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Risky Ayu Kristanti - One of the best experts on this subject based on the ideXlab platform.
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Identification of Metabolic Intermediates in Microbial Degradation of Chrysene by Armillaria sp. F022
2016Co-Authors: Tony Hadibarata, Risky Ayu Kristanti, Johor BahruAbstract:To degrade chrysene, a polycyclic aromatic hydrocarbon (PAH), Armillaria sp. F022, a fungus col-lected from a soil, was used. Maximal degradation (77%) was obtained when Armillaria sp. F022 was incubated in cultures agitated at 120 rpm for 30 days, as compared to just 41 % degradation in stationary culture. Furthermore, the degradation of chrysene was affected by the addition of surfactants. The mecha-nism of degradation was determined through identification of the intermediates. Several enzymes (manga-nese peroxidase, lignin peroxidase, laccase, 1,2-dioxygenase and 2,3-dioxygenase) produced by Armillaria sp. F022 were detected in the culture. The highest level of activity was shown by 1,2-dioxygenase after 20 days (143.6 U l-1). These ligninolytic and dioxygenase enzymes played an important role in the oxidation of chrysene. Chrysene was indeed degraded by Armillaria sp. F022 through several intermediates, chrysenequinone, 2-((1E,3E)-4-carboxy-3-hydroxybuta-1,3-dien-1-yl)-1-naphthoic acid, 1-hydroxy-2-naphthoic acid, and gentisic acid
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ORIGINAL PAPER Biodegradation and metabolite transformation of pyrene by basidiomycetes fungal isolate Armillaria sp. F022
2016Co-Authors: Tony Hadibarata, Risky Ayu KristantiAbstract:Abstract Armillaria sp. F022 is a white-rot fungus iso-lated from a tropical rain forest in Indonesia that is capable of utilizing pyrene as a source of carbon and energy. Enzymes production during the degradation process by Armillaria sp. F022 was certainly related to the increase in biomass. In the first week after incubation, the growth rate rapidly increased, but enzyme production decreased. After 7 days of incubation, rapid growth was observed, whereas, the enzymes were produced only after a good amount of biomass was generated. About 63 % of pyrene underwent biodegradation when incubated with this fungus in a liquid medium on a rotary shaker (120 rpm, 25 C) for 30 days; during this period, pyrene was transformed to five stable metabolic products. These metabolites were extracted in ethyl acetate, isolated by column chromatography, and then identified using thin layer chromatography (TLC) and gas chromatography–mass spectrometry (GC–MS). 1-Hydrox-ypyrene was directly identified by GC–MS, while 4-phe-nanthroic acid, 1-hydroxy-2-naphthoic acid, phthalic acid, and protocatechuic acid were identified to be present in their derivatized forms (methylated forms and silylated forms). Protocatechuic acid was the end product of pyrene degradation by Armillaria sp. F022. Dynamic profiles of two key enzymes, namely laccase and 1,2-dioxygenase, were revealed during the degradation process, and the results indicated the presence of a complicated mechanism in the regulation of pyrene-degrading enzymes. In con-clusion, Armillaria sp. F022 is a white-rot fungus with potential for application in the degradation of polycyclic aromatic hydrocarbons such as pyrene in the environment
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fluorene biodegradation and identification of transformation products by white rot fungus Armillaria sp f022
Biodegradation, 2014Co-Authors: Tony Hadibarata, Risky Ayu KristantiAbstract:A diverse surfactant, including the nonionic Tween 80 and Brij 30, the anionic sodium dodecyl sulphate, the cationic surfactant Tetradecyltrimethylammonium bromide, and biosurfactant Rhamnolipid were investigated under fluorine-enriched medium by Armilaria sp. F022. The cultures were performed at 25 °C in malt extract medium containing 1 % of surfactant and 5 mg/L of fluorene. The results showed among the tested surfactants, Tween-80 harvested the highest cell density and obtained the maximum specific growth rate. This due Tween-80 provide a suitable carbon source for fungi. Fluorane was also successfully eliminated (>95 %) from the cultures within 30 days in all flasks. During the experiment, laccase production was the highest among other enzymes and Armillaria sp. F022-enriched culture containing Non-ionic Tween 80 showed a significant result for laccase activity (1,945 U/L). The increased enzyme activity was resulted by the increased biodegradation activity as results of the addition of suitable surfactants. The biotransformation of fluorene was accelerated by Tween 80 at the concentration level of 10 mg/L. Fluorene was initially oxidized at C-2,3 positions resulting 9-fluorenone. Through oxidative decarboxylation, 9-fluorenone subjected to meta-cleavage to form salicylic acid. One metabolite detected in the end of experiment, was identified as catechol. Armillaria sp. F022 evidently posses efficient, high effective degrader and potential for further application on the enhanced bioremediation technologies for treating fluorene-contaminated soil.
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biodegradation and metabolite transformation of pyrene by basidiomycetes fungal isolate Armillaria sp f022
Bioprocess and Biosystems Engineering, 2013Co-Authors: Tony Hadibarata, Risky Ayu KristantiAbstract:Armillaria sp. F022 is a white-rot fungus isolated from a tropical rain forest in Indonesia that is capable of utilizing pyrene as a source of carbon and energy. Enzymes production during the degradation process by Armillaria sp. F022 was certainly related to the increase in biomass. In the first week after incubation, the growth rate rapidly increased, but enzyme production decreased. After 7 days of incubation, rapid growth was observed, whereas, the enzymes were produced only after a good amount of biomass was generated. About 63 % of pyrene underwent biodegradation when incubated with this fungus in a liquid medium on a rotary shaker (120 rpm, 25 °C) for 30 days; during this period, pyrene was transformed to five stable metabolic products. These metabolites were extracted in ethyl acetate, isolated by column chromatography, and then identified using thin layer chromatography (TLC) and gas chromatography–mass spectrometry (GC–MS). 1-Hydroxypyrene was directly identified by GC–MS, while 4-phenanthroic acid, 1-hydroxy-2-naphthoic acid, phthalic acid, and protocatechuic acid were identified to be present in their derivatized forms (methylated forms and silylated forms). Protocatechuic acid was the end product of pyrene degradation by Armillaria sp. F022. Dynamic profiles of two key enzymes, namely laccase and 1,2-dioxygenase, were revealed during the degradation process, and the results indicated the presence of a complicated mechanism in the regulation of pyrene-degrading enzymes. In conclusion, Armillaria sp. F022 is a white-rot fungus with potential for application in the degradation of polycyclic aromatic hydrocarbons such as pyrene in the environment.
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identification of naphthalene metabolism by white rot fungus Armillaria sp f022
Journal of Environmental Sciences-china, 2012Co-Authors: Tony Hadibarata, Abdull Rahim Mohd Yusoff, Azmi Aris, Risky Ayu KristantiAbstract:Armillaria sp. F022, a white rot fungus isolated from tropical rain forest (Samarinda, Indonesia) was used to biodegrade naphthalene in cultured medium. Transformation of naphthalene by Armillaria sp. F022 which is able to use naphthalene, a two ring-polycyclic aromatic hydrocarbon (PAH) as a source of carbon and energy was investigated. The metabolic pathway was elucidated by identifying metabolites, biotransformation studies and monitoring enzyme activities in cell-free extracts. The identification of metabolites suggests that Armillaria sp. F022 initiates its attack on naphthalene by dioxygenation at its C-1 and C-4 positions to give 1,4-naphthoquinone. The intermediate 2-hydroxybenzaldehyde and salicylic acid, and the characteristic of the meta-cleavage of the resulting diol were identified in the long-term incubation. A part from typical metabolites of naphthalene degradation known from mesophiles, benzoic acid was identified as the next intermediate for the naphthalene pathway of this Armillaria sp. F022. Neither phthalic acid, catechol and cis,cis-muconic acid metabolites were detected in culture extracts. Several enzymes (manganese peroxidase, lignin peroxidase, laccase, 1,2-dioxygenase and 2,3-dioxygenase) produced by Armillaria sp. F022 were detected during the incubation.
Tony Hadibarata - One of the best experts on this subject based on the ideXlab platform.
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Identification of Metabolic Intermediates in Microbial Degradation of Chrysene by Armillaria sp. F022
2016Co-Authors: Tony Hadibarata, Risky Ayu Kristanti, Johor BahruAbstract:To degrade chrysene, a polycyclic aromatic hydrocarbon (PAH), Armillaria sp. F022, a fungus col-lected from a soil, was used. Maximal degradation (77%) was obtained when Armillaria sp. F022 was incubated in cultures agitated at 120 rpm for 30 days, as compared to just 41 % degradation in stationary culture. Furthermore, the degradation of chrysene was affected by the addition of surfactants. The mecha-nism of degradation was determined through identification of the intermediates. Several enzymes (manga-nese peroxidase, lignin peroxidase, laccase, 1,2-dioxygenase and 2,3-dioxygenase) produced by Armillaria sp. F022 were detected in the culture. The highest level of activity was shown by 1,2-dioxygenase after 20 days (143.6 U l-1). These ligninolytic and dioxygenase enzymes played an important role in the oxidation of chrysene. Chrysene was indeed degraded by Armillaria sp. F022 through several intermediates, chrysenequinone, 2-((1E,3E)-4-carboxy-3-hydroxybuta-1,3-dien-1-yl)-1-naphthoic acid, 1-hydroxy-2-naphthoic acid, and gentisic acid
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ORIGINAL PAPER Biodegradation and metabolite transformation of pyrene by basidiomycetes fungal isolate Armillaria sp. F022
2016Co-Authors: Tony Hadibarata, Risky Ayu KristantiAbstract:Abstract Armillaria sp. F022 is a white-rot fungus iso-lated from a tropical rain forest in Indonesia that is capable of utilizing pyrene as a source of carbon and energy. Enzymes production during the degradation process by Armillaria sp. F022 was certainly related to the increase in biomass. In the first week after incubation, the growth rate rapidly increased, but enzyme production decreased. After 7 days of incubation, rapid growth was observed, whereas, the enzymes were produced only after a good amount of biomass was generated. About 63 % of pyrene underwent biodegradation when incubated with this fungus in a liquid medium on a rotary shaker (120 rpm, 25 C) for 30 days; during this period, pyrene was transformed to five stable metabolic products. These metabolites were extracted in ethyl acetate, isolated by column chromatography, and then identified using thin layer chromatography (TLC) and gas chromatography–mass spectrometry (GC–MS). 1-Hydrox-ypyrene was directly identified by GC–MS, while 4-phe-nanthroic acid, 1-hydroxy-2-naphthoic acid, phthalic acid, and protocatechuic acid were identified to be present in their derivatized forms (methylated forms and silylated forms). Protocatechuic acid was the end product of pyrene degradation by Armillaria sp. F022. Dynamic profiles of two key enzymes, namely laccase and 1,2-dioxygenase, were revealed during the degradation process, and the results indicated the presence of a complicated mechanism in the regulation of pyrene-degrading enzymes. In con-clusion, Armillaria sp. F022 is a white-rot fungus with potential for application in the degradation of polycyclic aromatic hydrocarbons such as pyrene in the environment
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fluorene biodegradation and identification of transformation products by white rot fungus Armillaria sp f022
Biodegradation, 2014Co-Authors: Tony Hadibarata, Risky Ayu KristantiAbstract:A diverse surfactant, including the nonionic Tween 80 and Brij 30, the anionic sodium dodecyl sulphate, the cationic surfactant Tetradecyltrimethylammonium bromide, and biosurfactant Rhamnolipid were investigated under fluorine-enriched medium by Armilaria sp. F022. The cultures were performed at 25 °C in malt extract medium containing 1 % of surfactant and 5 mg/L of fluorene. The results showed among the tested surfactants, Tween-80 harvested the highest cell density and obtained the maximum specific growth rate. This due Tween-80 provide a suitable carbon source for fungi. Fluorane was also successfully eliminated (>95 %) from the cultures within 30 days in all flasks. During the experiment, laccase production was the highest among other enzymes and Armillaria sp. F022-enriched culture containing Non-ionic Tween 80 showed a significant result for laccase activity (1,945 U/L). The increased enzyme activity was resulted by the increased biodegradation activity as results of the addition of suitable surfactants. The biotransformation of fluorene was accelerated by Tween 80 at the concentration level of 10 mg/L. Fluorene was initially oxidized at C-2,3 positions resulting 9-fluorenone. Through oxidative decarboxylation, 9-fluorenone subjected to meta-cleavage to form salicylic acid. One metabolite detected in the end of experiment, was identified as catechol. Armillaria sp. F022 evidently posses efficient, high effective degrader and potential for further application on the enhanced bioremediation technologies for treating fluorene-contaminated soil.
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biodegradation and metabolite transformation of pyrene by basidiomycetes fungal isolate Armillaria sp f022
Bioprocess and Biosystems Engineering, 2013Co-Authors: Tony Hadibarata, Risky Ayu KristantiAbstract:Armillaria sp. F022 is a white-rot fungus isolated from a tropical rain forest in Indonesia that is capable of utilizing pyrene as a source of carbon and energy. Enzymes production during the degradation process by Armillaria sp. F022 was certainly related to the increase in biomass. In the first week after incubation, the growth rate rapidly increased, but enzyme production decreased. After 7 days of incubation, rapid growth was observed, whereas, the enzymes were produced only after a good amount of biomass was generated. About 63 % of pyrene underwent biodegradation when incubated with this fungus in a liquid medium on a rotary shaker (120 rpm, 25 °C) for 30 days; during this period, pyrene was transformed to five stable metabolic products. These metabolites were extracted in ethyl acetate, isolated by column chromatography, and then identified using thin layer chromatography (TLC) and gas chromatography–mass spectrometry (GC–MS). 1-Hydroxypyrene was directly identified by GC–MS, while 4-phenanthroic acid, 1-hydroxy-2-naphthoic acid, phthalic acid, and protocatechuic acid were identified to be present in their derivatized forms (methylated forms and silylated forms). Protocatechuic acid was the end product of pyrene degradation by Armillaria sp. F022. Dynamic profiles of two key enzymes, namely laccase and 1,2-dioxygenase, were revealed during the degradation process, and the results indicated the presence of a complicated mechanism in the regulation of pyrene-degrading enzymes. In conclusion, Armillaria sp. F022 is a white-rot fungus with potential for application in the degradation of polycyclic aromatic hydrocarbons such as pyrene in the environment.
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identification of naphthalene metabolism by white rot fungus Armillaria sp f022
Journal of Environmental Sciences-china, 2012Co-Authors: Tony Hadibarata, Abdull Rahim Mohd Yusoff, Azmi Aris, Risky Ayu KristantiAbstract:Armillaria sp. F022, a white rot fungus isolated from tropical rain forest (Samarinda, Indonesia) was used to biodegrade naphthalene in cultured medium. Transformation of naphthalene by Armillaria sp. F022 which is able to use naphthalene, a two ring-polycyclic aromatic hydrocarbon (PAH) as a source of carbon and energy was investigated. The metabolic pathway was elucidated by identifying metabolites, biotransformation studies and monitoring enzyme activities in cell-free extracts. The identification of metabolites suggests that Armillaria sp. F022 initiates its attack on naphthalene by dioxygenation at its C-1 and C-4 positions to give 1,4-naphthoquinone. The intermediate 2-hydroxybenzaldehyde and salicylic acid, and the characteristic of the meta-cleavage of the resulting diol were identified in the long-term incubation. A part from typical metabolites of naphthalene degradation known from mesophiles, benzoic acid was identified as the next intermediate for the naphthalene pathway of this Armillaria sp. F022. Neither phthalic acid, catechol and cis,cis-muconic acid metabolites were detected in culture extracts. Several enzymes (manganese peroxidase, lignin peroxidase, laccase, 1,2-dioxygenase and 2,3-dioxygenase) produced by Armillaria sp. F022 were detected during the incubation.
Michael J Wingfield - One of the best experts on this subject based on the ideXlab platform.
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Armillaria root rot pathogens species boundaries and global distribution
Pathogenetics, 2018Co-Authors: Martin Petrus Albertus Coetzee, Brenda D Wingfield, Michael J WingfieldAbstract:This review considers current knowledge surrounding species boundaries of the Armillaria root-rot pathogens and their distribution. In addition, a phylogenetic tree using translation elongation factor subunit 1-alpha (tef-1α) from isolates across the globe are used to present a global phylogenetic framework for the genus. Defining species boundaries based on DNA sequence-inferred phylogenies has been a central focus of contemporary mycology. The results of such studies have in many cases resolved the biogeographic history of species, mechanisms involved in dispersal, the taxonomy of species and how certain phenotypic characteristics have evolved throughout lineage diversification. Such advances have also occurred in the case of Armillaria spp. that include important causal agents of tree root rots. This commenced with the first phylogeny for Armillaria that was based on IGS-1 (intergenic spacer region one) DNA sequence data, published in 1992. Since then phylogenies were produced using alternative loci, either as single gene phylogenies or based on concatenated data. Collectively these phylogenies revealed species clusters in Armillaria linked to their geographic distributions and importantly species complexes that warrant further research.
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phylogenetic relationships among biological species of Armillaria from china
Mycoscience, 2015Co-Authors: Martin Petrus Albertus Coetzee, Brenda D Wingfield, Jun Zhao, Sophia Johanna Van Coller, Michael J WingfieldAbstract:Fourteen Chinese Biological Species (CBS) of Armillaria were previously identified in a collection of Chinese isolates. CBS C, F, G, H, J, L, N and O remained unnamed, while the remaining isolates included A. borealis, A. cepistipes, A. gallica, A. mellea, A. sinapina and A. tabescens. CBS F was suggested to represent A. singula based on basidiocarp morphology. In this study, phylogenetic relationships between Chinese Armillaria isolates and those from other parts of the world were determined based on DNA sequence data. Results of this study suggest that CBS F might not represent A. singula, and that A. monadelpha (a name applied to the North American form of A. tabescens by some authors) and A. tabescens should be treated as a single species. Four main phylogenetic lineages, referred to as the A. ostoyae, A. gallica, A. tabescens and A. mellea clusters, were identified on the phylogenetic trees. The unnamed biological species grouped within the “A. gallica cluster” and were phylogenetically closely related. The results of this study contribute to our current understanding of the systematics of Armillaria from South East Asia where these fungi are relatively poorly known.
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phylogenetic relationships among Armillaria species inferred from partial elongation factor 1 alpha dna sequence data
Australasian Plant Pathology, 2006Co-Authors: Lancelot Maphosa, Brenda D Wingfield, Martin Petrus Albertus Coetzee, Eddie Mwenje, Michael J WingfieldAbstract:Armillaria species are important root rot pathogens with a wide host range and a worldwide distribution. The taxonomy of these fungi has been problematic for many years but the understanding of the relationships between them has been substantially improved through the application of DNA sequence comparisons. In this study, relationships between different Armillaria species were determined using elongation factor 1-alpha DNA sequence data for the first time. A total of 42 isolates, representing the majority of Armillaria species, with diverse geographic distributions and hosts, were included in this study. PCR amplification yielded products of 600 bp for all the isolates. Phylogenetic trees resulting from parsimony analysis showed that this gene region is useful for studying relationships between species. Generally, results were similar to those emerging from previous comparisons using ITS and IGS-1 sequence data. Phylogenetic trees generated from the dataset grouped the African taxa in a strongly supported clade, basal to the rest of the Armillaria species included in the study. The Armillaria species originating from the Northern Hemisphere formed a monophyletic group. Within this group, isolates of A. mellea constituted four subclades, representing their geographical origin. The phylogenetic relationships among species from the Southern Hemisphere were not entirely resolved. However, A. pallidula, A. fumosa and A. hinnulea grouped in a strongly supported clade and isolates of A. limonea formed a sister clade with those of A. luteobubalina. This is the first time a single-copy protein coding gene has been used to study phylogenetic relationships in Armillaria, and overall the data support previously held views regarding the relationships between species.
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discovery of two northern hemisphere Armillaria species on proteaceae in south africa
Plant Pathology, 2003Co-Authors: Martin Petrus Albertus Coetzee, Brenda D Wingfield, Jolanda Roux, P W Crous, S Denman, Michael J WingfieldAbstract:Armillaria root rot symptoms were observed on native Protea and Leucadendron (Proteaceae) species in Kirstenbosch Botanical Gardens in the Western Cape Province of South Africa. Intergenic spacer (IGS)-1 polymerase chain reaction (PCR) restriction fragment-length polymorphism (RFLP) profiling indicated the presence of at least two Armillaria species. The profiles of two isolates were identical to those of A. mellea s. str., originating in Europe. Phylogenetic analyses incorporating internal transcribed spacer (ITS) and IGS-1 sequence data identified the remaining isolates as closely related to A. calvescens , A. gallica , A. jezoensis and A. sinapina . These isolates displayed mating compatibility with A. gallica. From the RFLP profiles, sequencing results and sexual compatibility studies, it is concluded that the two species on Proteaceae in Kirstenbosch represent A. mellea and A. gallica . These are northern hemisphere fungi that have apparently been accidentally introduced into South Africa. This is the second report of Armillaria being introduced into South Africa. The introduction probably occurred early in the colonization of Cape Town, when potted plants from Europe were used to establish gardens.
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molecular identification and phylogeny of Armillaria isolates from south america and indo malaysia
Mycologia, 2003Co-Authors: Martin Petrus Albertus Coetzee, Brenda D Wingfield, Paulette Bloomer, Geoff S Ridley, Michael J WingfieldAbstract:Armillaria root rot is a serious disease, chiefly of woody plants, caused by many species of Armillaria that occur in temperate, tropical and sub- tropical regions of the world. Very little is known about Armillaria in South America and Southeast Asia, although Armillaria root rot is well known in these areas. In this study, we consider previously un- identified isolates collected from trees with symptoms of Armillaria root rot in Chile, Indonesia and Malay- sia. In addition, isolates from basidiocarps resembling A. novae-zelandiae and A. limonea, originating from Chile and Argentina, respectively, were included in this study because their true identity has been uncer- tain. All isolates in this study were compared, based on their similarity in ITS sequences with previously sequenced Armillaria species, and their phylogenetic relationship with species from the Southern Hemi- sphere was considered. ITS sequence data for Armil- laria also were compared with those available at GenBank. Parsimony and distance analyses were con- ducted to determine the phylogenetic relationships between the unknown isolates and the species that showed high ITS sequence similarity. In addition, IGS-1 sequence data were obtained for some of the species to validate the trees obtained from the ITS data set. Results of this study showed that the ITS sequences of the isolates obtained from basidiocarps
Martin Petrus Albertus Coetzee - One of the best experts on this subject based on the ideXlab platform.
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Armillaria root rot pathogens species boundaries and global distribution
Pathogenetics, 2018Co-Authors: Martin Petrus Albertus Coetzee, Brenda D Wingfield, Michael J WingfieldAbstract:This review considers current knowledge surrounding species boundaries of the Armillaria root-rot pathogens and their distribution. In addition, a phylogenetic tree using translation elongation factor subunit 1-alpha (tef-1α) from isolates across the globe are used to present a global phylogenetic framework for the genus. Defining species boundaries based on DNA sequence-inferred phylogenies has been a central focus of contemporary mycology. The results of such studies have in many cases resolved the biogeographic history of species, mechanisms involved in dispersal, the taxonomy of species and how certain phenotypic characteristics have evolved throughout lineage diversification. Such advances have also occurred in the case of Armillaria spp. that include important causal agents of tree root rots. This commenced with the first phylogeny for Armillaria that was based on IGS-1 (intergenic spacer region one) DNA sequence data, published in 1992. Since then phylogenies were produced using alternative loci, either as single gene phylogenies or based on concatenated data. Collectively these phylogenies revealed species clusters in Armillaria linked to their geographic distributions and importantly species complexes that warrant further research.
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ima genome f 6 draft genome sequences of Armillaria fuscipes ceratocystiopsis minuta ceratocystis adiposa endoconidiophora laricicola e polonica and penicillium freii daomc 242723
IMA fungus, 2016Co-Authors: Brenda D Wingfield, Tuan A. Duong, Fourie Joubert, Almuth Hammerbacher, Alistair R. Mctaggart, Kershney Naidoo, Jon Ambler, Martin Petrus Albertus Coetzee, Wilhelm Z De Beer, Hai D. T. NguyenAbstract:The genomes of Armillaria fuscipes, Ceratocystiopsis minuta, Ceratocystis adiposa, Endoconidiophora laricicola, E. polonica, and Penicillium freii DAOMC 242723 are presented in this genome announcement. These six genomes are from plant pathogens and otherwise economically important fungal species. The genome sizes range from 21 Mb in the case of Ceratocystiopsis minuta to 58 Mb for the basidiomycete Armillaria fuscipes. These genomes include the first reports of genomes for the genus Endoconidiophora. The availability of these genome data will provide opportunities to resolve longstanding questions regarding the taxonomy of species in these genera. In addition these genome sequences through comparative studies with closely related organisms will increase our understanding of how these pathogens cause disease.
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phylogenetic relationships among biological species of Armillaria from china
Mycoscience, 2015Co-Authors: Martin Petrus Albertus Coetzee, Brenda D Wingfield, Jun Zhao, Sophia Johanna Van Coller, Michael J WingfieldAbstract:Fourteen Chinese Biological Species (CBS) of Armillaria were previously identified in a collection of Chinese isolates. CBS C, F, G, H, J, L, N and O remained unnamed, while the remaining isolates included A. borealis, A. cepistipes, A. gallica, A. mellea, A. sinapina and A. tabescens. CBS F was suggested to represent A. singula based on basidiocarp morphology. In this study, phylogenetic relationships between Chinese Armillaria isolates and those from other parts of the world were determined based on DNA sequence data. Results of this study suggest that CBS F might not represent A. singula, and that A. monadelpha (a name applied to the North American form of A. tabescens by some authors) and A. tabescens should be treated as a single species. Four main phylogenetic lineages, referred to as the A. ostoyae, A. gallica, A. tabescens and A. mellea clusters, were identified on the phylogenetic trees. The unnamed biological species grouped within the “A. gallica cluster” and were phylogenetically closely related. The results of this study contribute to our current understanding of the systematics of Armillaria from South East Asia where these fungi are relatively poorly known.
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secrets of the subterranean pathosystem of Armillaria
Molecular Plant Pathology, 2011Co-Authors: Kendra Baumgartner, Martin Petrus Albertus Coetzee, Dirk HoffmeisterAbstract:SUMMARY Armillaria root disease affects fruit and nut crops, timber trees and ornamentals in boreal, temperate and tropical regions of the world. The causal pathogens are members of the genus Armillaria (Basidiomycota, Physalacriaceae). This review summarizes the state of knowledge and highlights recent advances in Armillaria research. Taxonomy:Armillaria includes more than 40 morphological species. However, the identification and delineation of species on the basis of morphological characters are problematic, resulting in many species being undetected. Implementation of the biological species' concept and DNA sequence comparisons in the contemporary taxonomy of Armillaria have led to the discovery of a number of new species that are not linked to described morphological species. Host range:Armillaria exhibits a range of symbioses with both plants and fungi. As plant pathogens, Armillaria species have broad host ranges, infecting mostly woody species. Armillaria can also colonize orchids Galeola and Gastrodia but, in this case, the fungus is the host and the plant is the parasite. Similar to its contrasting relationships with plants, Armillaria acts as either host or parasite in its interactions with other fungi. Disease control: Recent research on post-infection controls has revealed promising alternatives to the former pre-plant eradication attempts with soil fumigants, which are now being regulated more heavily or banned outright because of their negative effects on the environment. New study tools for genetic manipulation of the pathogen and characterization of the molecular basis of the host response will greatly advance the development of resistant rootstocks in a new stage of research. The depth of the research, regardless of whether traditional or genomic approaches are used, will depend on a clear understanding of where the different propagules of Armillaria attack a root system, which of the pathogen's diverse biolymer-degrading enzymes and secondary metabolites facilitate infection, and how the course of infection differs between resistant and susceptible hosts.
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phylogenetic relationships among Armillaria species inferred from partial elongation factor 1 alpha dna sequence data
Australasian Plant Pathology, 2006Co-Authors: Lancelot Maphosa, Brenda D Wingfield, Martin Petrus Albertus Coetzee, Eddie Mwenje, Michael J WingfieldAbstract:Armillaria species are important root rot pathogens with a wide host range and a worldwide distribution. The taxonomy of these fungi has been problematic for many years but the understanding of the relationships between them has been substantially improved through the application of DNA sequence comparisons. In this study, relationships between different Armillaria species were determined using elongation factor 1-alpha DNA sequence data for the first time. A total of 42 isolates, representing the majority of Armillaria species, with diverse geographic distributions and hosts, were included in this study. PCR amplification yielded products of 600 bp for all the isolates. Phylogenetic trees resulting from parsimony analysis showed that this gene region is useful for studying relationships between species. Generally, results were similar to those emerging from previous comparisons using ITS and IGS-1 sequence data. Phylogenetic trees generated from the dataset grouped the African taxa in a strongly supported clade, basal to the rest of the Armillaria species included in the study. The Armillaria species originating from the Northern Hemisphere formed a monophyletic group. Within this group, isolates of A. mellea constituted four subclades, representing their geographical origin. The phylogenetic relationships among species from the Southern Hemisphere were not entirely resolved. However, A. pallidula, A. fumosa and A. hinnulea grouped in a strongly supported clade and isolates of A. limonea formed a sister clade with those of A. luteobubalina. This is the first time a single-copy protein coding gene has been used to study phylogenetic relationships in Armillaria, and overall the data support previously held views regarding the relationships between species.
Da-wei Zhang - One of the best experts on this subject based on the ideXlab platform.
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transcriptome analysis of genes involved in defence response in polyporus umbellatus with Armillaria mellea infection
Scientific Reports, 2015Co-Authors: Yong-mei Xing, Da-wei ZhangAbstract:Polyporus umbellatus, a species symbiotic with Armillaria mellea and it also exhibits substantial defence response to Armillaria mellea infection. There are no genomics resources databases for understanding the molecular mechanism underlying the infection stress of P. umbellatus. Therefore, we performed a large-scale transcriptome sequencing of this fungus with A. mellea infection using Illumina sequencing technology. The assembly of the clean reads resulted in 120,576 transcripts, including 38,444 unigenes. Additionally, we performed a gene expression profiling analysis upon infection treatment. The results indicated significant differences in the gene expression profiles between the control and the infection group. In total, 10933 genes were identified between the two groups. Based on the differentially expressed genes, a Gene Ontology annotation analysis showed many defence-relevant categories. Meanwhile, the Kyoto Encyclopedia of Genes and Genomes pathway analysis uncovered some important pathways. Furthermore, the expression patterns of 13 putative genes that are involved in defence response resulting from quantitative real-time PCR were consistent with their transcript abundance changes as identified by RNA-seq. The sequenced genes covered a considerable proportion of the P. umbellatus transcriptome, and the expression results may be useful to strengthen the knowledge on the defence response of this fungus defend against Armillaria mellea invasion.
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Genetic diversity of Armillaria spp. symbiotic with Polyporus umbellatus in China
Biochemical Systematics and Ecology, 2015Co-Authors: Yong-mei Xing, Xu Zeng, Da-wei ZhangAbstract:The growth and development of Polyporus umbellatus sclerotia is dependt on a symbiotic relationship with Armillaria, a species of forest pathogenic fungus. Our aim was to identify the Armillaria spp. that are symbiotic with Polyporus umbellatus in China. Samples of Armillaria spp. were isolated from Polyporus umbellatus from 31 districts among 13 provinces in China. Armillaria spp. were identified using DNA-based methods targeting the IGS region of ribosomal DNA. Genotypes were differentiated by the Inter-simple sequence repeat (ISSR) analysis. The results showed that Armillaria gallica and Armillaria cepistipes were the species most frequently observed to be symbiotic with P. umbellatus in China. Two dendrograms were generated based on the similarity matrix by the Unweighted Pair Group Method with Arithmetic Mean (UPGMA), wherein the genotypes of A. gallica were grouped into four clusters and the genotypes of A. cepistipes were grouped into three clusters. This study showed that there is genetic diversity among the genotypes of A. cepistipes and A. gallica that are symbiotic with P. umbellatus.
