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The phylogeny of Phoma lingam and Phoma betae, the type species of Phoma sections Plenodomus and Pilosa, based on the strict consensus tree from a Bayesian analysis of 48 LSU/SSU sequences. The Bayesian posterior probabilities are given at the nodes. The tree was rooted to Sporormiella minima (CBS 524.50).
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The anamorphic genus Phoma was subdivided into nine sections based on morphological characters, and included teleomorphs in Didymella, Leptosphaeria, Pleospora and Mycosphaerella, suggesting the polyphyly of the genus. Recent molecular, phylogenetic studies led to the conclusion that Phoma should be restricted to Didymellaceae. The pre...
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... mud Mozambique respectively. The tree ( Fig. 1) was rooted to Sporormiella minima (CBS 524.50). The Bayesian analysis resulted in 6 5442 trees after 3 272 000 generations, from which the burn-in was discarded and the consensus tree and posterior probabilities were calculated based on 56 028 trees (Fig. 1). The families that belong to Pleosporineae, represented by the species ...Context 2
... mud Mozambique respectively. The tree ( Fig. 1) was rooted to Sporormiella minima (CBS 524.50). The Bayesian analysis resulted in 6 5442 trees after 3 272 000 generations, from which the burn-in was discarded and the consensus tree and posterior probabilities were calculated based on 56 028 trees (Fig. 1). The families that belong to Pleosporineae, represented by the species grouping in clades A-G, clustered in a strongly supported clade (99 % posterior probability). Clade A, representing those species classified in Pleosporaceae, was strongly supported (100 %) and included two subclades. www.studiesinmycology.org Phoma sections ...Citations
... In a previous study on P. tracheiphilus, similar results were obtained despite using a different database, necessitating analysis of sequences alongside taxonomically related taxa [40]. These species could not be differentiated based on the ITS sequence, but are pathogenic to different hosts [82,83]. In addition, P. tracheiphilus was detected in our soil samples using species-specific qPCR, suggesting that this ASV actually belongs to the species P. tracheiphilus. ...
Mal secco is a vascular disease of citrus caused by the mitosporic fungus Plenodomus tracheiphilus. Soil containing infected plant material constitutes an inoculum source for root infections. In this study, the soil bacterial and fungal communities of five lemon orchards located in Syracuse Province (Sicily, Italy) affected by mal secco were analyzed. Soil samples were collected under lemon tree canopies and subjected to total genomic DNA extraction. The fungal DNA was detected through qPCR in all orchards, with variable concentrations. Bacterial and fungal communities were profiled using 16S and ITS amplicon-based high-throughput sequencing, respectively. According to our results, the relative abundances of the most represented bacterial phyla (e.g., Proteobacteria, Actinobacteriota, Acidobacteriota) changed across the orchards, while in the fungal community, the phylum Ascomycota was dominant, with Basidiomycota and Mortierellomycota abundances fluctuating. On the whole, β diversity analysis showed significant variation in the composition of the soil microbial communities across the orchards. This result was confirmed by the analysis of the core community (taxa present at ≥ 75% of total samples), where putative beneficial bacteria resulted in significantly enriched fungus-infected soil samples, suggesting complex microbial interactions. Our findings shed light on the composition and diversity of the soil microbiome in lemon orchards with the occurrence of mal secco infections.
... Undoubtedly, more will be discovered with time. A particular problem among Fungi was the previous individual naming of sexual and asexual forms, but it's believed that most of the anamorph (asexual) -teleomorph (sexual) anomalies have been recognised (de Gruyter et al. 2013, Ertz et al. 2015, Jayasiri et al. 2015. ...
... Mal secco disease is caused by the fungus Plenodomus tracheiphilus Petri Gruyter, Aveskamp, and Verkley (De Gruyter et al. 2013). It is a xylem disease that affects different citrus species, mainly lemon (Citrus limon). ...
Mal secco, caused by the fungus Plenodomus tracheiphilus , is a xylem disease that is a limiting factor for lemon production in the Mediterranean. Resistance or field tolerance are major goals for lemon breeders; however, there is scant information regarding the heritability of mal secco resistance in breeding populations. As with other vascular diseases, phenotyping is the bottleneck for ascertaining resistance and susceptibility, and a validated protocol for greenhouse phenotyping would be valuable to accelerate the selection of tolerant trees before field evaluation. We report phenotyping of 148 hybrids of Khasi papeda ( Citrus latipes ; tolerant to mal secco) × lemon (susceptible to the disease) in field and greenhouse conditions. Field evaluation was performed on all hybrids for 2 to 3 consecutive years on trees subjected to high natural-pathogen pressure. Detection of the fungal infection was performed by visual observation and real-time polymerase chain reaction (PCR). The first infections occurred ≈6 months after planting, but 2 years of observations were needed for a reliable estimation of susceptibility. The spread of the disease did not occur uniformly throughout the plot, with patterns of spread within rows, probably resulting from infections from plant to plant. The possible errors in the estimation of susceptibility as a result of the uneven distribution of infections in the plot were reduced by using more than one replicate tree per hybrid. The correlation between phenotyping scores and cycle threshold values was weak ( r = –0.48, P < 0.001). Three years after planting, hybrids clustered into three groups—susceptible, tolerant, and intermediate—based on symptom progression. A subset of 65 self-rooted hybrids was also subjected to stem inoculation in an unheated greenhouse, with two to seven biological replicates per hybrid. Three months after inoculation, the samples were monitored for symptoms appearance and subjected to real-time PCR pathogen quantification. We observed a weak ( r = 0.41) but significant ( P < 0.001) correlation between phenotypes in the field and the greenhouse, indicating that, in our conditions, field evaluation remains the best method for phenotyping. However, artificial inoculations might help to discard the highly susceptible hybrids before field evaluation.
... The members of Neohendersoniaceae are endophytic or saprobic fungi on plants, and human pathogens (Tanaka et al. 2017, Hongsanan et al. 2020. For example, Neohendersonia kickxii has been reported as a specific endophyte from beech twigs in Europe (Danti et al. 2002, Sieber 2007, Medicopsis romeroi was found to be a human pathogen (de Gruyter et al. 2013), and Brevicollum hyalosporum was known as saprobic on dead twigs of Syzygium samarangense (Myrtaceae) in Japan (Tanaka et al. 2017). Most genera of the family have sexual morphs except for Neohendersonia and Neomedicopsis (Crous et al. 2019). ...
During an investigation of ascomycetous fungi from decaying wood in southwest China, seven taxa with sexual morphs were found to be saprobic from terrestrial habitats. These taxa were identified based on morphology, phylogeny, and cultural characteristics. The morphology and phylogenetic evidence placed these new fungal collections in Neohendersoniaceae, distributing in the genera Crassiparies and Neobrevicollum. The phylogenetic analyses of a combined ITS, LSU, SSU, RPB2, and TEF1-α sequence dataset also confirmed their taxonomic placement. A new species, Neobrevicollum biancaeae is introduced to accommodate the two taxa, which have thin-walled ascomata without ostiole, and smaller asci and ascospores compared to the type species, N. oleae. The other five samples were identified as Crassiparies quadrisporus and N. oleae representing three and two taxa, respectively. The identification and establishment of these species are justified based on morpho-molecular analyses. In addition, the new host records of C. quadrisporus and N. oleae were reported. Detailed descriptions and illustrations are provided for collected taxa. This study contributed to the microfungal diversity in Southwest China.
... Meanwhile, the taxonomic position of 15 strains of L. biglobosa was also clarified based on molecular phylogenies with the DNA sequences of ITS, LSU, tub2, and rpb2, and they all belong to L. biglobosa (anamorph: Plenodomus) [49]. Phylogenetic analysis with the DNA sequences of ITS and LSU also showed that the 15 strains of L. biglobosa are more closely related to L. biglobosa 'brassicae'. ...
Eight fungal strains (P1 to P8) were isolated from rapeseed stems (Brassica napus) infected with the blackleg pathogen Leptosphaeria biglobosa (Lb). They formed pycnidia with similar morphology to those of Lb, and thus were considered as Lb relatives (LbRs). The species-level identification of these strains was performed. Their virulence on rapeseed and efficacy in the suppression of Lb infection were determined, and the biocontrol potential and biocontrol mechanisms of strain P2 were investigated. The results showed that the LbRs belong to two teleomorphic genera in the family Didymellaceae, Didymella for P1 to P7 and Boeremia for P8. Pathogenicity tests on rapeseed cotyledons and stems indicated the LbRs were weakly virulent compared to L. biglobosa. Co-inoculation assays on rapeseed cotyledons demonstrated that P1 to P7 (especially P1 to P4) had a suppressive effect on Lb infection, whereas P8 had a marginal effect on infection by L. biglobosa. Moreover, D. macrostoma P2 displayed a more aggressive behavior than L. biglobosa in the endophytic colonization of healthy rapeseed cotyledons. Cultures of P2 in potato dextrose broth (PDB) and pycnidiospore mucilages exuded from P2 pycnidia showed antifungal activity to L. biglobosa. Further leaf assays revealed that antifungal metabolites (AM) of strain P2 from PDB cultures effectively suppressed infection by L. biglobosa, Botrytis cinerea (gray mold), and Sclerotinia sclerotiorum (white mold). An antifungal metabolite, namely penicillither, was purified and identified from PDB cultures and detected in pycnidiospore mucilages of strain P2. This study suggests that the LbRs are a repertoire for screening biocontrol agents (BCAs) against rapeseed diseases, and D. macrostoma P2 is a multi-functional BCA, a penicillither producer, and an endophyte.
... Aveskamp et al. (2010) revised the monophyletic clades within the family based on molecular phylogenetic analyses utilising the ITS, LSU, SSU, and tub2 loci. Its generic boundaries were clarified through subsequent studies conducted by Aveskamp et al. (2010) and De Gruyter et al. (2009, 2013. Chen et al. (2015) applied RNA polymerase II (rpb2) gene, ITS, LSU and tub2 towards a robust backbone support for taxon differentiation in Didymellaceae. ...
... Morphological characters coupled with multi-gene phylogeny presented in this study introduce new host records of Didymellaceae isolated from leaf litter of N. zizyphifolium (Malvaceae), D. cultrata and A. xylocarpa (Fabaceae) from Doi Tung, Chiang Rai. Previous studies reported several ambiguities in phoma-like fungi due to identifications based only on morphology (Aveskamp et al. , 2010De Gruyter et al. 2009, 2013Chen et al. 2015). Therefore, occupying multi-locus (LSU, ITS, rpb2, and tub2) sequence phylogeny aided in verifying the placement and identification of the species. ...
... Didymella coffeae-arabicae (MFLUCC 23-0080, MFLUCC 23-0081) was described as the first reported sexual morph for the species for the first time ( Figures 2 and 3, Figures 5 and 6). The present results further validated the attempts of Aveskamp and De Gruyter (2008), Aveskamp et al. (2010), De Gruyter et al. (2009, 2013 and Chen et al. (2015) by robust and reliable species delimitation within phoma and allied genera using multi-gene phylogeny. ...
Studying the taxonomy, diversity and host preference of leaf litter inhabiting microfungi contributes towards elucidating hidden taxa, their host affinities and recovering novel life modes dwelling inside forest ecosystems. Leaf litter-inhabiting microfungi also play a crucial role in forest ecosystems through decomposition and nutrient recycling. This study resulted in the introduction of saprobic Didymellaceae microfungi from Doi Tung Forest Reserve, Chiang Rai, northern Thailand. Fungal isolates were characterised based on morphology and molecular phylogeny of the nuclear ribosomal DNA (ITS, LSU) and protein-coding genes (tub2, rpb2). Allophoma tropica and Remotididymella ageratinae are recorded from dead leaves of Nayariophyton zizyphifolium (Malvaceae), and Didymella coffeae-arabicae from Dalbergia cultrata and Afzelia xylocarpa (Fabaceae). This study also reports the sexual morph of Allophoma tropica and Didymella coffeae-arabicae and provides molecular evidence for the first reports of sexual morphs from Thailand.
... P. chrysanthemicola can cause leaf spot disease and root rot, as well as promote plant chlorophyll synthesis and increase plant resistance to salt and heavy metal stresses [14,17,19,21]. P chrysanthemicola was originally classified in the genus Phoma, but reassigned based on morphological and molecular characteristics [50,51]. Members of ...
... P. chrysanthemicola can cause leaf spot disease and root rot, as well as promote plant chlorophyll synthesis and increase plant resistance to salt and heavy metal stresses [14,17,19,21]. P chrysanthemicola was originally classified in the genus Phoma, but reassigned based on morphological and molecular characteristics [50,51]. Members of Phoma sect. ...
... Members of Phoma sect. Paraphoma were transferred to a range of genera, including Paraphoma [51]. Ph. chrysanthemicola was also renamed to P. chrysanthemicola [23]. ...
Paraphoma chrysanthemicola is a newly identified endophytic fungus. The focus of most studies on P. chrysanthemicola has been on its isolation, identification and effects on plants. However, the limited genomic information is a barrier to further research. Therefore, in addition to studying the morphological and physiological characteristics of P. chrysanthemicola, we sequenced its genome and compared it with that of Paraphoma sp. The results showed that sucrose, peptone and calcium phosphate were suitable sources of carbon, nitrogen and phosphorus for this strain. The activities of amylase, cellulase, chitosanase, lipase and alkaline protease were also detected. Sequencing analysis revealed that the genome of P. chrysanthemicola was 44.1 Mb, with a scaffold N50 of 36.1 Mb and 37,077 protein-coding genes. Gene Ontology (GO) annotation showed that mannose-modified glycosylation was predominant in monosaccharide utilisation. The percentage of glycoside hydrolase (GH) modules was the highest in the carbohydrate-active enzymes database (CAZy) analysis. Secondary metabolite-associated gene cluster analysis identified melanin, dimethylcoprogen and phyllostictine A biosynthetic gene clusters (>60% similarity). The results indicated that P. chrysanthemicola had a mannose preference in monosaccharide utilisation and that melanin, dimethylcoprogen and phyllostictine A were important secondary metabolites for P. chrysanthemicola as an endophytic fungus.
... 4 Phoma stem canker is caused by two closely related fungal pathogen species, Leptosphaeria maculans (Plenodomus lingam) and Leptosphaeria biglobosa (Plenodomus biglobosus). [5][6][7] In Europe, phoma stem canker epidemics are initiated by ascospores released from mature pseudothecia developed on previous crop debris in autumn. 8,9 These ascospores get dispersed by wind, land on leaf surfaces and upon successful infection, cause phoma leaf spots. ...
BACKGROUND
Phoma stem canker is an economically important disease of oilseed rape, caused by two co‐existing fungal pathogen species, Leptosphaeria maculans (Plenodomus lingam) and Leptosphaeria biglobosa (Plenodomus biglobosus). Leptosphaeria maculans produces a phytotoxin called sirodesmin PL. Our previous work showed that L. biglobosa has an antagonistic effect on the production of sirodesmin PL if it is simultaneously co‐inoculated with L. maculans. However, the effects of sequential co‐inoculation on interspecific interactions between the two pathogens are not understood.
RESULTS
The interactions between L. maculans and L. biglobosa were investigated in liquid culture by inoculation with L. maculans first, followed by L. biglobosa sequentially at 1, 3, 5 or 7 days later and vice versa; the controls were inoculated with L. maculans only, L. biglobosa only, or L. maculans and L. biglobosa simultaneously. The results showed that L. biglobosa inhibited the growth of L. maculans, the production of both sirodesmin PL and its precursors if L. biglobosa was inoculated before, or simultaneously with, L. maculans. However, the antagonistic effects of L. biglobosa were lost if it was co‐inoculated 5 or 7 days after L. maculans.
CONCLUSION
For the first time, the results of this study provided evidence that the timing when L. maculans and L. biglobosa meet significantly influences the outcome of the interspecific competition between them. Leptosphaeria biglobosa can inhibit the production of sirodesmin PL and the growth of L. maculans if it is inoculated before L. maculans or less than 3 days after L. maculans in liquid culture. There is a need to further investigate the timing of co‐inoculation on interactions between L. maculans and L. biglobosa in their host plants for improving the control of phoma stem canker. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
... Paraconiothyrium species have various morphologies including conidiomata which are eustromatic to pycnidial, conidiogenous cells that are phialidic or annelidic, and the conidia smooth-walled or minutely warted and hyaline to brown at later stages of development (Verkley et al. 2004;Gruyter et al. 2013;Liu et al. 2015). Therefore, species delineation of this genus should be incorporated with morphology and molecular phylogeny. ...
... Previous research also investigated Didymellaceae based on their morphology and phylogenetic analyses, but it did not distinguish any closely related taxa within several species complexes [33]. Therefore, the phylogenetic positions of Didymellaceae were subsequently revised based on morphological studies and multiple gene sequences obtained from four loci, including the internal transcribed spacer region (ITS) sequences, partial large subunit nrRNA gene (28S nrDNA; LSU), RNA polymerase II second largest subunit (rpb2) and partial beta-tubulin gene (tub2) [24,34]. The approach combining molecular phylogenetic analysis with morphological characters can effectively improve the scientific classification of species. ...
Members of Didymellaceae have a wide geographical distribution throughout different ecosystems, and most species are associated with fruit, leaf, stem and root diseases of land plants. However, species that occur in aquatic plants are not clearly known. During a survey of the diversity of endophytes in aquatic plants in Yunnan, Sichuan, and Guizhou provinces, we obtained 51 isolates belonging to Didymellaceae based on internal transcribed spacer region (ITS) sequences. Further, the phylogenetic positions of these isolates were determined by combined sequences composed of ITS, partial large subunit nrRNA gene (28S nrDNA; LSU), RNA polymerase II second largest subunit (rpb2) and partial beta-tubulin gene (tub2). Combining morphological characteristics and multi-locus phylogenetic analyses, two new varieties belong to Boeremia and 12 new species distributed into seven genera were recognized from 51 isolates, i.e., Cumuliphoma, Didymella, Dimorphoma, Ectophoma, Leptosphaerulina, Remotididymella, and Stagonosporopsis. Among these species, only one species of Stagonosporopsis and two species of Leptosphaerulina show teleomorphic stages on OA, but have no anamorphic state. Each new species is described in detail, and the differences between new species and their phylogenetically related species are discussed here. The high frequency of new species indicates that aquatic plants may be a special ecological niche which highly promotes species differentiation. At the same time, the frequent occurrence of new species may indicate the need for extensive investigation of fungal resources in those aquatic environments where fungal diversity may be underestimated.
