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

Endophytic species of Colletotrichum associated with cashew tree in northeastern Brazil

Anthracnose caused by Colletotrichum is the most severe and widely occurring cashew disease in Brazil. Colletotrichum species are commonly found as pathogens, endophytes and occasionally as saprophytes in a wide range of hosts. The endophytic species associated with cashew trees are poorly studied. In this study, we report the Colletotrichum endophytic species associated with cashew trees in two locations in the state of Pernambuco, their prevalence in different plant organs (leaves, veins, branches and inflorescences), and compare the species in terms of pathogenicity and aggressiveness using different inoculation methods (wounded × unwounded). Six species of Colletotrichum were identified according to multilocus phylogenetic analyses, including Colletotrichum asianum, Colletotrichum chrysophilum, Colletotrichum karsti, Colletotrichum siamense, Colletotrichum theobromicola, and Colletotrichum tropicale. There were differences in the percentage of isolation in relation to the prevalence of colonized tissues and collection locations. C. tropicale was the prevalent species in both geographic areas and plant tissues collected, with no pattern of distribution of species between areas and plant tissues. All isolates were pathogenic in injured tissues of cashew plants. The best method to test the pathogenicity of Colletotrichum species was utilizing the combination of leaves + presence of wounds + conidial suspension, as it better represents the natural infection process. C. siamense was the most aggressive species.

First Report of Colletotrichum fructicola, C. rhizophorae sp. nov. and C. thailandica sp. nov. on Mangrove in Thailand

Colletotrichum, a genus within the phylum Ascomycota (Fungi) and family Glomerellaceae are important plant pathogens globally. In this paper, we detail four Colletotrichum species found in mangrove ecosystems. Two new species, Colletotrichum rhizophorae and C. thailandica, and a new host record for Colletotrichum fructicola were identified in Thailand. Colletotrichum tropicale was collected from Taiwan's mangroves and is a new record for Rhizophora mucronata. These identifications were established through a combination of molecular analysis and morphological characteristics. This expanded dataset for Colletotrichum enhances our understanding of the genetic diversity within this genus and its associations with mangrove ecosystems. The findings outlined herein provide data on our exploration of mangrove pathogens in Asia.

Diversity of Colletotrichum species associated with torch ginger anthracnose

Anthracnose caused by Colletotrichum species is one of the most important diseases of torch ginger. The disease leads to loss of aesthetic and commercial value of torch ginger stems. This study aimed to characterize Colletotrichum species associated with torch ginger anthracnose in the production areas of Pernambuco and Ceará. A total of 48 Colletotrichum isolates were identified using molecular techniques. Pathogenicity tests were performed on torch ginger with representative isolates. Phylogenetic analyses based on seven loci-DNA lyase (APN2), intergenic spacer between DNA lyase and the mating-type locus MAT1-2-1 (APN2/MAT-IGS), calmodulin (CAL), intergenic spacer between glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and a hypothetical protein (GAP2-IGS), glutamine synthetase (GS), and β-tubulin (TUB2)-revealed that they belong to five known Colletotrichum species, namely, C. chrysophilum, C. fructicola, C. siamense, C. theobromicola, and C. tropicale, and three newly discovered species, described here as C. atlanticum, C. floscerae, and C. zingibericola. Of these, C. atlanticum was the most dominant. Pathogenicity assays showed that all isolates were pathogenic to torch ginger bracts. All species are reported for the first time associated with torch ginger in Brazil. The present study contributes to the current understanding of the diversity of Colletotrichum species associated with anthracnose on torch ginger and demonstrates the importance of accurate species identification for effective disease management strategies.

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

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

Genomic Resources of Four Colletotrichum Species (C. fioriniae, C. chrysophilum, C. noveboracense, and C. nupharicola) Threatening Commercial Apple Production in the Eastern United States

The genus Colletotrichum includes nine major clades with 252 species and 15 major phylogenetic lineages, also known as species complexes. Colletotrichum spp. are one of the top fungal plant pathogens causing anthracnose and pre- and postharvest fruit rots worldwide. Apple orchards are imperiled by devastating losses from apple bitter rot, ranging from 24 to 98%, which is a serious disease caused by several Colletotrichum species. Bitter rot is also a major postharvest rot disease, with C. fioriniae causing from 2 to 14% of unmarketable fruit in commercial apple storages. Dominant species causing apple bitter rot in the Mid-Atlantic United States are C. fioriniae from the Colletotrichum acutatum species complex and C. chrysophilum and C. noveboracense from the C. gloeosporioides species complex (CGSC). C. fioriniae is the dominant species causing apple bitter rot in the Northeastern and Mid-Atlantic states. C. chrysophilum was first identified on banana and cashew but has been recently found as the second most dominant species causing apple bitter rot in the Mid-Atlantic. As the third most dominant pathogen, C. noveboracense MB 836581 was identified as a novel species in the CGSC, causing apple bitter rot in the Mid-Atlantic. C. nupharicola is a sister group to C. fructicola and C. noveboracense, also causing bitter rot on apple. We deliver the resources of 10 new genomes, including two isolates of C. fioriniae, three isolates of C. chrysophilum, three isolates of C. noveboracense, and two isolates of C. nupharicola collected from apple fruit, yellow waterlily, and Juglans nigra. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Novel Harzia ixtarensis Fungus on Annona cherimola Fruit in Mexico and Its Synergistic Relationship with Colletotrichum fragariae

Since 2005 in Íxtaro, Michoacán, symptoms of Harzia infection have been observed on immature Annona cherimola fruit with Colletotrichum fragariae-induced anthracnose lesions and mummified fruit. This study aimed to identify the Harzia sp. and evaluate its pathogenicity. Four isolates were obtained from fruit exhibiting symptoms, cultured in four types of agar under various conditions, and characterized based on concatenated internal transcribes spacer (ITS) + large subunit and ITS + small subunit sequences. Additionally, the isolates were compared with two CBS species (two-type strains and two isolates) of Harzia patula and H. tenella under the same conditions as the Harzia isolates, and all known Harzia spp. in culture were included in two phylogenetic analyses. H. ixtarensis sp. nov. was proposed. Compared with H. patula CBS isolate 121524 which was the most closely phylogenetically related species, H. ixtarensis was characterized by slower colony growth (white to salmonish-beige), different percentages of two forms of conidia (elongated and globose; unicellular and hyaline to subhyaline), and smaller conidia. The conidia mainly germinated with two hyaline tubes without an appressorium. In situ inoculations (1 × 10⁶ ml^-1 conidia suspension) of fruit showed that fruit with wounds developed larger lesions than those without wounds. Harzia inoculation on anthracnose lesions (induced by prior inoculation with C. fragariae) produced larger anthracnose lesions than C. fragariae alone. When C. fragariae or H. ixtarensis was inoculated alone, the lesion size was 51 and 99% smaller, respectively, indicating synergy between C. fragariae and H. ixtarensis. Thus, H. ixtarensis may have a parasitic-synergistic and necrotrophic lifestyle, and exhibited symptoms on anthracnose lesions.

Reclassification of the Main Causal Agent of Glomerella Leaf Spot on Apple into Colletotrichum chrysophilum in Southern Brazil and Uruguay

Glomerella leaf spot (GLS) is one of the most important diseases of apple, affecting a wide range of economically important cultivars, particularly Golden Delicious and its descendants. Caused mainly by species of the Colletotrichum gloeosporioides species complex (CGSC), C. fructicola has been described as the most prevalent and aggressive species associated with GLS and apple bitter rot (ABR) in Brazil and Uruguay. Recently, new CGSC species, closely related to C. fructicola, have been identified causing ABR. To verify the accuracy of species identification within the CGSC, we aimed to reevaluate the identity of representative GLS-causing isolates from Brazilian and Uruguayan populations, previously identified as C. fructicola. Multilocus phylogenetic analysis based on APN2, ApMAT, CAL, GAPDH, GS, ITS, and TUB2 allocated these isolates in a monophyletic clade with C. chrysophilum. This species was first described as the causal agent of anthracnose in banana fruits in Brazil, and recent reports indicate its association with ABR in the United States. This is the first report of C. chrysophilum causing GLS disease on apple worldwide.

Pest categorisation of Colletotrichum aenigma, C. alienum, C. perseae, C. siamense and C. theobromicola

The EFSA Plant Health Panel performed a pest categorisation of Colletotrichum aenigma, C. alienum, C. perseae, C. siamense and C. theobromicola, five clearly defined fungi of the C. gloeosporioides complex causing anthracnose. The pathogens are widely distributed in at least three continents. C. aenigma and C. siamense are reported from Italy and C. alienum from Portugal, including the Madeira Islands, with a restricted distribution. C. perseae and C. theobromicola are not known to be present in the EU. However, there is uncertainty on the status of the pathogens worldwide and in the EU because of the taxonomic re-evaluation of the genus Colletotrichum and the lack of specific surveys. The pathogens are not included in Commission Implementing Regulation (EU) 2019/2072 and there are no reports of interceptions in the EU. With the exception of C. perseae, which has a very limited number of hosts, the other four Colletotrichum species have relatively wide host ranges. Therefore, this pest categorisation focused on those hosts for which there is robust evidence that the pathogens were formally identified by a combination of morphology, pathogenicity and multilocus sequence analysis. Host plants for planting and fresh fruits are the main entry pathways into the EU. Host availability and climate suitability factors occurring in some parts of the EU are favourable for the establishment of the pathogens. No yield losses have been reported so far in the EU but in non-EU areas of their current distribution, the pathogens have a direct impact on cultivated hosts that are also relevant for the EU. Phytosanitary measures are available to prevent the further introduction and spread of C. aenigma, C. alienum and C. siamense into the EU as well as the introduction and spread of C. perseae and C. theobromicola. C. aenigma, C. alienum, C. perseae, C. siamense and C. theobromicola satisfy the criteria that are within the remit of EFSA to assess for these species to be regarded as potential Union quarantine pests.

Predicting Species Boundaries and Assessing Undescribed Diversity in Pneumocystis, an Obligate Lung Symbiont

Far more biodiversity exists in Fungi than has been described, or could be described in several lifetimes, given current rates of species discovery. Although this problem is widespread taxonomically, our knowledge of animal-associated fungi is especially lacking. Fungi in the genus Pneumocystis are obligate inhabitants of mammal lungs, and they have been detected in a phylogenetically diverse array of species representing many major mammal lineages. The hypothesis that Pneumocystis cospeciate with their mammalian hosts suggests that thousands of Pneumocystis species may exist, potentially equal to the number of mammal species. However, only six species have been described, and the true correspondence of Pneumocystis diversity to host species boundaries is unclear. Here, we use molecular species delimitation to estimate the boundaries of Pneumocystis species sampled from 55 mammal species representing eight orders. Our results suggest that Pneumocystis species often colonize several closely related mammals, especially those in the same genus. Using the newly estimated ratio of fungal to host diversity, we estimate ≈4600 to 6250 Pneumocystis species inhabit the 6495 currently recognized extant mammal species. Additionally, we review the literature and find that only 240 (~3.7%) mammal species have been screened for Pneumocystis, and many detected Pneumocystis lineages are not represented by any genetic data. Although crude, our findings challenge the dominant perspective of strict specificity of Pneumocystis to their mammal hosts and highlight an abundance of undescribed diversity.

Pest categorisation of Colletotrichum fructicola

The EFSA Plant Health Panel performed a pest categorisation of Colletotrichum fructicola Prihast., a well-defined polyphagous fungus of the C. gloeosporioides complex which has been reported from all the five continents to cause anthracnose, bitter rot and leaf spotting diseases on over 90 cultivated and non-cultivated woody or herbaceous plant species. The pathogen is not included in EU Commission Implementing Regulation 2019/2072. Because of the very wide host range, this pest categorisation focused on Camellia sinensis, Citrus sinensis, C. reticulata, Fragaria × ananassa, Malus domestica, M. pumila, Persea americana, Prunus persica, Pyrus pyrifolia and P. bretschneideri for which there was robust evidence that C. fructicola was formally identified by morphology and multilocus gene sequencing analysis. Host plants for planting and fresh fruits are the main pathways for the entry of the pathogen into the EU. There are no reports of interceptions of C. fructicola in the EU. The pathogen has been reported from Italy and France. The host availability and climate suitability factors occurring in some parts of the EU are favourable for the establishment of the pathogen. Economic impact on the production of the main hosts is expected if establishment occurs. Phytosanitary measures are available to prevent the re-introduction of the pathogen into the EU. Although the pathogen is present in the EU, there is a high uncertainty on its actual distribution in the territory because of the re-evaluation of Colletotrichum taxonomy and the lack of systematic surveys. Therefore, the Panel cannot conclude with certainty on whether C. fructicola satisfies the criterium of being present but not widely distributed in the EU to be regarded as a potential Union quarantine pest unless systematic surveys for C. fructicola are conducted and Colletotrichum isolates from the EU in culture collections are re-evaluated.

First Report of Colletotrichum chrysophilum Causing Anthracnose on Blueberry in Brazil

Highbush (Vaccinium corymbosum L.) and rabbiteye (V. ashei R.) blueberry are the most important export small fruit crops in southern Brazil. Anthracnose has been considered one of the most destructive disease and exclusively associated with C. karstii in Brazil (Rios et al. 2014). In November 2019, severe anthracnose symptoms including leaf spots but particularly twig blights and fruit rots were observed on all blueberry plants (V. ashei) in one organic orchard in Santa Catarina state, Brazil (27º43'48.96"S, 49º0'57.79"W). Four isolates were obtained from necrotic lesions and monosporic cultures were grown on potato dextrose agar at 25°C and with a 12 h photoperiod under near ultra violet light. After 15 days, colonies showed upper surface color varying from grayish-white to pale-orange and the reverse side pale-orange. Conidia were hyaline, cylindrical with rounded ends, and their length and width ranged from 9.5 to 15.5 µm (x ̅=11.8) and 6.5 to 3.5 µm (x ̅=4.9), respectively. The isolates were identified by multilocus phylogenetic analyses using nucleotide sequences of actin (ACT), β-tubulin (TUB2), calmodulin (CAL), glyceraldehyde-3-phosphate-dehydrogenase (GAPDH), glutamine synthetase (GS), internal transcribed spacer (ITS) and the intergenic spacer between DNA lyase and the mating-type locus MAT1-2-1 (ApMAT). Nucleotide sequences exhibited from 95 to 100% sequence identity to Colletotrichum chrysophilum ex-type (CMM4268) and were deposited in GenBank database (MW868219 to MW868222, MW868211 to MW868214, MW868215 to MW868218, MW868223 to MW868226, MW868202 to MW868205, MW793353 to MW793356, and MW868207 to MW868210). C. chrysophilum belongs to the C. gloeosporioides species complex and was previously described as C. ignotum in banana and other tropical fruits in Brazil (Vieira et al. 2017; Veloso et al. 2018). In addition, this species was recently reported on apple fruit in New York, USA (Khodadadi et al. 2020). To confirm pathogenicity, one-year-old blueberry plants were inoculated by spraying a suspension of 1×106 conidia/ml, incubated in a moist chamber in the dark for 48 h and then kept in the greenhouse. Plants sprayed with sterile distilled water served as control. Additionally, fruits were immersed for 2 min in a conidial suspension (1×106 conidia/ml) and incubated at 25°C and 12 h photoperiod for 20 days. Inoculated plants exhibited first symptoms in twigs at 10 days after inoculation (dai). Infected twigs showed initially dark brown spots that coalesced and became necrotic. On leaves, reddish-brown lesions with less than 2 mm appeared at low intensity at 15 dai. On fruits, sunken areas associated with an abundant orange mucilaginous mass of acervuli and conidia were seen at 7 dai. Symptoms on plants were identical to those observed under field conditions, and the pathogen was re-isolated from lesions fulfilling Koch's postulates. To the best knowledge, this is the first report of C. chrysophilum causing anthracnose on blueberries in Brazil. The identification of this species causing blueberry anthracnose is crucial to improve the disease control strategies and resistance breeding.

First report of Colletotrichum tropicale causing anthracnose on Passiflora edulis in Brazil

Brazil is the world's largest producer and consumer of yellow passion fruit (Passiflora edulis f. flavicarpa), mainly for the manufacture of concentrate and frozen juice as well as for fresh consumption (Faleiro et al. 2005). Between June and July 2018, passion fruit plants with symptoms of anthracnose were observed in commercial planting in the municipality of Coruripe (20 ha), northeastern state of Alagoas, Brazil. Approximately 70% of the plants showed leaves with relatively large, watery, circular spots that affected 30% of the leaf surface. Small fragments taken from the transition region of symptomatic tissue were superficially disinfected in 70% ethanol for 30 s and in 1% NaClO for 1 min, rinsed in sterile distilled water (SDW), dried on filter paper, plated on potato dextrose agar (PDA-Kasvi) incubated at 25°C under white light and 12 h photoperiod, for 3 days. Two isolates were obtained and deposited in the Collection of Phytopathogens at the Universidade Federal de Alagoas (COUFAL0281 and COUFAL0282). To identify the isolates, partial sequences of the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and β-tubulin (TUB2) genes and of the rDNA-ITS (ITS) region were amplified by PCR. The partial sequences were deposited at GenBank (MT299339, MT334694, MT310553, MT299340, MT334695 and MT310554). Based on the BLASTn analysis, sequences of the PCR products showed high nucleotide similarity with sequences of the species C. tropicale (CBS 124949/ex-type and ICMP 18672), for GAPDH (98.94% and 100%), TUB2 (99 and 100%) genes and ITS (100%). This result was also confirmed in the phylogenetic tree of Bayesian Inference assembled with concatenated data (GAPDH, TUB2 and ITS). The colonies of the isolates were white with a white reverse, with dense mycelium, and mean growth rate of 7.54 mm/day, after 7 days on PDA medium at 25° C. Conidia were subcylindrical with rounded ends, hyaline, smooth walls and measured 13.63-20.59μm (= 17.54μm; n= 50) in length and 4.40-7.93 μm (= 5.88 μm; n= 50) in width. Appressoria were melanized, subglobose, irregular and measured 7.44 - 18.57 μm (= 10.04 μm; n= 50) in length and 5.49-10.16 μm (= 7.66 μm; n= 50) in width. These morphological characteristics were consistent with those described for Colletotrichum tropicale E.I. Rojas, S.A. Rehner & Samuels (Rojas et al. 2010). To confirm pathogenicity, 30 µL of a 106 conidia/mL sterile distilled water (SDW) conidia suspension, together with a drop of 20% Tween were deposited on the adaxial surface of passion fruit leaves wounded with a sterile needle, with four repetitions. The control consisted of leaves inoculated only with SDW. The leaves were placed in a plastic Gerbox box with sterilized filter paper moistened with SDW and maintained in a Biochemistry Oxygen Demand (BOD) incubator stove at 25 ºC and photoperiod of 12 h. After 7 days, typical anthracnose symptoms were observed on inoculated leaves. The pathogen was re-isolated and confirmed by morphological characterization, according to Koch's postulates. No symptoms were observed in the negative control. The occurrence of this species has been frequently reported in several other crops grown in northeastern Brazil (Silva et al. 2017; Veloso et al. 2018; Vieira et al. 2018; Costa et al. 2019). Additionally, many of these crops are grown in close proximity to the passion fruit orchards, thus favoring pathogen movement between hosts, probably, due to the anthropic influence, circulation of animals and insects, as well as wind driven rain splashes. However, this is first report of C. tropicale in Passiflora edulis in the world.

First report of Colletotrichum chrysophillum causing cassava anthracnose in Brazil

Cassava (Manihot esculenta Crantz) has significant socioeconomic relevance in Brazil and other developing countries, as one of the main sources of carbohydrates for human and animal consumption (De Oliviera et al., 2011). Among the cassava crop diseases, anthracnose is one of the main limiting factors for production and may be caused by species like Colletotrichum plurivorum, C. karstii, C. fructicola, and C. siamense (Bragança et al., 2016; Liu et al., 2019; Oliveira et al., 2016; Sangpueak; Phansak; Buensanteai, 2018). Severity in the field is variable, depending on the resistance of the variety used and is also highly influenced by the climate, being the most severe disease under high humidity and high temperature. Under these conditions, it can cause losses of up to 100%. In 2019, cassava leaves presenting dark brown necrotic injuries of different sizes and irregular borders-typical anthracnose symptoms- were collected from commercial plantations in the states of Pará and Tocantins, Brazil. Symptomatic tissue fragments were superficially disinfected, placed in plates with potato dextrose agar (PDA), and incubated under 25 ± 2 °C for seven days. In the 56 isolates used in the morphological identification, the colonies were white and gray at the top and dark gray in the bottom with sector formation. The conidia were hyaline, cylindrical, and aseptic, 10.04 to 17.83 μm long × 3.29 to 5.75 μm wide. These phenotypical characteristics were similar to those of C. gloeosporioides lato sensu species (Weir et al., 2012). Genomic DNA was extracted from two representative isolates (UFT/Coll69, collected in the municipality of Casa de Tábua-PA; UFT/Coll82, collected in Pau Darco-PA) and the APN2 / MAT-IGS, DNA lyase (Apn2), and glyceraldehyde-3-phosphate dehydrogenase-IGS (GAP2-IG) intergenic spacers were amplified and sequenced. The nucleotide sequences were deposited in the GenBank (accession numbers: MT409462, MT396231, MT759633, MT396239, MT396232, MT800846). The BLASTn (Basic Local Alignment Search Tool) showed a 99 to 100% similarity with Colletotrichum chrysophillum. The maximum likelihood phylogenetic analysis grouped the isolates in the C. chrysophillum clade, with a high bootstrap value (98%). Based on morphocultural characteristics and the phylogenetic analysis, the isolates associated with M. esculenta anthracnose were identified as C. chrysophillum, with a frequency of 6.67% among Colletotrichum colonies isolated from cassava leaves. The inoculation of three isolates was carried out in three plants, three leaves for each plant, by spraying spore solution with a concentration of 1×106 conidia / ml, without wounding the leaves and placed in a humid chamber at 25 ° C for ten days. Control plants were inoculated with sterile distilled water. From the 2nd day after inoculation, small irregular necrotic lesions appeared that increased in size over time, while control plants remained asymptomatic. Both were pathogenic and the symptoms caused after inoculation were similar to each other and to those observed in the field. In Brazil, anthracnose by C. chrysophillum was reported in cashew (Veloso et al., 2018) and banana trees (Vieira et al., 2017). To our knowledge, this is the first report of cassava anthracnose disease by C. chrysophillum.

Identification and characterization of Colletotrichum destructivum causing anthracnose on sunflower

Sunflower is one of the most economically important oil crops. Recently, sunflower anthracnose caused by Colletotrichum destructivum was reported and suggested to be a potential threat to the quality of oil and edible seeds derived from sunflower in the field and even on the ornamentals in the residential gardens. Colletotrichum destructivum, as the causal agent of sunflower anthracnose, has been rarely studied. In this study, the vegetative growth and sporulation of this fungal species were investigated by assessing the requirements of nutrition and other environmental conditions, such as temperature, ambient pH, and lightness regime. Additionally, the sensitivity of C. destructivum to several fungicides was assessed. The results will provide a baseline for better understanding of the biology and etiology of C. destructivum. This study will be the first reference for a sustainable management strategy according to the occurrence and prevalence of the sunflower anthracnose.

Colletotrichum species associated with mango in southern China

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

Optimal markers for the identification of Colletotrichum species

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