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Bruce D L Fitt - One of the best experts on this subject based on the ideXlab platform.
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Effects of a penthiopyrad and picoxystrobin fungicide mixture on Phoma stem canker (Leptosphaeria spp.) on UK winter oilseed rape
European Journal of Plant Pathology, 2016Co-Authors: Thomas R Sewell, Steven Moloney, Mike Ashworth, Faye Ritchie, Alla Mashanova, Henrik U. Stotz, Yongju Huang, Bruce D L FittAbstract:In the UK, fungicides are often used to control Phoma stem canker on winter oilseed rape. Field trials were established near Boxworth, Cambridgeshire for four cropping seasons (2011/2012, 2012/2013, 2013/2014 and 2014/15) to test the efficacy of a new fungicide mixture Refinzar® (penthiopyrad + picoxystrobin) by comparison to an existing fungicide Proline 275® (prothioconazole) against Phoma stem canker (Leptosphaeria spp.) and the effect on winter oilseed rape (cv. Catana) yield. In each season, weather data were collected from a weather station at Boxworth and the release of ascospores was monitored using a nearby Burkard spore sampler. The patterns of ascospore release differed between seasons and related to weather conditions. Fungicides penthiopyrad + picoxystrobin and prothioconazole were applied in October/November when 10 % of plants had Phoma leaf spotting (T1, early), 4/8 weeks after T1 (T2, late) or at both T1 and T2 (combined). When Phoma leaf spot symptoms were assessed in autumn/winter, penthiopyrad + picoxystrobin and prothioconazole both decreased numbers of Phoma leaf spots caused by L. maculans; there were few leaf spots caused by L. biglobosa. Penthiopyrad + picoxystrobin and prothioconazole both reduced Phoma stem canker severity before harvest compared to the untreated control but did not increase yield in these seasons when epidemics were not severe. In 2013/2014, the presence of L. maculans and L. biglobosa in upper stem lesions or stem base cankers was determined by species-specific PCR. The proportions of stems with L. maculans DNA were much greater than those with L. biglobosa DNA for both upper stem lesions and basal stem cankers. These results suggest that both penthiopyrad + picoxystrobin and prothioconazole can decrease Phoma stem canker severity on winter oilseed rape in severe disease seasons.
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Relating plant and pathogen development to optimise fungicide control of Phoma stem canker (Leptosphaeria maculans) on winter oilseed rape (Brassica napus)
European Journal of Plant Pathology, 2007Co-Authors: J. M. Steed, Andreas Baierl, Bruce D L FittAbstract:In winter oilseed rape experiments at Rothamsted in 2000/01 to 2002/03 growing seasons, the severity of Phoma stem canker epidemics in summer depended on the timing of Phoma leaf spot epidemics in the previous autumn, and hence on the timing of Leptosphaeria maculans ascospore release. The first major release of L. maculans ascospores was earlier in 2000 (26 September) and 2001 (18 September) than in 2002 (21 October). Consequently, the autumn Phoma leaf spot epidemic was also earlier in 2000 and 2001 than in 2002. The resulting stem canker epidemics were severe by harvest (July) in 2001 and 2002 but not in 2003. No correlation was found between the severity or duration of Phoma leaf spotting (lesion days or lesion °C-days) and the subsequent severity of Phoma stem canker epidemics. Rates of leaf production and loss were similar in the three growing seasons. Out of ca. 25 leaves produced on plants during each season, leaf numbers 10–14 generally remained on plants for the longest. Treatment with flusilazole + carbendazim in autumn decreased the severity of Phoma leaf spotting for several weeks after treatment, decreased the severity of stem canker the following summer and increased yield significantly in 2001 and 2002 but not in 2003. The most effective timings for flusilazole + carbendazim application were when leaves 7–11 were present on most plants and at least 10% of plants were affected by Phoma leaf spot. Two half-dose applications of fungicide reduced Phoma stem canker and increased yield more than a single full dose application when Phoma leaf spot epidemics were early (
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resistance to leptosphaeria maculans Phoma stem canker in brassica napus oilseed rape induced by l biglobosa and chemical defence activators in field and controlled environments
Plant Pathology, 2006Co-Authors: Bruce D L Fitt, N Evans, S J Foster, Yj Huang, A O Latundedada, J A LucasAbstract:Effects of pretreatment of Brassica napus leaves with ascospores of Leptosphaeria biglobosa or chemical defence activators [acibenzolar-S-methyl (ASM) or menadione sodium bisulphite (MSB)] on infection by ascospores of Leptosphaeria maculans (Phoma stem canker) and development of disease were studied in controlled-environment (Phoma leaf spot) and field (Phoma leaf spot and stem canker) experiments. In controlled-environment experiments, pretreatment of oilseed rape leaves (cv. Madrigal) with L. biglobosa, ASM or MSB delayed the appearance of L. maculans Phoma leaf spot lesions. These pretreatments also decreased the Phoma leaf spot lesion area in both pretreated leaves (local effect) and untreated leaves (systemic effect). In winter oilseed rape field experiments in the 2002/03 and 2003/04 growing seasons, pretreatment with L. biglobosa or ASM in October/November decreased not only the number of Phoma leaf spot lesions per leaf caused by L. maculans in autumn/winter, but also the severity of Phoma stem canker in the subsequent spring/summer. Effects were greater in 2002/03 (when natural L. maculans ascospore release began in September 2002) than in 2003/04 (when ascospore release began in December following a period of dry weather in August/September 2003). These results suggest that pretreatment with biological or chemical defence activators can induce local and systemic resistance to L. maculans, with both short-term effects on the development of Phoma leaf spotting and long-term effects on the development of stem canker 8 months later.
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relationships between Phoma leaf spot and development of stem canker leptosphaeria maculans on winter oilseed rape brassica napus in southern england
Annals of Applied Biology, 2000Co-Authors: Bruce D L Fitt, P Gladders, S J WelhamAbstract:Models were constructed to describe the relationships between incidence of Phoma leaf spot at different growth stages in autumn/winter or early spring and incidence of stem canker (basal canker or stem lesions) in summer on winter oilseed rape in southern England. Model 1, describing the Phoma leaf spot/basal canker relationship, was y(1) = beta (0) + beta (1)x(1) + beta (2)(x(2) - x(1)) if x(2) > x(1), and y(1) = beta (0) + beta (0) + beta (1)x(1) if x(2) less than or equal to x(1), in which y(1) was the incidence (Ic plants affected) of basal canker at harvest,x(1) was the maximum incidence of Phoma leaf spot during the period from sowing to growth stage (G.S.) 1,6-1,7 (about 100 days after sowing) and x(2) was the maximum incidence of Phoma leaf spot between G.S. 1,7 and G.S. 2,0 (start of stem extension). Model 2, describing the Phoma leaf spot/stem lesion relationship, was y(2) = alpha (0) + alpha (1)x(3) + alpha (2)x(4), in which y(2) was the incidence of stem lesions at harvest, x(3) was the incidence of Phoma leaf spot at G.S. 3,3-3,5 (flower buds visible) and x(4) was the incidence of Phoma leaf spot at G.S. 4,5-5,5 (flower buds opening). Data from field experiments with four winter oilseed rape cultivars at Boxworth or Rothamsted in the 1992/93, 1993/94, 1996/97, 1997/98 or 1998/99 seasons were used to test the models. The values of R-2 for the regression equations testing model 1 for the Phoma leaf spot/basal canker relationship were 0.75, 0.93, 0.91 and 0.89 for cvs Apex, Bristol, Capitol and Envol, respectively. The values of R-2 for the regression equations testing model 2 for the Phoma leaf spot/stem lesion relationship were 0.58, 0.57, 0.54 and 0.71 for cvs Apex, Bristol, Capitol and Envol, respectively. The Phoma leaf spot/basal canker relationship (model 1) could also be fitted to the combined data set for all four cultivars (R-2 = 0.65), whereas the Phoma leaf spot/stem lesion relationship (model 2) could not to be fitted to the combined data set for the four cultivars. The relationships between incidence and severity of stem canker were examined and the values of R-2 for the regressions of severity on incidence were 0.91 for basal canker and 0.89 for stern lesions.
S J Welham - One of the best experts on this subject based on the ideXlab platform.
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relationships between Phoma leaf spot and development of stem canker leptosphaeria maculans on winter oilseed rape brassica napus in southern england
Annals of Applied Biology, 2000Co-Authors: Bruce D L Fitt, P Gladders, S J WelhamAbstract:Models were constructed to describe the relationships between incidence of Phoma leaf spot at different growth stages in autumn/winter or early spring and incidence of stem canker (basal canker or stem lesions) in summer on winter oilseed rape in southern England. Model 1, describing the Phoma leaf spot/basal canker relationship, was y(1) = beta (0) + beta (1)x(1) + beta (2)(x(2) - x(1)) if x(2) > x(1), and y(1) = beta (0) + beta (0) + beta (1)x(1) if x(2) less than or equal to x(1), in which y(1) was the incidence (Ic plants affected) of basal canker at harvest,x(1) was the maximum incidence of Phoma leaf spot during the period from sowing to growth stage (G.S.) 1,6-1,7 (about 100 days after sowing) and x(2) was the maximum incidence of Phoma leaf spot between G.S. 1,7 and G.S. 2,0 (start of stem extension). Model 2, describing the Phoma leaf spot/stem lesion relationship, was y(2) = alpha (0) + alpha (1)x(3) + alpha (2)x(4), in which y(2) was the incidence of stem lesions at harvest, x(3) was the incidence of Phoma leaf spot at G.S. 3,3-3,5 (flower buds visible) and x(4) was the incidence of Phoma leaf spot at G.S. 4,5-5,5 (flower buds opening). Data from field experiments with four winter oilseed rape cultivars at Boxworth or Rothamsted in the 1992/93, 1993/94, 1996/97, 1997/98 or 1998/99 seasons were used to test the models. The values of R-2 for the regression equations testing model 1 for the Phoma leaf spot/basal canker relationship were 0.75, 0.93, 0.91 and 0.89 for cvs Apex, Bristol, Capitol and Envol, respectively. The values of R-2 for the regression equations testing model 2 for the Phoma leaf spot/stem lesion relationship were 0.58, 0.57, 0.54 and 0.71 for cvs Apex, Bristol, Capitol and Envol, respectively. The Phoma leaf spot/basal canker relationship (model 1) could also be fitted to the combined data set for all four cultivars (R-2 = 0.65), whereas the Phoma leaf spot/stem lesion relationship (model 2) could not to be fitted to the combined data set for the four cultivars. The relationships between incidence and severity of stem canker were examined and the values of R-2 for the regressions of severity on incidence were 0.91 for basal canker and 0.89 for stern lesions.
László Irinyi - One of the best experts on this subject based on the ideXlab platform.
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Advances in Taxonomy of Genus Phoma: Polyphyletic Nature and Role of Phenotypic Traits and Molecular Systematics
Indian Journal of Microbiology, 2014Co-Authors: Vaibhav V. Tiwari, László Irinyi, György János KövicsAbstract:Phoma is a highly polyphyletic genus with its unclear species boundaries. The conventional system of identification is functional but it has its limitations. Besides morphological studies, chemotaxonomy, secondary metabolite and protein profiling have been assessed for the classification and identification of these fungi. Molecular datasets have provided a better outlook towards the phylogenetic and evolutionary trends of Phoma . Molecular markers such as ITS-rDNA, tubulin, actin, translation elongation factor have been widely used by the taxonomists to demarcate species. However, outcomes gained up till now represent preliminary step towards the study of Phoma systematics and a combined approach would be beneficial in the understanding of this polyphyletic group members. Lately, on the base of molecular phylogeny of the type species of the seven Phoma sections a new teleomorph family, Didymellaceae has been established, besides the Phaeosphaeriaceae related to sect. ParaPhoma anamorphs, and the Leptosphaeriaceae to sect. Heterospora anamorphs. The estimated ratio is about 70 % of the recognized Phoma -like species can be associated with the Didymellaceae ascomycetous family.
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Phoma-like fungi on soybeans
Critical Reviews in Microbiology, 2013Co-Authors: György János Kövics, Mahendra Rai, Erzsébet Sándor, László IrinyiAbstract:Numerous coelomycetous fungi classified in Ascochyta, Phoma and Phyllosticta, and lately established and/or re-classified genera and species, namely Boeremia and Peyronellaea have been recorded from spots on leaves and pods of soybeans. These rarely observed pathogens are cosmopolitan, ubiquitous species on diseased and dead plant materials, and define frequently as weak or opportunistic parasites. Based on the Genealogical Concordance Phylogenetic Species Recognition, the authors summarize the re-evaluation of the taxonomic status of Phoma sojicola (syn. Ascochyta sojicola) and Phyllosticta sojicola. Inspite of the former delimitation of Ph. sojicola based on small differences in morphological features, it has proved to be identical to Peyronellaea pinodella (syn. Phoma pinodella). Similarly, it was also confirmed that Ph. sojicola was identical to Boeremia exigua var. exigua (syn. Phoma exigua var. exigua). The authors and co-workers contributed to the identification of Phoma-like fungi by combined conventional and molecular methods. Protein-encoding genes (TEF1 and β-tubulin) were successfully applied within the Phoma genus to infer phylogenetic relationships.
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Phylogenetic studies of soybean pathogen Phoma species by Bayesian analysis
Acta Agraria Debreceniensis, 2009Co-Authors: László Irinyi, György János Kövics, Erzsébet SándorAbstract:We carried out phylogenetic study analyzing sequences of genetic markers in the taxonomy of Phoma and Phoma-like fungi. Different species of Phoma and Phoma-like fungi occurring on soybean (Phoma pinodella, Phoma sojicola, Phyllosticta sojicola, Phoma exigua var. exigua) are difficult to identy because of their high morphological and symptomatic similarities.Twenty-two isolates of nine different Phoma species were obtained from reference culture collections. Seven of them were isolated from soybean, the others were collected from different hosts.The Phoma isolates were firstly characterised by morphologically, and then we employed a part of the gene responsible for the synthesis of translation elongation factor 1 subunit alpha protein (tef1), ITS region, as well as β-tubulin partial sequences as potential genetic markers to inferphylogenetic relationships among different Phoma species..Finally, their ITS and tef1 sequences were sequenced and analysed by Bayesian approaches.According to phylogenetic trees inferred by Bayesian analysis of tef1, ITS and β-tubulin sequences, different Phoma species can be separated proving that these phylogenetic markers are well suited for phylogenetic studies of Phoma species. However, the phylogenetic tree does not support the traditional Phoma sections based on morphological characterization.Bayesian analyses of the three sequences confirmed that the Phyllosticta sojicola species is clustered with the Phoma exigua var. exigua group and the Phoma sojicola is grouped with Phoma pinodella group. The molecular data provide evidence for reclassification of formerly mentioned soybean pathogens.
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Phoma Saccardo: distribution, secondary metabolite production and biotechnological applications.
Critical Reviews in Microbiology, 2009Co-Authors: Mahendra Rai, György János Kövics, Prajakta Deshmukh, Aniket Gade, Avinash P. Ingle, László IrinyiAbstract:Phoma Sacc. is an ubiquitous fungus, which has been reported from plants, soil, human beings, animals, and air. Some species of Phoma like P. sorghina, P. herbarum, P. exigua var. exigua, P. macrostoma, P. glomerata, Phoma macdonaldii, Phoma tracheiphila, Phoma proboscis, P. multirostrata, and Phoma foveata secrete phytotoxin and anthraquinone pigments as secondary metabolites, which have great potential for the biological control of weeds, and can be exploited for the production of mycopesticides, agrophytochemicals, and dyes. Some other species produce pharmaceutically active metabolites, viz., Sirodesmins, Phomenoic acid, Phomenolactone, Phomadecalins, Phomactin A, Phomasetin, Squalestatin-1 (S1), and Squalestatin-2 (S2). The secondary metabolites secreted by some species of Phoma are antitumor, antimicrobial, and anti-HIV. Equisetin and Phomasetin obtained from species of Phoma are useful against AIDS. The main goal of the present review is to discuss secondary metabolite production by species of Phoma and their utilization as antibiotics and as biocontrol agents.
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Taxonomical re-evaluation of Phoma-like soybean pathogenic fungi.
Mycological Research, 2009Co-Authors: László Irinyi, György János Kövics, Erzsébet SándorAbstract:Coelomycetous fungi classified in Ascochyta, Phoma, and Phyllosticta have been recorded from spots on leaves and pods of soybeans. Based on the Genealogical Concordance Phylogenetic Species Concept, the authors suggest the re-evaluation of the taxonomic status of Phoma sojicola (syn. = Ascochyta sojicola) and Phyllosticta sojicola. In spite of the former delimitation of Phoma sojicola based on small differences in morphological features, it has proved to be identical to Phoma pinodella. Similarly, it was also confirmed that Phyllosticta sojicola was identical to Phoma exigua var. exigua. The authors supply tools for identification of Phoma-like fungi by combined conventional and molecular methods. Protein-encoding genes (tef1 and β-tubulin) were successfully applied within the Phoma genus to infer phylogenetic relationships.
J. De Gruyter - One of the best experts on this subject based on the ideXlab platform.
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Redisposition of Phoma-like anamorphs in Pleosporales
Studies in Mycology, 2013Co-Authors: J. De Gruyter, Gerard J M Verkley, Johannes Z Groenewald, M.m. Aveskamp, J.h.c. Woudenberg, Pedro W CrousAbstract:UNLABELLED: 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 present study focuses on the taxonomy of excluded Phoma species, currently classified in Phoma sections Plenodomus, Heterospora and Pilosa. Species of Leptosphaeria and Phoma section Plenodomus are reclassified in Plenodomus, Subplenodomus gen. nov., Leptosphaeria and Paraleptosphaeria gen. nov., based on the phylogeny determined by analysis of sequence data of the large subunit 28S nrDNA (LSU) and Internal Transcribed Spacer regions 1 & 2 and 5.8S nrDNA (ITS). Phoma heteromorphospora, type species of Phoma section Heterospora, and its allied species Phoma dimorphospora, are transferred to the genus Heterospora stat. nov. The Phoma acuta complex (teleomorph Leptosphaeria doliolum), is revised based on a multilocus sequence analysis of the LSU, ITS, small subunit 18S nrDNA (SSU), β-tubulin (TUB), and chitin synthase 1 (CHS-1) regions. Species of Phoma section Pilosa and allied Ascochyta species were determined to belong to Pleosporaceae based on analysis of actin (ACT) sequence data. Anamorphs that are similar morphologically to Phoma and described in Ascochyta, Asteromella, Coniothyrium, Plectophomella, PleuroPhoma and Pyrenochaeta are included in this study. Phoma-like species, which grouped outside the Pleosporineae based on a LSU sequence analysis, are transferred to the genera Aposphaeria, Paraconiothyrium and Westerdykella. The genera Medicopsis gen. nov. and Nigrograna gen. nov. are introduced to accommodate the medically important species formerly known as Pyrenochaeta romeroi and Pyrenochaeta mackinnonii, respectively. TAXONOMIC NOVELTIES: New genera: Medicopsis Gruyter, Verkley & Crous, Nigrograna Gruyter, Verkley & Crous, Paraleptosphaeria Gruyter, Verkley & Crous, Subplenodomus Gruyter, Verkley & Crous. New species: Aposphaeria corallinolutea Gruyter, Aveskamp & Verkley, Paraconiothyrium maculicutis Verkley & Gruyter. New combinations: Coniothyrium carteri (Gruyter & Boerema) Verkley & Gruyter, C. dolichi (Mohanty) Verkley & Gruyter, C. glycines (R.B. Stewart) Verkley & Gruyter, C. multiporum (V.H. Pawar, P.N. Mathur & Thirum.) Verkley & Gruyter, C. telephii (Allesch.) Verkley & Gruyter, Heterospora (Boerema, Gruyter & Noordel.) Gruyter, Verkley & Crous, H. chenopodii (Westend.) Gruyter, Aveskamp & Verkley, H. dimorphospora (Speg.) Gruyter, Aveskamp & Verkley, Leptosphaeria errabunda (Desm.) Gruyter, Aveskamp & Verkley, L. etheridgei (L.J. Hutchison & Y. Hirats.) Gruyter, Aveskamp & Verkley, L. macrocapsa (Trail) Gruyter, Aveskamp & Verkley, L. pedicularis (Fuckel) Gruyter, Aveskamp & Verkley, L. rubefaciens (Togliani) Gruyter, Aveskamp & Verkley, L. sclerotioides (Sacc.) Gruyter, Aveskamp & Verkley, L. sydowii (Boerema, Kesteren & Loer.) Gruyter, Aveskamp & Verkley, L. veronicae (Hollos) Gruyter, Aveskamp & Verkley, Medicopsis romeroi (Borelli) Gruyter, Verkley & Crous, Nigrograna mackinnonii (Borelli) Gruyter, Verkley & Crous, Paraconiothyrium flavescens (Gruyter, Noordel. & Boerema) Verkley & Gruyter, Paracon. fuckelii (Sacc.) Verkley & Gruyter, Paracon. fusco-maculans (Sacc.) Verkley & Gruyter, Paracon. lini (Pass.) Verkley & Gruyter, Paracon. tiliae (F. Rudolphi) Verkley & Gruyter, Paraleptosphaeria dryadis (Johanson) Gruyter, Aveskamp & Verkley, Paralept. macrospora (Thum.) Gruyter, Aveskamp & Verkley, Paralept. nitschkei (Rehm ex G. Winter) Gruyter, Aveskamp & Verkley, Paralept. orobanches (Schweinitz: Fr.) Gruyter, Aveskamp & Verkley, Paralept. praetermissa (P. Karst.) Gruyter, Aveskamp & Verkley, Plenodomus agnitus (Desm.) Gruyter, Aveskamp & Verkley, Plen. biglobosus (Shoemaker & H. Brun) Gruyter, Aveskamp & Verkley, Plen. chrysanthemi (Zachos, Constantinou & Panag.) Gruyter, Aveskamp & Verkley, Plen. collinsoniae (Dearn. & House) Gruyter, Aveskamp & Verkley, Plen. confertus (Niessl ex Sacc.) Gruyter, Aveskamp & Verkley, Plen. congestus (M.T. Lucas) Gruyter, Aveskamp & Verkley, Plen. enteroleucus (Sacc.) Gruyter, Aveskamp & Verkley, Plen. fallaciosus (Berl.) Gruyter, Aveskamp & Verkley, Plen. hendersoniae (Fuckel) Gruyter, Aveskamp & Verkley, Plen. influorescens (Boerema & Loer.) Gruyter, Aveskamp & Verkley, Plen. libanotidis (Fuckel) Gruyter, Aveskamp & Verkley, Plen. lindquistii (Frezzi) Gruyter, Aveskamp & Verkley, Plen. lupini (Ellis & Everh.) Gruyter, Aveskamp & Verkley, Plen. pimpinellae (Lowen & Sivan.) Gruyter, Aveskamp & Verkley, Plen. tracheiphilus (Petri) Gruyter, Aveskamp & Verkley, Plen. visci (Moesz) Gruyter, Aveskamp & Verkley, Pleospora fallens (Sacc.) Gruyter & Verkley, Pleo. flavigena (Constantinou & Aa) Gruyter & Verkley, Pleo. incompta (Sacc. & Martelli) Gruyter & Verkley, Pyrenochaetopsis pratorum (P.R. Johnst. & Boerema) Gruyter, Aveskamp & Verkley, Subplenodomus apiicola (Kleb.) Gruyter, Aveskamp & Verkley, Subplen. drobnjacensis (Bubak) Gruyter, Aveskamp & Verkley, Subplen. valerianae (Henn.) Gruyter, Aveskamp & Verkley, Subplen. violicola (P. Syd.) Gruyter, Aveskamp & Verkley, Westerdykella capitulum (V.H. Pawar, P.N. Mathur & Thirum.) de Gruyter, Aveskamp & Verkley, W. minutispora (P.N. Mathur ex Gruyter & Noordel.) Gruyter, Aveskamp & Verkley. New names: Pleospora angustis Gruyter & Verkley, Pleospora halimiones Gruyter & Verkley.
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Revised taxonomy of Phoma and allied genera
2012Co-Authors: J. De GruyterAbstract:The anamorphic genus Phoma includes many important plant pathogens. The identification of Phoma species based on studies in pure culture is difficult and time consuming and the in vitro characters are often variable. Moreover, the present classification of Phoma species into sections is ambiguous and morphological characters are shared with related genera. In the present study the molecular phylogeny of species of Phoma and allied genera was examined and the results obtained were used to revise the taxonomy. The DNA sequence data obtained provide tools for the development of detection and identification methods. Chapter 1 provides a general introduction of the anamorph genus Phoma and the research that has been performed in The Netherlands during the last decades is described. Phoma is characterised by producing hyaline conidia in fruiting bodies called pycnidia. The genus includes many important plant pathogens. The taxonomy of Phoma has been studied intensively at the Plant Protection Service in the Netherlands for more than 50 years, resulting in the development of a generic concept in 1997 as an outline for identification of Phoma species. In this concept species of the genus Phoma are classified based on their morphological characters into the nine sections Phoma, Heterospora, Macrospora, ParaPhoma, Peyronellaea, Phyllostictoides, Pilosa, Plenodomus and Sclerophomella. The species placed in each of the sections were systematically described culminating in the publication of the “Phoma Identification Manual” in 2004, with the descriptions of 223 specific and infra-specific taxa of Phoma, and more than 1000 synonyms in other coelomycetous genera. In the Netherlands the late Gerhard Boerema, former head of the Mycology Department at the Plant Protection Service, has been the driving force behind this Phoma research for decades. The Phoma Identification Manual is a valuable tool for the morphological identification of isolates, but in vitro studies are very time consuming and need a high level of expertise. Moreover, the classification of Phoma species in sections based on morphological characters appeared artificial and several species can be classified in more than one section because of their multiple “section-specific” characters. In addition, distinctive characters of Phoma sections are shared among morphologically related coelomycetous genera including Ascochyta, Asteromella, Microsphaeropsis, Phomopsis, Phyllosticta, PleuroPhoma, Pyrenochaeta and Stagonospora. Phoma sections are related to diverse teleomorph genera including Didymella, Leptosphaeria, Mycosphaerella and Pleospora. Synanamorphs of Phoma species have been recognised amongst the genera Phaeomoniella, Stagonosporopsis, Epicoccum, Phialophora and Sclerotium illustrating their heterogeneity. A large, well-studied Phoma culture collection established at the Plant Protection Service and the “Centraalbureau voor Schimmelcultures” includes more than 1100 strains of Phoma species. This collection formed the basis of an intensive molecular phylogenetic study of the genus Phoma and morphologically similar genera, which commenced in 2006. Furthermore, a literature study identified sequences of genes that are suitable for phylogenic studies and elucidation of the evolutionary history of the genus Phoma. Several potentially informative regions of the genome were sequenced in the first phase of the project as has been described in chapters 2–4. The phylogeny and DNA sequence data obtained have provided tools for the development of fast and reliable molecular detection and identification methods. The development of Real-time TaqMan PCR methods for the detection and identification of two important plant pathogenic (quarantine) species formerly described in Phoma, Stagonosporopsis andigena and S. crystalliniformis, is described in Chapter 5. In chapter 2 several genes were studied to elucidate the molecular phylogeny of Phoma and allied genera. Sequence data of the 18S nrDNA (SSU) and 28S nrDNA (LSU) regions of the type species of the Phoma sections and morphologically similar coelomycetes and related teleomorphs were compared. The results justified the introduction of the new family Didymellaceae to accommodate the generic type species Didymella exigua and Phoma herbarum. The type species of the Phoma sections Phyllostictoides, Sclerophomella, Macrospora and Peyronellaea also grouped in Didymellaceae. The generic type species Ascochyta pisi and Microsphaeropsis olivacea also grouped in Didymellaceae and it shows that these genera are closely allied to Phoma. The type species of Phoma sections Heterospora, ParaPhoma, Pilosa and Plenodomus grouped in various families outside Didymellaceae and were subject of following studies. Chapter 3 provides a molecular phylogenetic re-evaluation on Phoma-like species that appeared only distantly related to the generic type species Phoma herbarum and its related Didymella teleomorph (Didymellaceae). Phoma section ParaPhoma, characterised by setose pycnidia, resembles species of Pyrenochaeta and PleuroPhoma. Sequence data from the SSU and LSU regions of the species classified in Phoma section ParaPhoma were compared with those of representative isolates of Pyrenochaeta and PleuroPhoma, and with those of the type species of the Phoma sections Phoma, Pilosa and Plenodomus. Unnamed, often sterile Phomalike strains in the collections were included. The molecular phylogeny of species that were classified in Phoma section ParaPhoma appeared to be highly polyphyletic and a thorough reclassification of the species is provided. ParaPhoma was reinstalled and grouped with the new genera NeosetoPhoma and SetoPhoma in Phaeosphaeriaceae. Pyrenochaeta and the new genus Pyrenochaetopsis, including mainly taxa formerly described in Phoma section ParaPhoma, were closely allied in Cucurbitariaceae. In chapter 4 the molecular phylogeny of species of Phoma sections Plenodomus, Pleospora and Heterospora was determined using LSU, SSU and ITS. In a “one species = one name” approach, the species described in Phoma section Plenodomus and its teleomorph Leptosphaeria were reclassified in Leptosphaeria, Plenodomus and the new genera Paraleptosphaeria and Subplenodomus in Leptosphaeriaceae. Two species of Phoma section Heterospora, the type species Phoma heteromorphospora and its allied species Ph. dimorphospora, were transferred to the new genus Heterospora that also grouped in Leptosphaeriaceae. Leptosphaeria doliolum comprises a species complex that was revised based on multilocus sequence data of LSU, ITS, SSU, s-tubulin, and chitin synthase 1. The molecular phylogeny of species classified in Ascochyta and Phoma, section Pilosa in Pleosporaceae that produce morphologically similar pilose pycnidia, was determined based on analysis of actin sequence data. Several Phoma-like species grouped outside the suborder Pleosporineae in a LSU sequence analysis and were transferred to the genera Aposphaeria (Melanommataceae), Paraconiothyrium (Montagnulaceae) and Westerdykella (Sporormiaceae). Coniothyrium palmarum and related species were described in Coniothyriaceae. The new genera Medicopsis (Trematosphaeriaceae) and Nigrograna, of which the family is still unknown, are introduced to accommodate two medically important species formerly classified in Pyrenochaeta. In chapter 5 specific real-time (TaqMan) PCR assays were developed for the detection of the pathogens Stagonosporopsis andigena and S. crystalliniformis in leaves of potato and tomato. The molecular phylogeny with related species of Stagonosporopsis, Boeremia and Phoma based on sequence polymorphisms in the actine gene, was determined. The reliability of the DNA extraction and TaqMan PCRs for the detection of S. andigena and S. crystalliniformis in leaf material was tested in performance studies and demonstrated the specificity, analytical sensitivity, reproducibility, repeatability and robustness of both assays.
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Phoma Identification Manual: Differentiation of Specific and Infra-specific Taxa in Culture
2004Co-Authors: G. H. Boerema, J. De Gruyter, M. E. Noordeloos, M. E. C. HamersAbstract:This book is a practical manual to aid identification of Phoma species, and will be useful for researchers working in the areas of mycology, plant pathology and microbiology. It provides line drawings and keys for the identification of 223 specific and infraspecific taxa of Phoma, including common pathogenic and saprophytic species, with references to additional diagnostic literature, representative cultures and documentation of the numerous synonyms formerly used in the mycological and phytopathological literature. Methods for identification and differentiation of species in vitro are covered, then species are described under the following sections: Phoma, Heterospora, ParaPhoma, Peyronellaea, Phyllostictoides, Sclerophomella, Plenodomus, Macrospora, Pilosa and miscellaneous.
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Contributions towards a monograph of Phoma (Coelomycetes) VIII. Section ParaPhoma: Taxa with setose pycnidia
Persoonia, 2002Co-Authors: J. De Gruyter, G. H. BoeremaAbstract:In this paper eleven species of Phoma with obvious setose pycnidia, grouped in the section ParaPhoma, are documented and described. Most of these species were formerly classified in Pyrenochaeta. The following new taxa have been proposed: Phoma briardii nom. nov., Phoma carteri nom. nov., Phoma glycinicola nom. nov., Phoma indica (T.S. Viswan.) comb, nov., Phoma setariae (H.C. Greene) comb. nov. and Phoma leveillei var. microspora var. nov. Indices on host/substratum-fungus and fungus-host relations are included and short comments on the ecology and distribution of the taxa are given.
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Contributions towards a monograph of Phoma (Coelomycetes) VI — 2. Section Phyllostictoides: Outline of its taxa
Persoonia, 2002Co-Authors: J. De Gruyter, G. H. Boerema, H. A. Van Der AaAbstract:Thirty taxa in Phoma sect. Phyllostictoides, characterised by secondary septation of a variable number of conidia, are described in vitro. Two Phyllostictoides-like species are (re)classified in sect. Sclerophomella on account of certain pycnidial characteristics. Short notes on the ecology and distribution are added. Newly proposed taxa are: Phoma acetosellae (A. L. Sm. & Ramsb.) Aa & Boerema comb, nov., Phoma argillacea (Bres.) Aa & Boerema comb. nov. (teleomorph Didymella applanata (Niessl) Sacc.), Phoma nepeticola (Melnik) Dorenb. & de Gruyter comb, nov. (teleomorph Didymella catariae (Cooke & Ellis) Sacc.), Phoma destructiva var. diversispora de Gruyter & Boerema var. nov., Phoma heliopsidis (H.C. Greene) Aa & Boerema comb, nov., Phoma laundoniae Boerema & De Gruyter spec. nov. and Phoma rhei (Ellis & Everh.) Aa & Boerema comb. nov. A key is given to the cultural characteristics of all species and varieties at present recognised within the section (including the two Phywllostictoides-like species of Sclerophomella), as well as indices on host-fungus and fungus-host relations.
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Phoma-like fungi on soybeans
Critical Reviews in Microbiology, 2013Co-Authors: György János Kövics, Mahendra Rai, Erzsébet Sándor, László IrinyiAbstract:Numerous coelomycetous fungi classified in Ascochyta, Phoma and Phyllosticta, and lately established and/or re-classified genera and species, namely Boeremia and Peyronellaea have been recorded from spots on leaves and pods of soybeans. These rarely observed pathogens are cosmopolitan, ubiquitous species on diseased and dead plant materials, and define frequently as weak or opportunistic parasites. Based on the Genealogical Concordance Phylogenetic Species Recognition, the authors summarize the re-evaluation of the taxonomic status of Phoma sojicola (syn. Ascochyta sojicola) and Phyllosticta sojicola. Inspite of the former delimitation of Ph. sojicola based on small differences in morphological features, it has proved to be identical to Peyronellaea pinodella (syn. Phoma pinodella). Similarly, it was also confirmed that Ph. sojicola was identical to Boeremia exigua var. exigua (syn. Phoma exigua var. exigua). The authors and co-workers contributed to the identification of Phoma-like fungi by combined conventional and molecular methods. Protein-encoding genes (TEF1 and β-tubulin) were successfully applied within the Phoma genus to infer phylogenetic relationships.
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Phylogenetic studies of soybean pathogen Phoma species by Bayesian analysis
Acta Agraria Debreceniensis, 2009Co-Authors: László Irinyi, György János Kövics, Erzsébet SándorAbstract:We carried out phylogenetic study analyzing sequences of genetic markers in the taxonomy of Phoma and Phoma-like fungi. Different species of Phoma and Phoma-like fungi occurring on soybean (Phoma pinodella, Phoma sojicola, Phyllosticta sojicola, Phoma exigua var. exigua) are difficult to identy because of their high morphological and symptomatic similarities.Twenty-two isolates of nine different Phoma species were obtained from reference culture collections. Seven of them were isolated from soybean, the others were collected from different hosts.The Phoma isolates were firstly characterised by morphologically, and then we employed a part of the gene responsible for the synthesis of translation elongation factor 1 subunit alpha protein (tef1), ITS region, as well as β-tubulin partial sequences as potential genetic markers to inferphylogenetic relationships among different Phoma species..Finally, their ITS and tef1 sequences were sequenced and analysed by Bayesian approaches.According to phylogenetic trees inferred by Bayesian analysis of tef1, ITS and β-tubulin sequences, different Phoma species can be separated proving that these phylogenetic markers are well suited for phylogenetic studies of Phoma species. However, the phylogenetic tree does not support the traditional Phoma sections based on morphological characterization.Bayesian analyses of the three sequences confirmed that the Phyllosticta sojicola species is clustered with the Phoma exigua var. exigua group and the Phoma sojicola is grouped with Phoma pinodella group. The molecular data provide evidence for reclassification of formerly mentioned soybean pathogens.
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Taxonomical re-evaluation of Phoma-like soybean pathogenic fungi.
Mycological Research, 2009Co-Authors: László Irinyi, György János Kövics, Erzsébet SándorAbstract:Coelomycetous fungi classified in Ascochyta, Phoma, and Phyllosticta have been recorded from spots on leaves and pods of soybeans. Based on the Genealogical Concordance Phylogenetic Species Concept, the authors suggest the re-evaluation of the taxonomic status of Phoma sojicola (syn. = Ascochyta sojicola) and Phyllosticta sojicola. In spite of the former delimitation of Phoma sojicola based on small differences in morphological features, it has proved to be identical to Phoma pinodella. Similarly, it was also confirmed that Phyllosticta sojicola was identical to Phoma exigua var. exigua. The authors supply tools for identification of Phoma-like fungi by combined conventional and molecular methods. Protein-encoding genes (tef1 and β-tubulin) were successfully applied within the Phoma genus to infer phylogenetic relationships.
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Taxonomical re-evaluation of Phoma-like soybean pathogenic fungi.
Mycological research, 2008Co-Authors: László Irinyi, György János Kövics, Erzsébet SándorAbstract:Coelomycetous fungi classified in Ascochyta, Phoma, and Phyllosticta have been recorded from spots on leaves and pods of soybeans. Based on the Genealogical Concordance Phylogenetic Species Concept, the authors suggest the re-evaluation of the taxonomic status of Phoma sojicola (syn.=Ascochyta sojicola) and Phyllosticta sojicola. In spite of the former delimitation of Phoma sojicola based on small differences in morphological features, it has proved to be identical to Phoma pinodella. Similarly, it was also confirmed that Phyllosticta sojicola was identical to Phoma exigua var. exigua. The authors supply tools for identification of Phoma-like fungi by combined conventional and molecular methods. Protein-encoding genes (tef1 and beta-tubulin) were successfully applied within the Phoma genus to infer phylogenetic relationships.
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Phylogenetic studies of Phoma species by maximum likelihood analysis
Acta Agraria Debreceniensis, 2008Co-Authors: László Irinyi, György János Kövics, Erzsébet SándorAbstract:The cosmopolitan Phoma genus contains mainly phytopathogenic, opportunistic parasite, and saprophyte fungal species. Up to now the characterization of Phoma species and other taxa of Phoma has so far been determined on the basis of morphology on standardized media, and gene sequence analysis was only used as a confirmative or distinctive complement.In this study we have tried to study phylogenetic relationships by maximum likelihood method in the Phoma genus. We employed a part of the gene responsible for the synthesis of translation elongation factor 1 subunit alpha protein (tef1) containing both introns and exons, a part of the gene responsible for synthesis of tubulin protein and ITS region containing the internal transcribed spacer regions 1 and 2 and the 5.8S rDNA as potential genetic markers to infer phylogenetic relationships among different Phoma taxa. Twenty-four isolates of eleven different Phoma species were firstly characterised by morphologically, and then their tef1, tubulin and ITS sequences were sequenced and analysed by maximum likelihood method carried out by PAUP*4.0b program. According to constructed phylogenetic trees, the different Phoma taxons are well separated. However these trees do not support the traditional Phoma sections based on morphological characterization.The maximum likelihood analyses of all three sequences confirmed that the Phyllosticta sojicola species is clustered with the Phoma exigua var. exigua group and the Phoma sojicola is grouped with Phoma pinodella group. The experienced molecular evidences initiate the demand of reclassification of formerly mentioned soybean pathogens.