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Kolařík M, Vrublevskaya M, Kajzrová S, Kulišová M, Kolouchová IJ. Taxonomic analysis reveals host preference of rare fungi in endophytes of Vitis vinifera from the Czech Republic. Folia Microbiol (Praha) 2023; 68:961-975. [PMID: 37289415 DOI: 10.1007/s12223-023-01066-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/20/2023] [Indexed: 06/09/2023]
Abstract
This paper represents the results of screening a diversity of fungal endophytes associated with Vitis vinifera leaves and canes in the Czech Republic. The characterization of strains is based on morphological and phylogenetic analyses of ITS, EF1α and TUB2 sequence data. Our strain selection covers 16 species and seven orders belonging to Ascomycota and Basidiomycota. Together with ubiquitous fungi, we report on several poorly known plant-associated fungi, Angustimassarina quercicola (= A. coryli, a synonym proposed in this study) and Pleurophoma pleurospora. Other species, such as Didymella negriana, D. variabilis, Neosetophoma sp. (species identical or sister to N. rosae), Phragmocamarosporium qujingensis and Sporocadus rosigena, have so far been little known and rarely found, but are frequent on V. vinifera in different parts of the world and obviously belong to a microbiota with a strong preference for this plant. Detailed taxonomical identification allowed us to identify species with apparent stable associations with V. vinifera, for which further interactions with V. vinifera can be expected. Our study is the first to focus on V. vinifera endophytes in Central Europe and expands the knowledge about their taxonomy, ecology and geography.
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Affiliation(s)
- Miroslav Kolařík
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 14220, Prague, Czech Republic.
| | - Maria Vrublevskaya
- Department of Biotechnology, University of Chemistry and Technology, Technická 5, 166 28, Prague, Czech Republic
| | - Soňa Kajzrová
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 14220, Prague, Czech Republic
| | - Markéta Kulišová
- Department of Biotechnology, University of Chemistry and Technology, Technická 5, 166 28, Prague, Czech Republic
| | - Irena Jarošová Kolouchová
- Department of Biotechnology, University of Chemistry and Technology, Technická 5, 166 28, Prague, Czech Republic
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Deng X, Yang J, Wan Y, Han Y, Tong H, Chen Y. Characteristics of Leaf Spot Disease Caused by Didymella Species and the Influence of Infection on Tea Quality. Phytopathology 2023; 113:516-527. [PMID: 36972529 DOI: 10.1094/phyto-06-22-0202-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Leaf spots are the most damaging and common foliar diseases of tea and are caused by several species of fungi. During 2018 to 2020, leaf spot diseases showing different symptoms (large and small spots) were observed in commercial tea plantations in Guizhou and Sichuan provinces of China. The pathogen causing the two different sized leaf spots was identified as the same species (Didymella segeticola) based on morphological characteristics, pathogenicity, and multilocus phylogenetic analysis using the combined ITS, TUB, LSU, and RPB2 gene regions. Microbial diversity analysis of lesion tissues from small spots on naturally infected tea leaves further confirmed Didymella to be present as the main pathogen. Results of sensory evaluation and quality-related metabolite analysis of tea shoots infected with the small leaf spot symptom indicated that D. segeticola negatively affected the quality and flavor of tea by changing the composition and content of caffeine, catechins, and amino acids. In addition, the significantly reduced amino acid derivatives in tea are confirmed to be positively associated with the enhanced bitter taste. The results improve our understanding of the pathogenicity of Didymella species and the influence of Didymella on the host plant, Camellia sinensis.
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Affiliation(s)
- Xinyi Deng
- Department of Tea Science, College of Food Science, Southwest University, Chongqing, 400715, China
| | - Juan Yang
- Tea Research Institute, Chongqing Academy of Agricultural Sciences, Yongchuan, Chongqing, 402160, China
| | - Yuhe Wan
- Department of Tea Science, College of Food Science, Southwest University, Chongqing, 400715, China
| | - Yuxin Han
- Department of Tea Science, College of Food Science, Southwest University, Chongqing, 400715, China
| | - Huarong Tong
- Department of Tea Science, College of Food Science, Southwest University, Chongqing, 400715, China
| | - Yingjuan Chen
- Department of Tea Science, College of Food Science, Southwest University, Chongqing, 400715, China
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You MP, Eshete BB, Kemal SA, Barbetti MJ. Faba Bean Gall Pathogen Physoderma viciae: New Primers Reveal Its Puzzling Association with the Field Pea Ascochyta Complex. Plant Dis 2022; 106:2299-2303. [PMID: 35124995 DOI: 10.1094/pdis-11-21-2576-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Recent morphological and molecular studies confirmed Physoderma viciae, and not Olpidium viciae, to be the causative agent of the devastating Faba Bean Gall (FBG) disease on faba bean (Vicia faba) in Ethiopia and also highlighted its ability to cross-infect with other host genera such as Pisum and Trifolium. In this study, the first pair of specific primer 'Physo 1' and primer pair 'Physo D' are reported from molecular sequences of this pathogen from the conserved LSU (S28) gene. Whereas 'Physo 1' readily detects P. viciae, 'Physo D', clearly separates its identity from the common and confounding presence of Didymella/Phoma spp. The study also reports the presence of the Ascochyta blight pathogen complex, symptomless but almost universal on field pea (Pisum sativum), within faba bean infested by P. viciae. We emphasize historical evidence confirming such unique association in other legumes, such as the subterranean clover (Trifolium subterraneum). This new finding has significant implications for rotations involving different legume crop and/or forage legume genera and possibly provides the first explanation for the widespread occurrence of the field pea Ascochyta blight pathogen complex even in the absence of field pea cropping for many years.
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Affiliation(s)
- Ming Pei You
- School of Agriculture and Environment and the UWA Institute of Agriculture, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | | | - Seid Ahmed Kemal
- International Center for Agricultural Research in the Dry Areas, Station Exp. Institut National de Recherche Agronomique (INRA)-Quich, Rue Hafiane Cherkaoui Agdal, Rabat Instituts, Rabat, Morocco
| | - Martin J Barbetti
- School of Agriculture and Environment and the UWA Institute of Agriculture, The University of Western Australia, Crawley, Western Australia 6009, Australia
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He Y, Li Y, Song Y, Hu X, Liang J, Shafik K, Ni D, Xu W. Amplicon Sequencing Reveals Novel Fungal Species Responsible for a Controversial Tea Disease. J Fungi (Basel) 2022; 8:782. [PMID: 35893150 DOI: 10.3390/jof8080782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/22/2022] [Accepted: 07/24/2022] [Indexed: 12/10/2022] Open
Abstract
Amplicon sequencing is a powerful tool for analyzing the fungal composition inside plants, whereas its application for the identification of etiology for plant diseases remains undetermined. Here, we utilize this strategy to clarify the etiology responsible for tea leaf brown-black spot disease (LBSD), a noticeable disease infecting tea plants etiology that remains controversial. Based on the ITS-based amplicon sequencing analysis, Didymella species were identified as separate from Pestalotiopsis spp. and Cercospora sp., which are concluded as the etiological agents. This was further confirmed by the fungal isolation and their specific pathogenicity on diverse tea varieties. Based on the morphologies and phylogenetic analysis constructed with multi-loci (ITS, LSU, tub2, and rpb2), two novel Didymella species—tentatively named D. theae and D. theifolia as reference to their host plants—were proposed and characterized. Here, we present an integrated approach of ITS-based amplicon sequencing in combination with fungal isolation and fulfillment of Koch’s postulates for etiological identification of tea plant disease, revealing new etiology for LBSD. This contributes useful information for further etiological identification of plant disease based on amplicon sequencing, as well as understanding, prevention, and management of this economically important disease.
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Zelaya-Molina LX, Sanchez-Lima AD, Arteaga-Garibay RI, Bustamante-Brito R, Vásquez-Murrieta MS, Martínez-Romero E, Ramos-Garza J. Functional characterization of culturable fungi from microbiomes of the "conical cobs" Mexican maize (Zea mays L.) landrace. Arch Microbiol 2021; 204:57. [PMID: 34939131 DOI: 10.1007/s00203-021-02680-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/23/2021] [Accepted: 10/25/2021] [Indexed: 11/29/2022]
Abstract
Mexican maize landraces, produced for local consumption, are adapted to different environmental conditions, and their yield is affected by abiotic and biotic factors, including the use of agrochemicals. The search for sustainable alternatives to agrochemicals includes the study of the culturable microbial communities. In this study, the fungal communities associated with 2 Mexican maize landraces reddish and bluish "conical cobs" were found to be comprised of Ascomycota fungi, represented by 89 strains within 6 orders (Pleosporales, Hypocreales, Onygenales, Capnodiales, Helotiales, and Eurotiales) and 16 genera. Cellulases and metallophores production were the primary enzymatic products and plant growth-promoting activities were detected among the isolates. Penicillium, Didymella, and Fusarium strains had the most active enzymatic and plant growth promoting activities, however, Aspergillus sp. HES2-2.2, Talaromyces sp. RS1-7, and Penicillium sp. HFS3-3 showed antagonistic activity against the four phytopathogenic Fusarium strains Fusarium oxysporum, Fusarium sambucinum, Fusarium fujikuroi and Fusarium incarnatum-equiseti and also a high and diverse production of enzymatic and plant growth promoting activities; here we identified fungal strains as candidates to promote maize growth.
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Affiliation(s)
- Lily X Zelaya-Molina
- Laboratorio de Recursos Genéticos Microbianos, Centro Nacional de Recursos Genéticos-INIFAP, Boulevard de la Biodiversidad No. 400, C.P. 47600, Tepatitlán de Morelos, Jalisco, México
| | - Alejandra D Sanchez-Lima
- Laboratorio de Microbiología 314, Universidad del Valle de México, Campus Chapultepec. Observatorio No. 400, C.P. 11810, Ciudad de México, México
| | - Ramón I Arteaga-Garibay
- Laboratorio de Recursos Genéticos Microbianos, Centro Nacional de Recursos Genéticos-INIFAP, Boulevard de la Biodiversidad No. 400, C.P. 47600, Tepatitlán de Morelos, Jalisco, México
| | - Rafael Bustamante-Brito
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad S/N, C.P. 62210, Cuernavaca, Morelos, México
| | - María S Vásquez-Murrieta
- Departamento de Microbiología, Laboratorio de Biotecnología Microbiana. Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio Y Plan de Ayala S/N, C.P. 11340, Ciudad de México, México
| | - Esperanza Martínez-Romero
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad S/N, C.P. 62210, Cuernavaca, Morelos, México
| | - Juan Ramos-Garza
- Laboratorio de Microbiología 314, Universidad del Valle de México, Campus Chapultepec. Observatorio No. 400, C.P. 11810, Ciudad de México, México. .,Laboratorio de Recursos Genéticos Microbianos, Centro Nacional de Recursos Genéticos-INIFAP, Boulevard de la Biodiversidad No. 400, C.P. 47600, Tepatitlán de Morelos, Jalisco, México.
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Mravlje J, Regvar M, Starič P, Mozetič M, Vogel-Mikuš K. Cold Plasma Affects Germination and Fungal Community Structure of Buckwheat Seeds. Plants (Basel) 2021; 10:851. [PMID: 33922511 PMCID: PMC8145130 DOI: 10.3390/plants10050851] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/18/2021] [Accepted: 04/20/2021] [Indexed: 01/27/2023]
Abstract
Crop seeds are frequently colonised by fungi from the field or storage places. Some fungi can cause plant diseases or produce mycotoxins, compromising the use of seeds as seeding material, food or feed. We have investigated the effects of cold plasma (CP) on seed germination and diversity of seed-borne fungi in common and Tartary buckwheat. The seeds were treated with CP for 15, 30, 45, 60, 90, and 120 s in a low-pressure radiofrequency system using oxygen as the feed gas. The fungi from the seed surface and fungal endophytes were isolated using potato dextrose agar plates. After identification by molecular methods, the frequency and diversity of fungal strains were compared between CP treated and chemically surface-sterilised (30% of H2O2) seeds. CP treatments above 60 s negatively affected the germination of both buckwheat species. A significant reduction in fungal frequency and diversity was observed after 90 s and 120 s in common and Tartary buckwheat, respectively. The filamentous fungi of genera Alternaria and Epicoccum proved to be the most resistant to CP. The results of our study indicate that CP treatment used in our study may be applicable in postharvest and food production, but not for further seed sowing.
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Affiliation(s)
- Jure Mravlje
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia; (M.R.); (K.V.-M.)
| | - Marjana Regvar
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia; (M.R.); (K.V.-M.)
| | - Pia Starič
- Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia; (P.S.); (M.M.)
| | - Miran Mozetič
- Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia; (P.S.); (M.M.)
| | - Katarina Vogel-Mikuš
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia; (M.R.); (K.V.-M.)
- Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia; (P.S.); (M.M.)
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Kim W, Chen W. Phytotoxic Metabolites Produced by Legume-Associated Ascochyta and Its Related Genera in the Dothideomycetes. Toxins (Basel) 2019; 11:E627. [PMID: 31671808 DOI: 10.3390/toxins11110627] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/27/2019] [Accepted: 10/28/2019] [Indexed: 12/20/2022] Open
Abstract
Phytotoxins, secondary metabolites toxic to plants and produced by fungi, are believed to play an important role in disease development by targeting host cellular machineries and/or interfering with host immune responses. The Ascochyta blight diseases on different legume plants are caused by Ascochyta and related taxa, such as Phoma. The causal agents of the Ascochyta blight are often associated with specific legume plants, showing a relatively narrow host range. The legume-associated Ascochyta and Phoma are known to produce a diverse array of polyketide-derived secondary metabolites, many of which exhibited significant phytotoxicity and have been claimed as virulence or pathogenicity factors. In this article, we reviewed the current state of knowledge on the diversity and biological activities of the phytotoxic compounds produced by Ascochyta and Phoma species. Also, we touched on the secondary metabolite biosynthesis gene clusters identified thus far and discussed the role of metabolites in the fungal biology.
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Abstract
The Didymellaceae was established in 2009 to accommodate Ascochyta, Didymella and Phoma, as well as several related phoma-like genera. The family contains numerous plant pathogenic, saprobic and endophytic species associated with a wide range of hosts. Ascochyta and Phoma are morphologically difficult to distinguish, and species from both genera have in the past been linked to Didymella sexual morphs. The aim of the present study was to clarify the generic delimitation in Didymellaceae by combing multi-locus phylogenetic analyses based on ITS, LSU, rpb2 and tub2, and morphological observations. The resulting phylogenetic tree revealed 17 well-supported monophyletic clades in Didymellaceae, leading to the introduction of nine genera, three species, two nomina nova and 84 combinations. Furthermore, 11 epitypes and seven neotypes were designated to help stabilise the taxonomy and use of names. As a result of these data, Ascochyta, Didymella and Phoma were delineated as three distinct genera, and the generic circumscriptions of Ascochyta, Didymella, Epicoccum and Phoma emended. Furthermore, the genus Microsphaeropsis, which is morphologically distinct from the members of Didymellaceae, grouped basal to the Didymellaceae, for which a new family Microsphaeropsidaceae was introduced.
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Affiliation(s)
- Q. Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Rd, Chaoyang District, Beijing 100101, China
| | - J.R. Jiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Rd, Chaoyang District, Beijing 100101, China
| | - G.Z. Zhang
- College of Agriculture and Biotechnology, China Agricultural University, No. 2 West Yuanmingyuan Rd, Haidian District, Beijing 100193, China
| | - L. Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Rd, Chaoyang District, Beijing 100101, China
| | - P.W. Crous
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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Stewart JE, Andrew M, Bao X, Chilvers MI, Carris LM, Peever TL. Development of sequence characterized amplified genomic regions (SCAR) for fungal systematics: proof of principle using Alternaria, Ascochyta and Tilletia. Mycologia 2013; 105:1077-86. [PMID: 23449078 DOI: 10.3852/12-287] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
SCARs were developed by cloning RAPD-PCR amplicons into commercially available vectors, sequencing them and designing specific primers for PCR, direct sequencing and phylogenetic analysis. Eighteen to seventy percent of cloned RAPD-PCR amplicons were phylogenetically informative among closely related small-spored Alternaria spp., Ascochyta spp. and Tilletia spp., taxa that have been resistant to phylogenetic analysis with universally primed, protein-coding sequence data. Selected SCARs were sequenced for larger, population-scale samples of each taxon and demonstrated to be useful for phylogenetic inference. Variation observed in the cloned SCARs generally was higher than variation in nuclear ribosomal internal transcribed spacer (ITS) and several protein-coding sequences commonly used in lower level fungal systematics. Sequence data derived from SCARs will provide sufficient resolution to address lower level phylogenetic hypotheses in Alternaria, Ascochyta, Tilletia and possibly many other fungal groups and organisms.
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Affiliation(s)
- Jane E Stewart
- Department of Plant Pathology, Washington State University, Pullman, WA, USA
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Tanaka K, Hirayama K, Yonezawa H, Hatakeyama S, Harada Y, Sano T, Shirouzu T, Hosoya T. Molecular taxonomy of bambusicolous fungi: Tetraplosphaeriaceae, a new pleosporalean family with Tetraploa-like anamorphs. Stud Mycol 2011; 64:175-209. [PMID: 20169030 PMCID: PMC2816973 DOI: 10.3114/sim.2009.64.10] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
A new pleosporalean family Tetraplosphaeriaceae is established to
accommodate five new genera; 1) Tetraplosphaeria with small ascomata
and anamorphs belonging to Tetraploa s. str., 2)
Triplosphaeria characterised by hemispherical ascomata with rim-like
side walls and anamorphs similar to Tetraploa but with three conidial
setose appendages, 3) Polyplosphaeria with large ascomata surrounded
by brown hyphae and anamorphs producing globose conidia with several setose
appendages, 4) Pseudotetraploa, an anamorphic genus, having
obpyriform conidia with pseudosepta and four to eight setose appendages, and
5) Quadricrura, an anamorphic genus, having globose conidia with one
or two long setose appendages at the apex and four to five short setose
appendages at the base. Fifteen new taxa in these genera mostly collected from
bamboo are described and illustrated. They are linked by their Tetraploa
s. l. anamorphs. To infer phylogenetic placement in the
Pleosporales, analyses based on a combined dataset of small- and
large-subunit nuclear ribosomal DNA (SSU+LSU nrDNA) was carried out.
Tetraplosphaeriaceae, however, is basal to the main pleosporalean
clade and therefore its relationship with other existing families was not
completely resolved. To evaluate the validity of each taxon and to clarify the
phylogenetic relationships within this family, further analyses using
sequences from ITS-5.8S nrDNA (ITS), transcription elongation factor 1-α
(TEF), and β-tubulin (BT), were also conducted. Monophyly of the family
and that of each genus were strongly supported by analyses based on a combined
dataset of the three regions (ITS+TEF+BT). Our results also suggest that
Tetraplosphaeria (anamorph: Tetraploa s. str.) is an
ancestral lineage within this family. Taxonomic placement of the bambusicolous
fungi in Astrosphaeriella, Kalmusia, Katumotoa, Massarina,
Ophiosphaerella, Phaeosphaeria, Roussoella, Roussoellopsis, and
Versicolorisporium, are also discussed based on the SSU+LSU
phylogeny.
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Affiliation(s)
- K Tanaka
- Faculty of Agriculture & Life Sciences, Hirosaki University, Bunkyo-cho 3, Hirosaki, Aomori 036-8561, Japan
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Aveskamp M, de Gruyter J, Woudenberg J, Verkley G, Crous P. Highlights of the Didymellaceae: A polyphasic approach to characterise Phoma and related pleosporalean genera. Stud Mycol 2010; 65:1-60. [PMID: 20502538 PMCID: PMC2836210 DOI: 10.3114/sim.2010.65.01] [Citation(s) in RCA: 273] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Fungal taxonomists routinely encounter problems when dealing with asexual fungal species due to poly- and paraphyletic generic phylogenies, and unclear species boundaries. These problems are aptly illustrated in the genus Phoma. This phytopathologically significant fungal genus is currently subdivided into nine sections which are mainly based on a single or just a few morphological characters. However, this subdivision is ambiguous as several of the section-specific characters can occur within a single species. In addition, many teleomorph genera have been linked to Phoma, three of which are recognised here. In this study it is attempted to delineate generic boundaries, and to come to a generic circumscription which is more correct from an evolutionary point of view by means of multilocus sequence typing. Therefore, multiple analyses were conducted utilising sequences obtained from 28S nrDNA (Large Subunit - LSU), 18S nrDNA (Small Subunit - SSU), the Internal Transcribed Spacer regions 1 & 2 and 5.8S nrDNA (ITS), and part of the beta-tubulin (TUB) gene region. A total of 324 strains were included in the analyses of which most belonged to Phoma taxa, whilst 54 to related pleosporalean fungi. In total, 206 taxa were investigated, of which 159 are known to have affinities to Phoma. The phylogenetic analysis revealed that the current Boeremaean subdivision is incorrect from an evolutionary point of view, revealing the genus to be highly polyphyletic. Phoma species are retrieved in six distinct clades within the Pleosporales, and appear to reside in different families. The majority of the species, however, including the generic type, clustered in a recently established family, Didymellaceae. In the second part of this study, the phylogenetic variation of the species and varieties in this clade was further assessed. Next to the genus Didymella, which is considered to be the sole teleomorph of Phoma s. str., we also retrieved taxa belonging to the teleomorph genera Leptosphaerulina and Macroventuria in this clade. Based on the sequence data obtained, the Didymellaceae segregate into at least 18 distinct clusters, of which many can be associated with several specific taxonomic characters. Four of these clusters were defined well enough by means of phylogeny and morphology, so that the associated taxa could be transferred to separate genera. Aditionally, this study addresses the taxonomic description of eight species and two varieties that are novel to science, and the recombination of 61 additional taxa.
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Affiliation(s)
- M.M. Aveskamp
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The
Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of
Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The
Netherlands
| | - J. de Gruyter
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The
Netherlands
- Dutch Plant Protection Service (PD), Geertjesweg 15, 6706 EA Wageningen,
The Netherlands
| | - J.H.C. Woudenberg
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The
Netherlands
| | - G.J.M. Verkley
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The
Netherlands
| | - P.W. Crous
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The
Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of
Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The
Netherlands
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