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Ten species of Phomopsis have previously been identified from grapevines. Of these, P. viticola, the causal agent of Phomopsis cane and leaf spot, and P. vitimegaspora, the causal agent of swelling arm of grapevines, have been confirmed as severe pathogens of this host. Earlier taxonomic
treatments of Phomopsis species chiefly distinguished taxa ba...
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... colours were described from isolates of each species incubated at 25 • C for 7 days, using the colour scheme of Rayner (1970). Cultures are maintained in the culture collection of the Department of Plant Pathology, University of Stellenbosch (STE-U), and the Centraalbureau voor Schimmelcultures, Utrecht, Netherlands (CBS) ( Table 1). ...
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... acid was extracted from 63 isolates, which were isolated from symptomatic and asymptomatic material, and subjected to sequencing (Table 1). All isolates sporulated on PDA and WAV after being incubated at 25 • C under nuv light in a 12 h light-darkness regime for 2-3 weeks. ...
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... to the inclusion of sequences from GenBank that were shorter on the 5 and 3 ends, the complete sequences determined in this study were not used in the phylogenetic analysis. Sequences were deposited in GenBank (Table 1), and the alignment in TreeBASE (SN 1693). The neighbour-joining analysis resulted in a phylogenetic tree delimiting six main clades and several sub-groups (Fig. 1). ...
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... is known from grapevines in Australia, Portugal and South Africa, and also occurs on proteas and pears in the latter country (Mostert et al. 2001;Figs 40, 41). Presently this species appears to have a wide host range, and it is probable that future studies will be able to link these cultures (Table 1) to an established name. ...
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... species was treated in detail by Mostert et al. (2001). Although it is morphologically distinct given the shape of its alpha conidia (Mostert et al. 2001; Fig. 46), we decline to name it as new as it is presently known from only one collection (Table 1). ...
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... This species is presently known from a single collection (STE-U 4407) (Table 1), and has ellipsoidal, non-guttulate alpha conidia, (5-)6-8(-9) × (2-)2.5-3 µm (Fig. 10A). ...
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... This species is known from a single collection from vines in South Africa (STE-U 5464) (Table 1). It is characterised by having fusoid-ellipsoidal alpha conidia that are multiguttulate, and taper from an obtusely rounded apex to a subtruncate base, (6-)7-9(-10) × 2-2.5(-3) µm, and straight, curved or hamate beta conidia, 25-30 × 1-1.5 µm (Fig. 10B). ...
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... appressed, convex with smooth, even margins, white on the surface, and white to olivaceous (21''m Notes. This species is known from several collections obtained from grapevines in South Africa (STE-U 5346, 5463, 5345, 5465, 5496) ( Table 1). Alpha conidia are 6-8(-9) × 2(-2.5) ...
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... sp. 6 appears to be common on grapevines in South Africa (STE-U 5348, 5133, 5160, 5467, 5134, 5466, 5347, 5135, 5158, 5461), but also occurs on other hosts such as Rosa (South Africa), and Vaccinium (USA) ( Table 1). This species has relatively large, fusoid-ellipsoidal alpha conidia, (6-)7-9(-10) × 2-2.5 µm (Fig. 10D), being slightly shorter than those of P. viticola (Mostert et al. 2001). ...
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... This species is presently known from a single South African collection (STE-U 5495) (Table 1). Morphologically, it is characterised by having slender, fusoid-ellipsoidal alpha conidia, (8-)9-10(-11) × 2-2.5(-3) µm, being slightly narrower than those of P. viticola (Mostert et al. 2001) (Fig. 10E). ...
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... Based on phylogeny obtained here, the grapevine isolate (STE-U 5462) (Table 1) clustered with a Phomopsis sp. that is regarded as a serious pathogen of pears and plums in the USA ( Uddin et al. 1998). Morphologically, it had alpha conidia that were slender, fusoid to narrowly ellipsoidal, with acutely rounded apices and subtruncate bases, (6-)7-9 × 2-2.5(-3) µm (Fig. 10F). ...
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... Of these, the stem canker pathogen Diaporthe australafricana resides in the Diaporthe rudis species complex. This pathogen occurs on blueberry and hazelnut in Chile (Guerrero and Pérez 2013;Elfar et al. 2013) and grapevine in South Africa, Australia, and northern California (Van Niekerk et al. 2005;Gomes et al. 2013;Lawrence et al. 2015). ...
The pace at which Next Generation Sequence data is being produced continues to accelerate as technology improves. As a result, such data are increasingly becoming accessible to biologists outside of the field of bioinformatics. In contrast, access to training in the methods of genome assembly and annotation are not growing at a similar rate. In this issue, we report on a Genome Assembly Workshop for Mycologists that was held at the Forestry and Agricultural Biotechnology Institute (FABI) at the University of Pretoria, South Africa and make available the 12 draft genome sequences emanating from the event. With the aim of making the process of genome assembly and annotation more accessible to biologists, we provide a step-by-step guide to both genome assembly and annotation, intended to encourage and empower mycologists to use genome data in their research.
... Fungal development was then observed over a six-week period. Taxonomic classification of resulting fungi was carried out at the family level based on culture and morphological characteristics for Botryosphaeriaceae (Phillips et al., 2013), Diaporthaceae (van Niekerk et al., 2005), Diatrypaceae (Trouillas et al., 2010), Nectriaceae (Chaverri et al., 2011;Grafenhan et al., 2011), Phaeomoniellaceae (Chen et al., 2022), Togniniaceae (Gramaje et al., 2015), or the Basidiomycota Fomitiporia mediterranea (Fischer et al., 2005). (Pouzoulet et al., 2013). ...
en (2024) Grapevine pruning strategy affects trunk disease symptoms, wood pathobiome and mycobiome. † These authors contributed equally. Summary. Vine training and pruning are cultural strategies that can be deployed to manage grapevine trunk diseases (GTDs). Forty-year-old commercial vineyards in the Cognac region, France, trained to either Guyot-Arcure (severe pruning) or Guyot-Poussard (minimal pruning), were studied to determine how the two systems affected trunk disease symptomatology. Effects of pruning practices on the pathobiome and mycobiome of asymptomatic grapevines were also assessed, using culture-and ampli-con-based Illumina sequencing approaches. The hypothesis examined was that severe pruning of Guyot-Arcure increases trunk diseases incidence and severity, and causes higher pathogen load and microbial diversity, compared to Guyot-Poussard. Numbers of symptomatic and asymptomatic vines for the two training systems were recorded over 3 years, including numbers of vines with esca foliar symptoms, and partially unproductive and dead vines. Six asymptomatic vines from each pruning method were selected, and culturing and sequencing data were obtained from 27 samples per vine. Fungi in the Phaeomoniellaceae, Togniniaceae, and Botryosphaeriaceae were the most frequently identified. The data indicated that severe pruning increased risk of pathogen infections, with Phaeomoniella chlamydospora, Phaeoacremonium minimum and Diplodia sp. being the most commonly identified fungi. Greater numbers of dead or dying vines were recorded in the severely pruned vineyard, indicating that this strategy shortens vine longevity. Results also showed that severe pruning increased endophytic microbial diversity, and that the pruning methods influenced mycobiome community composition. This knowledge will improve recommendations to growers for practical and cost-effective ways to manage GTDs.
... The most studied Diaporthe spp. are those associated with soybean (Santos et al., 2011;Zhang et al., 1998), sunflower (Thompson et al., 2011), citrus (Udayanga et al., 2014), grapes (Baumgartner et al., 2013;van Niekerk et al., 2005), sweet potato (Huang et al., 2021) and blueberry (Hilário et al., 2021). ...
... Diaporthe/Phomopsis spp. may use more than one plant species as a host (van Niekerk et al., 2005), either as endophytes, pathogens or saprobes (Santos et al., 2011;Thompson et al., 2011). In addition to soybean, D. aspalathi isolates have been obtained from other hosts, including blue lupin (Yorinori, 1990) and rooibos (van Rensburg et al., 2006). ...
Soybean stem canker (SSC) is an important disease caused by different Diaporthe spp., including D . aspalathi , D . caulivora and D . longicolla , that leads to soybean ( Glycine max ) yield losses around the world. Most studies have been focused on the morphological characterization and molecular identification of Diaporthe spp. present in SSC lesions. Several soybean resistance loci to Diaporthe spp. causing SSC have been identified, although the molecular identities of the resistance genes are at present unknown. In this review, we summarize the current knowledge on SSC disease, the molecular characterization of Diaporthe spp. and their evolutionary relationships. We highlight how recent genomic and transcriptomic information is allowing significant progress in our understanding of the molecular components and mechanisms underlying Diaporth e infection strategies as well as soybean disease resistance. The information generated, combined with available resources enabling functional genomics, will contribute to the development of breeding strategies for disease resistance, leading to a more sustainable agriculture.
... Moreover, plasticity of morphological characters in these genera makes identification to species difficult (43). Accordingly, Phomopsis and Diaporthe species are currently identified primarily by molecular phylogenies (12,46,47,53,61). ...
... Although Castlebury et al. (8) previously reported the ITS region not to be particularly informative in Phomopsis, most of the molecular approaches to identify Phomopsis/Diaporthe spp. over the last decade have relied only on ITS sequences, since they are the most common in databases (8,12,24,47,57,61,64). More recently, several studies have shown multi-locus phylogenetic analyses to provide better resolution for Phomopsis/Diaporthe spp. ...
... This study reported for the first time the occurrence of D. ambigua, D. eres, and D. neotheicola on grapevines in California. Previous pathogenicity studies conducted in vitro on green shoots showed D. ambigua to cause lesions similar to the nonpathogen Clonostachys rosea (Link) Schroers, Samuels, Seifert & W. Gams and the noninoculated controls (61). Although the anamorph of D. neotheicola, Phomopsis theicola Curzi, was reported from escainfected grapevines in South Africa, no pathogenicity studies were conducted (64). ...
... There are six major GTDs, each caused by different fungi, and include the Esca complex, Eutypa dieback, Botryosphaeria dieback, and Phomopsis dieback. The black-foot and Petri diseases affect primarily young grapevine (<5 years old) (Glawe and Rogers, 1982;Mostert et al., 2005;Van Niekerk et al., 2005;Bruez et al., 2013;Gramaje et al., 2018). ...
Grapevines (Vitis vinifera) are important fruit producers in Jordan, and grapevine trunk diseases (GTDs) are suspected to cause problems in many Jordanian vineyards. This study aimed to estimate GTDs incidence and severity in selected vineyards, and to isolate and identify the causal agents associated with GTDs in this country. Field surveys were carried out and representative samples of diseased vines showing GTDs symptoms were collected to isolate and identify the causal organisms. Molecular analyses of DNA sequences of the Internal Transcribed Spacer (ITS) regions of fungal ribosomal DNA (rDNA) were used to confirm the morphological identifications of the fungal isolates. GTDs were present in all the surveyed vineyards. Mean GTD incidence was 44% across all the fields evaluated, ranging from 9 to 69% in individual vineyards. Disease severity ranged from 52–74% (mean = 62%) across all vineyards and locations. A total of 325 fungal isolates were recovered from infected grapevines. The most prevalent pathogens identified were those associated with Botryosphaeria dieback, including Diplodia seriata, Lasiodiplodia theobromae and Neofusicoccum parvum, followed by the Esca disease pathogens Phaeoacremonium parasiticum, P. aleophilum, P. rubrigenum, and Fomitiporia spp. Ilyonectria liriodendri and I. spp., known to be associated with black foot of grapevines, were also isolated. Plant pathogens causing vascular wilts and root rots, including Fusarium proliferatum, F. oxysporum, Verticillium spp., and Rhizoctonia solani, were also identified from diseased plant samples, and were found in mixed infections with GTDs pathogens. Most of the identified pathogens, except those associated with vascular wilt and root rot, are reported for the first time in Jordan. Results of this study indicate that GTDs are widespread in Jordan, and that there is urgent need to adopt a “national strategy” for GTD management in this country.
... The species has semi-immersed stromata, 5-12 gregarious perithecia in a stroma, ostiolate, lanceolate to clavate, subsessile asci, 64-80 × 8-9 µm, clavate to fusoid, straight, often unequal, 1-(3)-septate, scarcely constricted in the middle, hyaline ascospores, 13-15 × 4 µm (Saccardo 1882a). There are no other important morphological characters to distinguish it from other Diaporthe species (Niessl 1876c, van Niekerk et al. 2005. Diaporthe perjuncta was considered as an important pathogen of grapevines worldwide (Moleleki et al. 2003). ...
Diaporthe is a large and taxonomically complex genus, with over a thousand epithets listed in Index Fungorum. The placement of many Diaporthe species remains confusing, and there is a lack of consensus on their taxonomy and phylogeny. In this study, we provide annotated notes on accepted or presumed species of Diaporthe up to 2023. Our notes cover 832 species and include information on their morphology, ecology, geographic distribution, molecular data, and pathogenicity, where available. Diaporthe cyatheae comb. nov., D. pseudobauhiniae nom. nov., D. xishuangbannaensis nom. nov., D. krabiensis sp. nov., and D. pseudobiguttulata nom. nov. are introduced in this paper. In addition, we list 331 species that were previously classified as Diaporthe but are no longer accepted as members of the genus. Our comprehensive review of Diaporthe species provides a resource for researchers and taxonomists, enabling accurate identification and classification, and enhancing our understanding ecological roles of these fungi.
... The different trunk diseases include Botryosphaeria dieback (caused by species of the Botryosphaeriaceae family) (Van Niekerk et al., 2004;Úrbez-Torres et al., 2006), Eutypa dieback (caused by species of the Diatrypaceae family) (Petzoldt et al., 1981;Pitt et al., 2010;Trouillas & Gubler, 2010), Petri disease (caused by P. chlamydospora (Crous & Gams, 2000) and Phaeoacremonium spp. (Gramaje et al., 2015)), esca (caused by wood-rotting species of the Hymenochaetales, together with Petri disease fungi) (Surico, 2009, White et al., 2011Cloete et al., 2015) and Phomopsis dieback (caused by various species of the genus Diaporthe) (Van Niekerk et al., 2005, Úrbez-Torres et al., 2013Lesuthu et al., 2019). ...
... It is well known that D. ampelina infects green shoots and leaves of grapevines during spring (Hewitt & Pearson, 1988). Diaporthe ampelina can also infect grapevines via active or wounded buds (Hewitt & Pearson 1988;Uddin et al., 1997) and wounded green shoots (Mostert et al., 2001;Van Niekerk et al., 2005). It has been shown that species of the Botryosphaeriaceae can also infect and cause lesions on green shoots (Van Niekerk et al., 2004;Amponsah et al., 2012). ...
Grapevine trunk disease fungi infect vines through openings, primarily pruning wounds. The main objective of this study was to understand the role of sucker wounds and wounds made by the removal of green shoots from the stems of potted grapevines as potential points of infection for grapevine trunk disease pathogens. Six wine and four table grape vineyards of different ages were sampled in different production areas in the Western Cape grape region of South Africa. Isolations were made from 161 sucker wounds, and fungal pathogens were identified using morphology and DNA sequence analysis of the internal transcribed spacers (ITS1 and ITS2) and the 5.8S ribosomal RNA gene, the translation elongation factor 1alpha or the partial β-tubulin gene. The results show that 62% of the sucker wounds were infected by trunk disease pathogens, including Diaporthe ampelina, Diplodia seriata, Phaeomoniella chlamydospora, Phaeoacremonium minimum, Eutypella microtheca, Cryptovalsa ampelina and Neofusicoccum australe. Diaporthe ampelina was the most common, followed by D. seriata and P. chlamydospora, in both the wine and table grape sucker wounds. Under glasshouse conditions, wounds made by the removal of young green shoots on one-year-old potted grapevine plants were inoculated with spore suspensions of D. ampelina, E. lata, N. parvum, P. minimum and P. chlamydospora. After four months, all the inoculated pathogens could be re-isolated. This study shows that grapevine sucker and green shoot wounds are susceptible to different grapevine trunk disease pathogens and may therefore play a role in the epidemiology of trunk diseases.
... GTDs are disease complexes caused by pathogenic wood fungi belonging to approximately 174 species and comprising 32 genera, including Phaeoacremonium, Botryosphaeria, Eutypa, Diaporthe, and Dactylonectria [1]. Important GTDs include the Esca disease complex (ESCA) [2], Botryosphaeria dieback [3], Eutypa dieback [4], Diaporthe dieback [5], and black foot disease [6]. GTD pathogens often colonize the wood tissues of perennial organs as endophytes, and then transition to pathogens that cause wood necrosis, wood discoloration, vascular infections, and white decay under appropriate conditions [7]. ...
... GTDs are disease complexes caused by pathogenic wood fungi belonging to approximately 174 species and comprising 32 genera, including Phaeoacremonium, Botryosphaeria, Eutypa, Diaporthe, and Dactylonectria [1]. Important GTDs include the Esca disease complex (ESCA) [2], Botryosphaeria dieback [3], Eutypa dieback [4], Diaporthe dieback [5], and black foot disease [6]. GTD pathogens often colonize the wood tissues of perennial organs as endophytes, and then transition to pathogens that cause wood necrosis, wood discoloration, vascular infections, and white decay under appropriate conditions [7]. ...
Abstract Background Grapevine trunk diseases (GTDs) are disease complexes that are major threats to viticulture in most grapevine growing regions. The microbiomes colonizing plant belowground components form complex associations with plants, play important roles in promoting plant productivity and health in natural environments, and may be related to GTD development. To investigate associations between belowground fungal communities and GTD symptomatic or asymptomatic grapevines, fungal communities associated with three soil–plant compartments (bulk soils, rhizospheres, and roots) were characterized by ITS high-throughput amplicon sequencing across two years. Results The fungal community diversity and composition differs according to the soil–plant compartment type (PERMANOVA, p
... Meanwhile, phylogenetic relationships among the 15 analyzed species are consistent with our data obtained at the whole-genome level, assuming that evolution of the Diaporthe genus is host-independent. In fact, as previously reported, the different Diaporthe species can occupy a single host and the same species of this genus can be found in different hosts (Rehner et al. 1994;Crous 2005;Niekerk et al. 2005;Diogo et al. 2010;Udayanga et al. 2014b;Santos et al. 2009;Gomes et al. 2013;Mostert et al. 2001). Furthermore, the Diaporthe species analyzed here share the same core protein-coding genes including more than 60% of predicted virulence factors, implying that adaptation to different hosts is likely determined by variation in the primary structure of common (core) genes rather than by differences in speciesspecific genes. ...
Diaporthe caulivora is an economically important fungal pathogen and a causal agent of soybean stem canker and seed decay. Here, the genome of a Russian Far Eastern isolate of D. caulivora was sequenced, assembled, and announced. Assembly quality was enough for advanced annotation, including prediction of potential disease-related genes encoding virulence factors and molecular determinants contributing to pathogen-host selection, interactions, and adaptation. Comparative analysis of 15 Diaporthe species was conducted regarding general genome properties, collinearity, and proteomes, and included detailed investigation of interspersed repeats. A notable feature of this analysis is a high recombinant variability of Diaporthe genomes, determined by the number and distribution of interspersed repeats, which also proved to be responsible for the diversity of GC content and genome size. This variability is assumed the main determinant of the divergence of Diaporthe genomes. A Bayesian multi-gene phylogeny was inferred for the 15 Diaporthe species on the basis of twenty thousand polymorphic sites of > 100 orthologous genes using independently adjusted evolutionary models. This allowed for the most accurate determination of evolutionary relationships and species boundaries for effective reporting about these plant pathogens. The evidence, obtained by different genome analysis techniques, implies the host-independent evolution of Diaporthe species.
Key points
• The genome of a Far Eastern isolate of D. caulivora was announced.
• A high degree of recombinant variability determines genomic divergence in Diaporthe genus.
• The multi-gene phylogeny implies host-independent evolution of Diaporthe species.
