A multi-locus phylogenetic evaluation of Diaporthe (Phomopsis)

Phylogenetic and Haplotype Network Analyses of Diaporthe eres Species in China Based on Sequences of Multiple Loci

Diaporthe eres is considered one of the most important causal agents of many plant diseases, with a broad host range worldwide. In this study, multiple sequences of ribosomal internal transcribed spacer region (ITS), translation elongation factor 1-α gene (EF1-α), beta-tubulin gene (TUB2), calmodulin gene (CAL), and histone-3 gene (HIS) were used for multi-locus phylogenetic analysis. For phylogenetic analysis, maximum likelihood (ML), maximum parsimony (MP), and Bayesian inferred (BI) approaches were performed to investigate relationships of D. eres with closely related species. The results strongly support that the D. eres species falls into a monophyletic lineage, with the characteristics of a species complex. Phylogenetic informativeness (PI) analysis showed that clear boundaries could be proposed by using EF1-α, whereas ITS showed an ineffective reconstruction and, thus, was unsuitable for speciating boundaries for Diaporthe species. A combined dataset of EF1-α, CAL, TUB2, and HIS showed strong resolution for Diaporthe species, providing insights for the D. eres complex. Accordingly, besides D. biguttusis, D. camptothecicola, D. castaneae-mollissimae, D. cotoneastri, D. ellipicola, D. longicicola, D. mahothocarpus, D. momicola, D. nobilis, and Phomopsis fukushii, which have already been previously considered the synonymous species of D. eres, another three species, D. henanensis, D. lonicerae and D. rosicola, were further revealed to be synonyms of D. eres in this study. In order to demonstrate the genetic diversity of D. eres species in China, 138 D. eres isolates were randomly selected from previous studies in 16 provinces. These isolates were obtained from different major plant species from 2006 to 2020. The genetic distance was estimated with phylogenetic analysis and haplotype networks, and it was revealed that two major haplotypes existed in the Chinese populations of D. eres. The haplotype networks were widely dispersed and not uniquely correlated to specific populations. Overall, our analyses evaluated the phylogenetic identification for D. eres species and demonstrated the population diversity of D. eres in China.

Morphological and phylogenetic analyses reveal three new species of Diaporthe from Yunnan, China

Species of Diaporthe have often been reported as plant pathogens, endophytes or saprobes, commonly isolated from a wide range of plant hosts. Sixteen strains isolated from species of ten host genera in Yunnan Province, China, represented three new species of Diaporthe, D. chrysalidocarpi, D. machili and D. pometiae as well as five known species D. arecae, D. hongkongensis, D. middletonii, D. osmanthi and D. pandanicola. Morphological comparisons with known species and DNA-based phylogenies based on the analysis of a multigene (ITS, TUB, TEF, CAL and HIS) dataset support the establishment of the new species. This study reveals that a high species diversity of Diaporthe with wide host ranges occur in tropical rainforest in Yunnan Province, China.

Diaporthe species causing stem gray blight of red-fleshed dragon fruit (Hylocereus polyrhizus) in Malaysia

This study aimed to characterize the new fungal disease on the stem of red-fleshed dragon fruit (Hylocereus polyrhizus) in Malaysia, which is known as gray blight through morphological, molecular and pathogenicity analyses. Nine fungal isolates were isolated from nine blighted stems of H. polyrhizus. Based on morphological characteristics, DNA sequences and phylogeny (ITS, TEF1-α, and β-tubulin), the fungal isolates were identified as Diaporthe arecae, D. eugeniae, D. hongkongensis, D. phaseolorum, and D. tectonendophytica. Six isolates recovered from the Cameron Highlands, Pahang belonged to D. eugeniae (DF1 and DF3), D. hongkongensis (DF9), D. phaseolorum (DF2 and DF12), and D. tectonendophytica (DF7), whereas three isolates from Bukit Kor, Terengganu were recognized as D. arecae (DFP3), D. eugeniae (DFP4), and D. tectonendophytica (DFP2). Diaporthe eugeniae and D. tectonendophytica were found in both Pahang and Terengganu, D. phaseolorum and D. hongkongensis in Pahang, whereas D. arecae only in Terengganu. The role of the Diaporthe isolates in causing stem gray blight of H. polyrhizus was confirmed. To date, only D. phaseolorum has been previously reported on Hylocereus undatus. This is the first report on D. arecae, D. eugeniae, D. hongkongensis, D. phaseolorum, and D. tectonendophytica causing stem gray blight of H. polyrhizus worldwide.

Endophytic Diaporthe Associated With Citrus grandis cv. Tomentosa in China

Diaporthe species are associated with Citrus as endophytes, pathogens, and saprobes worldwide. However, little is known about Diaporthe as endophytes in Citrus grandis in China. In this study, 24 endophytic Diaporthe isolates were obtained from cultivated C. grandis cv. "Tomentosa" in Huazhou, Guangdong Province in 2019. The nuclear ribosomal internal transcribed spacer (ITS), partial sequences of translation elongation factor 1-α (tef1), β-tubulin (tub2), and partial calmodulin (cal) gene regions were sequenced and employed to construct phylogenetic trees. Based on morphology and combined multigene phylogeny, eleven Diaporthe species were identified including two new species, Diaporthe endocitricola and D. guangdongensis. These are the first report of D. apiculata, D. aquatica, D. arecae, D. biconispora, D. limonicola, D. masirevicii, D. passifloricola, D. perseae, and D. sennae on C. grandis. This study provides the first intensive study of endophytic Diaporthe species on C. grandis cv. tomentosa in China. These results will improve the current knowledge of Diaporthe species associated with C. grandis. The results obtained in this study will also help to understand the potential pathogens and biocontrol agents and to develop a platform in disease management.

Diaporthe amygdali, a species complex or a complex species?

Delimitation of species boundaries within the fungal genus Diaporthe has been challenging, but the analyses of combined multilocus DNA sequences has become an important tool to infer phylogenetic relationships and to circumscribe species. However, analyses of congruence between individual gene genealogies and the application of the genealogical concordance principle have been somehow overlooked. We noted that a group of species including D. amygdali, D. garethjonesii, D. sterilis, D. kadsurae, D. ternstroemia, D. ovoicicola, D. fusicola, D. chongqingensis and D. mediterranea, commonly known as D. amygdali complex, occupy a monophyletic clade in Diaporthe phylogenies but the limits of all species within the complex are not entirely clear. To assess the boundaries of species within this complex we employed the Genealogical Concordance Phylogenetic Species Recognition principle (GCPSR) and coalescence-based models: General Mixed Yule-Coalescent (GMYC) and Poisson Tree Processes (PTP). The incongruence detected between individual gene phylogenies, as well as the results of coalescent methods do not support the recognition of lineages within the complex as distinct species. Moreover, results support the absence of reproductive isolation and barriers to gene flow in this complex, thus providing further evidence that the D. amygdali species complex constitutes a single species. This study highlights the relevance of the application of the GCPSR principle, showing that concatenation analysis of multilocus DNA sequences, although being a powerful tool, might lead to an erroneous definition of species limits. Additionally, it further shows that coalescent methods are useful tools to assist in a more robust delimitation of species boundaries in the genus Diaporthe.

Morphology Characterization, Molecular Phylogeny, and Pathogenicity of Diaporthe passifloricola on Citrus reticulata cv. Nanfengmiju in Jiangxi Province, China

The Nanfengmiju (Citrus reticulata cv. Nanfengmiju), a high-quality local variety of mandarin, is one of the major fruit crops in Jiangxi Province, China. Citrus melanose and stem-end rot, two common fungal diseases of Nanfengmiju, are both caused by Diaporthe spp. (syn. Phomopsis spp.). Identification of the Diaporthe species is essential for epidemiological studies, quarantine measures, and management of diseases caused by these fungi. Melanose disease was observed on Nanfengmiju fruit in Jiangxi Province of China in 2016. Based on morphological characterization and multi-locus phylogenetic analyses, three out of 39 isolates from diseased samples were identified as D. passifloricola. Since these three isolates did not cause melanose on citrus fruit in the pathogenicity tests, they were presumed to be endophytic fungi present in the diseased tissues. However, our results indicate that D. passifloricola may persist as a symptom-less endophyte in the peel of citrus fruit, yet it may cause stem-end if it invades the stem end during fruit storage. To the best of our knowledge, this is the first report of D. passifloricola as the causal agent of the stem-end rot disease in Citrus reticulata cv. Nanfengmiju.

Morphological and molecular identification of Diaporthe species in south-western China, with description of eight new species

Diaporthe species have often been reported as plant pathogens, endophytes and saprophytes, commonly isolated from a wide range of infected plant hosts. In the present study, twenty strains obtained from leaf spots of twelve host plants in Yunnan Province of China were isolated. Based on a combination of morphology, culture characteristics and multilocus sequence analysis of the rDNA internal transcribed spacer region (ITS), translation elongation factor 1-α (TEF), β-tubulin (TUB), calmodulin (CAL), and histone (HIS) genes, these strains were identified as eight new species: Diaporthe camelliae-sinensis, D. grandiflori, D. heliconiae, D. heterostemmatis, D. litchii, D. lutescens, D. melastomatis, D. pungensis and two previously described species, D. subclavata and D. tectonendophytica. This study showed high species diversity of Diaporthe in tropical rain forests and its hosts in south-western China.

Unravelling Diaporthe Species Associated with Woody Hosts from Karst Formations (Guizhou) in China

Though several Diaporthe species have been reported in China, little is known about the species associated with nature reserves in Guizhou province. During a survey of fungi in six nature reserves in Guizhou province of China, thirty-one Diaporthe isolates were collected from different woody hosts. Based on morphology, culture characteristics and molecular phylogenetic analysis, these isolates were characterized and identified. Phylogenetic analysis of internal transcribed spacer region (ITS), combined with translation elongation factor 1-alpha (tef), β-tubulin (tub), calmodulin (cal) and histone H3 (his) gene regions identified five known Diaporthe species and seven distinct lineages representing novel Diaporthe species. The details of five known species: Diaporthe cercidis, D. cinnamomi, D. conica, D. nobilis and D. sackstonii are given and the seven new species D. constrictospora, D. ellipsospora, D. guttulata, D. irregularis, D. lenispora, D. minima, and D. minusculata are introduced with detailed descriptions and illustrations. This study revealed a high diversity of previously undescribed Diaporthe species associated with woody hosts in various nature reserves of Guizhou province, indicating that there is a potential of Diaporthe species remains to be discovered in this unique landform (Karst formations) in China. Interestingly, the five known Diaporthe species have been reported as pathogens of various hosts, and this could indicate that those newly introduced species in this study could be potentially pathogenic pending further studies to confirm.

The Identification of a New Species, Diaporthe humulicola, a Pathogen Causing Diaporthe Leaf Spot on Common Hop

Common hop, Humulus lupulus, is a commercially important crop in the United States, with an increasing number of hop yards being established in the Northeast. In 2018, a new fungal disease was observed at two research hop yards in Connecticut. This new pathogen affected all hop cultivars being grown and caused leaf spots and browning of cones. The causal organism was isolated and Koch's postulates were performed to confirm pathogenicity. The disease symptoms were similar to the previously described Phoma wilt; however, morphological and phylogenetic analyses placed the causal organism as a new species of Diaporthe. We propose the name Diaporthe humulicola. The disease increased under hot, humid conditions (around 24°C and 90% relative humidity), which prevail during the summer in the northeastern United States as well as other parts of the country. An in vitro preliminary assessment of fungicide sensitivity revealed that pyraclostrobin and boscalid inhibited D. humulicola growth in culture and should be further assessed for field efficacy against this new disease of hop. The proper identification and monitoring of this pathogen will be important to inform hop growers of this new threat.

Identification and Characterization of Diaporthe spp. Associated with Twig Cankers and Shoot Blight of Almonds in Spain

Two hundred and twenty-five Diaporthe isolates were collected from 2005 to 2019 in almond orchards showing twig cankers and shoot blight symptoms in five different regions across Spain. Multilocus DNA sequence analysis with five loci (ITS, tub, tef-1α, cal and his), allowed the identification of four known Diaporthe species, namely: D. amygdali, D. eres, D. foeniculina and D. phaseolorum. Moreover, a novel phylogenetic species, D. mediterranea, was described. Diaporthe amygdali was the most prevalent species, due to the largest number of isolates (85.3%) obtained from all sampled regions. The second most frequent species was D. foeniculina (10.2%), followed by D. mediterranea (3.6%), D. eres and D. phaseolorum, each with only one isolate. Pathogenicity tests were performed using one-year-old almond twigs cv. Vayro and representative isolates of the different species. Except for D. foeniculina and D. phaseolorum, all Diaporthe species were able to cause lesions significantly different from those developed on the uninoculated controls. Diaporthe mediterranea caused the most severe symptoms. These results confirm D. amygdali as a key pathogen of almonds in Spain. Moreover, the new species, D. mediterranea, should also be considered as a potential important causal agent of twig cankers and shoot blight on this crop.

Polyphasic studies of new species of Diaporthe from native forest in Chile, with descriptions of Diaporthe araucanorum sp. nov., Diaporthe foikelawen sp. nov. and Diaporthe patagonica sp. nov

During a survey of fungi in native forests in Chile, several unidentified isolates of Diaporthe were collected from different hosts. The isolates were characterized based on DNA comparisons, morphology, culture characteristics and host affiliation, in accordance with previous descriptions. Phylogenetic analysis of the ITS region, combined with partial tub2 and tef1 genes, showed that the isolates formed three distinct groups representing three new taxa. The three new species of Diaporthe, Diaporthe araucanorum on Araucaria araucana, Diaporthe foikelawen on Drimys winteri and Diaporthe patagonica on Aristotelia chilensis are described and illustrated in the present study.

Analysis of the species spectrum of the Diaporthe/Phomopsis complex in European soybean seeds

Phytopathogenic fungal species of the Diaporthe/Phomopsis complex (DPC) are associated with three highly destructive diseases on soybean: seed decay, pod and stem blight, and stem canker. They are responsible for poor seed quality and significant yield reduction in most soybean-producing areas. Precise identification and classification of DPC species are important in understanding the epidemiology of disease and to develop effective control measures. Although cultural and morphological characteristics of DPC-associated pathogens have been described, establishing a more accurate taxonomic framework seems necessary for a revaluation of the taxonomy and phylogeny of DPC species. In this study, we focused on morphological and molecular analyses of species from DPC-damaged European soybean seeds obtained from several locations throughout Europe. Colony characteristics, conidia dimensions, existence of α- and β-conidia, and formation of perithecia were evaluated in order to assign the isolates to a species morphologically. Phylogenetic relationships were determined based on sequences from beta-tubulin (TUB), translation elongation factor 1-alpha (TEF1), and nuclear ribosomal DNA internal transcribed spacers (ITS). All isolates were tested for pathogenicity on soybean with positive results. In this study, we present updated taxonomic data by combining morphological observations and molecular tools which placed 32 Diaporthe isolates into four DPC species: D. longicolla, D. caulivora, D. eres, and D. novem, which are well-known soybean pathogens.

Variations in Fungal Community and Diversity in Doushen With Different Flavors

Doushen, a traditional Chinese fermented soybean product, may be spiced or spicy depending on whether pepper powder is added. While numerous studies have investigated the microbial communities of other fermented foods, little is known on the fungal diversity of Doushen. Therefore, in this study, we investigated the fungal community and diversity in both spiced and spicy Doushen. Our results revealed that fungal species richness significantly differed between the samples with different flavors. A total of nine phyla and 188 fungal genera were identified, and Ascomycota and Aspergillus were predominant in all samples. Based on linear discriminant analysis, a total of 57 OTUs were significantly different between the two samples. Results of non-metric multidimensional scaling and unweighted pair-group analysis suggested that the presence of pepper powder affects the microbial community in Doushen. Network analysis showed that microbial interactions between fungal communities in Doushen with different flavors were significantly different. The results on the enumeration and identification of fungi were consistent with the composition of the dominant genera in the samples with different flavors. This study provides a theoretical basis for future research on food ecology in Doushen.

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

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

Molecular Characterization of Diaporthe Species Associated With Hazelnut Defects

Fungi of the genus Diaporthe have been reported as the main causative agent of hazelnut defects in the Caucasus area. This study aimed to define which fungal species are present in defective hazelnuts grown in Turkey and confirm the role of Diaporthe spp. Seven hazelnut orchards were selected, with each one located in a different Turkish Province (Düzce, Giresun, Ordu, Samsun, Sakarya, Trabzon, and Zonguldak), and hazelnuts were collected at early and full ripening. Fungal isolation and identification were performed at the genus level based on morphological characteristics. Several genera were isolated, with Diaporthe spp. being among the prevalent. This was the only genus with increasing incidence from early to full ripening, and incidence at full ripening was positively correlated both with internal (ρ = 0.86) and visible defects (ρ = 0.81), which confirmed its role as the key causative agent of hazelnut defects. The correlation of defect occurrence with rainfall, reported in previous study, was not confirmed, possibly due to the low defect incidence. A total of 86 Diaporthe monosporic strains isolated from Turkish hazelnut samples, together with 33 strains collected in the Caucasus region and 6 from Italy, were analyzed with a multi-locus phylogeny based on three genomic loci (ITS, EF1-α, and tub). The results showed that Diaporthe strains can be grouped into 7 distinct clades, with a majority of Turkish strains (95%) being placed into a single clade related with D. eres. These samples were organized into several sub-clades, which indicates the existence of genetically diverse sub-populations.

Freshwater Sordariomycetes

Sordariomycetes is one of the largest classes of Ascomycota that comprises a highly diverse range of fungi mainly characterized by perithecial ascomata and inoperculate unitunicate asci. Freshwater Sordariomycetes play an important role in ecosystems and some of them have the potential to produce bioactive compounds. This study documents and reviews the freshwater Sordariomycetes, which is one of the largest and important groups of fungi in aquatic habitats. Based on evidence from DNA sequence data and morphology, we introduce a new order Distoseptisporales, two new families, viz. Ceratosphaeriaceae and Triadelphiaceae, three new genera, viz. Aquafiliformis, Dematiosporium and Neospadicoides, 47 new species, viz. Acrodictys fluminicola, Aquafiliformis lignicola, Aquapteridospora fusiformis, Arthrinium aquaticum, Ascosacculus fusiformis, Atractospora aquatica, Barbatosphaeria lignicola, Ceratosphaeria aquatica, C. lignicola, Chaetosphaeria aquatica, Ch. catenulata, Ch. guttulata, Ch. submersa, Codinaea yunnanensis, Conioscypha aquatica, C. submersa, Cordana aquatica, C. lignicola, Cosmospora aquatica, Cylindrotrichum submersum, Dematiosporium aquaticum, Dictyochaeta cangshanensis, D. ellipsoidea, D. lignicola, D. submersa, Distoseptispora appendiculata, D. lignicola, D. neorostrata, D. obclavata, Hypoxylon lignicola, Lepteutypa aquatica, Myrmecridium aquaticum, Neospadicoides aquatica, N. lignicola, N. yunnanensis, Ophioceras submersum, Peroneutypa lignicola, Phaeoisaria filiformis, Pseudostanjehughesia lignicola, Rhodoveronaea aquatica, Seiridium aquaticum, Sporidesmiella aquatica, Sporidesmium lageniforme, S. lignicola, Tainosphaeria lunata, T. obclavata, Wongia aquatica, two new combinations, viz. Acrodictys aquatica, Cylindrotrichum aquaticum, and 9 new records, viz. Chaetomium globosum, Chaetosphaeria cubensis, Ch. myriocarpa, Cordana abramovii, Co. terrestris, Cuspidatispora xiphiago, Sporidesmiella hyalosperma, Stachybotrys chartarum,S. chlorohalonata. A comprehensive classification of the freshwater Sordariomycetes is presented based on updated literature. Phylogenetic inferences based on DNA sequence analyses of a combined LSU, SSU, RPB2 and TEF1α dataset comprising species of freshwater Sordariomycetes are provided. Detailed information including their habitats distribution, diversity, holotype, specimens collected and classification are provided.

Association mapping of a locus that confers southern stem canker resistance in soybean and SNP marker development

BACKGROUND

Southern stem canker (SSC), caused by Diaporthe aspalathi (E. Jansen, Castl. & Crous), is an important soybean disease that has been responsible for severe losses in the past. The main strategy for controlling this fungus involves the introgression of resistance genes. Thus far, five main loci have been associated with resistance to SSC. However, there is a lack of information about useful allelic variation at these loci. In this work, a genome-wide association study (GWAS) was performed to identify allelic variation associated with resistance against Diaporthe aspalathi and to provide molecular markers that will be useful in breeding programs.

RESULTS

We characterized the response to SSC infection in a panel of 295 accessions from different regions of the world, including important Brazilian elite cultivars. Using a GBS approach, the panel was genotyped, and we identified marker loci associated with Diaporthe aspalathi resistance through GWAS. We identified 19 SNPs associated with southern stem canker resistance, all on chromosome 14. The peak SNP showed an extremely high degree of association (p-value = 6.35E-27) and explained a large amount of the observed phenotypic variance (R2 = 70%). This strongly suggests that a single major gene is responsible for resistance to D. aspalathi in most of the lines constituting this panel. In resequenced soybean materials, we identified other SNPs in the region identified through GWAS in the same LD block that clearly differentiate resistant and susceptible accessions. The peak SNP was selected and used to develop a cost-effective molecular marker assay, which was validated in a subset of the initial panel. In an accuracy test, this SNP assay demonstrated 98% selection efficiency.

CONCLUSIONS

Our results suggest relevance of this locus to SSC resistance in soybean cultivars and accessions from different countries, and the SNP marker assay developed in this study can be directly applied in MAS studies in breeding programs to select materials that are resistant against this pathogen and support its introgression.

Diaporthalean fungi associated with canker and dieback of trees from Mount Dongling in Beijing, China

Diaporthales is a fungal order comprising important plant pathogens, saprobes and endophytes on a wide range of woody hosts. It is often difficult to differentiate the pathogens in this order, since both the morphology and disease symptoms are similar among the various species. In the current study, we obtained 15 representative diaporthalean isolates from six tree hosts belonging to plant families Betulaceae, Fagaceae, Juglandaceae, Rosaceae, and Ulmaceae from Mount Dongling in China. Six species were identified residing in four families of Diaporthales (Diaporthaceae, Erythrogloeaceae, Juglanconidaceae and Melanconidaceae). Based on morphological comparison and the phylogenetic analyses of partial ITS, LSU, cal, his3, rpb2, tef1-α and tub2 gene sequences, we identified five known species (Diaporthe betulina, D. eres, D. rostrata, Juglamconis oblonga and Melanconis stilbostoma) and one novel species (Dendrostoma donglinensis). These results represent the first study of diaporthalean fungi associated with canker and dieback symptoms from Mount Dongling in Beijing, China.

Diaporthe species in south-western China

Three strains of the genus Diaporthe were isolated from different plant hosts in south-western China. Phylogenetic analyses of the combined ITS, β-tubulin, tef1 and calmoudulin dataset indicated that these strains represented three independent lineages in Diaporthe. Diaporthemillettiaesp. nov. clustered with D.hongkongensis and D.arecae, Diaportheosmanthisp. nov. grouped with D.arengae, D.pseudomangiferae and D.perseae and Diaporthe strain GUCC9146, isolated from Camelliasinensis, was grouped in the D.eres species complex with a close relationship to D.longicicola. These species are reported with taxonomic descriptions and illustrations.

Diaporthe nebulae sp. nov. and First Report of D. cynaroidis D. novem, and D. serafiniae on Grapevines in South Africa

Diaporthe species cause Phomopsis cane and leaf spot as well as Phomopsis dieback on grapevines. Symptoms of Phomopsis dieback have increasingly been observed over the past few years. In order to assess the current status of Diaporthe on grapevines in the Western Cape Province of South Africa, isolations were made from dormant grafted nursery vines, dormant rootstock canes, and dying or dead spurs of field vines. Cultures identified as Diaporthe based on morphological features were further identified to species level by sequencing the internal transcribed spacers (ITS) 1 and 2 and 5.8S rRNA and, for a representative subsample of isolates, the partial beta-tubulin (tub2) and translation elongation factor 1-alpha (EF1-α) genes. Phylogenetic analysis of the combined ITS, tub2, and EF1-α data revealed nine Diaporthe species associated with grapevines during this survey. One of these represents a new species, D. nebulae sp. nov., and three other species, namely D. novem, D. cynaroidis, and D. serafiniae, are reported on grapevines in South Africa for the first time. Species-specific primers were designed for PCR identification of D. ampelina, D. ambigua, and D. foeniculina. Pathogenicity studies conducted on detached grapevine shoots indicated D. ampelina, D. novem, and D. nebulae sp. nov. as the most virulent species.

Diversity of Endophytic Fungi of the Coastal Plant Vitex rotundifolia in Taiwan

Vitex rotundifolia L. f. (Lamiaceae), which commonly grows at sand coasts, is important for coast protection and the prevention of erosion. However, the diversity and roles of fungi associated with this plant remain unclear. A total of 1,052 endophytic isolates from 1,782 plants tissues from two sand beaches in northern Taiwan were classified into 76 morphospecies based on culture morphology and ITS or LSU rRNA gene sequence comparisons. Critical species were further identified using protein gene sequences and microscopy. Most of the isolates at both sites belonged to the phylum Ascomycota, with Pleosporales having the most species (15 species). The largest number of isolates (47.7%) was from the stems, followed by the roots (22.5%), leaves (16.6%), and branches (13.1%). The three species with the highest isolation frequencies at both sites were Alternaria alternata, Aspergillus terreus, and an undescribed species of Alpestrisphaeria. A. terreus was found in all organs. A. alternata was detected in all organs, except the roots. Alpestrisphaeria sp. was only found in the roots and stems. In the stems and roots, strain numbers from cortical tissues were approximately two-fold higher than those from the corresponding woody tissue. The overall colonization rate in the stems was significantly higher than those that in the roots and leaves. The majority of fungi appeared to be saprobes, which may play important roles in nutrient recycling during sand burial and mediate further stress factors in the coastal habitat.

Identification and Characterization of Fungal Pathogens Causing Fruit Rot of Deciduous Holly

Cut branches of deciduous holly (Ilex spp. L.) harboring colorful berries are traditionally used as ornaments in holiday decorations. Since 2012, a fruit rot of unspecified cause has resulted in significant yield reduction and economic losses across Midwestern and Eastern U.S. nurseries. In this study, symptomatic fruit samples collected from nine different locations over five years were analyzed, and several fungal species were isolated. A combination of morphological characterization, multilocus phylogenetic analyses, and pathogenicity assays revealed that Alternaria alternata and Diaporthe ilicicola sp. nov. were the primary pathogens associated with symptomatic fruit. Other fungi including A. arborescens, Colletotrichum fioriniae, C. nymphaeae, Epicoccum nigrum, and species in the D. eres species complex appeared to be minor pathogens in this disease complex. In detached fruit pathogenicity assays testing the role of wounding and inoculum concentration on disease development, disease incidence and severity increased when fruit was wounded and inoculated with a higher inoculum concentration. These findings indicate that management strategies that can protect fruit from injury or reduce inoculum may lower disease levels in the field. This research established the basis for further studies on this emerging disease and the design of research-based management strategies. To our knowledge, it also represents the first report of species of Alternaria, Colletotrichum, Diaporthe, and Epicoccum causing fruit rot of deciduous holly.

Identification and antifungal sensitivity of two new species of Diaporthe isolated

Diaporhte species are plant pathogens rarely involved in human diseases, especially eye diseases. We report our findings in two undescribed Diaporhte species. Both were identified by their morphological characteristics and by DNA sequence analyses. In Case 1, an 81-year-old male farmer who had pterygium surgery 7 years earlier developed keratitis and the causal fungus was identified as a new species of Diaporthe, D. oculi. This species can be distinguished from the closely related D. limonicola on Citrus limon (Rutaceae) by the ITS, tef1, and TUB (515/520 = 99.0% in ITS, 315/324 = 97.2% in tef1, and 601/614 = 97.9% in TUB). The isolate from Case 2, a 68-year-old man with a rose thorn injury, was also identified as a new Diaporthe species, D. pseudooculi. Phylogenetically, D. pseudooculi is different from the closely related D. podocarpi-macrophylli by the ITS, tef1, and TUB (525/531 = 98.9% in ITS, 314/333 = 94.3% in tef1, and 436/442 = 98.6% in TUB). We report on the identification, drug sensitivity, and treatment outcomes for these two new species of Diaporthe, D. oculi and D. pseudooculi.

High diversity of Diaporthe species associated with dieback diseases in China, with twelve new species described

Diaporthe species have often been reported as important plant pathogens, saprobes and endophytes on a wide range of plant hosts. Although several Diaporthe species have been recorded in China, little is known about species able to infect forest trees. Therefore, extensive surveys were recently conducted in Beijing, Heilongjiang, Jiangsu, Jiangxi, Shaanxi and Zhejiang Provinces. The current results emphasised on 15 species from 42 representative isolates involving 16 host genera using comparisons of DNA sequence data for the nuclear ribosomal internal transcribed spacer (ITS), calmodulin (cal), histone H3 (his3), partial translation elongation factor-1α (tef1) and β-tubulin (tub2) gene regions, as well as their morphological features. Three known species, D.biguttulata, D.eres and D.unshiuensis, were identified. In addition, twelve novel taxa were collected and are described as D.acerigena, D.alangii, D.betulina, D.caryae, D.cercidis, D.chensiensis, D.cinnamomi, D.conica, D.fraxinicola, D.kadsurae, D.padina and D.ukurunduensis. The current study improves the understanding of species causing diebacks on ecological and economic forest trees and provides useful information for the effective disease management of these hosts in China.

Multiloci identification of Diaporthe fungi isolated from the medicinal plant Costus spiralis (Jacq.) Roscoe (Costaceae)

AIMS

The purpose of this study is to identify species from genus Diaporthe associated with a medicinal plant Costus spiralis by ITS, EF 1-α, TUB and CAL gens.

METHODS AND RESULTS

The 30 isolates from the genus Diaporthe associated with the medicinal plant Costus spiralis were characterized based on morphological characters and the microculture technique and grouped by DNA fingerprinting with the ISSP gene. Afterwards, a total of 12 isolates were selected for the identification of the species based on the comparative research on the blast through the sequences of the ITS gene. Phylogenetic Tree of Maximum Likelihood were generated with the ITS gene individually and with the genes ITS, TUB, CAL and EF1-α combined with the Diaporthe species recognized and with the additional sequences obtained from GenBank for these species.

CONCLUSIONS

It was not possible to characterize the 30 isolates microscopically and macromorphologically through the microculture technique and the macromorphological characteristics. The 12 isolates selected based on the DNA fingerprinting profile identified phylogenetically, revealed five distinct species of Diaporthe which are present in C. spiralis.

SIGNIFICANCE AND IMPACT OF THE STUDY

The molecular analyses used in this study are excellent alternatives for species-level identification of Diaporthe associated with medicinal plants.

Identification of endophytic fungi from leaves of Pandanaceae based on their morphotypes and DNA sequence data from southern Thailand

The authors established the taxonomic status of endophytic fungi associated with leaves of Pandanaceae collected from southern Thailand. Morphotypes were initially identified based on their characteristics in culture and species level identification was done based on both morphological characteristics and phylogenetic analyses of DNA sequence data. Twenty-two isolates from healthy leaves were categorised into eight morphotypes. Appropriate universal primers were used to amplify specific gene regions and phylogenetic analyses were performed to identify these endophytes and established relationships with extant fungi. The authors identified both ascomycete and basidiomycete species, including one new genus, seven new species and nine known species. Morphological descriptions, colour plates and phylogenies are given for each taxon.

Identification of endophytic fungi from leaves of Pandanaceae based on their morphotypes and DNA sequence data from southern Thailand

The authors established the taxonomic status of endophytic fungi associated with leaves of Pandanaceae collected from southern Thailand. Morphotypes were initially identified based on their characteristics in culture and species level identification was done based on both morphological characteristics and phylogenetic analyses of DNA sequence data. Twenty-two isolates from healthy leaves were categorised into eight morphotypes. Appropriate universal primers were used to amplify specific gene regions and phylogenetic analyses were performed to identify these endophytes and established relationships with extant fungi. The authors identified both ascomycete and basidiomycete species, including one new genus, seven new species and nine known species. Morphological descriptions, colour plates and phylogenies are given for each taxon.

Emerging citrus diseases in Europe caused by species of Diaporthe

Species of Diaporthe are considered important plant pathogens, saprobes, and endophytes on a wide range of plant hosts. Several species are well-known on citrus, either as agents of pre- or post-harvest infections, such as dieback, melanose and stem-end rot on fruit. In this study we explored the occurrence, diversity and pathogenicity of Diaporthe species associated with Citrus and allied genera in European orchards, nurseries, and gardens. Surveys were carried out during 2015 and 2016 in Greece, Italy, Malta, Portugal, and Spain. A total of 79 Diaporthe strains were isolated from symptomatic twigs, branches and trunks. A multi-locus phylogeny was established based on five genomic loci (ITS, tef1, cal, his3 and tub2), and the morphological characters of the isolates determined. Preliminary pathogenicity tests were performed on lemon, lime, and orange plants with representative isolates. The most commonly isolated species were D. foeniculina and D. baccae, while only four isolates of D. novem were collected. Two new Diaporthe species, described here as D. limonicola and D. melitensis spp. nov. were found associated with a new devastating dieback disease of lemon plants. Furthermore, one cluster of sterile Diaporthe isolates was renamed as D. infertilis. Pathogenicity tests revealed most of the Citrus species as susceptible to D. baccae, D. foeniculina, and D. novem. Moreover, D. limonicola and D. melitensis caused serious cankers affecting all the Citrus species tested. This study is the first report of D. baccae and D. novem on citrus in Europe, and the first detection of a new Diaporthe canker disease of citrus in Europe. However, no isolates of D. citri were found. The study improves our understanding of the species associated with several disease symptoms on citrus plants, and provides useful information for effective disease management.

Fungal Endophyte Communities in Begonia Species from the Brazilian Atlantic Rainforest

Tropical plants represent hotspots of endophytic fungal species diversity. Based on culture-dependent methods, we evaluated the endophytic fungal communities in leaves of three plant species found in the Brazilian Atlantic Rainforest: Begonia fischeri, Begonia olsoniae, and Begonia venosa. These species are found in two distant sites: a continental region and an insular area. A total of 426 fungal endophytes in 19 genera were isolated in pure culture including Colletotrichum (51.6% of isolates) and Diaporthe (22.5%) as the most abundant, followed by Phyllosticta (3.5%), Neopestalotiopsis (1.8%), Stagonospora (1.8%), and Nigrospora (1.6%) among the genera found in minor abundance. The diversity and composition of fungal taxa differed across plant hosts. Richness and diversity of fungi were higher in B. fischeri in comparison to B. olsoniae and B. venosa. Discriminatory analysis revealed that fungal communities are structured according to hosts, which means that each plant species had its distinct endophytic communities, but dominated by common fungal taxa. This is the first study to report fungal endophytes in begonia leaves and characterize their communities.

Identification and Characterization of Diaporthe ambigua, D. australafricana, D. novem, and D. rudis Causing a Postharvest Fruit Rot in Kiwifruit

Diaporthe spp. are important plant pathogens causing wood cankers, blight, dieback, and fruit rot in a wide range of hosts. During surveys conducted during the 2013 and 2014 seasons, a postharvest rot in Hayward kiwifruit (Actinidia deliciosa) was observed in Chile. In order to identify the species of Diaporthe associated with this fruit rot, symptomatic fruit were collected from seven kiwifruit packinghouses located between San Francisco de Mostazal and Curicó (central Chile). Twenty-four isolates of Diaporthe spp. were identified from infected fruit based on morphological and cultural characters and analyses of nucleotides sequences of three loci, including the internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2), a partial sequences of the β-tubulin, and translation elongation factor 1-α genes. The Diaporthe spp. identified were Diaporthe ambigua, D. australafricana, D. novem, and D. rudis. Multilocus phylogenetic analysis revealed that Chilean isolates were grouped in separate clades with their correspondent ex-types species. All species of Diaporthe were pathogenic on wounded kiwifruit after 30 days at 0°C under normal and controlled-atmosphere (2% O₂ and 5% CO₂) storage and they were sensitive to benomyl, pyraclostrobin, and tebuconazole fungicides. D. ambigua isolates were the most virulent based on the lesion length measured in inoculated Hayward and Jintao kiwifruit. These findings confirm D. ambigua, D. australafricana, D. novem, and D. rudis as the causal agents of kiwifruit rot during cold storage in Chile. The specie D. actinidiae, a common of Diaporthe sp. found associated with kiwifruit rot, was not identified in the present study.

Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe

BACKGROUND

Species identification is essential for controlling disease, understanding epidemiology, and to guide the implementation of phytosanitary measures against fungi from the genus Diaporthe. Accurate Diaporthe species separation requires using multi-loci phylogenies. However, defining the optimal set of loci that can be used for species identification is still an open problem.

METHODS

Here we addressed that problem by identifying five loci that have been sequenced in 142 Diaporthe isolates representing 96 species: TEF1, TUB, CAL, HIS and ITS. We then used every possible combination of those loci to build, analyse, and compare phylogenetic trees.

RESULTS

As expected, species separation is better when all five loci are simultaneously used to build the phylogeny of the isolates. However, removing the ITS locus has little effect on reconstructed phylogenies, identifying the TEF1-TUB-CAL-HIS 4-loci tree as almost equivalent to the 5-loci tree. We further identify the best 3-loci, 2-loci, and 1-locus trees that should be used for species separation in the genus.

DISCUSSION

Our results question the current use of the ITS locus for DNA barcoding in the genus Diaporthe and suggest that TEF1 might be a better choice if one locus barcoding needs to be done.

High genetic variability in endophytic fungi from the genus Diaporthe isolated from common bean (Phaseolus vulgaris L.) in Brazil

AIMS

The goals of the present study were to identify, to analyse the phylogenetic relations and to evaluate the genetic variability in Diaporthe endophytic isolates from common bean.

METHODS AND RESULTS

Diaporthe sp., D. infecunda and D. phaseolorum strains were identified using multilocus phylogeny (rDNA ITS region; EF1-α, β-tubulin, and calmodulin genes). IRAP (Inter-Retrotransposon Amplified Polymorphism) and REMAP (Retrotransposon-Microsatellite Amplified Polymorphism) molecular markers reveal the existence of high genetic variability, especially among D. infecunda isolates.

CONCLUSIONS

It was concluded that the multilocus phylogenetic approach was more effective than individual analysis of ITS sequences, in identifying the isolates to species level, and that IRAP and REMAP markers can be used for studying the genetic variability in the genus Diaporthe particularly at the intraspecific level.

SIGNIFICANCE AND IMPACT OF THE STUDY

The combined use of molecular tools such as multilocus phylogenetic approach and molecular markers, as performed in this study, is the best way to distinguish endophytic strains of Diaporthe isolated from common bean (Phaseolus vulgaris L.).

Chemical constituents and their antibacterial activity from the tropical endophytic fungus Diaporthe sp. F2934

AIMS

To isolate, characterize and determine the antibacterial activities of compounds produced by the endophytic fungus Diaporthe sp. F2934, cultivated on malt extract agar.

METHODS AND RESULTS

The fungus was cultivated aseptically in Petri dishes containing malt extract agar at 25°C for 15 days. Crude extract was obtained from mycelium using ethyl acetate and sonication, and was fractioned using classic chromatography and HPLC. The structures of phomosines and chromanones were established by NMR experiments including HMQC, HMBC and COSY. Their molecular formulas were determined by ESI-TOFMS. We obtained six compounds: (1) 4H-1-benzopyra-4-one-2,3-dihydro-5-hydroxy-2,8-dimetyl, (2) 4H-1-benzopyran-4-one-2,3-dihydro-5-hydroxy-8-(hydroxylmethyl)-2-methyl, (3) 4H-1-benzopyra-4-one-2,3-dihydro-5-methoxyl-2,8-dimetyl, (4) phomosine A, (5) phomosine D and (6) phomosine C. Isolated compounds 1, 2 and 5 were inactive against 15 micro-organisms, but phomosines A and C were active against diverse Gram-negative and Gram-positive bacteria.

CONCLUSIONS

A group of new chromanones and known phomosines have been isolated from the genus Diaporthe (Diaporthe sp. F2934). The results obtained confirm the wide chemical diversity produced by endophytic fungi, specifically the genus Diaporthe. In addition, phomosines A and C may be considered as antimicrobial agents that can be used to guide the development of new antibiotics.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our phylogenetic analysis places Diaporthe sp. F2934 as sister to the Diaporthe cynaroidis clade. Three chromanones were isolated and identified, for the first time, using crude extract obtained from Diaporthe F2934. From this extract phomosines A, C and D were also purified. Regarding Staphylococcus aureus, the inhibition zone diameter (IZD) for phomosine A was 20% higher than the standard drug, vancomycin. When cultivated as described here, Diaporthe sp. F2934 produced new and antimicrobial compounds.

Species boundaries in plant pathogenic fungi: a Colletotrichum case study

BACKGROUND

Accurate delimitation of plant pathogenic fungi is critical for the establishment of quarantine regulations, screening for genetic resistance to plant pathogens, and the study of ecosystem function. Concatenation analysis of multi-locus DNA sequence data represents a powerful and commonly used approach to recognizing evolutionary independent lineages in fungi. It is however possible to mask the discordance between individual gene trees, thus the speciation events might be erroneously estimated if one simply recognizes well supported clades as distinct species without implementing a careful examination of species boundary. To investigate this phenomenon, we studied Colletotrichum siamense s. lat., which is a cosmopolitan pathogen causing serious diseases on many economically important plant hosts. Presently there are significant disagreements among mycologists as to what constitutes a species in C. siamense s. lat., with the number of accepted species ranging from one to seven.

RESULTS

In this study, multiple approaches were used to test the null hypothesis "C. siamense is a species complex", using a global strain collection. Results of molecular analyses based on the Genealogical Concordance Phylogenetic Species Recognition (GCPSR) and coalescent methods (e.g. Generalized Mixed Yule-coalescent and Poisson Tree Processes) do not support the recognition of any independent evolutionary lineages within C. siamense s. lat. as distinct species, thus rejecting the null hypothesis. This conclusion is reinforced by the recognition of genetic recombination, cross fertility, and the comparison of ecological and morphological characters. Our results indicate that reproductive isolation, geographic and host plant barriers to gene flow are absent in C. siamense s. lat.

CONCLUSIONS

This discovery emphasized the importance of a polyphasic approach when describing novel species in morphologically conserved genera of plant pathogenic fungi.

Biological and Molecular Characterization of Five Phomopsis Species Associated with Pear Shoot Canker in China

In recent years, a widespread canker disease that infects the branches of pear trees has been observed in many provinces in China; it kills the branches and results in high losses in fruit production. Symptomatic branches were collected for etiological isolation from 11 varieties of three pear species and from Malus pumila. Samples were collected from six provinces in China. In total, 143 Phomopsis isolates were obtained from 181 samples and these were identified as belonging to five species: Phomopsis fukushii (n = 69 isolates), Diaporthe eres (n = 31), P. amygdali (n = 22), P. longicolla (n = 13), and D. neotheicola (n = 8). Pathogenicity tests showed that only the first three species induced lesions on nonwounded branches of Pyrus pyrifolia var. Cuiguan. All the fungal species induced branch cankers following wound inoculations, and tests with additional pear varieties showed significantly higher virulence levels for the first three species than the latter two. A host range evaluation suggested that the five species could infect most fruit trees belonging to the Rosaceae family as well as some non-Rosaceous species. Virulence varied depending on the species of both host and pathogen. Isolates of Phomopsis amygdali had significantly higher virulence in all the tested Rosaceae plants. Correlations among the host, pathogen, and sampling regions were noted, and the morphology, growth rate, and sporulation of these species in varied media were also characterized. This study presents the first attempt to perform a broad survey and characterization of the Phomopsis spp. associated with the pear shoot cankers in China. This study shows that D. eres and P. amygdali are just as responsible for the pear shoot canker diseases as P. fukushii, and it expands the host and geographic ranges of the five species. This report provides useful information for understanding and improving management strategies for controlling this economically important disease.