp. at the latent infection stage in the nursery. Previous PCR-based methods developed for the diagnosis or detection of Colletotrichum acutatum and Colletotrichum gloeosporioides have used primers targeting the internal transcribed spacer region of ribosomal DNA, β-tubulin gene, or mating type gene. In this study, to specifically detect Colletotrichum siamense and Colletotrichum fructicola, the most predominant and virulent Colletotrichum species causing strawberry anthracnose in Taiwan, we conducted a comparative genomics analysis of 29 Colletotrichum spp. and identified a non-conserved 1157-bp intergenic region suitable for designing specific primers for a nested PCR assay. In silico analysis and actual tests suggested that the new nested PCR assay could detect pathogenic C. siamense and C. fructicola, but not other strawberry pathogens (Botrytis sp., Fusarium spp., Neopestalotiopsis rosae, and Phytophthora sp.) or ubiquitous saprophytes (Fusarium spp. and Trichoderma spp.). The inner to outer primer ratio was optimized to 1:10 to eliminate unexpected bands and enhance the signal. The assay could detect as little as 1 pg of C. siamense genomic DNA, which corresponds to ~15 cells. Application of the new detection assay on 747 leaf samples collected from 18 strawberry nurseries in 2019 and 2020 showed that an average of 20% of strawberry mother plants in Taiwan were latently infected by C. siamense or C. fructicola. The newly developed assay is being applied to facilitate the production of healthy strawberry runner plants in Taiwan.

Publicly Available and Validated DNA Reference Sequences Are Critical to Fungal Identification and Global Plant Protection Efforts: A Use-Case in Colletotrichum

Publicly available and validated DNA reference sequences useful for phylogeny estimation and identification of fungal pathogens are an increasingly important resource in the efforts of plant protection organizations to facilitate safe international trade of agricultural commodities. Colletotrichum species are among the most frequently encountered and regulated plant pathogens at U.S. ports-of-entry. The RefSeq Targeted Loci (RTL) project at NCBI (BioProject no. PRJNA177353) contains a database of curated fungal internal transcribed spacer (ITS) sequences that interact extensively with NCBI Taxonomy, resulting in verified name-strain-sequence type associations for >12,000 species. We present a publicly available dataset of verified and curated name-type strain-sequence associations for all available Colletotrichum species. This includes an updated GenBank Taxonomy for 238 species associated with up to 11 protein coding loci and an updated RTL ITS dataset for 226 species. We demonstrate that several marker loci are well suited for phylogenetic inference and identification. We improve understanding of phylogenetic relationships among verified species, verify or improve phylogenetic circumscriptions of 14 species complexes, and reveal that determining relationships among these major clades will require additional data. We present detailed comparisons between phylogenetic and similarity-based approaches to species identification, revealing complex patterns among single marker loci that often lead to misidentification when based on single-locus similarity approaches. We also demonstrate that species-level identification is elusive for a subset of samples regardless of analytical approach, which may be explained by novel species diversity in our dataset and incomplete lineage sorting and lack of accumulated synapomorphies at these loci.

Colletotrichum Spp. Diversity Between Leaf Anthracnose and Crown Rot From the Same Strawberry Plant

Leaf anthracnose (LA) and anthracnose crown rot (ACR) represent serious fungal diseases that pose significant threats to strawberry production. To characterize the pathogen diversity associated with above diseases, 100 strawberry plants, including varieties of "Hongjia," "Zhangji," and "Tianxianzui," were sampled from Jiande and Zhoushan, the primary plantation regions of Zhejiang province, China. A total of 309 Colletotrichum isolates were isolated from crown (150 isolates) and leaves (159 isolates) of affected samples. Among these, 100 isolates obtained from the plants showing both LA and CR symptoms were selected randomly for further characterization. Based on the morphological observations combined with phylogenetic analysis of multiple genes (ACT, ITS, CAL, GAPDH, and CHS), all the 100 tested isolates were identified as C. gloeosporioides species complex, including 91 isolates of C. siamense, 8 isolates of C. fructicola causing both LA and ACR, and one isolate of C. aenigma causing ACR. The phenotypic characteristics of these isolated species were investigated using the BIOLOG phenotype MicroArray (PM) and a total of 950 different metabolic phenotype were tested, showing the characteristics among these isolates and providing the theoretical basis for pathogenic biochemistry and metabolism. The pathogenicity tests showed that even the same Colletotrichum species isolated from different diseased tissues (leaves or crowns) had significantly different pathogenicity toward strawberry leaves and crown. C. siamense isolated from diseased leaves (CSLA) was more aggressive than C. siamense isolated from rotted crown (CSCR) during the infection on "Zhangji" leaves. Additionally, C. fructicola isolated from affected leaf (CFLA) caused more severe symptoms on the leaves of four strawberry varieties compared to C. fructicola isolated from diseased crown (CFCR). For crown rot, the pathogenicity of CSCR was higher than that of CSLA.

Fungal and Oomycete Diseases of Minor Tropical Fruit Crops

Minor tropical fruits are grown on a small scale and provide income to smallholder farmers. The cultivation of these fruit crops indirectly contributes to the economy of producing countries as well as to food and crop security. Dragon fruits, guava, passionfruit, lychee, longan, mangosteen, durian, and rambutan are common minor fruit crops. In recent years, the international trade of some of these minor tropical fruits, particularly dragon fruit, passionfruit, guava, and lychee, has increased due to their nutritional value, with various health benefits. Similar to other crops, minor fruit crops are susceptible to fungal and oomycete diseases. These diseases negatively affect the yield and quality of fruit crops, leading to substantial losses. In this context, the knowledge of disease types and causal pathogens is fundamental to develop suitable disease management practices in the field as well as appropriate post-harvest treatments.

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.

First Report of Colletotrichum nymphaeae Causing Walnut Anthracnose in China

Walnut (Juglans regia L.) is a high quality woody nut and edible oil tree with a planting area of about 5,000,000 hectare in China. Walnut anthracnose is a serious disease, infecting approximately 50% of the fruits and causing a great yield losses (Wang et al. 2016). In 2019 to 2020, walnut fruits with anthracnose symptoms were collected from walnut orchards in province of Hubei, Sichuan procinve and Chongqing municipality, China. Symptoms on fruits were circular or subcircular or irregular shaped, with brown to black water soaked and sunken lesions. The black lesions enlarged and amalgamated into large necrotic areas. The older spots in the center became blackish with acervuli causing the complete mummification of the fruit, and orange conidial masses appeared under wet conditions. Necrotic tissues of the fruits were sterilized in 75% ethanol solution for 30 s, then sterilized in 4% sodium hypochlorite for 1min, and washed 3 times with sterile distilled water. The tissues were put on potato dextrose agar (PDA) and incubated at 25℃. Pure cultures were obtained by single-spore culturing method and the isolate HBBK4-4 was deposited into the China's Forestry Culture Collection Center (CFCC 57388). On PDA, the colonies were cottony, white to pale gray with aerial mycelium on the upper side and pink with black spots on the reverse. The mycelial growth rate was 9.6 mm/day at 25°C. Conidia were 1-celled, colorless, smooth-walled, straight, cylindrical to cylindrical-clavate with acute ends, 12.5 to 18.2 × 3.9 to 5.4 μm (mean 15.3 ± 3.7 × 4.9 ± 0.6 μm, n = 40). Most conidia germinated and developed one pleurogenous, 1-celled appressorium. Appressoria were single, medium brown, smooth-walled, ovate to ellipsoid, 5.4 to 7.8 × 5.4 to 7.8 μm (mean 6.7 ± 0.6 × 6.3 ± 0.5 μm, n = 30). These morphological characteristics were in concordance with published descriptions of Collectotrichum acutatum species complex. To further confirm the identity, internal transcribed spacer (ITS), beta-tubulin (TUB2), chitin synthase 1 (CHS-I) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) genes were amplified and sequenced (Damm et al. 2012). The ITS (OM189549) and TUB2 (OM273642) sequences of isolate HBBK4-4 showed 100% similarity, and GAPDH (OM249791) and CHS-1 (OM273641) sequences showed 98.7% and 99.6% similarity with C. nymphaeae CBS100064 respectively. A maximum likelihood phylogenetic tree was generated based on combining all sequenced loci in MEGA5. 18 isolates including HBBK4-4 fell in the C. nymphaeae clade with 96% bootstrap support. To verify Koch's postulates, six isolates were used for pathogenicity test, and 20 healthy fruits and 15 fully expanded leaves for each isolate were inoculated with 5-mm-diameter mycelial plugs. Controls consisted of detached premature fruits inoculated with a PDA plug without the fungus. Six days after inoculation, all fruits and leaves developed anthracnose symptoms similar to those observed in the field, while the controls remained healthy. The pathogenicity tests were repeated twice with the same results. The morphology of the reisolated fungi was consistent with the inoculated one, fulfilling Koch's postulates. The isolate HBBK4-4 was identified as C. nymphaeae, based on the description by Damm et al. (2012). The species C. nymphaeae has been previously reported to cause severe anthracnose on walnut in France (Da Lio et al., 2018), Brazil (Savian et al., 2019) and Italy (Luongo et al., 2022). To our knowledge, this is the first report of C. nymphaeae as a pathogen of walnut anthracnose in China. The result provided crucial information for epidemiologic studies and management of this disease.

Comparative transcriptome analysis reveals significant differences in gene expression between pathogens of apple Glomerella leaf spot and apple bitter rot

Background

Apple Glomerella leaf spot (GLS) and apple bitter rot (ABR) are two devastating foliar and fruit diseases on apples. The different symptoms of GLS and ABR could be related to different transcriptome patterns. Thus, the objectives of this study were to compare the transcriptome profiles of Colletotrichum gloeosporioides species complex isolates GC20190701, FL180903, and FL180906, the pathogen of GLS and ABR, and to evaluate the involvement of the genes on pathogenicity.

Results

A relatively large difference was discovered between the GLS-isolate GC20190701 and ABR-isolates FL180903, FL180906, and quite many differential expression genes associated with pathogenicity were revealed. The DEGs between the GLS- and ABR-isolate were significantly enriched in GO terms of secondary metabolites, however, the categories of degradation of various cell wall components did not. Many genes associated with secondary metabolism were revealed. A total of 17 Cytochrome P450s (CYP), 11 of which were up-regulated while six were down-regulated, and five up-regulated methyltransferase genes were discovered. The genes associated with the secretion of extracellular enzymes and melanin accumulation were up-regulated. Four genes associated with the degradation of the host cell wall, three genes involved in the degradation of cellulose, and one gene involved in the degradation of xylan were revealed and all up-regulated. In addition, genes involved in melanin syntheses, such as tyrosinase and glucosyltransferase, were highly up-regulated.

Conclusions

The penetration ability, pathogenicity of GLS-isolate was greater than that of ABR-isolate, which might indicate that GLS-isolate originated from ABR-isolates by mutation. These results contributed to highlighting the importance to investigate such DEGs between GLS- and ABR-isolate in depth.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08493-w.

Monitoring Colletotrichum Colonization and Reproduction in Different Rubber Tree Clones

Anthracnose, caused by fungi of the genus Colletotrichum, is present in the major rubber tree crop areas in Brazil, especially in São Paulo, Mato Grosso do Sul, Paraná, Minas Gerais, Espírito Santo, and northern states. This disease can affect different tissues of the rubber tree, leading to production losses. Thus, a better understanding of the pathosystem Colletotrichum x rubber tree can provide evidence to subsequent epidemiological research and phytosanitary management studies of this disease in the field. The present study aimed to investigate C.tamarilloi colonization and reproduction steps in resistant clones (IAC 502, IAC 507, RRIM 937) and in one susceptible clone (RRIM 600) of the rubber tree, verifying the influence of temperature up to 48 h after inoculation of the fungus, under 24 h wetness. Samples were analyzed under a light, a UV and a scanning electron microscope. Data indicated that the fungus had a delay in its development in resistant clones and, although colonization was expressive 48 h after inoculation, the new spore formation rate in the analyzed samples was lower in resistant clones. For RRIM 600, rapid colonization and intensive sporulation could be observed.

First report of Colletotrichum fioriniae causing anthracnose on the fruit of omija (schisandra) in South Korea

Omija or Schisandra (Schisandra chinensis Baillon) is one of Korea's most unique fruits and have been used in herbal medicine. It is also used for making cold drinks during summer and hot tea during winter. Among the different diseases, anthracnose poses great threat for omija production as it reduces the yield and market quality of fruits. In September 2021, severe anthracnose symptoms were observed in some commercial farmer fields (36°36'14.9"N 127°59'31.3"E) in Mungyeong and disease incidence was approximately 30 to 35%. The symptoms on fruits were manifested as small sunken lesions. The presumed fungi were isolated from necrotic tissues on potato dextrose agar (PDA) and purified using the single spore isolation technique (Cai et al. 2009; Hassan et al.2019). A total of 20 morphological similar isolates were obtained from 18 sampled fruits. The cultures were incubated at 25°C in the dark for 5 to 7 days. The colonies were pink with white aerial mycelium on the upper side and pink with black zones on the reverse. All the colonies produced fusiform conidia measuring 12.7 to 17.5 × 4.7 to 7.4 μm (n=50). The appressoria were brown, globose to ellipsoid and measuring 6.3 to 12 × 5.9 to 9.7 μm (n=30). Morphological characteristics of present isolates were in concordance with that of Colletotrichum acutatum sensu lato (Damm et al., 2012). For molecular identification, genomic DNA of five representative isolates was extracted for sequencing of target markers and the phylogenetic tree was constructed. For amplification and sequencing of internal transcribed spacers (ITS), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin (ACT) chitin synthase-1 (CHS-1), histone 3 (HIS3) and beta-tubulin (TUB2), the primer pairs ITS1/ITS4, GDF1/GDR1, ACT-512F/ACT-783R, CHS1-79F/CHS-1-354R, CYLH3F /CYLH3R and BT2a /BT2b were used respectively (Damm et al., 2012). The resulting sequences were deposited in GenBank with accession numbers LC680890 to LC680914 and LC687627 to LC687631. The maximum likelihood tree based on concatenated sequences of the five genes shows that present isolates were grouped in the C. fioriniae. Pathogenicity on red schisandra fruits was confirmed using the two isolates OR1 and O59. Fruit clusters (20-30 fruits/ cluster) were surface sterilized by dipping them in 1% NaOCl for 3 minutes, rinsing in sterile distilled water, and placing them in a sterile plastic box containing moist paper tissues. All the fruits in each cluster were inoculated with 10 μl of 106 conidia/ml suspensions of each isolate by following either the wounded or un- wounded method (Hassan et al.2019). Fruit clusters treated with sterile distilled water served as a control. Three fruit clusters were inoculated per isolate for each method. With the wounding method, all the inoculated fruits showed typical anthracnose symptoms after 4 days of incubation at 25 ± 1°C in the dark, while the control and un- wounded fruits remained symptomless. This test was repeated twice. The species C. fioriniae were reisolated from the infected fruit. The morphology and ITS sequences of the reisolated fungi were consistent with the original one, fulfilling Koch's postulates. The species C. fioriniae have been described as a causal agent of anthracnose of numerous hosts worldwide including South Korea (Damm et al., 2012; Hassan et al.2019; Oo et al. 2016; Lee et al. 2020). To our knowledge, this is the first report of C. fioriniae as causal agent of omija anthracnose in South Korea. As this disease results in deterioration of fruits quality, management practices should be tailored to address C. fioriniae management. Acknowledgments This research was supported by Kyungpook National University Research Fund, 2021. References Cai, L., et al. 2009. Fungal Divers. 39:183. Damm, U., et al. 2012. Stud. Mycol. 73:37. Hassan, O., et al. 2019. Sci. Rep. 9:12089. Lee, D., et al. 2020. Mycobiology. 48: 210. Oo, M.M., et al. 2016. Mycobiology. 44: 325.

First Report of Colletotrichum fioriniae Causing Anthracnose on Rhododendron delavayi in China

Rhododendron delavayi Franch, a member of Ericaceae family, is globally famous for its garden flowers with significant ornamental value (Liu et al., 2020). In July 2020 and 2021, a disease survey of R. delavayi groves was conducted in Baili Azalea Forest Area (N27°10'-27°20', E 105°04'-106°04'). We arbitrarily selected an area with around 280 R. delavayi trees covering 2.5 hectares in R. delavayi grove where 20-35% of leaves showed symptoms of anthracnose. Typical symptoms included elliptical to irregularly shaped brown lesions on leaves and masses of black dots clustered on it. About 30 pieces of leaves with anthracnose lesions were collected. A few black dots were picked from the lesions with a sterilized needle, plated on water agar and incubated at 25℃ for 12 h to observe spore germination (Fang, 2007). Then the germinated spores were transferred onto PDA medium for further purification and morphological observation. Fourteen single-spore isolates with similar morphology were obtained. The surface of the colony was white or gray and spongy; the edge was smooth; and the back side was pinkish brown after 7 days of growth on PDA. Conidia were spindle-shaped, transparent, 11.1-16.6×3.6-4.9 μm (n=50). Appressorium from conidia was nearly ovate or proximate, brown or dark brown in color, 4.3-10.3 ×3.2-7.6 μm (n=50). These characteristics are consistent with Colletotrichum fioriniae reported by Shivas and Tan (2009). DNA was extracted from a representative isolate MYDJ12. The internal transcribed spacer region (ITS), the glyceraldehyde-3-phosphate dehydrogenase (GAPDH), β-tubulin (TUB), actin (ACT), and chitin synthase 1 (CHS-1) genes were amplified using primer pairs described by Damm et al. (2012). The sequences were deposited in GenBank with accession number MW692854 (ITS), MW727518 (GAPDH), MW727519 (TUB2), MW727520 (ACT), and MW727521 (CHS-1). BLASTN searches of the ITS, GADPH, TUB2, ACT and CHS-1 genes revealed 100% (540/540 nucleotides), 100% (254/254 nucleotides), 99.38% (4488/491 nucleotides), 98.77% (242/245 nucleotides) and 100% (282/282 nucleotides) homology with those of C. fioriniae CBS:128517T in GenBank (NR_111747, JQ948622, JQ949943, JQ949613 and JQ948953 respectively). The phylogenetic tree showed the isolate MYDJ12 to cluster with C. fioriniae CBS:128517T. Finally, two-year old R. delavayi plants (n=5) were inoculated by wounding with a syringe needle and placing 10 μL of spore suspension (106 spores per mL) of the isolate MYDJ12 on three leaves per plant. Control leaves were inoculated with sterile water. The experiment was conducted twice. Inoculated leaves were wrapped in parafilm tape and then the plants were placed in a greenhouse at 25°C with high relative humidity (90 to 95%). Seven days after incubation, brown lesions appeared, similar to those observed in the grove. Black dots clustered on the lesions after 15 days. Re-isolation was conducted 20 days after inoculation. From all the five inoculated plants, similar symptoms were observed, and the same pathogen was re-isolated. One of the isolates was selected for morphological observation and multi-gene (ITS, GAPDH, ACT, TUB2 and CHS-1) analysis indicated the reisolated fungus to be C. fioriniae. No fungal pathogens were isolated from mock inoculated plants. This study can provide effective management and useful information for the control of this disease on R. delavayi in Baili Azalea Forest Area. References: Damm, U., et al. 2012. Stud Mycol 73: 37. Fang, Z. D. 2007. Research Methods of Plant Diseases (Third edition). China Agriculture Press. Liu, J., et al. 2020. Mitochondrial DNA B 5:37. Shivas, R, G; Tan, Y, P. 2009. Fungal Divers 39:111.

First report of Colletotrichum scovillei causing anthracnose fruit rot on Eriobotrya japonicain in Zhejiang province, China

Loquat (Eriobotrya japonica (Thunb.) Lindl.) is a fruit tree of high economic impotance in China. In May 2021, fruit rot on cv. "Baozhu" was observed in Yuhang district (119°40'E, 30°09'N), Zhejiang province, at an incidence of more than 30% within five orchards (the total affected area were about 121, 000 m2). Early symptoms of naturally affected fruits were dark brown, necrotic lesion (Fig. 1 A). Lesions subsequently expanded, and orange conidia were observed (Fig. 1 B). Conidia were transferred using a sterilized needle into sterile water, diluted to several conidia (approximately 10 conidia/µL) in the field of light microscope, and spread onto potato dextrose agar (PDA). After 24 h, single colonies were transferred, and six single-spore strain isolated from different fruits or locations were obtained. Six-day old colonies grown on PDA at 27°C had gray-green centers with white edges, and on the reverse side, the centers were brown (Fig. 1 C). Isolate PPGS2 was selected for further characterization. Conidia were unicellular, smooth-walled, hyaline, cylindrical with one rounded and one acute end, or with both ends rounded and they (n = 30) measured 11.1 to 16.0 µm (mean = 13.3 µm) × 3.0 to 4.6 µm (mean = 4.1) (Fig. 1 D). Appressoria were single or in smalln groups, light brown to dark brown, ovoid or elliptical with a smooth or undulate outline, and measured (n = 30) 4.6 to 8.7 µm (mean = 6.5 µm) × 4.0 to 5.6 µm (mean = 4.9 µm) (Fig. 1 H). These features of PPGS2 were consistent with species of the Colletotrichum acutatum species complex (Damm et al. 2012). For species identification, the internal transcribed spacer (ITS), beta-tubulin (TUB), chitin synthase (CHS-1), calmodulin (CAL), and actin (ACT) genes were sequenced (O'Donnell et al. 2000; Weir et al. 2012). The five sequences were deposited in GenBank (OK054581, OK077960, OK077987, OK077988 and OK077989, respectively). A BLAST search of these sequences showed 99% identity with sequences of the ex-holotype C. scovillei CBS126529 (Damm et al. 2012). The evolutionary tree shown that PPGS2 and C. scovillei CBS126529 were clustered in a branch (SH-aLRT/approximate Bayes test/bootstrap support = 88.6/0.999/96). Combining morphological characteristics with phylogenetic analysis, PPGS2 was identified as C. scovillei. To fulfill Koch's postulates, E. japonica fruit were disinfected with 75% alcohol and air-dried for 5 mins to allow the alcohol to volatilize. A conidial suspension (10 mL of 1 × 106 conidia/ml) of PPGS2 was sprayed onto six fruits, and six fruit sprayed with sterilized water served as controls. The experiment was repeated three times. Fruits were kept on a mist bench at 27°C and 80% relative humidity for 5 days. Inoculated fruit developed dark brown necrotic lesions that later fused and expanded (Fig. 1, E-G), whereas control fruit remained symptomless. C. scovillei was re-isolated from lesions of inoculated fruit. C. scovillei has been reported from fruit of Capsicum sp., Musa sp., Mangifera indica, and Clausena lansium in China (Farr and Rossman 2021). To our knowledge, this is the first report of C. scovillei causing anthracnose fruit rot of E. japonica in China. This disease results in severe economic losses both in the field and after harvest, and it is necessary to develop more effective prevention and control strategies.

Colletotrichum Species Associated with Peaches in China

Colletotrichum is regarded as one of the 10 most important genera of plant pathogens in the world. It causes diseases in a wide range of economically important plants, including peaches. China is the largest producer of peaches in the world but little is known about the Colletotrichum spp. affecting the crop. In 2017 and 2018, a total of 286 Colletotrichum isolates were isolated from symptomatic fruit and leaves in 11 peach production provinces of China. Based on multilocus phylogenetic analyses (ITS, ACT, CAL, CHS-1, GAPDH, TUB2, and HIS3) and morphological characterization, the isolates were identified to be C. nymphaeae, C. fioriniae, and C. godetiae of the C. acutatum species complex, C. fructicola and C. siamense of the C. gloeosporioides species complex, C. karsti of the C. boninense species complex, and one newly identified species, C. folicola sp. nov. This study is the first report of C. karsti and C. godetiae in peaches, and the first report of C. nymphaeae, C. fioriniae, C. fructicola, and C. siamense in peaches in China. C. nymphaeae is the most prevalent species of Colletotrichum in peaches in China, which may be the result of fungicide selection. Pathogenicity tests revealed that all species found in this study were pathogenic on both the leaves and fruit of peaches, except for C. folicola, which only infected the leaves. The present study substantially improves our understanding of the causal agents of anthracnose on peaches in China.

RNA-Seq and Gene Regulatory Network Analyses Uncover Candidate Genes in the Early Defense to Two Hemibiotrophic Colletorichum spp. in Strawberry

Two hemibiotrophic pathogens, Colletotrichum acutatum (Ca) and C. gloeosporioides (Cg), cause anthracnose fruit rot and anthracnose crown rot in strawberry (Fragaria × ananassa Duchesne), respectively. Both Ca and Cg can initially infect through a brief biotrophic phase, which is associated with the production of intracellular primary hyphae that can infect host cells without causing cell death and establishing hemibiotrophic infection (HBI) or quiescent (latent infections) in leaf tissues. The Ca and Cg HBI in nurseries and subsequent distribution of asymptomatic infected transplants to fruit production fields is the major source of anthracnose epidemics in North Carolina. In the absence of complete resistance, strawberry varieties with good fruit quality showing rate-reducing resistance have frequently been used as a source of resistance to Ca and Cg. However, the molecular mechanisms underlying the rate-reducing resistance or susceptibility to Ca and Cg are still unknown. We performed comparative transcriptome analyses to examine how rate-reducing resistant genotype NCS 10-147 and susceptible genotype ‘Chandler’ respond to Ca and Cg and identify molecular events between 0 and 48 h after the pathogen-inoculated and mock-inoculated leaf tissues. Although plant response to both Ca and Cg at the same timepoint was not similar, more genes in the resistant interaction were upregulated at 24 hpi with Ca compared with those at 48 hpi. In contrast, a few genes were upregulated in the resistant interaction at 48 hpi with Cg. Resistance response to both Ca and Cg was associated with upregulation of MLP-like protein 44, LRR receptor-like serine/threonine-protein kinase, and auxin signaling pathway, whereas susceptibility was linked to modulation of the phenylpropanoid pathway. Gene regulatory network inference analysis revealed candidate transcription factors (TFs) such as GATA5 and MYB-10, and their downstream targets were upregulated in resistant interactions. Our results provide valuable insights into transcriptional changes during resistant and susceptible interactions, which can further facilitate assessing candidate genes necessary for resistance to two hemibiotrophic Colletotrichum spp. in strawberry.

First Report of Colletotrichum scovillei Causing Anthracnose on Watermelon (Citrullus lanatus) in Malaysia

Production of watermelon (Citrullus lanatus) in Malaysia was 150,000 mt in 2020 (Malaysian Department of Agriculture, 2021). In November 2019, nine locally produced watermelon fruit (red flesh, seedless) from five local stores in the states of Kelantan, Terengganu, and Penang exhibited sunken, circular, brown lesions that enlarged to1.5 to 10 cm in diameter with scattered orange masses of conidia. Lesions coalesced to cover approximately 50% of the fruit surface. Lesions were surface sterilized by spraying 70% alcohol onto the fruit followed by drying with sterilized paper towels. A total of 153 tissue segments (1×1 cm) were excised from the rind, immersed in 1% sodium hypochlorite for 3 min, rinsed twice for 1 min in sterilized distilled water, air-dried, transferred to potato dextrose agar (PDA) plates, and incubated at 25±1°C for 7 days. Single-spore transfers produced pure cultures, resulting in 12 isolates. Colonies on PDA were initially white and turned pale gray with age. Conidia were hyaline, one end round and the other narrowly acute, aseptate, smooth-walled, straight, cylindrical to clavate, 10.5-16.5 µm × 3-4.5 μm (n = 30). Observed morphological characters matched published description of Colletotrichum spp. (Damm et al. 2012). Internal transcribed spacer (ITS) and glyceraldehyde-phosphate dehydrogenase (GAPDH) genes were amplified using primer sets ITS1/ITS4 and GDF1/GDF2, respectively. All sequences were deposited in GenBank (MW856808 for ITS; MZ219296 for GAPDH). A BLASTn search of both sequences on GenBank showed 99% identity with C. scovillei along with other closely related Colletotrichum species. Phylogenetic analysis of ITS and GAPDH alignments, using maximum likelihood along with reference strains of closely related species from Mycobank, confirmed species identity as C. scovillei. A pathogenicity test was conducted on two healthy watermelon fruit (red flesh, seedless). A 6-mm-diameter mycelial plug of a colony on PDA was positioned on a 0.5-cm-long wound on each fruit; a sterile PDA plug placed on a similar wound on the opposite side served as a control. Fruit were incubated at 25±1°C for 7 days in plastic-wrapped trays above distilled water to maintain high humidity. Small, sunken, circular brown lesions appeared and expanded at inoculation sites within 7 days. Symptoms were identical to those produced by natural infections, and the controls were asymptomatic. Isolates from the lesions at the inoculation sites were confirmed as C. scovillei based on morphological characteristics, fulfilling Koch's postulates. The pathogenicity test was conducted four times with a total of eight fruit. Many species in the C. orbiculare complex cause watermelon anthracnose (Keinath, 2018). To our knowledge, this is the first report of C. scovillei (C. acutatum species complex; Damm et al. 2012) causing anthracnose on watermelon in Malaysia. Anthracnose caused by C. scovillei has been confirmed on other crops such as pepper (Toporek and Keinath, 2021), banana (Zhou et al., 2017), and chili (Oo et al., 2017). This insight will inform efforts to improve management of watermelon anthracnose in Malaysia.

Genome-wide association study reveals white lupin candidate gene involved in anthracnose resistance

GWAS identifies candidate gene controlling resistance to anthracnose disease in white lupin. White lupin (Lupinus albus L.) is a promising grain legume to meet the growing demand for plant-based protein. Its cultivation, however, is severely threatened by anthracnose disease caused by the fungal pathogen Colletotrichum lupini. To dissect the genetic architecture for anthracnose resistance, genotyping by sequencing was performed on white lupin accessions collected from the center of domestication and traditional cultivation regions. GBS resulted in 4611 high-quality single-nucleotide polymorphisms (SNPs) for 181 accessions, which were combined with resistance data observed under controlled conditions to perform a genome-wide association study (GWAS). Obtained disease phenotypes were shown to highly correlate with overall three-year disease assessments under Swiss field conditions (r > 0.8). GWAS results identified two significant SNPs associated with anthracnose resistance on gene Lalb_Chr05_g0216161 encoding a RING zinc-finger E3 ubiquitin ligase which is potentially involved in plant immunity. Population analysis showed a remarkably fast linkage disequilibrium decay, weak population structure and grouping of commercial varieties with landraces, corresponding to the slow domestication history and scarcity of modern breeding efforts in white lupin. Together with 15 highly resistant accessions identified in the resistance assay, our findings show promise for further crop improvement. This study provides the basis for marker-assisted selection, genomic prediction and studies aimed at understanding anthracnose resistance mechanisms in white lupin and contributes to improving breeding programs worldwide.

First Report of Anthracnose Disease Caused by Colletotrichum fioriniae on Barbary wolfberry (Lycium barbarum L.) in Gansu Province, China

Barbary wolfberry (Lycium barbarum L.) is a well-known edible and medicinal plant, widely grown in northwest China (Gao et al. 2021). During the summer of 2019, typical anthracnose symptoms were observed on fruits of barbary wolfberry in Baiyin, Gansu province, China. Approximately 30% of the barbary wolfberry fruits had typical anthracnose symptoms. Lesions on barbary wolfberry fruits were dark, circular or irregular, sunken, and necrotic or wilted, with the presence of orange to pink conidial masses under high humidity. Small pieces cut from the margins of lesions were surface disinfested with 75% ethanol for 10 s, and 1% NaClO solution for 1 min, rinsed three times in sterile distilled water, dried on sterile filter paper, placed onto potato dextrose agar (PDA), and incubated at 25 ± 1℃ for 5 days in the dark. The pure cultures were obtained by single-spore isolation. All isolates produced pale gray and dense aerial mycelia, in reverse orange to red, at times showing concentric rings on PDA at 25℃ after 10 days in the dark. Conidia (n=100) were colorless, smooth-walled, aseptate, fusiform elliptical with one or both ends, and 8.3 to 17.6 × 3.7 to 6.2 μm. Appressoria (n = 100) were solitary, pale to medium brown, smooth-walled, subglobose to elliptical, sometimes clavate or irregular, and 5.7 to 11.7 × 4.1 to 8.5 μm. The internal transcribed spacer (ITS) region of ribosomal DNA, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene, bate-tubulin 2 (TUB2) gene, actin (ACT) gene, calmodulin (CAL) gene, chitin synthase 1 (CHS-1) gene, and histone H3 (HIS3) gene of the two representative isolates BY19LB02 and BY19LB06 were amplified and sequenced with primers ITS1/ITS4, GDF1/GDR1, T1/Bt2b, ACT-512F/ACT-783R, CL1/CL2A, CHS-79F/CHS-354R, CYLH3F/CYLH3R, respectively (Damm et al. 2012), and deposited on GenBank (ITS, MZ496816 and MZ505524; ACT, MZ557422 and MZ557417; CHS-1, MZ557423 and MZ557418; GAPDH, MZ557424 and MZ557419; HIS3, MZ557425 and MZ557420; TUB2, MZ557426 and MZ557421). BLAST analysis of the resulting for all the sequences showed 98 to 100% similarity with those of C. fioriniae. Based on the above, the isolates BY19LB02 and BY19LB06 were identified as C. fioriniae. To confirm the pathogenicity, detached heathy barbary wolfberry fruits were surface-sterilized with 75% ethanol for 30s, rinsed three times in sterile distilled water, allowed to dry on sterile filter paper, and then wounded using sterilized needles. Fruits were inoculated by pipetting 10 μL of conidial suspension (1×106 conidia/mL) onto each wound, and controls were inoculated with 10 μL sterile distilled water. Each treatment had 30 fruit replicates. These fruits were kept in a moist chamber at 28°C in the dark. The experiment was repeated three times. After 5 days, anthracnose symptoms were observed on all of the inoculated fruits and identical to those observed in the field, whereas control fruits did not develop symptoms. Theathogen was re-isolated from the lesions of inoculated fruits, fulfilling Koch's postulates. To the best of our knowledge, this is the first report of C. fioriniae causing anthracnose on barbary wolfberry in Gansu Province, China. The same disease on barbary wolfberry was reported in Jilin Province, China (Liu et al. 2016). Gansu is one of the main barbary wolfberry producing areas in northwest China and its geographical area, climate and environmental conditions are different from Jilin Province. Considering that barbary wolfberry is the main source of income for growers in Gansu, this identification can aid in the selection of appropriate management measures for this disease.

Fourteen New Species of Foliar Colletotrichum Associated with the Invasive Plant Ageratinaadenophora and Surrounding Crops

Ageratina adenophora is one of the most invasive weeds in China. Following an outbreak in Yunnan in the 1960s, A. adenophora has been spreading in Southwest China at tremendous speed. Previous research indicated A. adenophora contained many Colletotrichum species as endophytes. In this study, we investigated the diversity of Colletotrichum in healthy and diseased leaves of the invasive plant A. adenophora and several surrounding crops in Yunnan, Guangxi, and Guizhou provinces in China, and obtained over 1000 Colletotrichum strains. After preliminary delimitation using the internal transcribed spacer region (ITS) sequences, 44 representative strains were selected for further study. Their phylogenetic positions were determined by phylogenetic analyses using combined sequences of ITS, actin (ACT), chitin synthase (CHS-1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and beta-tubulin (TUB2). Combined with morphological characteristics, 14 new Colletotrichum species were named as C. adenophorae, C. analogum, C. cangyuanense, C. dimorphum, C. gracile, C. nanhuaense, C. nullisetosum, C. oblongisporum, C. parvisporum, C. robustum, C. simulanticitri, C. speciosum, C. subhenanense, and C. yunajiangense.

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.