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Petersen RH, Hughes KW. Two new species of Collybiopsis (Agaricales, Omphalotaceae) from Eastern North America. MycoKeys 2024; 107:95-124. [PMID: 39081830 PMCID: PMC11287082 DOI: 10.3897/mycokeys.107.122634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 07/05/2024] [Indexed: 08/02/2024] Open
Abstract
Two small gymnopoid fungi from the southern Appalachian Mountains and Massachusetts, Collybiopsiscomplicata sp. nov. and C.prolapsis sp. nov., are identified and described. A new generic nrITS-LSU phylogeny of Collybiopsis places C.complicata and C.prolapsis in a small clade together with C.minor, and an unknown taxon from Arkansas. This clade adds to the growing circumscription of Collybiopsis (= Marasmiellus).
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Affiliation(s)
- Ronald H. Petersen
- Ecology & Evolutionary Biology, University of Tennessee, Knoxville, TN 37996-1100, USAUniversity of TennesseeKnoxvilleUnited States of America
| | - Karen W. Hughes
- Ecology & Evolutionary Biology, University of Tennessee, Knoxville, TN 37996-1100, USAUniversity of TennesseeKnoxvilleUnited States of America
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Yang WJ, Xu M, Zhang J, Zhou F, Le ZF, Tong WJ, Song HY, Jin ZH, Cheng QG, Zhou JP, Gao Y, Zhai ZJ, Hu HJ, Chen MH, Yin H, Wang J, Hu DM. Morphological and phylogenetic analyses reveal a new species of Anthracophyllum (Omphalotaceae, Agaricales) in Zhejiang Province, China. Arch Microbiol 2024; 206:63. [PMID: 38217700 DOI: 10.1007/s00203-023-03748-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 11/15/2023] [Accepted: 11/15/2023] [Indexed: 01/15/2024]
Abstract
During the investigations of macrofungi resources in Zhejiang Province, China, an interesting wood rot fungus was collected. Based on morphological and molecular phylogenetic studies, it is described as a new species, Anthracophyllum sinense. A. sinense is characterized by its sessile, charcoal black and pleurotoid pileus, sparse lamellae occasionally branching, clavate basidia with long sterigmata [(3-)6-7(-8) μm], and non-heteromorphous cystidia. A. sinense establishes a separate lineage close to A. archeri and A. lateritium in the phylogenetic tree.
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Affiliation(s)
- Wen-Juan Yang
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
| | - Miao Xu
- Jiangxi Engineering Research Center for Comprehensive Development of Forest Fungal Resources, Jiangxi Environmental Engineering Vocational College, Ganzhou, China
| | - Jing Zhang
- General Station for Forestry Technology Extension of Taizhou City, Zhejiang, Taizhou, 318000, Zhejiang, China
| | - Fan Zhou
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
| | - Zhi-Fang Le
- Ministry of Ecology and Environment of the People's Republic of China, Nanjing Institute of Environmental Sciences, Nanjing, 210042, China
| | - Wen-Jun Tong
- Ministry of Ecology and Environment of the People's Republic of China, Nanjing Institute of Environmental Sciences, Nanjing, 210042, China
| | - Hai-Yan Song
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China.
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, (Jiangxi Agricultural University), Ministry of Education of the P.R. China, 1101 Zhimin Road, Nanchang, 330045, China.
| | - Zhuo-Han Jin
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
| | - Qiu-Ge Cheng
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
| | - Jian-Ping Zhou
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
| | - Yang Gao
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
| | - Zhi-Jun Zhai
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
| | - Hai-Jing Hu
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
| | - Ming-Hui Chen
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
| | - Hua Yin
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
| | - Jiang Wang
- School of Life Sciences, Taizhou University, Taizhou, 318000, China
| | - Dian-Ming Hu
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China.
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China.
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China.
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3
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Zhang QY, Jin C, Zhou HM, Ma ZY, Zhang YZ, Liang JQ, Si J, Li HJ. Enlargement of the knowledge of Cortinarius section Anomali (Agaricales, Basidiomycota): introducing three new species from China. Front Cell Infect Microbiol 2023; 13:1215579. [PMID: 37377645 PMCID: PMC10291886 DOI: 10.3389/fcimb.2023.1215579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Cortinarius is a globally distributed agaricoid genus that has been well studied in Europe and America with over 1,000 described species. However, as part of an ongoing effort to investigate the diversity of Cortinarius section Anomali in China, the resource investigation and classification research are still limited, and the species diversity has not been clarified by far. During the re-examination of the Chinese Cortinarius specimens, C. cinnamomeolilacinus, C. subclackamasensis, and C. tropicus, belonging to the sect. Anomali, were described in China as new to science based on morphological examination and phylogenetic analysis. The three new species are described and illustrated in detail according to the Chinese materials. The phylogenetic analysis based on internal transcribed spacer sequences confirmed the placement of the three species in the Cortinarius sect. Anomali clade. Phylogenetically related and morphologically similar species to these three new species are discussed.
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Affiliation(s)
- Qiu-Yue Zhang
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Can Jin
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Hong-Min Zhou
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Zi-Yan Ma
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yi-Zhe Zhang
- National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jia-Qi Liang
- National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jing Si
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Hai-Jiao Li
- National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
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Li JP, Pan MC, Li Y, Deng CY, Wang XM, Zhang BX, Li CT, Li Y. Morpho-Molecular Evidence Reveals Four Novel Species of Gymnopus (Agaricales, Omphalotaceae) from China. J Fungi (Basel) 2022; 8:jof8040398. [PMID: 35448629 PMCID: PMC9028581 DOI: 10.3390/jof8040398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/11/2022] [Accepted: 04/11/2022] [Indexed: 01/27/2023] Open
Abstract
Nine collections of gymnopoid fungi were studied based on morpho-molecular characteristics. The macromorphology was made according to the photograph of fresh basidiomata and field notes, while the micromorphology was examined via an optical microscope. Simultaneously, the phylogenetic analyses were performed by maximum likelihood and Bayesian inference methods based on a combined dataset of nrITS1-nr5.8S-nrITS2-nrLSU sequences. Integrated analysis of these results was therefore, G. efibulatus belonging to sect. Androsacei, G. iodes and G. sinopolyphyllus belonging to sect. Impudicae and G. strigosipes belonging to sect. Levipedes are proposed as new to science. The detailed descriptions, colour photos of basidiomata and line-drawings of microscopic structures are provided. The comparisons with closely related species and a key to known species of Gymnopus s. str. reported with morpho-molecular evidence in China is also given.
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Affiliation(s)
- Ji-Peng Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China; (J.-P.L.); (M.-C.P.)
| | - Mei-Chen Pan
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China; (J.-P.L.); (M.-C.P.)
| | - Yi Li
- College of Food Science and Engineering, Yangzhou University, Yangzhou 225127, China;
| | - Chun-Ying Deng
- Guizhou Institute of Biology, Guizhou Academy of Sciences, Guiyang 550009, China;
| | - Xiao-Min Wang
- Soil and Fertilizer Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China; (X.-M.W.); (B.-X.Z.)
| | - Bang-Xi Zhang
- Soil and Fertilizer Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China; (X.-M.W.); (B.-X.Z.)
| | - Chang-Tian Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China; (J.-P.L.); (M.-C.P.)
- Correspondence: (C.-T.L.); (Y.L.)
| | - Yu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China; (J.-P.L.); (M.-C.P.)
- Correspondence: (C.-T.L.); (Y.L.)
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5
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Looney BP, Buyck B, Menolli N, Randrianjohany E, Hibbett D. Lentinula madagasikarensis sp. nov., a relative of shiitake mushrooms from Madagascar. Fungal Syst Evol 2022; 8:1-8. [PMID: 35005568 PMCID: PMC8687056 DOI: 10.3114/fuse.2021.08.01] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 05/03/2021] [Indexed: 11/26/2022] Open
Abstract
We describe the first species of Lentinula from Africa, Lentinula madagasikarensis sp. nov. The new taxon, which was collected from central Madagascar, is strikingly similar to L. edodes, the shiitake mushroom. A BLAST search using ITS sequences from L. madagasikarensis as the query retrieves a mix of Lentinula, Gymnopus, Marasmiellus, and other members of Omphalotaceae as the top hits. A 28S phylogeny of the Omphalotaceae confirms placement of L. madagasikarensis within Lentinula. An ITS phylogeny places L. madagasikarensis as the sister group of L. aciculospora, which is a neotropical species. Lentinula madagasikarensis is characterized by robust basidiomata with vinaceous pilei, prominent floccose scales near the pileus margin, florets of sphaeropedunculate cheilocystidia, and subcylindrical basidiospores. This report constitutes a 4 000-mile, trans-oceanic range extension for Lentinula.
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Affiliation(s)
- B P Looney
- Clark University, Department of Biology, Worcester, MA 01610, USA
| | - B Buyck
- Museìum national d'Histoire naturelle, CNRS, Sorbonne Universiteì, Institut de Systeìmatique, Eìcologie, Biodiversiteì (ISYEB), EPHE, 57 rue Cuvier, CP 39, F-75005, Paris, France
| | - N Menolli
- Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), Departamento de Ciências da Natureza e Matemática (DCM), Subárea de Biologia (SAB), Câmpus São Paulo, Rua Pedro Vicente 625, São Paulo, SP, 01109-010, Brazil.,Instituto de Botânica (IBt), Núcleo de Pesquisa em Micologia (NPM), Av. Miguel Stefano 3687, Água Funda, São Paulo, SP, 04301-012, Brazil
| | - E Randrianjohany
- Centre National de Recherche sur l'Environnement (CNRE), BP 1739, Lab. de Microbiologie de l'Environnement (LME), Antananarivo, Madagascar
| | - D Hibbett
- Clark University, Department of Biology, Worcester, MA 01610, USA
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Jofre GI, Singh A, Mavengere H, Sundar G, D'Agostino E, Chowdhary A, Matute DR. An Indian lineage of Histoplasma with strong signatures of differentiation and selection. Fungal Genet Biol 2022; 158:103654. [PMID: 34942368 DOI: 10.1016/j.fgb.2021.103654] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 12/06/2021] [Accepted: 12/11/2021] [Indexed: 01/04/2023]
Abstract
Histoplasma, a genus of dimorphic fungi, is the etiological agent of histoplasmosis, a pulmonary disease widespread across the globe. Whole genome sequencing has revealed that the genus harbors a previously unrecognized diversity of cryptic species. To date, studies have focused on Histoplasma isolates collected in the Americas with little knowledge of the genomic variation from other localities. In this report, we report the existence of a well-differentiated lineage of Histoplasma occurring in the Indian subcontinent. The group is differentiated enough to satisfy the requirements of a phylogenetic species, as it shows extensive genetic differentiation along the whole genome and has little evidence of gene exchange with other Histoplasma species. Next, we leverage this genetic differentiation to identify genetic changes that are unique to this group and that have putatively evolved through rapid positive selection. We found that none of the previously known virulence factors have evolved rapidly in the Indian lineage but find evidence of strong signatures of selection on other alleles potentially involved in clinically-important phenotypes. Our work serves as an example of the importance of correctly identifying species boundaries to understand the extent of selection in the evolution of pathogenic lineages. IMPORTANCE: Whole genome sequencing has revolutionized our understanding of microbial diversity, including human pathogens. In the case of fungal pathogens, a limiting factor in understanding the extent of their genetic diversity has been the lack of systematic sampling. In this piece, we show the results of a collection in the Indian subcontinent of the pathogenic fungus Histoplasma, the causal agent of a systemic mycosis. We find that Indian samples of Histoplasma form a distinct clade which is highly differentiated from other Histoplasma species. We also show that the genome of this lineage shows unique signals of natural selection. This work exemplifies how the combination of a robust sampling along with population genetics, and phylogenetics can reveal the precise genetic changes that differentiate lineages of fungal pathogens.
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Affiliation(s)
- Gaston I Jofre
- Department of Biology, University of North Carolina, Chapel Hill, NC, United States
| | - Ashutosh Singh
- National Reference Laboratory for Antimicrobial Resistance in Fungal Pathogens, Medical Mycology Unit, Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Heidi Mavengere
- Department of Biology, University of North Carolina, Chapel Hill, NC, United States
| | - Gandhi Sundar
- National Reference Laboratory for Antimicrobial Resistance in Fungal Pathogens, Medical Mycology Unit, Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Emmanuel D'Agostino
- Department of Biology, University of North Carolina, Chapel Hill, NC, United States
| | - Anuradha Chowdhary
- National Reference Laboratory for Antimicrobial Resistance in Fungal Pathogens, Medical Mycology Unit, Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Daniel R Matute
- Department of Biology, University of North Carolina, Chapel Hill, NC, United States.
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Species diversity, phylogeny, endemism and geography of the truffle genus Tuber in China based on morphological and molecular data. Persoonia - Molecular Phylogeny and Evolution of Fungi 2022. [DOI: 10.3767/persoonia.2022.48.05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The genus Tuber (Tuberaceae, Pezizales) is an important fungal group of Ascomycota both economically and ecologically. However, the species diversity, phylogenetic relationships, and geographic distribution of Tuber species in China remains poorly understood, primarily because descriptions of many new species relied heavily on morphological features with molecular data either not sought or ignored. The misapplication of European and North American names further added to confusion regarding the taxonomy of Chinese Tuber species. In this study, we examined more than 1000 specimens from China, and performed a comprehensive phylogenetic analysis for Chinese Tuber species using ITS sequences and multilocus sequence data. To infer the phylogeny of Chinese Tuber spp., 11 molecular datasets were assembled, including a concatenated internal transcribed spacers of the nuc rDNA (ITS), nuc rDNA 28S subunit (LSU), translation elongation factor 1-alpha (tef1-α), and RNA polymerase II subunit (rpb2) dataset as well as 10 ITS datasets (totally including 1435 sequences from 828 collections with 597 newly generated sequences, and 168 sequences from the types of 63 species). Our phylogenetic tree based on a concatenated multilocus dataset revealed that all Chinese Tuber species nested in nine phylogenetic clades (phylogroups), including Aestivum, Excavatum, Latisporum, Macrosporum, Maculatum, Melanosporum, Puberulum, Rufum and Turmericum. Of these, five phylogroups (Macrosporum, Maculatum, Melanosporum, Puberulum and Rufum) are shared across the continents of Asia, Europe and North America; two phylogroups (Aestivum and Excavatum) are shared by Europe and Asia; and the phylogroups Turmericum and Latisporum are endemic only to Asia. Phylogenetic trees based on 10 ITS datasets confirmed the presence of at least 82 phylogenetic species in China. Of these, 53 are identified as known species, including three new records for China, and 25 species are identified as new to science. Of the new species, nine are described and illustrated in this paper, and the others remain unnamed due to the paucity or absence of ascomatal materials. Accordingly, the confirmed, excluded and doubtful Tuber species in China are discussed. Tuber species showed high endemism. Of the 82 phylogenetic species found in China, 68 species occur only in China, six species are also found in other regions in Asia, and only eight species (T. anniae, T. excelsum-reticulatum, T. formosanum, T. maculatum, T. wenchuanense, Tuber sp. CHN-3, Tuber sp. CHN-10 and Tuber sp. CHN-11) are shared with other continents. Most Tuber species have a small and limited distribution in China, but a few, such as T. formosanum and T. parvomurphium, are widely distributed across China. Some phylogenetically closely related species, such as T. liaotongense and T. subglobosum, as well as T. xuanhuaense and T. lijiangense, show a pattern of allopatric distribution.
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Isolating ecological-specific fungi and creating fungus-seed bags for epiphytic orchid conservation. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01714] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Høyer AK, Hodkinson TR. Hidden Fungi: Combining Culture-Dependent and -Independent DNA Barcoding Reveals Inter-Plant Variation in Species Richness of Endophytic Root Fungi in Elymus repens. J Fungi (Basel) 2021; 7:jof7060466. [PMID: 34207673 PMCID: PMC8226481 DOI: 10.3390/jof7060466] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 01/04/2023] Open
Abstract
The root endophyte community of the grass species Elymus repens was investigated using both a culture-dependent approach and a direct amplicon sequencing method across five sites and from individual plants. There was much heterogeneity across the five sites and among individual plants. Focusing on one site, 349 OTUs were identified by direct amplicon sequencing but only 66 OTUs were cultured. The two approaches shared ten OTUs and the majority of cultured endophytes do not overlap with the amplicon dataset. Media influenced the cultured species richness and without the inclusion of 2% MEA and full-strength MEA, approximately half of the unique OTUs would not have been isolated using only PDA. Combining both culture-dependent and -independent methods for the most accurate determination of root fungal species richness is therefore recommended. High inter-plant variation in fungal species richness was demonstrated, which highlights the need to rethink the scale at which we describe endophyte communities.
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Nitare J, Ainsworth A, Larsson E, Parfitt D, Suz L, Svantesson S, Larsson KH. Four new species of Hydnellum ( Thelephorales, Basidiomycota) with a note on Sarcodon illudens. Fungal Syst Evol 2021; 7:233-254. [PMID: 34124626 PMCID: PMC8165966 DOI: 10.3114/fuse.2021.07.12] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/18/2021] [Indexed: 11/07/2022] Open
Abstract
Four new Hydnellum species are described. Hydnellum roseoviolaceum sp. nov. grows in dry pine heaths on acidic, sandy soil. It is close to H. fuligineoviolaceum, another pine-associated species, but differs by smaller spores, an initially rose-coloured instead of violet flesh in fresh basidiomata and a mild taste. Hydnellum scabrosellum sp. nov. grows in coniferous forests on calcareous soil. It shares a general morphology with H. scabrosum, which also is its closest relative. It differs by having smaller and slenderer basidiomata and by the yellowish ochraceous colour of flesh and spines in dried specimens compared to the whitish or reddish brown colour seen in H. scabrosum. Hydnellum fagiscabrosum sp. nov. is another species with morphological and phylogenetic affinities to H. scabrosum. However, it is associated with trees from Fagales whereas H. scabrosum is associated with Pinaceae. Hydnellum nemorosum sp. nov. is yet another species that associates with broadleaved trees. It seems to be a rare species, morphologically reminiscent of H. fuligineoviolaceum, H. ioeides and H. scabrosum, but it is phylogenetically close to H. fennicum. Sequences from the type specimens of H. glaucopus, H. lepidum, H. scabrosum, Sarcodon illudens and S. regalis are included in the analyses. Specimens given the provisional name "Sarcodon pseudoglaucopus" in Sweden are now shown to be referable to S. illudens. The analyses further showed that S. illudens is close to H. lepidum. The new combination Hydnellum illudens is proposed. Sarcodon regalis and H. lepidum are shown to be conspecific and, although their basionyms were simultaneously published, the name S. regalis was only validated in a later publication. Hydnellum lepidum therefore takes priority and S. regalis becomes a synonym. Citation: Nitare J, Ainsworth AM, Larsson E, Parfitt D, Suz LM, Svantesson S, Larsson K-H (2021). Four new species of Hydnellum (Thelephorales, Basidiomycota) with a note on Sarcodon illudens. Fungal Systematics and Evolution 7: 233-254. doi: 10.3114/fuse.2021.07.12.
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Affiliation(s)
- J. Nitare
- Skogsstyrelsen, SE-551 83 Jönköping, Sweden
| | - A.M. Ainsworth
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS UK
| | - E. Larsson
- Department of Biological and Environmental Sciences, University of Gothenburg, P.O. Box 461, SE-405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, P.O. Box 461, SE-405 30 Göteborg, Sweden
| | - D. Parfitt
- Cardiff School of Biosciences, Cardiff University, Cardiff, CF10 3AX UK
| | - L.M. Suz
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS UK
| | - S. Svantesson
- Department of Biological and Environmental Sciences, University of Gothenburg, P.O. Box 461, SE-405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, P.O. Box 461, SE-405 30 Göteborg, Sweden
| | - K.-H. Larsson
- Gothenburg Global Biodiversity Centre, P.O. Box 461, SE-405 30 Göteborg, Sweden
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, NO-0318 Oslo, Norway
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Giusti A, Ricci E, Gasperetti L, Galgani M, Polidori L, Verdigi F, Narducci R, Armani A. Building of an Internal Transcribed Spacer (ITS) Gene Dataset to Support the Italian Health Service in Mushroom Identification. Foods 2021; 10:foods10061193. [PMID: 34070525 PMCID: PMC8227961 DOI: 10.3390/foods10061193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/23/2021] [Accepted: 05/24/2021] [Indexed: 01/26/2023] Open
Abstract
This study aims at building an ITS gene dataset to support the Italian Health Service in mushroom identification. The target species were selected among those mostly involved in regional (Tuscany) poisoning cases. For each target species, all the ITS sequences already deposited in GenBank and BOLD databases were retrieved and accurately assessed for quality and reliability by a systematic filtering process. Wild specimens of target species were also collected to produce reference ITS sequences. These were used partly to set up and partly to validate the dataset by BLAST analysis. Overall, 7270 sequences were found in the two databases. After filtering, 1293 sequences (17.8%) were discarded, with a final retrieval of 5977 sequences. Ninety-seven ITS reference sequences were obtained from 76 collected mushroom specimens: 15 of them, obtained from 10 species with no sequences available after the filtering, were used to build the dataset, with a final taxonomic coverage of 96.7%. The other 82 sequences (66 species) were used for the dataset validation. In most of the cases (n = 71; 86.6%) they matched with identity values ≥ 97–100% with the corresponding species. The dataset was able to identify the species involved in regional poisoning incidents. As some of these species are also involved in poisonings at the national level, the dataset may be used for supporting the National Health Service throughout the Italian territory. Moreover, it can support the official control activities aimed at detecting frauds in commercial mushroom-based products and safeguarding consumers.
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Affiliation(s)
- Alice Giusti
- FishLab, Department of Veterinary Sciences, University of Pisa, Viale delle Piagge 2, 56124 Pisa, Italy; (M.G.); (A.A.)
- Correspondence: ; Tel.: +39-0502210204
| | - Enrica Ricci
- Experimental Zooprophylactic Institute of Lazio and Tuscany M. Aleandri, UOT Toscana Nord, SS Abetone e Brennero 4, 56124 Pisa, Italy; (E.R.); (L.G.)
| | - Laura Gasperetti
- Experimental Zooprophylactic Institute of Lazio and Tuscany M. Aleandri, UOT Toscana Nord, SS Abetone e Brennero 4, 56124 Pisa, Italy; (E.R.); (L.G.)
| | - Marta Galgani
- FishLab, Department of Veterinary Sciences, University of Pisa, Viale delle Piagge 2, 56124 Pisa, Italy; (M.G.); (A.A.)
| | - Luca Polidori
- Tuscany Mycological Groups Association, via Turi, 8 Santa Croce sull’Arno, 56124 Pisa, Italy; (L.P.); (R.N.)
| | - Francesco Verdigi
- North West Tuscany LHA (Mycological Inspectorate), via A. Cocchi, 7/9, 56124 Pisa, Italy;
| | - Roberto Narducci
- Tuscany Mycological Groups Association, via Turi, 8 Santa Croce sull’Arno, 56124 Pisa, Italy; (L.P.); (R.N.)
| | - Andrea Armani
- FishLab, Department of Veterinary Sciences, University of Pisa, Viale delle Piagge 2, 56124 Pisa, Italy; (M.G.); (A.A.)
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Mavengere H, Mattox K, Teixeira MM, Sepúlveda VE, Gomez OM, Hernandez O, McEwen J, Matute DR. Paracoccidioides Genomes Reflect High Levels of Species Divergence and Little Interspecific Gene Flow. mBio 2020; 11:e01999-20. [PMID: 33443110 PMCID: PMC8534288 DOI: 10.1128/mbio.01999-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/27/2020] [Indexed: 12/30/2022] Open
Abstract
The fungus Paracoccidioides is a prevalent human pathogen endemic to South America. The genus is composed of five species. In this report, we use 37 whole-genome sequences to study the allocation of genetic variation in Paracoccidioides We tested three genome-wide predictions of advanced speciation, namely, that all species should be reciprocally monophyletic, that species pairs should be highly differentiated along the whole genome, and that there should be low rates of interspecific gene exchange. We find support for these three hypotheses. Species pairs with older divergences show no evidence of gene exchange, while more recently diverged species pairs show evidence of modest rates of introgression. Our results indicate that as divergence progresses, species boundaries become less porous among Paracoccidioides species. Our results suggest that species in Paracoccidioides are at different stages along the divergence continuum.IMPORTANCEParacoccidioides is the causal agent of a systemic mycosis in Latin America. Most of the inference of the evolutionary history of Paracoccidioides has used only a few molecular markers. In this report, we evaluate the extent of genome divergence among Paracoccidioides species and study the possibility of interspecific gene exchange. We find that all species are highly differentiated. We also find that the amount of gene flow between species is low and in some cases is even completely absent in spite of geographic overlap. Our study constitutes a systematic effort to identify species boundaries in fungal pathogens and to determine the extent of gene exchange among fungal species.
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Affiliation(s)
- Heidi Mavengere
- Biology Department, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Kathleen Mattox
- Biology Department, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Marcus M Teixeira
- Núcleo de Medicina Tropical, Faculdade de Medicina, University of Brasília, Brasília, Brazil
| | - Victoria E Sepúlveda
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Oscar M Gomez
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
| | - Orville Hernandez
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- MICROBA Research Group, School of Microbiology, Universidad de Antioquia, Medellín, Colombia
| | - Juan McEwen
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, North Carolina, USA
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Fryssouli V, Zervakis GI, Polemis E, Typas MA. A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 2020; 75:71-143. [PMID: 33304123 PMCID: PMC7723883 DOI: 10.3897/mycokeys.75.59872] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 10/26/2020] [Indexed: 01/16/2023] Open
Abstract
Ganoderma P. Karst. is a cosmopolitan genus of white-rot fungi which comprises species with highly-prized pharmaceutical properties, valuable biotechnological applications and of significant phytopathological interest. However, the status of the taxonomy within the genus is still highly controversial and ambiguous despite the progress made through molecular approaches. A metadata analysis of 3908 nuclear ribosomal internal transcribed spacer (ITS) rDNA sequences obtained from GenBank/ENA/DDBJ and UNITE was performed by targeting sequences annotated as Ganoderma, but also sequences from environmental samples and from material examined for the first time. Ganoderma taxa segregated into five main lineages (Clades A to E). Clade A corresponds to the core of laccate species and includes G. shanxiense and three major well-supported clusters: Cluster A.1 ('G. lucidum sensu lato') consists of taxa from Eurasia and North America, Cluster A.2 of material with worldwide occurrence including G. resinaceum and Cluster A.3 is composed of species originating from all continents except Europe and comprises G. lingzhi. Clade B includes G. applanatum and allied species with a Holarctic distribution. Clade C comprises taxa from Asia and Africa only. Clade D consists of laccate taxa with tropical/subtropical occurrence, while clade E harbours the highest number of non-laccate species with a cosmopolitan distribution. The 92 Ganoderma-associated names, initially used for sequences labelling, correspond to at least 80 taxa. Amongst them, 21 constitute putatively new phylospecies after our application of criteria relevant to the robustness/support of the terminal clades, intra- and interspecific genetic divergence and available biogeographic data. Moreover, several other groups or individual sequences seem to represent distinct taxonomic entities and merit further investigation. A particularly large number of the public sequences was revealed to be insufficiently and/or incorrectly identified, for example, 87% and 78% of entries labelled as G. australe and G. lucidum, respectively. In general, ITS demonstrated high efficacy in resolving relationships amongst most of the Ganoderma taxa; however, it was not equally useful at elucidating species barriers across the entire genus and such cases are outlined. Furthermore, we draw conclusions on biogeography by evaluating species occurrence on a global scale in conjunction with phylogenetic structure/patterns. The sequence variability assessed in ITS spacers could be further exploited for diagnostic purposes.
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Affiliation(s)
- Vassiliki Fryssouli
- Agricultural University of Athens, Laboratory of General and Agricultural Microbiology, Iera Odos 75, 11855 Athens, Greece
| | - Georgios I. Zervakis
- Agricultural University of Athens, Laboratory of General and Agricultural Microbiology, Iera Odos 75, 11855 Athens, Greece
| | - Elias Polemis
- Agricultural University of Athens, Laboratory of General and Agricultural Microbiology, Iera Odos 75, 11855 Athens, Greece
| | - Milton A. Typas
- National and Kapodistrian University of Athens, Department of Genetics and Biotechnology, Faculty of Biology, Panepistemiopolis, Athens 15701, Greece
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Koch RA, Liu J, Brann M, Jumbam B, Siegel N, Aime MC. Marasmioid rhizomorphs in bird nests: Species diversity, functional specificity, and new species from the tropics. Mycologia 2020; 112:1086-1103. [PMID: 32897841 DOI: 10.1080/00275514.2020.1788892] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
In tropical and subtropical rainforests, vegetative fungal rhizomorphs from the Marasmiineae are routinely used as construction material in bird nests. Because rhizomorphs seldom produce mushrooms within nests, the fungal species involved remain largely unknown. In turn, this limitation has prevented us from resolving broader questions such as whether specific fungal species are selected by birds for different functional roles (i.e., attachment, or parasite control). To fill some of these gaps, we collected 74 rhizomorph-containing bird nests from the Neo- and Afrotropics and used nuc rDNA internal transcribed spacer ITS1-5.8S-ITS2 (ITS) sequences to discriminate between rhizomorph-forming species. In total we recovered 25 Marasmiineae species used by birds in nest construction, none of which were shared between the Neotropics and the Afrotropics. We also collected Marasmiineae basidiomes in the vicinity of nests and used ITS sequences to match these sporulating morphs with nest rhizomorphs for nine species. Basidiomes from an additional five species were found fruiting from rhizomorphs incorporated within bird nests. Finally, an additional six species were putatively identified based on publicly available sequence data. Rhizomorphs of five species were found to be utilized almost exclusively as lining material in nests. Lining material comes in direct contact with nestlings and is hypothesized to play a role in parasite control. Rhizomorphs from 10 species were used to attach and anchor nests to substrates; we matched six of those to fruiting litter trap-forming species collected in the understory. Litter traps hold large quantities of fallen litter material, suggesting that birds may preferentially use rhizomorphs that are adapted to bearing heavy loads for nest attachment. Finally, we describe two species of Marasmius-M. neocrinis-equi, sp. nov., and M. nidus-avis, sp. nov.-that are commonly found associated with bird nests and show that rhizomorph production is common across the genus.
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Affiliation(s)
- Rachel A Koch
- Department of Botany and Plant Pathology, Purdue University , West Lafayette, Indiana 47907
| | - Jingyu Liu
- Department of Botany and Plant Pathology, Purdue University , West Lafayette, Indiana 47907
| | - Mia Brann
- Department of Botany and Plant Pathology, Purdue University , West Lafayette, Indiana 47907
| | - Blaise Jumbam
- Department of Botany and Plant Pathology, Purdue University , West Lafayette, Indiana 47907
| | - Noah Siegel
- 25 Prospect Hill Road, Royalston , Massachusetts 01368
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University , West Lafayette, Indiana 47907
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15
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Cong B, Yin X, Deng A, Shen J, Tian Y, Wang S, Yang H. Diversity of Cultivable Microbes From Soil of the Fildes Peninsula, Antarctica, and Their Potential Application. Front Microbiol 2020; 11:570836. [PMID: 33013802 PMCID: PMC7495136 DOI: 10.3389/fmicb.2020.570836] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/17/2020] [Indexed: 12/02/2022] Open
Abstract
To explore the diversity and application potential of Antarctic microorganisms, 1208 strains bacteria and fungi were isolated from 5 samples collected from the Fildes Peninsula during China’s 27th and 31st Antarctic expeditions. By using 16S and ITS sequence similarity alignment, 83 strains bacteria belonging to 20 genera and 30 strains fungi belonging to 7 genera were identified. Among them, 1 strains bacteria and 6 strains fungi showed low sequence similarity to the database, suggesting that they might be novel species. Physiological-biochemical characteristics showed that the identified bacteria could utilize many kinds of carbohydrates and that the identified fungi could produce several kinds of extracellular enzymes. The fungal strain MS-19, identified as Aspergillus sydowii, possesses the potential to produce antifungal activity agents based on an activity-guided approach. Further isolation yielded four polyketones: versicone A (1), versicone B (2), 4-methyl-5,6-dihydro-2H-pyran-2-one (3), and (R)-(+)-sydowic acid (4). It should be noted that 1 displayed strong activity against Candida albicans, with an MIC value of 3.91 μg/mL.
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Affiliation(s)
- Bailin Cong
- The First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Xiaofei Yin
- The First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Aifang Deng
- The First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Jihong Shen
- The First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Yongqi Tian
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Shaoyun Wang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Huanghao Yang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
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16
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Yang WK, Li TQ, Wu SM, Finnegan PM, Gao JY. Ex situ seed baiting to isolate germination-enhancing fungi for assisted colonization in Paphiopedilum spicerianum, a critically endangered orchid in China. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01147] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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17
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Dulay RMR, Cabrera EC, Kalaw SP, Reyes RG. Nucleotide sequencing and identification of wild mushrooms from the Philippines. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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18
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Prunus trees in Germany—a hideout of unknown fungi? Mycol Prog 2020. [DOI: 10.1007/s11557-020-01586-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
AbstractPrunus belongs to the economically most important genera of fruit crops in Germany. Although wood pathogens possess the capability to damage the host substantially, the knowledge of the fungal pathogenic community and the mycobiome of Prunus wood in general is low. During a survey in important fruit production areas in Germany, branches with symptoms of fungal infection were sampled in Prunus avium, P. cerasus and P. domestica orchards, and 1018 fungal isolates were obtained primarily from the transition zone of symptomatic to non-symptomatic wood. By a combination of blastn searches and phylogenetic analyses based on ITS and LSU sequences with a strong focus on reliable reference data, a diversity of 172 fungal taxa belonging to Ascomycota, Basidiomycota and Mucoromycota were differentiated. The majority of the strains belonged to three classes of Ascomycota, namely Sordariomycetes, Leotiomycetes and Dothideomycetes. The dominant species were Aposphaeria corallinolutea (Dothideomycetes) and Pallidophorina paarla (Leotiomycetes) that were isolated more than a hundred times each, while all other taxa were isolated ≤ 30 times. Only part of them could be identified to species level. Because of the high plasticity of species boundaries, the identification certainty was divided into categories based on nucleotide differences to reference sequences. In total, 82 species were identified with high and 20 species with low (cf.) certainty. Moreover, about 70 species could not be assigned to a known species, which reveals Prunus wood to represent a habitat harbouring high numbers of potentially new species, even in a well-explored region like Germany.
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Wang T, Gao C, Cheng Y, Li Z, Chen J, Guo L, Xu J. Molecular Diagnostics and Detection of Oomycetes on Fiber Crops. PLANTS (BASEL, SWITZERLAND) 2020; 9:E769. [PMID: 32575466 PMCID: PMC7355704 DOI: 10.3390/plants9060769] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 11/16/2022]
Abstract
Fiber crops are an important group of economic plants. Traditionally cultivated for fiber, fiber crops have also become sources of other materials such as food, animal feed, cosmetics and medicine. Asia and America are the two main production areas of fiber crops in the world. However, oomycete diseases have become an important factor limiting their yield and quality, causing devastating consequences for the production of fiber crops in many regions. To effectively control oomycete pathogens and reduce their negative impacts on these crops, it is very important to have fast and accurate detection systems, especially in the early stages of infection. With the rapid development of molecular biology, the diagnosis of plant pathogens has progressed from relying on traditional morphological features to the increasing use of molecular methods. The objective of this paper was to review the current status of research on molecular diagnosis of oomycete pathogens on fiber crops. Our search of PubMed identified nearly 30 species or subspecies of oomycetes on fiber crops, among which the top three species were Phytophthora boehmeriae, Phytophthora nicotianae and Pythium ultimum. The gene regions that have been used for molecular identifications of these pathogens include the internal transcribed spacer (ITS) regions of the nuclear ribosomal RNA gene cluster, and genes coding for translation elongation factor 1α (EF-1α) and mitochondrial cytochrome c oxidase subunits I and II (Cox 1, Cox 2), etc. We summarize the molecular assays that have been used to identify these pathogens and discuss potential areas of future development for fast, specific, and accurate diagnosis of oomycetes on fiber crops.
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Affiliation(s)
- Tuhong Wang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (T.W.); (C.G.); (Y.C.); (Z.L.); (J.C.); (L.G.)
| | - Chunsheng Gao
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (T.W.); (C.G.); (Y.C.); (Z.L.); (J.C.); (L.G.)
| | - Yi Cheng
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (T.W.); (C.G.); (Y.C.); (Z.L.); (J.C.); (L.G.)
| | - Zhimin Li
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (T.W.); (C.G.); (Y.C.); (Z.L.); (J.C.); (L.G.)
| | - Jia Chen
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (T.W.); (C.G.); (Y.C.); (Z.L.); (J.C.); (L.G.)
| | - Litao Guo
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (T.W.); (C.G.); (Y.C.); (Z.L.); (J.C.); (L.G.)
| | - Jianping Xu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (T.W.); (C.G.); (Y.C.); (Z.L.); (J.C.); (L.G.)
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
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Cheng Y, Tang X, Gao C, Li Z, Chen J, Guo L, Wang T, Xu J. Molecular Diagnostics and Pathogenesis of Fungal Pathogens on Bast Fiber Crops. Pathogens 2020; 9:pathogens9030223. [PMID: 32197350 PMCID: PMC7157645 DOI: 10.3390/pathogens9030223] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/15/2020] [Accepted: 03/16/2020] [Indexed: 11/16/2022] Open
Abstract
Bast fibers and products derived from them are undergoing a resurgence in demand in the global market. However, fungal diseases have become an important factor limiting their yield and quality, causing devastating consequences for the production of bast fiber crops in many parts of the world. Thus, there is a high demand for effective control and prevention strategies against fungal pathogens. Having rapid, specific, sensitive, and cost-effective tests that can be used for early and accurate diagnosis of disease agents is an essential step of such strategies. The objective of this study was to review the current status of research on molecular diagnosis of fungal pathogens on bast fiber crops. Our search of PubMed identified nearly 20 genera of fungal pathogens on bast fiber crops, among which the five most common genera were Colletotrichum, Pythium, Verticillium, Fusarium, and Golovinomyces. The gene regions that have been used for molecular identifications of these fungi include internal transcribed spacer (ITS), translation elongation factor 1-α (EF-1α), ß-tubulin, calmodulin (CAL), histone subunit 3 (H3), glyceraldehydes-3-phosphate dehydrogenase (GAPDH), etc. We summarize the molecular assays that have been used to identify these fungi and discuss potential areas of future development for fast, specific, and accurate diagnosis of fungal pathogens on bast fiber crops.
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Affiliation(s)
- Yi Cheng
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
| | - Xiaoyu Tang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
| | - Chunsheng Gao
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
| | - Zhimin Li
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
| | - Jia Chen
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
| | - Litao Guo
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
| | - Tuhong Wang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
| | - Jianping Xu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
- Department of Biology, McMaster University, Hamilton, L8S 4K1, Canada
- Correspondence:
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21
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Song J, Liang JF, Mehrabi-Koushki M, Krisai-Greilhuber I, Ali B, Bhatt VK, Cerna-Mendoza A, Chen B, Chen ZX, Chu HL, Corazon-Guivin MA, da Silva GA, De Kesel A, Dima B, Dovana F, Farokhinejad R, Ferisin G, Guerrero-Abad JC, Guo T, Han LH, Ilyas S, Justo A, Khalid AN, Khodadadi-Pourarpanahi S, Li TH, Liu C, Lorenzini M, Lu JK, Mumtaz AS, Oehl F, Pan XY, Papp V, Qian W, Razaq A, Semwal KC, Tang LZ, Tian XL, Vallejos-Tapullima A, van der Merwe NA, Wang SK, Wang CQ, Yang RH, Yu F, Zapparoli G, Zhang M, Antonín V, Aptroot A, Aslan A, Banerjee A, Chatterjee S, Dirks AC, Ebrahimi L, Fotouhifar KB, Ghosta Y, Kalinina LB, Karahan D, Liu J, Maiti MK, Mookherjee A, Nath PS, Panja B, Saha J, Ševčíková H, Voglmayr H, Yazıcı K, Haelewaters D. Fungal Systematics and Evolution: FUSE 5. SYDOWIA 2019; 71:141-245. [PMID: 31975743 PMCID: PMC6978154 DOI: 10.12905/0380.sydowia71-2019-0141] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Thirteen new species are formally described: Cortinarius brunneocarpus from Pakistan, C. lilacinoarmillatus from India, Curvularia khuzestanica on Atriplex lentiformis from Iran, Gloeocantharellus neoechinosporus from China, Laboulbenia bernaliana on species of Apenes, Apristus, and Philophuga (Coleoptera, Carabidae) from Nicaragua and Panama, L. oioveliicola on Oiovelia machadoi (Hemiptera, Veliidae) from Brazil, L. termiticola on Macrotermes subhyalinus (Blattodea, Termitidae) from the DR Congo, Pluteus cutefractus from Slovenia, Rhizoglomus variabile from Peru, Russula phloginea from China, Stagonosporopsis flacciduvarum on Vitis vinifera from Italy, Strobilomyces huangshanensis from China, Uromyces klotzschianus on Rumex dentatus subsp. klotzschianus from Pakistan. The following new records are reported: Alternaria calendulae on Calendula officinalis from India; A. tenuissima on apple and quince fruits from Iran; Candelariella oleaginescens from Turkey; Didymella americana and D. calidophila on Vitis vinifera from Italy; Lasiodiplodia theobromae causing tip blight of Dianella tasmanica 'variegata' from India; Marasmiellus subpruinosus from Madeira, Portugal, new for Macaronesia and Africa; Mycena albidolilacea, M. tenuispinosa, and M. xantholeuca from Russia; Neonectria neomacrospora on Madhuca longifolia from India; Nothophoma quercina on Vitis vinifera from Italy; Plagiosphaera immersa on Urtica dioica from Austria; Rinodina sicula from Turkey; Sphaerosporium lignatile from Wisconsin, USA; and Verrucaria murina from Turkey. Multi-locus analysis of ITS, LSU, rpb1, tef1 sequences revealed that P. immersa, commonly classified within Gnomoniaceae (Diaporthales) or as Sordariomycetes incertae sedis, belongs to Magnaporthaceae (Magnaporthales). Analysis of a six-locus Ascomycota-wide dataset including SSU and LSU sequences of S. lignatile revealed that this species, currently in Ascomycota incertae sedis, belongs to Pyronemataceae (Pezizomycetes, Pezizales).
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Affiliation(s)
- Jie Song
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, P.R. China
| | - Jun-Feng Liang
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, P.R. China
| | - Mehdi Mehrabi-Koushki
- Department of Plant Protection, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran
- Biotechnology and Bioscience Research Center, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | | | - Barkat Ali
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
- Department of Biochemistry, Genetics and Microbiology, Division of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | | | - Agustín Cerna-Mendoza
- Laboratorio de Biología y Genética Molecular, Universidad Nacional de San Martín, Jr. Amorarca 315, Morales, Peru
| | - Bin Chen
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, P.R. China
| | - Zai-Xiong Chen
- Management Bureau of Danxiashan National Nature Reserve of Guangdong, Shaoguan 512300, China
| | - Hong-Long Chu
- College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, Yunnan 655011, China
| | - Mike Anderson Corazon-Guivin
- Laboratorio de Biología y Genética Molecular, Universidad Nacional de San Martín, Jr. Amorarca 315, Morales, Peru
| | - Gladstone Alves da Silva
- Departamento de Micologia, CB, Universidade Federal de Pernambuco, Av. da engenharia s/n, Cidade Universitária, 50740-600, Recife, PE, Brazil
| | - André De Kesel
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium
| | - Bálint Dima
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, H-1117 Budapest, Hungary
| | - Francesco Dovana
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, I-10125 Torino, Italy
| | - Reza Farokhinejad
- Department of Plant Protection, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | | | - Juan Carlos Guerrero-Abad
- Laboratorio de Biología y Genética Molecular, Universidad Nacional de San Martín, Jr. Amorarca 315, Morales, Peru
- Instituto Nacional de Innovación Agraria (INIA). Dirección General de Recursos Genéticos y Biotecnología. Av. La Molina 1981, La Molina - Lima, Peru
| | - Ting Guo
- Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Li-Hong Han
- College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, Yunnan 655011, China
| | - Sobia Ilyas
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Alfredo Justo
- New Brunswick Museum, 277 Douglas Ave., Saint John, New Brunswick, E2K 1E5, Canada
| | | | | | - Tai-Hui Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application & Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou 510070, China
| | - Chao Liu
- College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, Yunnan 655011, China
| | | | - Jun-Kun Lu
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, P.R. China
| | - Abdul Samad Mumtaz
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Fritz Oehl
- Agroscope, Competence Division for Plants and Plant Products, Ecotoxicology, Müller-Thurgau-Strasse 29, CH-8820 Wädenswil, Switzerland
| | - Xue-Yu Pan
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, P.R. China
| | - Viktor Papp
- Department of Botany, Szent István University, H-1518 Budapest, Hungary
| | - Wu Qian
- Bureau of Parks and Woods of Mt. Huangshan Administrative Committee, Huangshan, Anhui 245000, China
| | - Abdul Razaq
- Discipline of Botany, Faculty of Fisheries and Wildlife, University of Veterinary and Animal Sciences (UVAS), Ravi Campus, Pattoki, Pakistan
| | - Kamal C. Semwal
- Department of Biology, College of Sciences, Eritrea Institute of Technology, Mai Nafhi, Asmara, Eritrea
| | - Li-Zhou Tang
- College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, Yunnan 655011, China
| | - Xue-Lian Tian
- College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, Yunnan 655011, China
| | - Adela Vallejos-Tapullima
- Laboratorio de Biología y Genética Molecular, Universidad Nacional de San Martín, Jr. Amorarca 315, Morales, Peru
| | - Nicolaas A. van der Merwe
- Department of Biochemistry, Genetics and Microbiology, Division of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Sheng-Kun Wang
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, P.R. China
| | - Chao-Qun Wang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application & Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou 510070, China
| | - Rui-Heng Yang
- Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Fei Yu
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, P.R. China
| | - Giacomo Zapparoli
- Università degli Studi di Verona, Dipartimento di Biotecnologie, Italy
| | - Ming Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application & Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou 510070, China
| | - Vladimir Antonín
- Department of Botany, Moravian Museum, Zelný trh 6, CZ-659 37 Brno, Czech Republic
| | - André Aptroot
- ABL Herbarium G.v.d.Veenstraat, 107 NL-3762, XK Soest, The Netherlands
| | - Ali Aslan
- Yüzüncü Yıl University, Faculty of Pharmacy, 65080 Campus, Van, Turkey; Kyrgyz-Turkish Manas University, Faculty of Arts and Science, Dept. of Biology, Bishkek, Kyrgyzstan
| | - Arghya Banerjee
- Department of Plant Pathology, Bidhan Chandra Krishi Viswavidyalaya, Nadia-741252, West Bengal, India
| | - Subrata Chatterjee
- Department of Agricultural Entomology, Bidhan Chandra Krishi Viswavidyalaya, Nadia-741252, West Bengal, India
| | - Alden C. Dirks
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Avenue, 4050 Biological Sciences Building, Ann Arbor, MI 48109, USA
| | - Leila Ebrahimi
- Department of Entomology and Plant Pathology, Aburaihan Campus, University of Tehran, Tehran, 33916-53755, Iran
| | - Khalil-Berdi Fotouhifar
- Department of Plant Protection, Faculty of Agricultural Sciences and Engineering, College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-77871, Iran
| | - Youbert Ghosta
- Department of Plant Protection, Faculty of Agriculture, Urmia University, Urmia, P. O. Box 165, Iran
| | - Lyudmila B. Kalinina
- Russian Academy of Sciences, Komarov Botanical Institute, Prof. Popov Str. 2, St. Petersburg RU-197376, Russia
| | - Dilara Karahan
- Department of Biology, Faculty of Science, Karadeniz Technical University, 61080, Trabzon, Turkey
| | - Jingyu Liu
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
| | - Mrinal Kumar Maiti
- Department of Biotechnology, Indian Institute of Technology Kharagpur, 721302, West Bengal, India
| | - Abhirup Mookherjee
- Department of Biotechnology, Indian Institute of Technology Kharagpur, 721302, West Bengal, India
| | - Partha Sarathi Nath
- Department of Plant Pathology, Bidhan Chandra Krishi Viswavidyalaya, Nadia-741252, West Bengal, India
| | - Birendranath Panja
- Department of Plant Pathology, Bidhan Chandra Krishi Viswavidyalaya, Nadia-741252, West Bengal, India
| | - Jayanta Saha
- Department of Plant Pathology, Bidhan Chandra Krishi Viswavidyalaya, Nadia-741252, West Bengal, India
| | - Hana Ševčíková
- Department of Botany, Moravian Museum, Zelný trh 6, CZ-659 37 Brno, Czech Republic
| | - Hermann Voglmayr
- Department of Botany and Biodiversity Research, Universität Wien, Rennweg 14, 1030 Wien, Austria
- Institute of Forest Entomology, Forest Pathology and Forest Protection, BOKU-University of Natural Resources and Life Sciences, Peter-Jordan-Straße 82/I, 1190 Wien, Austria
| | - Kenan Yazıcı
- Department of Biology, Faculty of Science, Karadeniz Technical University, 61080, Trabzon, Turkey
| | - Danny Haelewaters
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
- Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA 02138, USA
- Herbario UCH, Universidad Autónoma de Chiriquí, Apartado Postal 0427, David, Panama
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Balboa, Panama
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Riccioni C, Paolocci F, Tulloss RE, Perini C. Molecular phylogenetic analyses show that Amanita ovoidea and Amanita proxima are distinct species and suggest their assignment to Roanokenses section. Mycol Prog 2019. [DOI: 10.1007/s11557-019-01521-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Fungal species boundaries in the genomics era. Fungal Genet Biol 2019; 131:103249. [PMID: 31279976 DOI: 10.1016/j.fgb.2019.103249] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 05/21/2019] [Accepted: 06/28/2019] [Indexed: 12/30/2022]
Abstract
Genomic data has opened new possibilities to understand how organisms change over time, and could enable the discovery of previously undescribed species. Although taxonomy used to be based on phenotypes, molecular data has frequently revealed that morphological traits are insufficient to describe biodiversity. Genomics holds the promise of revealing even more genetic discontinuities, but the parameters on how to describe species from genomic data remain unclear. Fungi have been a successful case in which the use of molecular markers has uncovered the existence of genetic boundaries where no crosses are possible. In this minireview, we highlight recent advances, propose a set of standards to use genomic sequences to uncover species boundaries, point out potential pitfalls, and present possible future research directions.
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Taxonomic update of Clitocybula sensu lato with a new generic classification. Fungal Biol 2019; 123:431-447. [DOI: 10.1016/j.funbio.2019.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 02/14/2019] [Accepted: 03/19/2019] [Indexed: 11/23/2022]
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Riccioni C, Rubini A, Türkoğlu A, Belfiori B, Paolocci F. Ribosomal DNA polymorphisms reveal genetic structure and a phylogeographic pattern in the Burgundy truffle Tuber aestivum Vittad. Mycologia 2019; 111:26-39. [PMID: 30676256 DOI: 10.1080/00275514.2018.1543508] [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: 02/04/2023]
Abstract
Ectomycorrhizal ascomycetes belonging to the genus Tuber produce edible fruiting bodies known as truffles. Tuber aestivum, in particular, is a fungus appreciated worldwide and has a natural distribution throughout Europe. Most of the molecular studies conducted on this species have been focused on the question as to whether or not T. aestivum and the morphologically similar T. uncinatum are conspecific. Conversely, only a handful of studies have assessed the level and distribution of genetic diversity and occurrence of phylogeographic patterns in this species. Here, we analyzed the genetic diversity of T. aestivum over a wide geographic range, performing an extensive sampling of specimens from Turkey, which is novel, to the best of our knowledge. We compared the internal transcribed spacer (ITS) profiles of 45 samples collected in different Turkish areas with those of 144 samples from all over Europe. We identified 63 haplotypes, 32 of which were exclusively present in Turkey. The majority of these haplotyes were also population specific. Haplotype network analysis and statistical tests highlighted the presence of a genetic structure and phylogeographic pattern, with three spatially distinct genetic clusters (northeastern Europe, southern Europe, and Turkey), with Turkey representing a diversity hotspot. Based on these results, we hypothesize the presence of glacial refugia for T. aestivum in Turkey, whereas European populations likely experienced a population bottleneck. The possible occurrence of cryptic species among Turkish T. aestivum samples also emerged. Our results are of practical relevance for the marketing of T. aestivum truffles and mycorrhizal seedlings and the preservation of the biodiversity of this species.
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Affiliation(s)
- Claudia Riccioni
- a Institute of Biosciences and Bioresources Perugia Division, National Research Council , Via Madonna Alta n. 130, 06128 Perugia , Italy
| | - Andrea Rubini
- a Institute of Biosciences and Bioresources Perugia Division, National Research Council , Via Madonna Alta n. 130, 06128 Perugia , Italy
| | - Aziz Türkoğlu
- b School of Environmental and Forest Sciences, Box 352100 University of Washington , Seattle , Washington 98195-2100
| | - Beatrice Belfiori
- a Institute of Biosciences and Bioresources Perugia Division, National Research Council , Via Madonna Alta n. 130, 06128 Perugia , Italy
| | - Francesco Paolocci
- a Institute of Biosciences and Bioresources Perugia Division, National Research Council , Via Madonna Alta n. 130, 06128 Perugia , Italy
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Meng YY, Shao SC, Liu SJ, Gao JY. Do the fungi associated with roots of adult plants support seed germination? A case study on Dendrobium exile (Orchidaceae). Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00582] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Sujkowska-Rybkowska M, Ważny R. Metal resistant rhizobia and ultrastructure of Anthyllis vulneraria nodules from zinc and lead contaminated tailing in Poland. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2018; 20:709-720. [PMID: 29723046 DOI: 10.1080/15226514.2017.1413336] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
This present paper studies the response of Anthyllis vulneraria-Rhizobium symbiosis to heavy metal stress. The symbiotic rhizobium bacteria isolated from root nodules of A. vulneraria from zinc and lead wastes were examined in this project. Light microscopy (LM) and transmission electron microscopy (TEM) were used to analyze the nodule anatomy and ultrastructure and conduct a comparison with nonmetal-treated nodules. 16S ribosomal DNA sequence analysis of bacteria isolated from metal-treated nodules revealed the presence of Rhizobium metallidurans and Bradyrhizobium sp. In regard to heavy metal resistance/tolerance, a similar tolerance to Pb was shown by both strains, and a high tolerance to Zn and a lower tolerance to Cd and Cu by R. metallidurans, whereas a high tolerance to Cd and Cu and a lower tolerance to Zn by Bradyrhizobium were found. The nodules of Anthyllis from metal-polluted tailing sites were identified as the typical determinate type of nodules. Observed under TEM microscopy changes in nodules ultrastructure like: (1) wall thickening; (2) infection thread reduction; (3) vacuole shrinkage; (4) synthesis of phenolics in vacuoles; (5) various differentiation of bacteroids and (6) simultaneous symbiosis with arbuscular mycorrhiza fungi could be considered as a form of the A.vulneraria-Rhizobium symbiosis adaptation to metal stress.
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Affiliation(s)
| | - Rafał Ważny
- b Małopolska Centre of Biotechnology, Jagiellonian University , Kraków , Poland
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Lücking R, Hawksworth DL. Formal description of sequence-based voucherless Fungi: promises and pitfalls, and how to resolve them. IMA Fungus 2018; 9:143-166. [PMID: 30018876 PMCID: PMC6048566 DOI: 10.5598/imafungus.2018.09.01.09] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 05/15/2018] [Indexed: 11/25/2022] Open
Abstract
There is urgent need for a formal nomenclature of sequence-based, voucherless Fungi, given that environmental sequencing has accumulated more than one billion fungal ITS reads in the Sequence Read Archive, about 1,000 times as many as fungal ITS sequences in GenBank. These unnamed Fungi could help to bridge the gap between 115,000 to 140,000 currently accepted and 2.2 to 3.8 million predicted species, a gap that cannot realistically be filled using specimen or culture-based inventories. The Code never aimed at placing restrictions on the nature of characters chosen for taxonomy, and the requirement for physical types is now becoming a constraint on the advancement of science. We elaborate on the promises and pitfalls of sequence-based nomenclature and provide potential solutions to major concerns of the mycological community. Types of sequence-based taxa, which by default lack a physical specimen or culture, could be designated in four alternative ways: (1) the underlying sample ('bag' type), (2) the DNA extract, (3) fluorescent in situ hybridization (FISH), or (4) the type sequence itself. Only (4) would require changes to the Code and the latter would be the most straightforward approach, complying with three of the five principal functions of types better than physical specimens. A fifth way, representation of the sequence in an illustration, has been ruled as unacceptable in the Code. Potential flaws in sequence data are analogous to flaws in physical types, and artifacts are manageable if a stringent analytical approach is applied. Conceptual errors such as homoplasy, intragenomic variation, gene duplication, hybridization, and horizontal gene transfer, apply to all molecular approaches and cannot be used as a specific argument against sequence-based nomenclature. The potential impact of these phenomena is manageable, as phylogenetic species delimitation has worked satisfactorily in Fungi. The most serious shortcoming of sequence-based nomenclature is the likelihood of parallel classifications, either by describing taxa that already have names based on physical types, or by using different markers to delimit species within the same lineage. The probability of inadvertently establishing sequence-based species that have names available is between 20.4 % and 1.5 % depending on the number of globally predicted fungal species. This compares favourably to a historical error rate of about 30 % based on physical types, and this rate could be reduced to practically zero by adding specific provisions to this approach in the Code. To avoid parallel classifications based on different markers, sequence-based nomenclature should be limited to a single marker, preferably the fungal ITS barcoding marker; this is possible since sequence-based nomenclature does not aim at accurate species delimitation but at naming lineages to generate a reference database, independent of whether these lineages represent species, closely related species complexes, or infraspecies. We argue that clustering methods are inappropriate for sequence-based nomenclature; this approach must instead use phylogenetic methods based on multiple alignments, combined with quantitative species recognition methods. We outline strategies to obtain higher-level phylogenies for ITS-based, voucherless species, including phylogenetic binning, 'hijacking' species delimitation methods, and temporal banding. We conclude that voucherless, sequence-based nomenclature is not a threat to specimen and culture-based fungal taxonomy, but a complementary approach capable of substantially closing the gap between known and predicted fungal diversity, an approach that requires careful work and high skill levels.
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Affiliation(s)
- Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Strasse 6–8, 14195 Berlin, Germany
| | - David L. Hawksworth
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; and Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Surrey TW9 3DS, UK; Jilin Agricultural University, Changchun, Jilin Province,130118 China
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Vasco-Palacios AM, Hernandez J, Peñuela-Mora MC, Franco-Molano AE, Boekhout T. Ectomycorrhizal fungi diversity in a white sand forest in western Amazonia. FUNGAL ECOL 2018. [DOI: 10.1016/j.funeco.2017.10.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Guzmán-Dávalos L, Pradeep CK, Vrinda KB, Manoj Kumar A, Ramírez-Cruz V, Herrera M, Villalobos-Arámbula AR, Soytong K, Baroni TJ, Aime MC. A new stipitate species of Crepidotus from India and Thailand, with notes on other tropical species. Mycologia 2018; 109:804-814. [PMID: 29345534 DOI: 10.1080/00275514.2017.1401834] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A new Asian species of Crepidotus (Basidiomycota, Agaricales), C. asiaticus, is presented based on morphological and nuc rDNA internal transcribed spacer (ITS1-5.8S-ITS2 = ITS) and large subunit (28S) sequence data. This new species, found in India and Thailand, is characterized by the centrally stipitate medium-sized basidiomata, orange to reddish brown pileus, white to brownish orange lamellae, and white stipe. Based on morphology, C. asiaticus is similar to the neotropical C. thermophilus. However, the microscopic characters, especially the size and shape of the basidiospores, can be used to distinguish these two taxa, as well as their geographic distributions. Further, the phylogenetic position of C. asiaticus is unique based on ITS and 28S nuc rDNA sequences. Melanomphalia argipoda, described by Singer from Ecuador, is also a stipitate Crepidotus based on an ITS sequence of the type specimen, so the new combination is proposed here. Phylogenetically, the three species form a monophyletic group with the Asiatic C. asiaticus forming the sister lineage to the neotropical C. argipodus and C. thermophilus.
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Affiliation(s)
- Laura Guzmán-Dávalos
- a Departamento de Botánica y Zoología , Universidad de Guadalajara , Apdo. Postal 1-139, Zapopan, Jal., 45101 , Mexico
| | - C K Pradeep
- b Jawaharlal Nehru Tropical Botanic Garden & Research Institute , Palode, Thiruvananthapuram , 695 562 , Kerala , India
| | - K B Vrinda
- b Jawaharlal Nehru Tropical Botanic Garden & Research Institute , Palode, Thiruvananthapuram , 695 562 , Kerala , India
| | - A Manoj Kumar
- b Jawaharlal Nehru Tropical Botanic Garden & Research Institute , Palode, Thiruvananthapuram , 695 562 , Kerala , India
| | - Virginia Ramírez-Cruz
- c Instituto de Estudios Ambientales, Universidad de la Sierra Juárez , Ixtlán de Juárez , Oaxaca , Mexico
| | - María Herrera
- a Departamento de Botánica y Zoología , Universidad de Guadalajara , Apdo. Postal 1-139, Zapopan, Jal., 45101 , Mexico
| | | | - Kasem Soytong
- e Faculty of Agricultural Technology , King Mongkut's Institute of Technology , Ladkrabang , Bangkok , Thailand
| | - Timothy J Baroni
- f Department of Biological Sciences , State University of New York-College at Cortland , Cortland , New York 13045
| | - M Catherine Aime
- g Department of Botany and Plant Pathology , Purdue University , West Lafayette , Indiana 47907
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Novotná A, Benítez Á, Herrera P, Cruz D, Filipczyková E, Suárez JP. High diversity of root-associated fungi isolated from three epiphytic orchids in southern Ecuador. MYCOSCIENCE 2018. [DOI: 10.1016/j.myc.2017.07.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Abstract
Histoplasma capsulatum is a pathogenic fungus that causes life-threatening lung infections. About 500,000 people are exposed to H. capsulatum each year in the United States, and over 60% of the U.S. population has been exposed to the fungus at some point in their life. We performed genome-wide population genetics and phylogenetic analyses with 30 Histoplasma isolates representing four recognized areas where histoplasmosis is endemic and show that the Histoplasma genus is composed of at least four species that are genetically isolated and rarely interbreed. Therefore, we propose a taxonomic rearrangement of the genus.IMPORTANCE The evolutionary processes that give rise to new pathogen lineages are critical to our understanding of how they adapt to new environments and how frequently they exchange genes with each other. The fungal pathogen Histoplasma capsulatum provides opportunities to precisely test hypotheses about the origin of new genetic variation. We find that H. capsulatum is composed of at least four different cryptic species that differ genetically and also in virulence. These results have implications for the epidemiology of histoplasmosis because not all Histoplasma species are equivalent in their geographic range and ability to cause disease.
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Morozova OV, Noordeloos ME, Popov ES, Alexandrova AV. Three new species within the genus Entoloma (Basidiomycota, Agaricales) with clamped basidia and a serrulatum-type lamellae edge, and their phylogenetic position. Mycol Prog 2017. [DOI: 10.1007/s11557-017-1364-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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35
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Turissini DA, Gomez OM, Teixeira MM, McEwen JG, Matute DR. Species boundaries in the human pathogen Paracoccidioides. Fungal Genet Biol 2017; 106:9-25. [PMID: 28602831 PMCID: PMC8335726 DOI: 10.1016/j.fgb.2017.05.007] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/12/2017] [Accepted: 05/31/2017] [Indexed: 12/29/2022]
Abstract
The use of molecular taxonomy for identifying recently diverged species has transformed the study of speciation in fungi. The pathogenic fungus Paracoccidioides spp has been hypothesized to be composed of five phylogenetic species, four of which compose the brasiliensis species complex. Nuclear gene genealogies support this divergence scenario, but mitochondrial loci do not; while all species from the brasiliensis complex are differentiated at nuclear coding loci, they are not at mitochondrial loci. We addressed the source of this incongruity using 11 previously published gene fragments, 10 newly-sequenced nuclear non-coding loci, and 10 microsatellites. We hypothesized and further demonstrated that the mito-nuclear incongruence in the brasiliensis species complex results from interspecific hybridization and mitochondrial introgression, a common phenomenon in eukaryotes. Additional population genetic analyses revealed possible nuclear introgression but much less than that seen in the mitochondrion. Our results are consistent with a divergence scenario of secondary contact and subsequent mitochondrial introgression despite the continued persistence of species boundaries. We also suggest that yeast morphology slightly-but significantly-differs across all five Paracoccidioides species and propose to elevate four of these phylogenetic species to formally described taxonomic species.
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Affiliation(s)
- David A Turissini
- Biology Department, University of North Carolina, Chapel Hill, NC, USA
| | - Oscar M Gomez
- Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia; Biology Institute, Universidad de Antioquia, Medellín, Colombia
| | - Marcus M Teixeira
- Northern Arizona Center for Valley Fever Research, Flagstaff, AZ, USA
| | - Juan G McEwen
- Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia; School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, NC, USA.
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Kuzdraliński A, Kot A, Szczerba H, Nowak M, Muszyńska M. A Review of Conventional PCR Assays for the Detection of Selected Phytopathogens of Wheat. J Mol Microbiol Biotechnol 2017; 27:175-189. [DOI: 10.1159/000477544] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/30/2017] [Indexed: 11/19/2022] Open
Abstract
Infection of phyllosphere (stems, leaves, husks, and grains) by pathogenic fungi reduces the wheat yield and grain quality. Detection of the main wheat pathogenic fungi provides information about species composition and allows effective and targeted plant treatment. Since conventional procedures for the detection of these organisms are unreliable and time consuming, diagnostic DNA-based methods are required. Nucleic acid amplification technologies are independent of the morphological and biochemical characteristics of fungi. Microorganisms do not need to be cultured. Therefore, a number of PCR-based methodologies have been developed for the identification of key pathogenic fungi, such as <i>Fusarium</i> spp., <i>Puccinia</i> spp., <i>Zymoseptoria tritici</i>, <i>Parastagonospora nodorum</i>,<i> Blumeria graminis </i>f. sp.<i> tritici</i>, and<i> Pyrenophora tritici-repentis</i>. This article reviews frequently used DNA regions for fungus identification and discusses already known PCR assays for detection of the aforementioned wheat pathogens. We demonstrate that PCR-based wheat pathogen identification assays require further research. In particular, the number of diagnostic tests for <i>Fusarium graminearum</i>, <i>Puccinia</i> spp., and <i>P. tritici-repentis</i> are insufficient.
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37
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Evaluating multilocus Bayesian species delimitation for discovery of cryptic mycorrhizal diversity. FUNGAL ECOL 2017. [DOI: 10.1016/j.funeco.2016.11.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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38
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Soteras F, Ibarra C, Geml J, Barrios-García MN, Domínguez LS, Nouhra ER. Mycophagy by invasive wild boar ( Sus scrofa ) facilitates dispersal of native and introduced mycorrhizal fungi in Patagonia, Argentina. FUNGAL ECOL 2017. [DOI: 10.1016/j.funeco.2016.11.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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39
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Liu LN, Wu L, Chen ZH, Bau T, Zhang P. The species of Lentaria (Gomphales, Basidiomycota) from China based on morphological and molecular evidence. Mycol Prog 2017. [DOI: 10.1007/s11557-017-1284-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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40
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Raja H, Miller AN, Pearce CJ, Oberlies NH. Fungal Identification Using Molecular Tools: A Primer for the Natural Products Research Community. JOURNAL OF NATURAL PRODUCTS 2017; 80:756-770. [PMID: 28199101 PMCID: PMC5368684 DOI: 10.1021/acs.jnatprod.6b01085] [Citation(s) in RCA: 373] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Indexed: 05/17/2023]
Abstract
Fungi are morphologically, ecologically, metabolically, and phylogenetically diverse. They are known to produce numerous bioactive molecules, which makes them very useful for natural products researchers in their pursuit of discovering new chemical diversity with agricultural, industrial, and pharmaceutical applications. Despite their importance in natural products chemistry, identification of fungi remains a daunting task for chemists, especially those who do not work with a trained mycologist. The purpose of this review is to update natural products researchers about the tools available for molecular identification of fungi. In particular, we discuss (1) problems of using morphology alone in the identification of fungi to the species level; (2) the three nuclear ribosomal genes most commonly used in fungal identification and the potential advantages and limitations of the ITS region, which is the official DNA barcoding marker for species-level identification of fungi; (3) how to use NCBI-BLAST search for DNA barcoding, with a cautionary note regarding its limitations; (4) the numerous curated molecular databases containing fungal sequences; (5) the various protein-coding genes used to augment or supplant ITS in species-level identification of certain fungal groups; and (6) methods used in the construction of phylogenetic trees from DNA sequences to facilitate fungal species identification. We recommend that, whenever possible, both morphology and molecular data be used for fungal identification. Our goal is that this review will provide a set of standardized procedures for the molecular identification of fungi that can be utilized by the natural products research community.
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Affiliation(s)
- Huzefa
A. Raja
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27402, United States
| | - Andrew N. Miller
- Illinois
Natural History Survey, University of Illinois, Champaign, Illinois 61820, United States
| | - Cedric J. Pearce
- Mycosynthetix,
Inc., 505 Meadowland
Drive, Suite 103, Hillsborough, North Carolina 27278, United States
| | - Nicholas H. Oberlies
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27402, United States
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41
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Hughes KW, Mather DA, Petersen RH. A new genus to accommodateGymnopus acervatus(Agaricales). Mycologia 2017; 102:1463-78. [DOI: 10.3852/09-318] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | - Ronald H. Petersen
- Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996-1100
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Desjardin DE, Peay KG, Bruns TD. Spongiforma squarepantsii, a new species of gasteroid bolete from Borneo. Mycologia 2017; 103:1119-23. [DOI: 10.3852/10-433] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Dennis E. Desjardin
- Department of Biology, San Francisco State University, 1600 Holloway Avenue, San Francisco, California 94131
| | - Kabir G. Peay
- Department of Plant Pathology, University of Minnesota, St Paul, Minnesota 55108
| | - Thomas D. Bruns
- Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, California 94720-3102
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Sheedy EM, Van de Wouw AP, Howlett BJ, May TW. Multigene sequence data reveal morphologically cryptic phylogenetic species within the genus Laccaria in southern Australia. Mycologia 2017; 105:547-63. [DOI: 10.3852/12-266] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | | | - Tom W. May
- Royal Botanic Gardens Melbourne, Private Bag 2000, South Yarra, Victoria 3141, Australia
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Yokoya K, Postel S, Fang R, Sarasan V. Endophytic fungal diversity of Fragaria vesca, a crop wild relative of strawberry, along environmental gradients within a small geographical area. PeerJ 2017; 5:e2860. [PMID: 28168102 PMCID: PMC5289447 DOI: 10.7717/peerj.2860] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 12/03/2016] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Fungal endophytes are highly diverse ubiquitous asymptomatic microorganisms, some of which appear to be symbiotic. Depending on abiotic conditions and genotype of the plant, the diversity of endophytes may confer fitness benefits to plant communities. METHODS We studied a crop wild relative (CWR) of strawberry, along environmental gradients with a view to understand the cultivable root-derived endophytic fungi that can be evaluated for promoting growth and tolerating stress in selected plant groups. The main objectives were to understand whether: (a) suboptimal soil types are drivers for fungal distribution and diversity; (b) high pH and poor nutrient availability lead to fungal-plant associations that help deliver fitness benefits; and (c) novel fungi can be identified for their use in improving plant growth, and alleviate stress in diverse crops. RESULTS The study revealed that habitats with high pH and low nutrient availability have higher fungal diversity, with more rare fungi isolated from locations with chalky soil. Plants from location G were the healthiest even though soil from this location was the poorest in nutrients. Study of environmental gradients, especially extreme habitat types, may help understand the root zone fungal diversity of different functional classes. Two small in vitro pilot studies conducted with two isolates showed that endophytic fungi from suboptimal habitats can promote plant growth and fitness benefits in selected plant groups. DISCUSSION Targeting native plants and crop wild relatives for research offers opportunities to unearth diverse functional groups of root-derived endophytic fungi that are beneficial for crops.
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Affiliation(s)
- Kazutomo Yokoya
- Natural Capital and Plant Health, Royal Botanic Gardens Kew , Richmond , Surrey , United Kingdom
| | - Sarah Postel
- Natural Capital and Plant Health, Royal Botanic Gardens Kew , Richmond , Surrey , United Kingdom
| | - Rui Fang
- Natural Capital and Plant Health, Royal Botanic Gardens Kew , Richmond , Surrey , United Kingdom
| | - Viswambharan Sarasan
- Natural Capital and Plant Health, Royal Botanic Gardens Kew , Richmond , Surrey , United Kingdom
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Overview of Phylogenetic Approaches to Mycorrhizal Biogeography, Diversity and Evolution. BIOGEOGRAPHY OF MYCORRHIZAL SYMBIOSIS 2017. [DOI: 10.1007/978-3-319-56363-3_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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46
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Petersen RH, Hughes KW. Micromphale sect. Perforantia (Agaricales, Basidiomycetes); Expansion and phylogenetic placement. MycoKeys 2016. [DOI: 10.3897/mycokeys.18.10007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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47
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Morgado LN, Semenova TA, Welker JM, Walker MD, Smets E, Geml J. Long-term increase in snow depth leads to compositional changes in arctic ectomycorrhizal fungal communities. GLOBAL CHANGE BIOLOGY 2016; 22:3080-3096. [PMID: 27004610 DOI: 10.1111/gcb.13294] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 01/16/2016] [Accepted: 03/02/2016] [Indexed: 06/05/2023]
Abstract
Many arctic ecological processes are regulated by soil temperature that is tightly interconnected with snow cover distribution and persistence. Recently, various climate-induced changes have been observed in arctic tundra ecosystems, e.g. shrub expansion, resulting in reduction in albedo and greater C fixation in aboveground vegetation as well as increased rates of soil C mobilization by microbes. Importantly, the net effects of these shifts are unknown, in part because our understanding of belowground processes is limited. Here, we focus on the effects of increased snow depth, and as a consequence, increased winter soil temperature on ectomycorrhizal (ECM) fungal communities in dry and moist tundra. We analyzed deep DNA sequence data from soil samples taken at a long-term snow fence experiment in Northern Alaska. Our results indicate that, in contrast with previously observed responses of plants to increased snow depth at the same experimental site, the ECM fungal community of the dry tundra was more affected by deeper snow than the moist tundra community. In the dry tundra, both community richness and composition were significantly altered while in the moist tundra, only community composition changed significantly while richness did not. We observed a decrease in richness of Tomentella, Inocybe and other taxa adapted to scavenge the soil for labile N forms. On the other hand, richness of Cortinarius, and species with the ability to scavenge the soil for recalcitrant N forms, did not change. We further link ECM fungal traits with C soil pools. If future warmer atmospheric conditions lead to greater winter snow fall, changes in the ECM fungal community will likely influence C emissions and C fixation through altering N plant availability, fungal biomass and soil-plant C-N dynamics, ultimately determining important future interactions between the tundra biosphere and atmosphere.
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Affiliation(s)
- Luis N Morgado
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, The Netherlands
- Section for Genetics and Evolutionary Biology (Evogene), Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, NO-0316, Oslo, Norway
| | - Tatiana A Semenova
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, The Netherlands
- Faculty of Science, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Jeffrey M Welker
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK, USA
| | | | - Erik Smets
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, The Netherlands
- Faculty of Science, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
- Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, Box 2437, 3001, Leuven, Belgium
| | - József Geml
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, The Netherlands
- Faculty of Science, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
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DNA barcoding for identification of consumer-relevant mushrooms: A partial solution for product certification? Food Chem 2016; 214:383-392. [PMID: 27507489 DOI: 10.1016/j.foodchem.2016.07.052] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 06/03/2016] [Accepted: 07/09/2016] [Indexed: 02/06/2023]
Abstract
One challenge in the dietary supplement industry is confirmation of species identity for processed raw materials, i.e. those modified by milling, drying, or extraction, which move through a multilevel supply chain before reaching the finished product. This is particularly difficult for samples containing fungal mycelia, where processing removes morphological characteristics, such that they do not present sufficient variation to differentiate species by traditional techniques. To address this issue, we have demonstrated the utility of DNA barcoding to verify the taxonomic identity of fungi found commonly in the food and dietary supplement industry; such data are critical for protecting consumer health, by assuring both safety and quality. By using DNA barcoding of nuclear ribosomal internal transcribed spacer (ITS) of the rRNA gene with fungal specific ITS primers, ITS barcodes were generated for 33 representative fungal samples, all of which could be used by consumers for food and/or dietary supplement purposes. In the majority of cases, we were able to sequence the ITS region from powdered mycelium samples, grocery store mushrooms, and capsules from commercial dietary supplements. After generating ITS barcodes utilizing standard procedures accepted by the Consortium for the Barcode of Life, we tested their utility by performing a BLAST search against authenticate published ITS sequences in GenBank. In some cases, we also downloaded published, homologous sequences of the ITS region of fungi inspected in this study and examined the phylogenetic relationships of barcoded fungal species in light of modern taxonomic and phylogenetic studies. We anticipate that these data will motivate discussions on DNA barcoding based species identification as applied to the verification/certification of mushroom-containing dietary supplements.
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Selosse MA, Vincenot L, Öpik M. Data processing can mask biology: towards better reporting of fungal barcoding data? THE NEW PHYTOLOGIST 2016; 210:1159-1164. [PMID: 26818207 DOI: 10.1111/nph.13851] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Affiliation(s)
- Marc-André Selosse
- Institut de Systématique, Évolution, Biodiversité (ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE), Muséum National d'Histoire Naturelle, Sorbonne Universités, 57 rue Cuvier, CP50, 75005, Paris, France
- Department of Plant Taxonomy and Nature Conservation, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Lucie Vincenot
- Ecodiv URA/IRSTEA/EA-1293, Normandie Université, SFR Scale 4116, UFR Sciences & Techniques, Université de Rouen, Mont-Saint-Aignan, 76821, France
| | - Maarja Öpik
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St., Tartu, 51005, Estonia
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50
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Woolfolk S, Stokes CE, Watson C, Baker G, Brown R, Baird R. Fungi Associated withSolenopsis invictaBuren (Red Imported Fire Ant, Hymenoptera: Formicidae) from Mounds in Mississippi. SOUTHEAST NAT 2016. [DOI: 10.1656/058.015.0203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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