101
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Physisporinus is an important mycorrhizal partner for mycoheterotrophic plants: Identification of mycorrhizal fungi of three Yoania species. MYCOSCIENCE 2020. [DOI: 10.1016/j.myc.2020.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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102
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Du P, Wu F, Tian XM. Three new species of Junghuhnia (Polyporales, Basidiomycota) from China. MycoKeys 2020; 72:1-16. [PMID: 32879617 PMCID: PMC7442768 DOI: 10.3897/mycokeys.72.51872] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/30/2020] [Indexed: 11/12/2022] Open
Abstract
In this study, taxonomic and phylogenetic analyses of Junghuhnia were performed. Three new species were characterised according to morphological characteristics and molecular phylogenetic analysis using ITS and nLSU sequences. They are J. austrosinensis sp. nov., J. nandinae sp. nov. and J. subcollabens sp. nov. Junghuhnia austrosinensis is characterised by resupinate, thin basidiomata with white to buff-yellow hymenophore, small pores (9-11 per mm), clamped generative hyphae possessing hymenial cystidia, ellipsoid basidiospores (2.5-3 × 1.7-2 µm) and growth on fallen bamboo or angiosperm branch. Junghuhnia nandinae is characterised by resupinate basidiomata with pink to salmon pores and a distinct white margin, clamp generative hyphae, interwoven tramal hyphae, ellipsoid basidiospores measuring 2.6-3.2 × 1.8-2 µm and growth on Nandina domestica. Junghuhnia subcollabens is characterised by resupinate basidiomata with pale salmon to brownish vinaceous hymenophore, small pores (10-12 per mm), generative hyphae with simple septa and clamp connections, interwoven tramal hyphae, lunate basidiospores measuring 2.9-3.4 × 1.6-1.8 µm and thriving on rotten wood of angiosperms.
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Affiliation(s)
- Ping Du
- College of Life Science and Technology, Yangtze Normal University, Chongqing 408100, ChinaYangtze Normal UniversityChongqingChina
| | - Fang Wu
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing 100083, ChinaBeijing Forestry UniversityBeijingChina
| | - Xue-Mei Tian
- Shandong Provincial Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao 266109, ChinaQingdao Agricultural UniversityQingdaoChina
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103
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Three new species of Phlebia (Polyporales, Basidiomycota) based on the evidence from morphology and DNA sequence data. Mycol Prog 2020. [DOI: 10.1007/s11557-020-01591-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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104
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Costa-Rezende DH, Robledo GL, Drechsler-Santos ER, Glen M, Gates G, de Madrignac Bonzi BR, Popoff OF, Crespo E, Góes-Neto A. Taxonomy and phylogeny of polypores with ganodermatoid basidiospores (Ganodermataceae). Mycol Prog 2020. [DOI: 10.1007/s11557-020-01589-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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105
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Ma X, Huang RX, Zhang Y, Zhao CL. WITHDRAWN: Hyphoderma fissuratum and H. mopanshanense spp. nov. (Polyporales) from southern China. MYCOSCIENCE 2020. [DOI: 10.1016/j.myc.2020.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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106
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Robledo GL, Palacio M, Urcelay C, Vasco-Palacios AM, Crespo E, Popoff O, Põldmaa K, Ryvarden L, Costa-Rezende DH. Mystery unveiled: Diacanthodes Singer – a lineage within the core polyporoid clade. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1776784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Gerardo Lucio Robledo
- BioTecA3 – Centro de Biotecnología Aplicada al Agro y Alimentos, Facultad de Ciencias, Agropecuarias – Univ. Nac. de Córdoba, Ing. Agr. Félix Aldo Marrone 746 – Planta Baja CC509 – CP 5000, Ciudad Universitaria, Córdoba, Argentina
- CONICET, Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina
- Fundación Fungicosmos, www.fungicosmos.org, Córdoba, Argentina
| | - Melissa Palacio
- Programa de Pós-Graduação em Botânica, Laboratório de Micologia, Departamento de Botânica, Universidade Federal do Rio Grande do Sul, Campus do Vale, CEP: 91501-970, Porto Alegre, Rio Grande do Sul, Brazil
| | - Carlos Urcelay
- Instituto Multidisciplinario de Biología Vegetal, Universidad Nacional de Córdoba, C.C.495, Córdoba, 5000, Argentina
| | - Aída M. Vasco-Palacios
- School of Microbiology, Microbiología Ambiental Group-BioMicro, University of Antioquia, Medellín, A.A.1226, Colombia
| | - Esteban Crespo
- Laboratorio de Microscopía Electrónica y Microanálisis (LABMEM) – CCT San Luis (CONICET), Universidad Nacional de San Luis, San Luis, Argentina
| | - Orlando Popoff
- Instituto de Botánica del Nordeste, Laboratorio de Micología, Universidad Nacional del Nordeste – CONICET, Corrientes, CC 209, (3400), Argentina
| | - Kadri Põldmaa
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, EE-51005, Estonia
| | - Leif Ryvarden
- Institute of Biological Sciences, University of Oslo, P.O. Box 1045, Blindern, Oslo, 0316, Norway
| | - Diogo H. Costa-Rezende
- Instituto de Ciências Biológicas (ICB), Departamento de Microbiologia, Laboratório de Biologia Molecular e Computacional de Fungos (LBMCF), Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Belo Horizonte, 31270-901, MG, Brazil
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107
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Ecology, Phylogeny, and Potential Nutritional and Medicinal Value of a Rare White “Maitake” Collected in a Mediterranean Forest. DIVERSITY 2020. [DOI: 10.3390/d12060230] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Albino Grifola frondosa (Dicks.) Gray “maitake” mushrooms (described as G. albicans Imazeki and then placed in synonymy with G. frondosa) are particularly rare, and the few pertinent records are not treated in scientific publications. A field investigation carried out in Sicily (Italy) led to the collection of an unusual white Grifola specimen at the base of a living tree of Quercus pubescens Willd. s.l. The outcome of sequencing the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA) indicated that it belongs to G. frondosa and provided an insight to the phylogenetic relationships within the genus. The results of nutritional composition analysis showed that the albino basidioma possesses relatively high contents of Ca, Fe, K, and Cu and is rather low in Na when compared with literature data on edible mushrooms. Vitamin (B1, B2, B3, B5, B9, and D2) contents ranged from 0.15 to 3.89 mg per 100 g of mushroom dry weight. The cold-water extract of this specimen was effective at inhibiting the growth of Staphylococcus epidermidis ATCC 12228 and Pseudomonas aeruginosa ATCC 15442 at the maximum screening concentration of 50% v/v. In addition, the extract slowed down the ability of Staphylococcus aureus ATCC 43300 to form biofilms. According to data hereby reported, the albino G. frondosa is a culinary-medicinal mushroom with a promising exploitation potential.
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108
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Oghenekaro AO, Kovalchuk A, Raffaello T, Camarero S, Gressler M, Henrissat B, Lee J, Liu M, Martínez AT, Miettinen O, Mihaltcheva S, Pangilinan J, Ren F, Riley R, Ruiz-Dueñas FJ, Serrano A, Thon MR, Wen Z, Zeng Z, Barry K, Grigoriev IV, Martin F, Asiegbu FO. Genome sequencing of Rigidoporus microporus provides insights on genes important for wood decay, latex tolerance and interspecific fungal interactions. Sci Rep 2020; 10:5250. [PMID: 32251355 PMCID: PMC7089950 DOI: 10.1038/s41598-020-62150-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/10/2020] [Indexed: 11/27/2022] Open
Abstract
Fungal plant pathogens remain a serious threat to the sustainable agriculture and forestry, despite the extensive efforts undertaken to control their spread. White root rot disease is threatening rubber tree (Hevea brasiliensis) plantations throughout South and Southeast Asia and Western Africa, causing tree mortality and severe yield losses. Here, we report the complete genome sequence of the basidiomycete fungus Rigidoporus microporus, a causative agent of the disease. Our phylogenetic analysis confirmed the position of R. microporus among the members of Hymenochaetales, an understudied group of basidiomycetes. Our analysis further identified pathogen's genes with a predicted role in the decay of plant cell wall polymers, in the utilization of latex components and in interspecific interactions between the pathogen and other fungi. We also detected putative horizontal gene transfer events in the genome of R. microporus. The reported first genome sequence of a tropical rubber tree pathogen R. microporus should contribute to the better understanding of how the fungus is able to facilitate wood decay and nutrient cycling as well as tolerate latex and utilize resinous extractives.
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Affiliation(s)
- Abbot O Oghenekaro
- Faculty of Life Sciences, Department of Plant Biology and Biotechnology, University of Benin, P.M.B 1154, Benin City, Nigeria
- Faculty of Agriculture and Forestry, Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014, Helsinki, Finland
- Department of Plant Science, University of Manitoba, MB R3T 2N2, Winnipeg, Canada
| | - Andriy Kovalchuk
- Faculty of Agriculture and Forestry, Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014, Helsinki, Finland
| | - Tommaso Raffaello
- Faculty of Agriculture and Forestry, Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014, Helsinki, Finland
| | - Susana Camarero
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, E28040, Madrid, Spain
| | - Markus Gressler
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich Schiller University, Jena, Germany
| | - Bernard Henrissat
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, CNRS, UMR 7257, 13288, Marseille, cedex 9, France
- USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, 23218, Jeddah, Saudi Arabia
| | - Juna Lee
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Mengxia Liu
- Faculty of Agriculture and Forestry, Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014, Helsinki, Finland
| | - Angel T Martínez
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, E28040, Madrid, Spain
| | - Otto Miettinen
- Mycology Unit, Botanical Museum, Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, Helsinki, Finland
| | - Sirma Mihaltcheva
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Fei Ren
- Faculty of Agriculture and Forestry, Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014, Helsinki, Finland
- Forestry experiment center of north China, Chinese Academy of Forestry, 102300, Beijing, China
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Francisco Javier Ruiz-Dueñas
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, E28040, Madrid, Spain
| | - Ana Serrano
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, E28040, Madrid, Spain
| | - Michael R Thon
- Universidad de Salamanca, Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Villamayor, Spain
| | - Zilan Wen
- Faculty of Agriculture and Forestry, Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014, Helsinki, Finland
| | - Zhen Zeng
- Faculty of Agriculture and Forestry, Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014, Helsinki, Finland
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Francis Martin
- Institut National de la Recherche Agronomique (INRA), Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE), UMR 1136, Champenoux, France
- University of Lorraine, Laboratory of Excellence ARBRE, UMR 1136, Champenoux, France
| | - Fred O Asiegbu
- Faculty of Agriculture and Forestry, Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014, Helsinki, Finland.
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109
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Cerebrosides and Steroids from the Edible Mushroom Meripilus giganteus with Antioxidant Potential. Molecules 2020; 25:molecules25061395. [PMID: 32204362 PMCID: PMC7144561 DOI: 10.3390/molecules25061395] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/16/2020] [Accepted: 03/18/2020] [Indexed: 11/17/2022] Open
Abstract
The detailed chemical analysis of the methanol extract of Meripilus giganteus (Pers.) P. Karst. led to the isolation of two new cerebrosides, mericeramides A (1) and B (2) together with cerebroside B (3), ergosterol (4), 3β-hydroxyergosta-7,22-diene (5), cerevisterol (6), 3β-hydroxyergosta-6,8(14),22-triene (7), 3β-O-glucopyranosyl-5,8-epidioxyergosta-6,22-diene (8) and (11E,13E)-9,10-dihydroxy-11,13-octadecadienoic acid (9). The structures of the compounds were determined on the basis of NMR and MS spectroscopic analysis. Mericeramide A (1) is the first representative of halogenated natural cerebrosides. The isolated fungal metabolites 1-9 were evaluated for their antioxidant activity using the oxygen radical absorbance capacity (ORAC) assay. Compounds 2, 5 and 9 proved to possess considerable antioxidant effects, with 2.50 ± 0.29, 4.94 ± 0.37 and 4.27 ± 0.05 mmol TE/g values, respectively. The result obtained gives a notable addition to the chemical and bioactivity profile of M. giganteus, highlighting the possible contribution of this species to a versatile and balanced diet.
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110
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Guan QX, Zhao TJ, Zhao CL. Morphological characters and phylogenetic analyses reveal two new species of Peniophorella from southern China. Mycol Prog 2020. [DOI: 10.1007/s11557-020-01568-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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111
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Wickramasinghe PCK, Munafo JP. Biosynthesis of Benzylic Derivatives in the Fermentation Broth of the Edible Mushroom, Ischnoderma resinosum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:2485-2492. [PMID: 32049524 DOI: 10.1021/acs.jafc.9b07218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Employing isotope incubation studies, the biosynthetic pathway leading to a series of benzylic derivatives was elucidated in the fermentation broth of the edible mushroom Ischnoderma resinosum (P. Karst). Twenty-six hydroxy- and methoxy- benzylic derivatives were screened by gas chromatography-mass spectrometry (GC-MS) of which 13 were detected in the culture media. Results from the isotope incubation studies showed the transformation of both benzyl alcohol and benzoic acid into benzaldehyde. Benzaldehyde was then converted into 4-methoxybenzaldehyde via hydroxylation and subsequent methylation of the 4-C position. The resulting 4-methoxybenzaldehyde was then hydroxylated in the 3-C position followed by methylation into 3,4-dimethoxybenzaldehyde. Based on these findings, a novel metabolic scheme for the biosynthesis of benzylic derivatives in I. resinosum was proposed. The knowledge of the biosynthetic pathway was utilized to produce 4-hydroxy-3-methoxybenzaldehyde (vanillin) from 4-hydroxy-3-methoxybenzoic acid (vanillic acid). This is the first report to elucidate the biosynthetic pathway of benzyl derivatives and production of vanillin from I. resinosum.
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Affiliation(s)
- Purni C K Wickramasinghe
- Department of Food Science , The University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - John P Munafo
- Department of Food Science , The University of Tennessee , Knoxville , Tennessee 37996 , United States
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112
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Zhang Y, Wang J, Yajun C, Zhou M, Wang W, Geng M, Xu D, Xu Z. Comparative Genomics Uncovers the Genetic Diversity and Synthetic Biology of Secondary Metabolite Production of Trametes. MYCOBIOLOGY 2020; 48:104-114. [PMID: 32363038 PMCID: PMC7178859 DOI: 10.1080/12298093.2020.1725361] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 01/02/2020] [Accepted: 01/22/2020] [Indexed: 05/27/2023]
Abstract
The carbohydrate-active enzyme (CAZyme) genes of Trametes contribute to polysaccharide degradation. However, the comprehensive analysis of the composition of CAZymes and the biosynthetic gene clusters (BGCs) of Trametes remain unclear. Here, we conducted comparative analysis, detected the CAZyme genes, and predicted the BGCs for nine Trametes strains. Among the 82,053 homologous clusters obtained for Trametes, we identified 8518 core genes, 60,441 accessory genes, and 13,094 specific genes. A large proportion of CAZyme genes were cataloged into glycoside hydrolases, glycosyltransferases, and carbohydrate esterases. The predicted BGCs of Trametes were divided into six strategies, and the nine Trametes strains harbored 47.78 BGCs on average. Our study revealed that Trametes exhibits an open pan-genome structure. These findings provide insights into the genetic diversity and explored the synthetic biology of secondary metabolite production for Trametes.
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Affiliation(s)
- Yan Zhang
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Jingjing Wang
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Chen Yajun
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Minghui Zhou
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Wei Wang
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Ming Geng
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Decong Xu
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Zhongdong Xu
- School of Life Sciences, Hefei Normal University, Hefei, China
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113
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Chen CC, Chen CY, Lim YW, Wu SH. Phylogeny and taxonomy of Ceriporia and other related taxa and description of three new species. Mycologia 2020; 112:64-82. [PMID: 31906813 DOI: 10.1080/00275514.2019.1664097] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Species of Ceriporia (Irpicaceae, Basidiomycota) are saprotrophs or endophytes in forest ecosystems. To evaluate the taxonomy and generic relationships of Ceriporia and other related taxa, we used morphology and multigene phylogenetic analyses based on sequence data from nuc rDNA internal transcribed spacer ITS1-5.8S-ITS2 (ITS) region, nuc 28S rDNA (28S), and RNA polymerase II largest subunit (rpb1). Our results show that Ceriporia sensu lato is polyphyletic and distributed across multiple clades in the Irpicaceae, Phanerochaetaceae, and Meruliaceae. Some species previously considered in Ceriporia are now recovered in Meruliopsis, resulting in four new combinations: M. albomellea, M. crassitunicata, M. nanlingensis, and M. pseudocystidiata. Two new species of Meruliopsis are described: M. leptocystidiata from northeast China and South Korea and M. parvispora from Taiwan. Ceriporia arbuscula is described as a new species from Taiwan. Ceriporia mellita and Meruliopsis nanlingensis are newly recorded from Japan and Taiwan, and M. taxicola is recorded from Taiwan for the first time.
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Affiliation(s)
- Che-Chih Chen
- Department of Plant Pathology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Chi-Yu Chen
- Department of Plant Pathology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Young Woon Lim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, Republic of Korea
| | - Sheng-Hua Wu
- Department of Plant Pathology, National Chung Hsing University, Taichung 40227, Taiwan.,Department of Biology, National Museum of Natural Science, Taichung 40419, Taiwan
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114
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Nguyen KA, Kumla J, Suwannarach N, Penkhrue W, Lumyong S. Optimization of high endoglucanase yields production from polypore fungus, Microporus xanthopus strain KA038 under solid-state fermentation using green tea waste. Biol Open 2019; 8:bio.047183. [PMID: 31784423 PMCID: PMC6899011 DOI: 10.1242/bio.047183] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Polypores are diverse macrofungi that have been extensively studied for their lignocellulolytic enzyme production capabilities. Currently, these enzymes are being used for many industrial purposes. However, the high cost associated with their production is the main barrier to their broader application. This work aimed to study the optimal medium and conditions for endoglucanase production using solid state fermentation. Seven polypore strains were used for endoglucanase activity screening. The fermentation experiments were carried out in 250 ml Erlenmeyer flasks with green tea waste as a substrate. Notably, Microporus xanthopus strain KA038 showed the best level of activity (38.62 IU/gds). Various parameters such as moisture content, nitrogen source, initial pH value, inoculum size and incubation time were considered to determine the optimal conditions for endoglucanase production. The optimal medium consisted of green tea leaves as a carbon source, beef extract as an organic nitrogen source, NH4H2PO4 as an inorganic nitrogen source, pH 7.0 and an incubation temperature at 30°C for 4 days resulted in a high enzyme yield with M. xanthopus strain KA038 (81.8 IU/gds).This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Kim Anh Nguyen
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand.,Master's Degree Program in Applied Microbiology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jaturong Kumla
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand.,Center of Excellence in Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nakarin Suwannarach
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand.,Center of Excellence in Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Watsana Penkhrue
- School of Preclinic, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Saisamorn Lumyong
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand .,Center of Excellence in Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand.,Academy of Science, The Royal Society of Thailand, Dusit, Bangkok 10300, Thailand
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115
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He MQ, Zhao RL, Hyde KD, Begerow D, Kemler M, Yurkov A, McKenzie EHC, Raspé O, Kakishima M, Sánchez-Ramírez S, Vellinga EC, Halling R, Papp V, Zmitrovich IV, Buyck B, Ertz D, Wijayawardene NN, Cui BK, Schoutteten N, Liu XZ, Li TH, Yao YJ, Zhu XY, Liu AQ, Li GJ, Zhang MZ, Ling ZL, Cao B, Antonín V, Boekhout T, da Silva BDB, De Crop E, Decock C, Dima B, Dutta AK, Fell JW, Geml J, Ghobad-Nejhad M, Giachini AJ, Gibertoni TB, Gorjón SP, Haelewaters D, He SH, Hodkinson BP, Horak E, Hoshino T, Justo A, Lim YW, Menolli N, Mešić A, Moncalvo JM, Mueller GM, Nagy LG, Nilsson RH, Noordeloos M, Nuytinck J, Orihara T, Ratchadawan C, Rajchenberg M, Silva-Filho AGS, Sulzbacher MA, Tkalčec Z, Valenzuela R, Verbeken A, Vizzini A, Wartchow F, Wei TZ, Weiß M, Zhao CL, Kirk PM. Notes, outline and divergence times of Basidiomycota. FUNGAL DIVERS 2019. [DOI: 10.1007/s13225-019-00435-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AbstractThe Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.
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Moiseenko KV, Glazunova OA, Shakhova NV, Savinova OS, Vasina DV, Tyazhelova TV, Psurtseva NV, Fedorova TV. Fungal Adaptation to the Advanced Stages of Wood Decomposition: Insights from the Steccherinum ochraceum. Microorganisms 2019; 7:E527. [PMID: 31694151 PMCID: PMC6921079 DOI: 10.3390/microorganisms7110527] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 10/29/2019] [Accepted: 10/31/2019] [Indexed: 12/15/2022] Open
Abstract
Steccherinum ochraceum is a white rot basidiomycete with wide ecological amplitude. It occurs in different regions of Russia and throughout the world, occupying different climatic zones. S. ochraceum colonizes stumps, trunks, and branches of various deciduous (seldom coniferous) trees. As a secondary colonizing fungus, S. ochraceum is mainly observed at the late decay stages. Here, we present the de novo assembly and annotation of the genome of S. ochraceum, LE-BIN 3174. This is the 8th published genome of fungus from the residual polyporoid clade and the first from the Steccherinaceae family. The obtained genome provides a first glimpse into the genetic and enzymatic mechanisms governing adaptation of S. ochraceum to an ecological niche of pre-degraded wood. It is proposed that increased number of carbohydrate-active enzymes (CAZymes) belonging to the AA superfamily and decreased number of CAZymes belonging to the GH superfamily reflects substrate preferences of S. ochraceum. This proposition is further substantiated by the results of the biochemical plate tests and exoproteomic study, which demonstrates that S. ochraceum assumes the intermediate position between typical primary colonizing fungi and litter decomposers or humus saprotrophs. Phylogenetic analysis of S. ochraceum laccase and class II peroxidase genes revealed the distinct evolutional origin of these genes in the Steccherinaceae family.
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Affiliation(s)
- Konstantin V. Moiseenko
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, Russia; (O.A.G.); (O.S.S.); (D.V.V.)
| | - Olga A. Glazunova
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, Russia; (O.A.G.); (O.S.S.); (D.V.V.)
| | - Natalia V. Shakhova
- Komarov Botanical Institute of the Russian Academy of Sciences, Professor Popov St. 2, St. Petersburg 197376, Russia;
| | - Olga S. Savinova
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, Russia; (O.A.G.); (O.S.S.); (D.V.V.)
| | - Daria V. Vasina
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, Russia; (O.A.G.); (O.S.S.); (D.V.V.)
| | - Tatiana V. Tyazhelova
- N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119071, Russia;
| | - Nadezhda V. Psurtseva
- Komarov Botanical Institute of the Russian Academy of Sciences, Professor Popov St. 2, St. Petersburg 197376, Russia;
| | - Tatiana V. Fedorova
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, Russia; (O.A.G.); (O.S.S.); (D.V.V.)
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117
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Luangharn T, Karunarathna SC, Mortimer PE, Hyde KD, Xu J. Additions to the knowledge of Ganoderma in Thailand: Ganoderma casuarinicola, a new record; and Ganoderma thailandicum sp. nov. MycoKeys 2019; 59:47-65. [PMID: 31662620 PMCID: PMC6811390 DOI: 10.3897/mycokeys.59.36823] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 09/05/2019] [Indexed: 11/19/2022] Open
Abstract
Ganoderma is a cosmopolitan genus of mushrooms, which can cause root and butt rot diseases on many tree species. Members of this genus are particularly diverse in tropical regions. Some Ganoderma spp. are medicinally active and therefore are used to treat human diseases or as a dietary supplement. In this study, three Ganoderma strains were collected in tropical southern Thailand. Phylogenetic analyses of combined ITS, LSU, TEF1α and RPB2 sequence data indicated that the three strains grouped in a distinct lineage within laccate Ganoderma. One strain was collected from Surat Thani Province clustered in the G.casuarinicola clade with high statistical support (MLBS = 100% / MPBS = 98% / PP = 0.96), while the other two strains of Ganoderma, collected from Nakhon Si Thammarat Province, formed a distinct well-supported clade (MLBS = 100% / MPBS = 100% / PP = 1.00) and are described here as a new species. Ganodermacasuarinicola is reported here as a new record to Thailand. Morphological differences of the two taxa and their closely related taxa are discussed. Colour photographs of macro and micro morphological characteristics and a phylogenetic tree to show the placement of the new record and new species are provided.
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Affiliation(s)
- Thatsanee Luangharn
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,East and Central Asia Regional Office, World Agroforestry Centre (ICRAF), Kunming 650201, Yunnan, China.,Centre for Mountain Futures (CMF), Kunming Institute of Botany, Kunming 650201, Yunnan, China
| | - Samantha C Karunarathna
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China.,East and Central Asia Regional Office, World Agroforestry Centre (ICRAF), Kunming 650201, Yunnan, China.,Centre for Mountain Futures (CMF), Kunming Institute of Botany, Kunming 650201, Yunnan, China
| | - Peter E Mortimer
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China.,Centre for Mountain Futures (CMF), Kunming Institute of Botany, Kunming 650201, Yunnan, China
| | - Kevin D Hyde
- East and Central Asia Regional Office, World Agroforestry Centre (ICRAF), Kunming 650201, Yunnan, China.,Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Jianchu Xu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China.,East and Central Asia Regional Office, World Agroforestry Centre (ICRAF), Kunming 650201, Yunnan, China.,Centre for Mountain Futures (CMF), Kunming Institute of Botany, Kunming 650201, Yunnan, China
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118
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Peintner U, Kuhnert-Finkernagel R, Wille V, Biasioli F, Shiryaev A, Perini C. How to resolve cryptic species of polypores: an example in Fomes. IMA Fungus 2019; 10:17. [PMID: 32647621 PMCID: PMC7325651 DOI: 10.1186/s43008-019-0016-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/27/2019] [Indexed: 01/02/2023] Open
Abstract
Species that cannot be easily distinguished based on morphology, but which form distinct phylogenetic lineages based on molecular markers, are often referred to as cryptic species. They have been proposed in a number of fungal genera, including the basidiomycete genus Fomes. The main aim of this work was to test new methods for species delimitation in cryptic lineages of polypores, and to define useful characters for species identification. A detailed examination of a number of different Fomes strains that had been collected and isolated from different habitats in Italy and Austria confirmed the presence of distinct lineages in the Fomes fomentarius clade. Our zero hypothesis was that the Mediterranean strains growing on Quercus represent a species which can be delimited based on morphological and physiological characters when they are evaluated in statistically relevant numbers. This hypothesis was tested based on phylogenetic analysis of the rDNA ITS region, morphological characters of basidiomes and pure cultures, growth rates and optimum growth temperature experiments, mycelial confrontation tests, enzyme activity tests and volatile organic compound (VOC) production. The Mediterranean lineage can unambiguously be delimited from F. fomentarius. A syntype of an obscure and previously synonymized name, Polyporus inzengae, represents the Mediterranean lineage that we recognize as Fomes inzengae, a distinct species. The rDNA ITS region is useful for delimitation of Fomes species. Moreover, also a variety of morphological characters including hymenophore pore size, basidiospore size, and diameter of skeletal hyphae are useful delimiting characters. The ecology is also very important, because the plant host appears to be a central factor driving speciation. Physiological characters turned also out to be species-specific, e.g. daily mycelial growth rates or the temperature range of pure cultures. The production of VOCs can be considered as a very promising tool for fast and reliable species delimitation in the future.
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Affiliation(s)
- Ursula Peintner
- University Innsbruck, Institute of Microbiology, Technikerstr. 25, 6020 Innsbruck, Austria
| | | | - Viana Wille
- University Innsbruck, Institute of Microbiology, Technikerstr. 25, 6020 Innsbruck, Austria
| | - Franco Biasioli
- Food Quality and Nutrition Department, Edmund Mach Foundation, Via Edmund Mach 1, 38010 San Michele all’ Adige, Italy
| | - Anton Shiryaev
- Vegetation & Mycobiota Diversity Department, Institute of Plant and Animal Ecology (IPAE), Ural Branch of the Russian Academy of Sciences (UrB RAS), 8 March str., 202/3, 620144 Ekaterinburg, Russia
| | - Claudia Perini
- Department of Life Sciences, University Siena, 53100 Siena, Italy
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119
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Westphalen MC, Tomšovský M, Gugliotta AM, Rajchenberg M. An overview of Antrodiella and related genera of Polyporales from the Neotropics. Mycologia 2019; 111:813-831. [PMID: 31525126 DOI: 10.1080/00275514.2019.1633895] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The genus Antrodiella includes resupinate and pileate species of polypores with a dimitic hyphal system, small, globose to cylindrical basidiospores, absence of cystidia, tetrapolar mating system, and haplo-dikaryotic nuclear behavior. Recent studies, however, indicate that Antrodiella is highly polyphyletic, so many of its species have been transferred to other genera. This study reviews the systematic status and diversity of Antrodiella from the Neotropics based, in part, on studies of type specimens. Collections from Brazil were used for molecular analysis of nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS), nuc 28S rDNA (28S), and portions of genes encoding translation elongation factor 1-α (tef1) and the second largest subunit of RNA polymerase II (rpb2). Eight genera are confirmed to include Neotropical species treated as Antrodiella in a broad sense: Aegis, Antrodiella s. str., Flaviporus, Metuloidea, Mycorrhaphium, Rickiopora, Trametopsis, and Trullella. Molecular data reveal the occurrence of two new species, described as Antrodiella trivialis, the only Neotropical species of Antrodiella s. str. known so far, and Mycorrhaphium hispidum. In addition, Antrodiella luteocontexta was found to nest in the genus Aegis, close to the Grifolaceae and Polyporaceae; therefore, the new combination Aegis luteocontexta is proposed. Comments on the eight Antrodiella-related genera as well as species with uncertain taxonomic position are provided, together with a key to their identification.
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Affiliation(s)
- Mauro C Westphalen
- Núcleo de Pesquisa em Micologia, Instituto de Botânica , Av. Miguel Estefano 3687, 04301-902 , São Paulo , São Paulo , Brazil
| | - Michal Tomšovský
- Faculty of Forestry and Wood Technology, Mendel University in Brno , Zemědělská 3, CZ-61300 , Czech Republic
| | - Adriana M Gugliotta
- Núcleo de Pesquisa em Micologia, Instituto de Botânica , Av. Miguel Estefano 3687, 04301-902 , São Paulo , São Paulo , Brazil
| | - Mario Rajchenberg
- National Research Council of Argentina (CONICET) and Área de Protección Forestal, Centro de Investigación y Extensión Forestal Andino Patagónico , C.C. 14, 9200 Esquel , Chubut , Argentina
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120
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Runnel K, Spirin V, Miettinen O, Vlasák J, Dai YC, Ryvarden L, Larsson KH. Morphological plasticity in brown-rot fungi: Antrodia is redefined to encompass both poroid and corticioid species. Mycologia 2019; 111:871-883. [PMID: 31433734 DOI: 10.1080/00275514.2019.1640532] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Most known brown rot-producing species of Polyporales belong to the so-called "Antrodia clade" that largely consists of poroid species. In this study, we use three genetic markers to revise Antrodia s. str., the core group of this clade. We show that a corticioid species with a smooth hymenophore, Phlebia griseoflavescens, belongs to Antrodia s. str. Accordingly, we revise the generic concept of Antrodia s. str. to accommodate this species and two recently described poroid taxa, A. tenerifensis and A. multiformis. In addition, we describe two new poroid species within Antrodia s. str., A. latebrosa from Africa and A. peregrina from East Asia, and provide new documentation for the Southeast Asian species A. parvula based on recent collections from the type location.
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Affiliation(s)
- Kadri Runnel
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu , Lai 40, EE-51015 Tartu , Estonia
| | - Viacheslav Spirin
- Botanical Unit (Mycology), Finnish Museum of Natural History, University of Helsinki , P.O. Box 7, FI-00014 , Helsinki , Finland
| | - Otto Miettinen
- Botanical Unit (Mycology), Finnish Museum of Natural History, University of Helsinki , P.O. Box 7, FI-00014 , Helsinki , Finland
| | - Josef Vlasák
- Biology Centre of the Academy of Sciences of the Czech Republic , Branišovská 31, 370 05 České Budějovice , Czech Republic
| | - Yu-Cheng Dai
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University , Beijing 100083 , China
| | - Leif Ryvarden
- Natural History Museum, University of Oslo , P.O. Box 1172, NO-0318 Oslo , Norway
| | - Karl-Henrik Larsson
- Natural History Museum, University of Oslo , P.O. Box 1172, NO-0318 Oslo , Norway
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121
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Fungal diversity notes 1036–1150: taxonomic and phylogenetic contributions on genera and species of fungal taxa. FUNGAL DIVERS 2019. [DOI: 10.1007/s13225-019-00429-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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122
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Mäkinen M, Kuuskeri J, Laine P, Smolander OP, Kovalchuk A, Zeng Z, Asiegbu FO, Paulin L, Auvinen P, Lundell T. Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi. BMC Genomics 2019; 20:430. [PMID: 31138126 PMCID: PMC6540522 DOI: 10.1186/s12864-019-5817-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/21/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The white rot fungus Phlebia radiata, a type species of the genus Phlebia, is an efficient decomposer of plant cell wall polysaccharides, modifier of softwood and hardwood lignin, and is able to produce ethanol from various waste lignocellulose substrates. Thus, P. radiata is a promising organism for biotechnological applications aiming at sustainable utilization of plant biomass. Here we report the genome sequence of P. radiata isolate 79 originally isolated from decayed alder wood in South Finland. To better understand the evolution of wood decay mechanisms in this fungus and the Polyporales phlebioid clade, gene content and clustering of genes encoding specific carbohydrate-active enzymes (CAZymes) in seven closely related fungal species was investigated. In addition, other genes encoding proteins reflecting the fungal lifestyle including peptidases, transporters, small secreted proteins and genes involved in secondary metabolism were identified in the genome assembly of P. radiata. RESULTS The PACBio sequenced nuclear genome of P. radiata was assembled to 93 contigs with 72X sequencing coverage and annotated, revealing a dense genome of 40.4 Mbp with approximately 14 082 predicted protein-coding genes. According to functional annotation, the genome harbors 209 glycoside hydrolase, 27 carbohydrate esterase, 8 polysaccharide lyase, and over 70 auxiliary redox enzyme-encoding genes. Comparisons with the genomes of other phlebioid fungi revealed shared and specific properties among the species with seemingly similar saprobic wood-decay lifestyles. Clustering of especially GH10 and AA9 enzyme-encoding genes according to genomic localization was discovered to be conserved among the phlebioid species. In P. radiata genome, a rich repertoire of genes involved in the production of secondary metabolites was recognized. In addition, 49 genes encoding predicted ABC proteins were identified in P. radiata genome together with 336 genes encoding peptidases, and 430 genes encoding small secreted proteins. CONCLUSIONS The genome assembly of P. radiata contains wide array of carbohydrate polymer attacking CAZyme and oxidoreductase genes in a composition identifiable for phlebioid white rot lifestyle in wood decomposition, and may thus serve as reference for further studies. Comparative genomics also contributed to enlightening fungal decay mechanisms in conversion and cycling of recalcitrant organic carbon in the forest ecosystems.
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Affiliation(s)
- Mari Mäkinen
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Campus, University of Helsinki, FI-00014, Helsinki, Finland.,Present address: VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | - Jaana Kuuskeri
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Campus, University of Helsinki, FI-00014, Helsinki, Finland
| | - Pia Laine
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, Viikki Campus, FI-00014, Helsinki, Finland
| | - Olli-Pekka Smolander
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, Viikki Campus, FI-00014, Helsinki, Finland.,Present address: Department of Chemistry and Biotechnology, Division of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Andriy Kovalchuk
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Viikki Campus, FI-00014, Helsinki, Finland
| | - Zhen Zeng
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Viikki Campus, FI-00014, Helsinki, Finland
| | - Fred O Asiegbu
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Viikki Campus, FI-00014, Helsinki, Finland
| | - Lars Paulin
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, Viikki Campus, FI-00014, Helsinki, Finland
| | - Petri Auvinen
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, Viikki Campus, FI-00014, Helsinki, Finland
| | - Taina Lundell
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Campus, University of Helsinki, FI-00014, Helsinki, Finland.
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123
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Crepatura ellipsospora gen. et sp. nov. in Phanerochaetaceae (Polyporales, Basidiomycota) bearing a tuberculate hymenial surface. Mycol Prog 2019. [DOI: 10.1007/s11557-019-01488-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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124
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125
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Phookamsak R, Hyde KD, Jeewon R, Bhat DJ, Jones EBG, Maharachchikumbura SSN, Raspé O, Karunarathna SC, Wanasinghe DN, Hongsanan S, Doilom M, Tennakoon DS, Machado AR, Firmino AL, Ghosh A, Karunarathna A, Mešić A, Dutta AK, Thongbai B, Devadatha B, Norphanphoun C, Senwanna C, Wei D, Pem D, Ackah FK, Wang GN, Jiang HB, Madrid H, Lee HB, Goonasekara ID, Manawasinghe IS, Kušan I, Cano J, Gené J, Li J, Das K, Acharya K, Raj KNA, Latha KPD, Chethana KWT, He MQ, Dueñas M, Jadan M, Martín MP, Samarakoon MC, Dayarathne MC, Raza M, Park MS, Telleria MT, Chaiwan N, Matočec N, de Silva NI, Pereira OL, Singh PN, Manimohan P, Uniyal P, Shang QJ, Bhatt RP, Perera RH, Alvarenga RLM, Nogal-Prata S, Singh SK, Vadthanarat S, Oh SY, Huang SK, Rana S, Konta S, Paloi S, Jayasiri SC, Jeon SJ, Mehmood T, Gibertoni TB, Nguyen TTT, Singh U, Thiyagaraja V, Sarma VV, Dong W, Yu XD, Lu YZ, Lim YW, Chen Y, Tkalčec Z, Zhang ZF, Luo ZL, Daranagama DA, Thambugala KM, Tibpromma S, Camporesi E, Bulgakov TS, Dissanayake AJ, Senanayake IC, Dai DQ, Tang LZ, Khan S, Zhang H, Promputtha I, Cai L, Chomnunti P, Zhao RL, Lumyong S, Boonmee S, Wen TC, Mortimer PE, Xu J. Fungal diversity notes 929–1035: taxonomic and phylogenetic contributions on genera and species of fungi. FUNGAL DIVERS 2019. [DOI: 10.1007/s13225-019-00421-w] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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126
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Distribution and conservation status of Grifola frondosa (Polyporales, Basidiomycota) in Ukraine. UKRAINIAN BOTANICAL JOURNAL 2019. [DOI: 10.15407/ukrbotj76.02.144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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127
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Wickramasinghe PCK, Munafo JP. Key Odorants from the Fermentation Broth of the Edible Mushroom Ischnoderma resinosum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:2036-2042. [PMID: 30735043 DOI: 10.1021/acs.jafc.8b06766] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Eighteen odorants were identified by applying aroma extract dilution analysis in the liquid fermentation broth of the edible mushroom Ischnoderma resinosum (P. Karst). Eight compounds with flavor dilution factors ≥16 were quantitated in a 16-day sample using stable isotope dilution assays. Odor activity values (OAV) revealed anise-smelling 4-methoxybenzaldehyde (OAV; 1639), vanilla-smelling 3,4-dimethoxybenzaldehyde (OAV; 51), and cherry-smelling benzaldehyde (OAV; 14) as key contributors to the pleasant "candy-like" odor of the fermentation broth. Odor simulation experiments revealed a mixture of five compounds in their natural concentrations mimicked the odor of a 16-day-old fermentation broth. A 30-day time course study was conducted to monitor the production of three odorants in the fungal fermentation broth, where it was revealed that both 3,4-dimethoxybenzaldehyde (10.7 ± 1.0 mg/kg) and benzaldehyde (4.5 ± 0.1 mg/kg) peaked on day 16, whereas 4-methoxybenzaldehyde peaked on day 24 (104.9 ± 4.9 mg/kg).
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Affiliation(s)
- Purni C K Wickramasinghe
- Department of Food Science , The University of Tennessee Institute of Agriculture , Knoxville , Tennessee 37996 , United States
| | - John P Munafo
- Department of Food Science , The University of Tennessee Institute of Agriculture , Knoxville , Tennessee 37996 , United States
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128
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Savinova OS, Moiseenko KV, Vavilova EA, Chulkin AM, Fedorova TV, Tyazhelova TV, Vasina DV. Evolutionary Relationships Between the Laccase Genes of Polyporales: Orthology-Based Classification of Laccase Isozymes and Functional Insight From Trametes hirsuta. Front Microbiol 2019; 10:152. [PMID: 30792703 PMCID: PMC6374638 DOI: 10.3389/fmicb.2019.00152] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/22/2019] [Indexed: 01/06/2023] Open
Abstract
Laccase is one of the oldest known and intensively studied fungal enzymes capable of oxidizing recalcitrant lignin-resembling phenolic compounds. It is currently well established that fungal genomes almost always contain several non-allelic copies of laccase genes (laccase multigene families); nevertheless, many aspects of laccase multigenicity, for example, their precise biological functions or evolutionary relationships, are mostly unknown. Here, we present a detailed evolutionary analysis of the sensu stricto laccase genes (CAZy - AA1_1) from fungi of the Polyporales order. The conducted analysis provides a better understanding of the Polyporales laccase multigenicity and allows for the systemization of the individual features of different laccase isozymes. In addition, we provide a comparison of the biochemical and catalytic properties of the four laccase isozymes from Trametes hirsuta and suggest their functional diversification within the multigene family.
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Affiliation(s)
- Olga S Savinova
- Laboratory of Molecular Aspects of Biotransformations, A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Konstantin V Moiseenko
- Laboratory of Molecular Aspects of Biotransformations, A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina A Vavilova
- Laboratory of Gene Expression Optimization, A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Andrey M Chulkin
- Laboratory of Gene Expression Optimization, A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana V Fedorova
- Laboratory of Molecular Aspects of Biotransformations, A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana V Tyazhelova
- Laboratory of Molecular Aspects of Biotransformations, A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Daria V Vasina
- Laboratory of Molecular Aspects of Biotransformations, A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
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129
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Evolution of substrate-specific gene expression and RNA editing in brown rot wood-decaying fungi. ISME JOURNAL 2019; 13:1391-1403. [PMID: 30718807 DOI: 10.1038/s41396-019-0359-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/14/2019] [Accepted: 01/17/2019] [Indexed: 02/07/2023]
Abstract
Fungi that decay wood have characteristic associations with certain tree species, but the mechanistic bases for these associations are poorly understood. We studied substrate-specific gene expression and RNA editing in six species of wood-decaying fungi from the 'Antrodia clade' (Polyporales, Agaricomycetes) on three different wood substrates (pine, spruce, and aspen) in submerged cultures. We identified dozens to hundreds of substrate-biased genes (i.e., genes that are significantly upregulated in one substrate relative to the other two substrates) in each species, and these biased genes are correlated with their host ranges. Evolution of substrate-biased genes is associated with gene family expansion, gain and loss of genes, and variation in cis- and trans- regulatory elements, rather than changes in protein coding sequences. We also demonstrated widespread RNA editing events in the Antrodia clade, which differ from those observed in the Ascomycota in their distribution, substitution types, and the genomic environment. Moreover, we found that substrates could affect editing positions and frequency, including editing events occurring in mRNA transcribed from wood-decay-related genes. This work shows the extent to which gene expression and RNA editing differ among species and substrates, and provides clues into mechanisms by which wood-decaying fungi may adapt to different hosts.
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130
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Assessment of white rot fungus mediated hardwood degradation by FTIR spectroscopy and multivariate analysis. J Microbiol Methods 2019; 157:123-130. [DOI: 10.1016/j.mimet.2019.01.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 01/11/2019] [Accepted: 01/14/2019] [Indexed: 01/26/2023]
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131
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Wu B, Xu Z, Knudson A, Carlson A, Chen N, Kovaka S, LaButti K, Lipzen A, Pennachio C, Riley R, Schakwitz W, Umezawa K, Ohm RA, Grigoriev IV, Nagy LG, Gibbons J, Hibbett D. Genomics and Development of Lentinus tigrinus: A White-Rot Wood-Decaying Mushroom with Dimorphic Fruiting Bodies. Genome Biol Evol 2018; 10:3250-3261. [PMID: 30398645 PMCID: PMC6305247 DOI: 10.1093/gbe/evy246] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2018] [Indexed: 12/23/2022] Open
Abstract
Lentinus tigrinus is a species of wood-decaying fungi (Polyporales) that has an agaricoid form (a gilled mushroom) and a secotioid form (puffball-like, with enclosed spore-bearing structures). Previous studies suggested that the secotioid form is conferred by a recessive allele of a single locus. We sequenced the genomes of one agaricoid (Aga) strain and one secotioid (Sec) strain (39.53–39.88 Mb, with 15,581–15,380 genes, respectively). We mated the Sec and Aga monokaryons, genotyped the progeny, and performed bulked segregant analysis (BSA). We also fruited three Sec/Sec and three Aga/Aga dikaryons, and sampled transcriptomes at four developmental stages. Using BSA, we identified 105 top candidate genes with nonsynonymous SNPs that cosegregate with fruiting body phenotype. Transcriptome analyses of Sec/Sec versus Aga/Aga dikaryons identified 907 differentially expressed genes (DEGs) along four developmental stages. On the basis of BSA and DEGs, the top 25 candidate genes related to fruiting body development span 1.5 Mb (4% of the genome), possibly on a single chromosome, although the precise locus that controls the secotioid phenotype is unresolved. The top candidates include genes encoding a cytochrome P450 and an ATP-dependent RNA helicase, which may play a role in development, based on studies in other fungi.
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Affiliation(s)
- Baojun Wu
- Biology Department, Clark University, Worcester, Massachusetts
| | - Zhangyi Xu
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, China
| | - Alicia Knudson
- Biology Department, Clark University, Worcester, Massachusetts
| | - Alexis Carlson
- Biology Department, Clark University, Worcester, Massachusetts
| | - Naiyao Chen
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, China
| | - Sam Kovaka
- Biology Department, Clark University, Worcester, Massachusetts
| | - Kurt LaButti
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California
| | - Anna Lipzen
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California
| | - Christa Pennachio
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California
| | - Robert Riley
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California
| | - Wendy Schakwitz
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California
| | - Kiwamu Umezawa
- Biology Department, Clark University, Worcester, Massachusetts.,Department of Environmental and Natural Resource Science, Tokyo University of Agriculture and Technology, Japan
| | - Robin A Ohm
- Department of Biology, Utrecht University, The Netherlands
| | - Igor V Grigoriev
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley
| | - László G Nagy
- Synthetic and Systems Biology Unit, Institute of Biochemistry, BRC-HAS, Szeged, Hungary
| | - John Gibbons
- Biology Department, Clark University, Worcester, Massachusetts
| | - David Hibbett
- Biology Department, Clark University, Worcester, Massachusetts
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132
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Taxonomy and phylogeny of Postia. Multi-gene phylogeny and taxonomy of the brown-rot fungi: Postia ( Polyporales, Basidiomycota) and related genera. Persoonia - Molecular Phylogeny and Evolution of Fungi 2018; 42:101-126. [PMID: 31551616 PMCID: PMC6712536 DOI: 10.3767/persoonia.2019.42.05] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 09/28/2018] [Indexed: 11/25/2022]
Abstract
Phylogenetic and taxonomic studies on the brown-rot fungi Postia and related genera, are carried out. Phylogenies of these fungi are reconstructed with multiple loci DNA sequences including the internal transcribed spacer regions (ITS), the large subunit (nLSU) and the small subunit (nSSU) of nuclear ribosomal RNA gene, the small subunit of mitochondrial rRNA gene (mtSSU), the translation elongation factor 1-α gene (TEF1), the largest subunit of RNA polymerase II (RPB1) and the second subunit of RNA polymerase II (RPB2). Ten distinct clades of Postia s.lat. are recognized. Four new genera, Amaropostia, Calcipostia, Cystidiopostia and Fuscopostia, are established, and nine new species, Amaropostia hainanensis, Cyanosporus fusiformis, C. microporus, C. mongolicus, C. piceicola, C. subhirsutus, C. tricolor, C. ungulatus and Postia sublowei, are identified. Illustrated descriptions of the new genera and species are presented. Identification keys to Postia and related genera, as well as keys to the species of each genus, are provided.
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133
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Wu SH, Chen CC, Wei CL. Three new species of Phanerochaete (Polyporales, Basidiomycota). MycoKeys 2018:91-106. [PMID: 30402037 PMCID: PMC6215025 DOI: 10.3897/mycokeys.41.29070] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/01/2018] [Indexed: 11/12/2022] Open
Abstract
Phanerochaetecanobrunnea, P.cystidiata and P.fusca are presented as new species, supported by morphological studies and two sets of phylogenetic analyses. The 5.8S+nuc 28S+rpb1 dataset shows the generic placement of the three species within the phlebioid clade of Polyporales. The ITS+nuc 28S dataset displays relationships for the new taxa within Phanerochaete s.s. Phanerochaetecanobrunnea grew on angiosperm branches in subtropical Taiwan and is characterised by greyish brown hymenial surface, brown generative hyphae and skeletal hyphae and absence of cystidia. Phanerochaetecystidiata grew on angiosperm branches above 1000 m in montane Taiwan and SW Yunnan Province of China and is characterised by cream to yellowish hymenial surface and more or less encrusted leptocystidia. Phanerochaetefusca grew on angiosperm branches at 1700 m in Hubei Province of China and is characterised by dark brown hymenial surface, leptocystidia, brown subicular hyphae and colourless to brownish basidiospores.
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Affiliation(s)
- Sheng-Hua Wu
- Department of Biology, National Museum of Natural Science, Taichung 40419, Taiwan National Chung Hsing University Taichung Taiwan.,Department of Plant Pathology, National Chung Hsing University, Taichung 40227, Taiwan National Museum of Natural Science Taichung Taiwan
| | - Che-Chih Chen
- Department of Plant Pathology, National Chung Hsing University, Taichung 40227, Taiwan National Museum of Natural Science Taichung Taiwan
| | - Chia-Ling Wei
- Department of Biology, National Museum of Natural Science, Taichung 40419, Taiwan National Chung Hsing University Taichung Taiwan
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134
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Chen CC, Wu SH, Chen CY. Hydnophanerochaete and Odontoefibula, two new genera of phanerochaetoid fungi (Polyporales, Basidiomycota) from East Asia. MycoKeys 2018:75-96. [PMID: 30271259 PMCID: PMC6160836 DOI: 10.3897/mycokeys.39.28010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 09/04/2018] [Indexed: 12/04/2022] Open
Abstract
Two new genera with phylogenetic affinities to Phanerochaete s.l. are presented, namely Hydnophanerochaete and Odontoefibula. The generic type of Hydnophanerochaete is Phanerochaeteodontoidea. Odontoefibula is established based on a new species: O.orientalis (generic type). Both genera have effused basidiocarps with odontioid hymenial surface, simple-septate generative hyphae, cystidia lacking, clavate basidia and ellipsoid basidiospores that are smooth, thin-walled, inamyloid, non-dextrinoid and acyanophilous. Hydnophanerochaete is additionally characterised by a compact texture in the subiculum with thick-walled generative hyphae and quasi-binding hyphae. Odontoefibula has a dense texture of subiculum with thin- to slightly thick-walled hyphae and further a dark reddish reaction of basidiocarps when treated with KOH. Multi-marker phylogenetic analyses based on sequences, inferred from the ITS+nuc 28S+rpb1+rpb2+tef1 dataset, indicate that Hydnophanerochaete and Odontoefibula are placed in the Meruliaceae and Donkia clades of Phanerochaetaceae, respectively. Phanerochaetesubodontoidea is a synonym of P.odontoidea, according to morphological and molecular evidence.
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Affiliation(s)
- Che-Chih Chen
- Department of Plant Pathology, National Chung Hsing University, Taichung 40227, Taiwan National Chung Hsing University Taichung Taiwan
| | - Sheng-Hua Wu
- Department of Plant Pathology, National Chung Hsing University, Taichung 40227, Taiwan National Chung Hsing University Taichung Taiwan.,Department of Biology, National Museum of Natural Science, Taichung 40419, Taiwan National Museum of Natural Science Taichung Taiwan
| | - Chi-Yu Chen
- Department of Plant Pathology, National Chung Hsing University, Taichung 40227, Taiwan National Chung Hsing University Taichung Taiwan
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135
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Luo H, Cai Q, Lüli Y, Li X, Sinha R, Hallen-Adams HE, Yang ZL. The MSDIN family in amanitin-producing mushrooms and evolution of the prolyl oligopeptidase genes. IMA Fungus 2018; 9:225-242. [PMID: 30622880 PMCID: PMC6317590 DOI: 10.5598/imafungus.2018.09.02.01] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 07/24/2018] [Indexed: 12/18/2022] Open
Abstract
The biosynthetic pathway for amanitins and related cyclic peptides in deadly Amanita (Amanitaceae) mushrooms represents the first known ribosomal cyclic peptide pathway in the Fungi. Amanitins are found outside of the genus in distantly related agarics Galerina (Strophariaceae) and Lepiota (Agaricaceae). A long-standing question in the field persists: why is this pathway present in these phylogenetically disjunct agarics? Two deadly mushrooms, A. pallidorosea and A. subjunquillea, were deep sequenced, and sequences of biosynthetic genes encoding MSDINs (cyclic peptide precursor) and prolyl oligopeptidases (POPA and POPB) were obtained. The two Amanita species yielded 29 and 18 MSDINs, respectively. In addition, two MSDIN sequences were cloned from L. brunneoincarnata basidiomes. The toxin MSDIN genes encoding amatoxins or phallotoxins from the three genera were compared, and a phylogenetic tree constructed. Prolyl oligopeptidase B (POPB), a key enzyme in the biosynthetic pathway, was used in phylogenetic reconstruction to infer the evolutionary history of the genes. Phylogenies of POPB and POPA based on both coding and amino acid sequences showed very different results: while POPA genes clearly reflected the phylogeny of the host species, POPB did not; strikingly, it formed a well-supported monophyletic clade, despite that the species belong to different genera in disjunct families. POPA, a known house-keeping gene, was shown to be restricted in a branch containing only Amanita species and the phylogeny resembled that of those Amanita species. Phylogenetic analyses of MSDIN and POPB genes showed tight coordination and disjunct distribution. A POPB gene tree was compared with a corresponding species tree, and distances and substitution rates were compared. The result suggested POPB genes have significant smaller distances and rates than the house-keeping rpb2, discounting massive gene loss. Under this assumption, the incongruency between the gene tree and species tree was shown with strong support. Additionally, k-mer analyses consistently cluster Galerina and Amanita POPB genes, while Lepiota POPB is distinct. Our result suggests that horizontal gene transfer (HGT), at least between Amanita and Galerina, was involved in the acquisition of POPB genes, which may shed light on the evolution of the α-amanitin biosynthetic pathway.
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Affiliation(s)
- Hong Luo
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | - Qing Cai
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | - Yunjiao Lüli
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuan Li
- Department of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650091, Yunnan, China
| | | | - Heather E Hallen-Adams
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Zhu L Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
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136
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Miyauchi S, Rancon A, Drula E, Hage H, Chaduli D, Favel A, Grisel S, Henrissat B, Herpoël-Gimbert I, Ruiz-Dueñas FJ, Chevret D, Hainaut M, Lin J, Wang M, Pangilinan J, Lipzen A, Lesage-Meessen L, Navarro D, Riley R, Grigoriev IV, Zhou S, Raouche S, Rosso MN. Integrative visual omics of the white-rot fungus Polyporus brumalis exposes the biotechnological potential of its oxidative enzymes for delignifying raw plant biomass. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:201. [PMID: 30061923 PMCID: PMC6055342 DOI: 10.1186/s13068-018-1198-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/06/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Plant biomass conversion for green chemistry and bio-energy is a current challenge for a modern sustainable bioeconomy. The complex polyaromatic lignin polymers in raw biomass feedstocks (i.e., agriculture and forestry by-products) are major obstacles for biomass conversions. White-rot fungi are wood decayers able to degrade all polymers from lignocellulosic biomass including cellulose, hemicelluloses, and lignin. The white-rot fungus Polyporus brumalis efficiently breaks down lignin and is regarded as having a high potential for the initial treatment of plant biomass in its conversion to bio-energy. Here, we describe the extraordinary ability of P. brumalis for lignin degradation using its enzymatic arsenal to break down wheat straw, a lignocellulosic substrate that is considered as a biomass feedstock worldwide. RESULTS We performed integrative multi-omics analyses by combining data from the fungal genome, transcriptomes, and secretomes. We found that the fungus possessed an unexpectedly large set of genes coding for Class II peroxidases involved in lignin degradation (19 genes) and GMC oxidoreductases/dehydrogenases involved in generating the hydrogen peroxide required for lignin peroxidase activity and promoting redox cycling of the fungal enzymes involved in oxidative cleavage of lignocellulose polymers (36 genes). The examination of interrelated multi-omics patterns revealed that eleven Class II Peroxidases were secreted by the fungus during fermentation and eight of them where tightly co-regulated with redox cycling enzymatic partners. CONCLUSION As a peculiar feature of P. brumalis, we observed gene family extension, up-regulation and secretion of an abundant set of versatile peroxidases and manganese peroxidases, compared with other Polyporales species. The orchestrated secretion of an abundant set of these delignifying enzymes and redox cycling enzymatic partners could contribute to the delignification capabilities of the fungus. Our findings highlight the diversity of wood decay mechanisms present in Polyporales and the potentiality of further exploring this taxonomic order for enzymatic functions of biotechnological interest.
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Affiliation(s)
- Shingo Miyauchi
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
- Present Address: Laboratoire d’Excellence ARBRE, UMR 1136, INRA-Université de Lorraine ‘Interactions Arbres/Microorganismes’, Champenoux, France
| | - Anaïs Rancon
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Elodie Drula
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Hayat Hage
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Delphine Chaduli
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
- CIRM-CF, UMR1163, INRA, Aix-Marseille Univ, Marseille, France
| | - Anne Favel
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
- CIRM-CF, UMR1163, INRA, Aix-Marseille Univ, Marseille, France
| | - Sacha Grisel
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Bernard Henrissat
- UMR 7257, CNRS, Aix-Marseille Univ, Marseille, France
- INRA, USC 1408, AFMB, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Isabelle Herpoël-Gimbert
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | | | - Didier Chevret
- INRA, UMR1319, Micalis, Plateforme d’Analyse Protéomique de Paris Sud-Ouest, Jouy-en-Josas, France
| | - Matthieu Hainaut
- UMR 7257, CNRS, Aix-Marseille Univ, Marseille, France
- INRA, USC 1408, AFMB, Marseille, France
| | - Junyan Lin
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Mei Wang
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Laurence Lesage-Meessen
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
- CIRM-CF, UMR1163, INRA, Aix-Marseille Univ, Marseille, France
| | - David Navarro
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
- CIRM-CF, UMR1163, INRA, Aix-Marseille Univ, Marseille, France
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA USA
| | - Simeng Zhou
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
- Present Address: Institut des Sciences Moléculaires de Marseille, UMR 7313, CNRS, Aix-Marseille Université, Marseille, France
| | - Sana Raouche
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Marie-Noëlle Rosso
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
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Korhonen A, Seelan JSS, Miettinen O. Cryptic species diversity in polypores: the Skeletocutis nivea species complex. MycoKeys 2018; 36:45-82. [PMID: 30057481 PMCID: PMC6060227 DOI: 10.3897/mycokeys.36.27002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 07/07/2018] [Indexed: 11/12/2022] Open
Abstract
We propose a taxonomic revision of the two closely related white-rot polypore species, Skeletocutis nivea (Jungh.) Jean Keller and S. ochroalba Niemelä (Incrustoporiaceae, Basidiomycota), based on phylogenetic analyses of nuclear ribosomal internal transcribed spacer (ITS) and translation elongation factor EF-1α sequences. We show that prevailing morphological species concepts of S. nivea and S. ochroalba are non-monophyletic and we delineate new species boundaries based on phylogenetic inference. We recognise eleven species within the prevailing species concept of S. nivea (S. calidasp. nov., S. coprosmae comb. nov., S. futilissp. nov., S. imperviasp. nov., S. ipuletiisp. nov., S. lepidasp. nov., S. nemoralissp. nov., S. nivea sensu typi, S. semipileata comb. nov., S. unguinasp. nov. and S. yuchengiisp. nov.) and assign new sequenced epitypes for S. nivea and S. semipileata. The traditional concept of S. ochroalba comprises two independent lineages embedded within the S. nivea species complex. The Eurasian conifer-dwelling species S. cummatasp. nov. is recognised as separate from the North American S. ochroalba sensu stricto. Despite comprehensive microscopic examination, the majority of the recognised species are left without stable diagnostic character combinations that would enable species identification based solely on morphology and ecology.
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Affiliation(s)
- Aku Korhonen
- Finnish Museum of Natural History, University of Helsinki, PO Box 7, 00014 University of Helsinki, Finland
- Natural Resources Institute Finland (Luke), PO Box 2 (Latokartanonkaari 9), FI-00791, Helsinki, Finland
| | - Jaya Seelan Sathiya Seelan
- Mycology and Pathology Laboratory, Institute for Tropical Biology and Conservation (ITBC), Universiti Malaysia Sabah, 88400 Kota Kinabalu, Sabah, Malaysia
| | - Otto Miettinen
- Finnish Museum of Natural History, University of Helsinki, PO Box 7, 00014 University of Helsinki, Finland
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138
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Evolutionary relationships of Bresadolia (Basidiomycota, Polyporales) based on molecular and morphological evidence. Mycol Prog 2018. [DOI: 10.1007/s11557-018-1416-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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139
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Ferreira DSS, Kato RB, Miranda FM, da Costa Pinheiro K, Fonseca PLC, Tomé LMR, Vaz ABM, Badotti F, Ramos RTJ, Brenig B, Azevedo VADC, Benevides RG, Góes-Neto A. Draft genome sequence of Trametes villosa (Sw.) Kreisel CCMB561, a tropical white-rot Basidiomycota from the semiarid region of Brazil. Data Brief 2018; 18:1581-1587. [PMID: 29904660 PMCID: PMC5998210 DOI: 10.1016/j.dib.2018.04.074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 04/12/2018] [Accepted: 04/19/2018] [Indexed: 11/16/2022] Open
Abstract
Herein, we present the draft genome of Trametes villosa isolate CCMB561, a wood-decaying Basidiomycota commonly found in tropical semiarid climate. The genome assembly was 57.98 Mb in size with an L50 of 691. A total of 16,711 putative protein-encoding genes was predicted, including 590 genes coding for carbohydrate-active enzymes (CAZy), directly involved in the decomposition of lignocellulosic materials. This is the first genome of this species of high interest in bioenergy research. The draft genome of Trametes villosa isolate CCMB561 will provide an important resource for future investigations in biofuel production, bioremediation and other green technologies.
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Affiliation(s)
| | - Rodrigo Bentes Kato
- Federal University of Minas Gerais, Institute of Biological Sciences, Belo Horizonte, MG 31270-901, Brazil
| | - Fábio Malcher Miranda
- Federal University of Minas Gerais, Institute of Biological Sciences, Belo Horizonte, MG 31270-901, Brazil
- Federal University of Pará, Computer Science Graduate Program, Belém, PA 66075-110, Brazil
| | | | | | - Luiz Marcelo Ribeiro Tomé
- Federal University of Minas Gerais, Institute of Biological Sciences, Belo Horizonte, MG 31270-901, Brazil
| | - Aline Bruna Martins Vaz
- Federal University of Minas Gerais, Institute of Biological Sciences, Belo Horizonte, MG 31270-901, Brazil
| | - Fernanda Badotti
- Federal Center of Technological Education of Minas Gerais (CEFET-MG), Belo Horizonte, MG 30421-169, Brazil
| | | | - Bertram Brenig
- University of Göttingen, Institute of Veterinary Medicine, Burckhardtweg 2, D-37077 Göttingen, Germany
| | | | - Raquel Guimarães Benevides
- State University of Feira de Santana, Departament of Biological Science, Feira de Santana, BA 44036-900, Brazil
| | - Aristóteles Góes-Neto
- State University of Feira de Santana, Departament of Biological Science, Feira de Santana, BA 44036-900, Brazil
- Federal University of Minas Gerais, Institute of Biological Sciences, Belo Horizonte, MG 31270-901, Brazil
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140
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Hussein JM, Tibuhwa DD, Tibell S. Phylogenetic position and taxonomy of Kusaghiporia usambarensis gen. et sp. nov. (Polyporales). Mycology 2018; 9:136-144. [PMID: 30123669 PMCID: PMC6059158 DOI: 10.1080/21501203.2018.1461142] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 04/02/2018] [Indexed: 10/25/2022] Open
Abstract
A large polyporoid mushroom from the West Usambara Mountains in North-eastern Tanzania produces dark brown, up to 60-cm large fruiting bodies that at maturity may weigh more than 10 kg. It has a high rate of mycelial growth and regeneration and was found growing on both dry and green leaves of shrubs; attached to the base of living trees, and it was also observed to degrade dead snakes and insects accidentally coming into contact with it. Phylogenetic analyses based on individual and concatenated data sets of nrLSU, nrSSU and the RPB2 and TEF1 genes showed it, together with Laetiporus, Phaeolus, Pycnoporellus and Wolfiporia, to form a monophyletic group in Polyporales. Based on morphological features and molecular data, it is described as Kusaghiporia usambarensis.
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Affiliation(s)
- Juma Mahmud Hussein
- Institute of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Department of Molecular Biology and Biotechnology, College of Natural & Applied Sciences, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Donatha Damian Tibuhwa
- Department of Molecular Biology and Biotechnology, College of Natural & Applied Sciences, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Sanja Tibell
- Institute of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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Revision of the taxonomic status of the genus Gloeoporus (Polyporales, Basidiomycota) reveals two new species. Mycol Prog 2018. [DOI: 10.1007/s11557-018-1400-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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142
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Miettinen O, Vlasák J, Rivoire B, Spirin V. Postia caesia complex ( Polyporales, Basidiomycota) in temperate Northern Hemisphere. Fungal Syst Evol 2018; 1:101-129. [PMID: 32490363 PMCID: PMC7259241 DOI: 10.3114/fuse.2018.01.05] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Taxonomy of the Postia caesia complex is revised based on morphology and two genetic markers, ITS and tef1. In total, we recognize 24 species, multiplying the known species diversity in the complex. We provide descriptions for 20 temperate Northern Hemisphere taxa. Identity of the core species, P. caesia, is re-established, and a neotype from the type locality is selected. Four new combinations are proposed, and 10 new species are described: P. arbuti, P. auricoma, P. bifaria, P. comata, P. cyanescens, P. glauca, P. livens, P. magna, P. populi, and P. yanae.
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Affiliation(s)
- O Miettinen
- Finnish Museum of Natural History, University of Helsinki, Finland
| | - J Vlasák
- Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | | | - V Spirin
- Finnish Museum of Natural History, University of Helsinki, Finland
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143
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Liu SL, Nakasone KK, Wu SH, He SH, Dai YC. Taxonomy and phylogeny of Lopharia s.s., Dendrodontia, Dentocorticium and Fuscocerrena (Basidiomycota, Polyporales). MycoKeys 2018:25-48. [PMID: 29681736 PMCID: PMC5904543 DOI: 10.3897/mycokeys.32.23641] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/08/2018] [Indexed: 11/25/2022] Open
Abstract
Eleven taxa of Lopharia s.s., Dendrodontia, Dentocorticium and Fuscocerrena in Polyporales are included in the phylogenetic analyses of nuc rDNA ITS1-5.8S-ITS2 (ITS), D1-D2 domains of nuc 28S rDNA (28S) and RNA polymerase II second-largest subunit (rpb2) sequences. New species Lophariaresupinata and L.sinensis are described and illustrated. Lophariaresupinata, from south-eastern China, is closely related to L.ayresii, and L.sinensis, from northern China, is related to L.cinerascens and L.mirabilis. Lophariamirabilis specimens from temperate to tropical areas with varied hymenophore configurations all cluster together in a fully supported clade. Dendrodontia and Fuscocerrena are shown to be synonyms of Dentocorticium, which is phylogenetically related to Lopharia. Four new combinations, Dentocorticiumbicolor, D.hyphopaxillosum, D.portoricense and D.taiwanianum, are proposed. Revised generic descriptions of Lopharia and Dentocorticium are provided with keys to the six accepted species in each genus. A list of all names in Lopharia and Dentocorticium are presented with their current taxonomic status. Type specimens of Dentocorticiumbrasiliense and D.irregulare were examined and determined to be later synonyms of Punctulariasubhepatica and Diplomitoporusdaedaleiformis, respectively.
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Affiliation(s)
- Shi-Liang Liu
- Institute of Microbiology, Beijing Forestry University, Beijing 100083, China
| | - Karen K Nakasone
- Center for Forest Mycology Research, Northern Research Station, U.S. Forest Service, One Gifford Pinchot Drive, Madison, WI 53726-2398, USA
| | - Sheng-Hua Wu
- Department of Biology, National Museum of Natural Science, Taichung 40419, Taiwan
| | - Shuang-Hui He
- Institute of Microbiology, Beijing Forestry University, Beijing 100083, China
| | - Yu-Cheng Dai
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
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144
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New systematic position of Aurantiporus alborubescens (Meruliaceae, Basidiomycota), a threatened old-growth forest polypore. Mycol Prog 2017. [DOI: 10.1007/s11557-017-1356-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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