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Xing RR, Bai WM, Hu D, Deng TT, Zhang JK, Chen Y. Using a DNA mini-barcode within the ITS region to identify toxic Amanita in mushroom poisoning cases. Appl Microbiol Biotechnol 2024; 108:376. [PMID: 38884656 PMCID: PMC11182838 DOI: 10.1007/s00253-024-13219-x] [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: 01/20/2024] [Revised: 05/28/2024] [Accepted: 06/02/2024] [Indexed: 06/18/2024]
Abstract
Mushroom poisoning contributes significantly to global foodborne diseases and related fatalities. Amanita mushrooms frequently cause such poisonings; however, identifying these toxic species is challenging due to the unavailability of fresh and intact samples. It is often necessary to analyze residues, vomitus, or stomach extracts to obtain DNA sequences for the identification of species responsible for causing food poisoning. This usually proves challenging to obtain usable DNA sequences that can be analyzed using conventional molecular biology techniques. Therefore, this study aimed to develop a DNA mini-barcoding method for the identification of Amanita species. Following the evaluation and optimization of universal primers for DNA mini-barcoding in Amanita mushrooms, we found that the internal transcribed spacer (ITS) gene sequence primer ITS-a was the most suitable DNA barcode primer for identifying Amanita species. Forty-three Amanita samples were subsequently amplified and sequenced. The sequences obtained were analyzed for intra- and inter-species genetic distances, and a phylogenetic tree was constructed. The findings indicated that the designed primers had strong universality among the Amanita samples and could accurately identify the target gene fragment with a length of 290 bp. Notably, the DNA mini-barcode accurately identified the 43 Amanita samples, demonstrating high consistency with the conventional DNA barcode. Furthermore, it effectively identified DNA from digested samples. In summary, this DNA mini-barcode is a promising tool for detecting accidental ingestion of toxic Amanita mushrooms. It may be used as an optimal barcode for species identification and traceability in events of Amanita-induced mushroom poisoning. KEY POINTS: • Development of a DNA mini-barcoding method for Amanita species identification without fresh samples. • The ITS-a primer set was optimized for robust universality in Amanita samples. • The mini-barcode is suitable for screening toxic mushroom species in mushroom poisoning cases.
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Affiliation(s)
- Ran-Ran Xing
- National Key Laboratory for Market Supervision (Food Authentication), Chinese Academy of Inspection and Quarantine, No. 11, Ronghua South Street, Daxing District, Beijing, 100176, China
| | - Wen-Ming Bai
- National Key Laboratory for Market Supervision (Food Authentication), Chinese Academy of Inspection and Quarantine, No. 11, Ronghua South Street, Daxing District, Beijing, 100176, China
- College of Food Science, South China Agricultural University, Guangzhou, 510642, China
| | - Di Hu
- National Key Laboratory for Market Supervision (Food Authentication), Chinese Academy of Inspection and Quarantine, No. 11, Ronghua South Street, Daxing District, Beijing, 100176, China
- Nanjing University of Finance and Economics, Nanjing, 210046, China
| | - Ting-Ting Deng
- National Key Laboratory for Market Supervision (Food Authentication), Chinese Academy of Inspection and Quarantine, No. 11, Ronghua South Street, Daxing District, Beijing, 100176, China
| | - Jiu-Kai Zhang
- National Key Laboratory for Market Supervision (Food Authentication), Chinese Academy of Inspection and Quarantine, No. 11, Ronghua South Street, Daxing District, Beijing, 100176, China
| | - Ying Chen
- National Key Laboratory for Market Supervision (Food Authentication), Chinese Academy of Inspection and Quarantine, No. 11, Ronghua South Street, Daxing District, Beijing, 100176, China.
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Ecological speciation of Japanese hedgehog mushroom: Hydnum subalpinum sp. nov. is distinguished from its sister species H. repando-orientale by means of integrative taxonomy. Mycol Prog 2022. [DOI: 10.1007/s11557-022-01844-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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3
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Cui YY, Ding XX, Kost G, Yang ZL. Tricholoma sect. Tricholoma (Tricholomataceae) from China: molecular phylogeny and taxonomy. Mycol Prog 2022. [DOI: 10.1007/s11557-022-01788-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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4
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Cao B, Haelewaters D, Schoutteten N, Begerow D, Boekhout T, Giachini AJ, Gorjón SP, Gunde-Cimerman N, Hyde KD, Kemler M, Li GJ, Liu DM, Liu XZ, Nuytinck J, Papp V, Savchenko A, Savchenko K, Tedersoo L, Theelen B, Thines M, Tomšovský M, Toome-Heller M, Urón JP, Verbeken A, Vizzini A, Yurkov AM, Zamora JC, Zhao RL. Delimiting species in Basidiomycota: a review. FUNGAL DIVERS 2021. [DOI: 10.1007/s13225-021-00479-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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5
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Zhao P, Ji SP, Cheng XH, Bau T, Dong HX, Gao XX. DNA Barcoding Mushroom Spawn Using EF-1α Barcodes: A Case Study in Oyster Mushrooms ( Pleurotus). Front Microbiol 2021; 12:624347. [PMID: 34093459 PMCID: PMC8176306 DOI: 10.3389/fmicb.2021.624347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 04/09/2021] [Indexed: 11/20/2022] Open
Abstract
Oyster mushrooms (genus Pleurotus) are widespread and comprise the most commonly cultivated edible mushrooms in the world. Species identification of oyster mushroom spawn based on cultural, morphological, and cultivated characteristics is time consuming and can be extraordinarily difficult, which has impeded mushroom breeding and caused economic loss for mushroom growers. To explore a precise and concise approach for species identification, the nuclear ribosomal internal transcribed spacer (ITS), 28S rDNA, and the widely used protein-coding marker translation elongation factor 1α (EF-1α) gene were evaluated as candidate DNA barcode markers to investigate their feasibility in identifying 13 oyster mushroom species. A total of 160 sequences of the candidate loci were analyzed. Intra- and interspecific divergences and the ease of nucleotide sequence acquisition were the criteria used to evaluate the candidate genes. EF-1α showed the best intra- and interspecific variation among the candidate markers and discriminated 84.6% of the species tested, only being unable to distinguish two closely related species Pleurotus citrinopileatus and Pleurotus cornucopiae. Furthermore, EF-1α was more likely to be acquired than ITS or 28S rDNA, with an 84% success rate of PCR amplification and sequencing. For ITS and 28S rDNA, the intraspecific differences of several species were distinctly larger than the interspecific differences, and the species identification efficiency of the two candidate markers was worse (61.5 and 46.2%, respectively). In addition, these markers had some sequencing problems, with 55 and 76% success rates of sequencing, respectively. Hence, we propose EF-1α as a possible DNA barcode marker for oyster mushroom spawn.
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Affiliation(s)
- Peng Zhao
- Key Laboratory of Shandong Province for Edible Mushroom Technology, School of Agriculture, Ludong University, Yantai, China
| | - Sen-Peng Ji
- Key Laboratory of Shandong Province for Edible Mushroom Technology, School of Agriculture, Ludong University, Yantai, China
| | - Xian-Hao Cheng
- Key Laboratory of Shandong Province for Edible Mushroom Technology, School of Agriculture, Ludong University, Yantai, China
| | - Tolgor Bau
- Institute of Mycology, Jilin Agricultural University, Changchun, China
| | - Hong-Xin Dong
- Key Laboratory of Shandong Province for Edible Mushroom Technology, School of Agriculture, Ludong University, Yantai, China
| | - Xing-Xi Gao
- Key Laboratory of Shandong Province for Edible Mushroom Technology, School of Agriculture, Ludong University, Yantai, China
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Genetic Diversity and DNA Barcoding of Wild Mushrooms from Northeast India. IRANIAN JOURNAL OF SCIENCE AND TECHNOLOGY, TRANSACTIONS A: SCIENCE 2021. [DOI: 10.1007/s40995-021-01067-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Li J, Han LH, Liu XB, Zhao ZW, Yang ZL. The saprotrophic Pleurotus ostreatus species complex: late Eocene origin in East Asia, multiple dispersal, and complex speciation. IMA Fungus 2020; 11:10. [PMID: 32617259 PMCID: PMC7325090 DOI: 10.1186/s43008-020-00031-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/31/2020] [Indexed: 12/02/2022] Open
Abstract
The Pleurotus ostreatus species complex is saprotrophic and of significant economic and ecological importance. However, species delimitation has long been problematic because of phenotypic plasticity and morphological stasis. In addition, the evolutionary history is poorly understood due to limited sampling and insufficient gene fragments employed for phylogenetic analyses. Comprehensive sampling from Asia, Europe, North and South America and Africa was used to run phylogenetic analyses of the P. ostreatus species complex based on 40 nuclear single-copy orthologous genes using maximum likelihood and Bayesian inference analyses. Here, we present a robust phylogeny of the P. ostreatus species complex, fully resolved from the deepest nodes to species level. The P. ostreatus species complex was strongly supported as monophyletic, and 20 phylogenetic species were recognized, with seven putatively new species. Data from our molecular clock analyses suggested that divergence of the genus Pleurotus probably occurred in the late Jurassic, while the most recent common ancestor of the P. ostreatus species complex diversified about 39 Ma in East Asia. Species of the P. ostreatus complex might migrate from the East Asia into North America across the North Atlantic Land Bridge or the Bering Land Bridge at different times during the late Oligocene, late Miocene and late Pliocene, and then diversified in the Old and New Worlds simultaneously through multiple dispersal and vicariance events. The dispersal from East Asia to South America in the middle Oligocene was probably achieved by a long-distance dispersal event. Intensification of aridity and climate cooling events in the late Miocene and Quaternary glacial cycling probably had a significant influence on diversification patterns of the complex. The disjunctions among East Asia, Europe, North America and Africa within Clade IIc are hypothesized to be a result of allopatric speciation. Substrate transitions to Apiaceae probably occurred no earlier than 6 Ma. Biogeographic analyses suggested that the global cooling of the late Eocene, intensification of aridity caused by rapid uplift of the QTP and retreat of the Tethys Sea in the late Miocene, climate cooling events in Quaternary glacial cycling, and substrate transitions have contributed jointly to diversification of the species complex.
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Affiliation(s)
- Jing Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201 Yunnan China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, 650201 Yunnan China
- State Key Laboratory of Conservation and Utilization for Bioresources in Yunnan, Yunnan University, Kunming, 650091 Yunnan China
| | - Li-Hong Han
- College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, 655011 Yunnan China
| | - Xiao-Bin Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201 Yunnan China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, 650201 Yunnan China
| | - Zhi-Wei Zhao
- State Key Laboratory of Conservation and Utilization for Bioresources in Yunnan, Yunnan University, Kunming, 650091 Yunnan China
| | - Zhu L. Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201 Yunnan China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, 650201 Yunnan China
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What is cultivated oyster mushroom? Phylogenetic and physiological study of Pleurotus ostreatus and related taxa. Mycol Prog 2019. [DOI: 10.1007/s11557-019-01515-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Wang S, Guo H, Li J, Li W, Wang Q, Yu X. Evaluation of five regions as DNA barcodes for identification of Lepista species (Tricholomataceae, Basidiomycota) from China. PeerJ 2019; 7:e7307. [PMID: 31341746 PMCID: PMC6637932 DOI: 10.7717/peerj.7307] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 06/17/2019] [Indexed: 12/13/2022] Open
Abstract
Background Distinguishing among species in the genus Lepista is difficult because of their similar morphologies. Methods To identify a suitable DNA barcode for identification of Lepista species, we assessed the following five regions: internal transcribed spacer (ITS), the intergenic spacer (IGS), nuclear ribosomal RNA subunit, mitochondrial small subunit rDNA, and tef1. A total of 134 sequences from 34 samples belong to eight Lepista species were analyzed. The utility of each region as a DNA barcode was assessed based on the success rates of its PCR amplification and sequencing, and on its intra- and inter-specific variations. Results The results indicated that the ITS region could distinguish all species tested. We therefore propose that the ITS region can be used as a DNA barcode for the genus Lepista. In addition, a phylogenetic tree based on the ITS region showed that the tested eight Lepista species, including two unrecognized species, formed eight separate and well-supported clades.
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Affiliation(s)
- Siyu Wang
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, China
| | - Hongbo Guo
- College of Life Engineering, Shenyang Institute of Technology, Fushun, China
| | - JiaJia Li
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, China
| | - Wei Li
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, China
| | - Qin Wang
- Liaoning Academy of Forestry, Shenyang, China
| | - Xiaodan Yu
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, China
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Pham MT, Huang CM, Kirschner R. The plant growth-promoting potential of the mesophilic wood-rot mushroom Pleurotus pulmonarius. J Appl Microbiol 2019; 127:1157-1171. [PMID: 31291682 DOI: 10.1111/jam.14375] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/09/2019] [Accepted: 06/26/2019] [Indexed: 11/27/2022]
Abstract
AIMS To demonstrate the plant growth-promoting potential of a wood-decay mushroom. METHODS AND RESULTS A wild strain of a white rot fungus (Pleurotus pulmonarius) was found to convert 10 mmol l-1 L-tryptophan (TRP) to approximately 15 μg ml-1 indole-3-acetic acid (IAA) under the optimal growth conditions of 30°C and pH 5 for 15 days. Results of gas chromatography-mass spectrometry indicated IAA synthesis through the indole-3-pyruvic acid pathway when using cellulose as a sole carbon source. The mycelium as well as the culture filtrate promoted the growth and chlorophyll content of seedlings. In a monocotyledonous plant (rice), the number of lateral roots was increased experimentally, whereas in a dicotyledonous plant (tomato), the fungus led to an increased length of shoots and roots. CONCLUSIONS TRP-dependent IAA production was demonstrated for the first time for P. pulmonarius and may be responsible for enhancing plant growth in vitro. SIGNIFICANCE AND IMPACT OF THE STUDY Synthesis of IAA as the most prevalent phytohormone in plants has been demonstrated for soil microfungi. Pleurotus pulmonarius is reported as an IAA-producing wood-decay macrofungus. The higher temperature optimum of P. pulmonarius isolated from subtropical environment compared to other Pleurotus species from temperate regions makes it more suitable for application in subtropical/tropical regions.
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Affiliation(s)
- M T Pham
- Department of Biomedical Sciences & Engineering, National Central University, Taoyuan City, Taiwan
| | - C-M Huang
- Department of Biomedical Sciences & Engineering, National Central University, Taoyuan City, Taiwan
| | - R Kirschner
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan
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Sekan AS, Myronycheva OS, Karlsson O, Gryganskyi AP, Blume Y. Green potential of Pleurotus spp. in biotechnology. PeerJ 2019; 7:e6664. [PMID: 30967974 PMCID: PMC6446892 DOI: 10.7717/peerj.6664] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/22/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The genus Pleurotus is most exploitable xylotrophic fungi, with valuable biotechnological, medical, and nutritional properties. The relevant features of the representatives of this genus to provide attractive low-cost industrial tools have been reported in numerous studies to resolve the pressure of ecological issues. Additionally, a number of Pleurotus species are highly adaptive, do not require any special conditions for growth, and possess specific resistance to contaminating diseases and pests. The unique properties of Pleurotus species widely used in many environmental technologies, such as organic solid waste recycling, chemical pollutant degradation, and bioethanol production. METHODOLOGY The literature study encompasses peer-reviewed journals identified by systematic searches of electronic databases such as Google Scholar, NCBI, Springer, ResearchGate, ScienceDirect, and ISI Web of Knowledge. The search scheme was divided into several steps, as described below. RESULTS In this review, we describe studies examining the biotechnological feasibility of Pleurotus spp. to elucidate the importance of this genus for use in green technology. Here, we review areas of application of the genus Pleurotus as a prospective biotechnological tool. CONCLUSION The incomplete description of some fungal biochemical pathways emphasises the future research goals for this fungal culture.
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Affiliation(s)
- Alona S. Sekan
- Institute of Food Biotechnology and Genomics, National Academy of Science of Ukraine, Kyiv, Ukraine
| | - Olena S. Myronycheva
- Division of Wood Science and Engineering, Department of Engineering Sciences and Mathematics, Lulea University of Technology, Skelleftea, Sweden
| | - Olov Karlsson
- Division of Wood Science and Engineering, Department of Engineering Sciences and Mathematics, Lulea University of Technology, Skelleftea, Sweden
| | | | - Yaroslav Blume
- Institute of Food Biotechnology and Genomics, National Academy of Science of Ukraine, Kyiv, Ukraine
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Holec J, Kunca V, Kolařík M. Tricholomopsis badinensis sp. nov. and T. sulphureoides—two rare fungi of European old-growth forests. Mycol Prog 2019. [DOI: 10.1007/s11557-018-1449-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Li J, Liu XB, Zhao ZW, Yang ZL. Genetic diversity, core collection and breeding history of Pleurotus ostreatus in China. MYCOSCIENCE 2019. [DOI: 10.1016/j.myc.2018.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Zervakis GI, Venturella G, Fryssouli V, Inglese P, Polemis E, Gargano ML. Pleurotus opuntiae revisited - An insight to the phylogeny of dimitic Pleurotus species with emphasis on the P. djamor complex. Fungal Biol 2018; 123:188-199. [PMID: 30798874 DOI: 10.1016/j.funbio.2018.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 12/04/2018] [Accepted: 12/20/2018] [Indexed: 10/27/2022]
Abstract
The name Pleurotus opuntiae is indiscriminately used for describing mushrooms with white to off-white to white-grey pilei with short or absent stipe and dimitic hyphal system, which grow on plants of the genera Opuntia, Yucca, Agave, Phytolacca etc. However, the outcome of the present study evidences that this name should be reserved for specimens deriving from the Mediterranean area only; an epitype originating from Italy on Opuntia ficus-indica is designated. Pertinent material was sequenced by using the internal transcribed spacer region (ITS) and found to be phylogenetically related to P. djamor from Kenya and Nigeria, while members of the P. djamor complex from other continents were clearly more distant. Results were further corroborated by examining the large subunit of nuclear ribosomal DNA (LSU) and the second subunit of RNA polymerase II (RPB2). The P. djamor complex shows high intraspecific polymorphism evidenced by sequence divergence and genetic distance values, presents a cosmopolitan distribution and also comprises material initially identified as P. flabellatus, P. opuntiae, P. ostreatoroseus, P. parsonsiae and P. salmoneostramineus. An ITS tree including representative specimens from all major Pleurotus species is provided for the first time and ambiguous taxa are discussed in the context of new findings.
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Affiliation(s)
- Georgios I Zervakis
- Agricultural University of Athens, Laboratory of General and Agricultural Microbiology, Iera Odos 75, 11855 Athens, Greece.
| | - Giuseppe Venturella
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Viale delle Scienze, Bldg 4, I-90128 Palermo, Italy.
| | - Vassiliki Fryssouli
- Agricultural University of Athens, Laboratory of General and Agricultural Microbiology, Iera Odos 75, 11855 Athens, Greece
| | - Paolo Inglese
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Viale delle Scienze, Bldg 4, I-90128 Palermo, Italy
| | - Elias Polemis
- Agricultural University of Athens, Laboratory of General and Agricultural Microbiology, Iera Odos 75, 11855 Athens, Greece
| | - Maria Letizia Gargano
- Department of Earth and Marine Sciences, University of Palermo, Viale delle Scienze, Bldg 5, I-90128 Palermo, Italy
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Phylogeny and species delimitation of Flammulina: taxonomic status of winter mushroom in East Asia and a new European species identified using an integrated approach. Mycol Prog 2018. [DOI: 10.1007/s11557-018-1409-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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