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Tremble K, Henkel T, Bradshaw A, Domnauer C, Brown LM, Thám LX, Furci G, Aime MC, Moncalvo JM, Dentinger B. A revised phylogeny of Boletaceae using whole genome sequences. Mycologia 2024; 116:392-408. [PMID: 38551379 DOI: 10.1080/00275514.2024.2314963] [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: 11/29/2023] [Accepted: 01/30/2024] [Indexed: 05/01/2024]
Abstract
The porcini mushroom family Boletaceae is a diverse, widespread group of ectomycorrhizal (ECM) mushroom-forming fungi that so far has eluded intrafamilial phylogenetic resolution based on morphology and multilocus data sets. In this study, we present a genome-wide molecular data set of 1764 single-copy gene families from a global sampling of 418 Boletaceae specimens. The resulting phylogenetic analysis has strong statistical support for most branches of the tree, including the first statistically robust backbone. The enigmatic Phylloboletellus chloephorus from non-ECM Argentinian subtropical forests was recovered as a new subfamily sister to the core Boletaceae. Time-calibrated branch lengths estimate that the family first arose in the early to mid-Cretaceous and underwent a rapid radiation in the Eocene, possibly when the ECM nutritional mode arose with the emergence and diversification of ECM angiosperms. Biogeographic reconstructions reveal a complex history of vicariance and episodic long-distance dispersal correlated with historical geologic events, including Gondwanan origins and inferred vicariance associated with its disarticulation. Together, this study represents the most comprehensively sampled, data-rich molecular phylogeny of the Boletaceae to date, establishing a foundation for future robust inferences of biogeography in the group.
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Affiliation(s)
- Keaton Tremble
- Natural History Museum of Utah and School of Biological Sciences, University of Utah, Salt Lake City, Utah 84108, USA
| | - Terry Henkel
- Department of Biological Sciences, California State Polytechnic University, Humboldt, Arcata 95521, California
| | - Alexander Bradshaw
- Natural History Museum of Utah and School of Biological Sciences, University of Utah, Salt Lake City, Utah 84108, USA
| | - Colin Domnauer
- Natural History Museum of Utah and School of Biological Sciences, University of Utah, Salt Lake City, Utah 84108, USA
| | - Lyda M Brown
- Natural History Museum of Utah and School of Biological Sciences, University of Utah, Salt Lake City, Utah 84108, USA
| | - Lê Xuân Thám
- Laboratory for Computation and Applications in Life Sciences, Institute for Computation Science and Artificial Intelligence, Van Lang University, Ho Chi Minh City 700000, Viet Nam
- Faculty of Applied Technology, School of Technology, Van Lang University, Ho Chi Minh City 700000, Viet Nam
| | | | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47906, USA
| | - Jean-Marc Moncalvo
- Department of Natural History, Royal Ontario Museum and Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 2C6, Canada
| | - Bryn Dentinger
- Natural History Museum of Utah and School of Biological Sciences, University of Utah, Salt Lake City, Utah 84108, USA
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Vadthanarat S, Raghoonundon B, Lumyong S, Raspé O. Rostrupomyces, a new genus to accommodate Xerocomussisongkhramensis, and a new Hemileccinum species (Xerocomoideae, Boletaceae) from Thailand. MycoKeys 2024; 103:129-165. [PMID: 38584717 PMCID: PMC10995610 DOI: 10.3897/mycokeys.103.107935] [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: 06/13/2023] [Accepted: 03/06/2024] [Indexed: 04/09/2024] Open
Abstract
A new genus, Rostrupomyces is established to accommodate Xerocomussisongkhramensis based on multiple protein-coding genes (atp6, cox3, tef1, and rpb2) analyses of a wide taxon sampling of Boletaceae. In our phylogeny, the new genus was sister to Rubinosporus in subfamily Xerocomoideae, phylogenetically distant from Xerocomus, which was highly supported as sister to Phylloporus in the same subfamily Xerocomoideae. Rostrupomyces is different from other genera in Boletaceae by the following combination of characters: rugulose to subrugulose pileus surface, white pores when young becoming pale yellow in age, subscabrous stipe surface scattered with granulose squamules, white basal mycelium, unchanging color in any parts, yellowish brown spore print, and broadly ellipsoid to ellipsoid, smooth basidiospores. In addition, Hemileccinuminferius, also from subfamily Xerocomoideae, is newly described. Detailed descriptions and illustrations of the new genus and new species are presented.
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Affiliation(s)
- Santhiti Vadthanarat
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Department of Biological Science, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, 34190, Thailand
| | | | - Saisamorn Lumyong
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Olivier Raspé
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok, Thailand
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium
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Halling R, Fechner N, Holmes G, Davoodian N. Kgaria ( Boletaceae, Boletoideae) gen. nov. in Australia: Neither a Tylopilus nor a Porphyrellus. Fungal Syst Evol 2023; 12:31-45. [PMID: 38455954 PMCID: PMC10918407 DOI: 10.3114/fuse.2023.12.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/23/2023] [Indexed: 03/09/2024] Open
Abstract
Kgaria is described as a new porphyrellus-like genus of Boletaceae to accommodate Tylopilus cyanogranulifer, a dark brown to dull lilac/violet, or rarely, nearly black bolete with a series of oxidation reactions progressing from blue to red then nearly black and a dark brown spore deposit. Idiosyncratic blue-green pigment encrustations (cyanogranules) and a similarly colored reaction of the hyphae located on pileus and stipe surfaces are also diagnostic. Phylogenetic analyses of nuclear large-subunit rDNA (nrLSU), translation elongation factor 1-alpha (tef-1), and the second largest subunit of RNA polymerase II (rpb2) infer Kgaria as a unique generic lineage with two species, one of which is newly described (K. similis). Tylopilus olivaceoporus, originally described at the same time and as distinct from T. cyanogranulifer, appears to be conspecific with the latter. Some darkly pigmented taxa with similar oxidation reactions that were recently described from Brazil, Guyana, and China are further supported by morphology and molecular data as discrete lineages in separate genera in subfamily Boletoideae. Citation: Halling RE, Fechner NA, Holmes G, Davoodian N (2023). Kgaria (Boletaceae, Boletoideae) gen. nov. in Australia: Neither a Tylopilus nor a Porphyrellus. Fungal Systematics and Evolution 12: 31-45. doi: 10.3114/fuse.2023.12.02.
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Affiliation(s)
- R.E. Halling
- Department of Research & Conservation, Denver Botanic Gardens, 909 York St, Denver CO 80206 USA; Institute of Systematic Botany, New York Botanical Garden, 2900 Southern Blvd, Bronx, NY 10458, USA
| | - N.A. Fechner
- Queensland Herbarium, Mt Coot-tha Road, Toowong, Brisbane, QLD 4066, Australia
| | - G. Holmes
- Royal Botanic Gardens Victoria, South Yarra, VIC 3141, Australia
| | - N. Davoodian
- Royal Botanic Gardens Victoria, South Yarra, VIC 3141, Australia
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Rubinosporus auriporus gen. et sp. nov. (Boletaceae: Xerocomoideae) from Tropical Forests of Thailand, Producing Unusual Dark Ruby Spore Deposits. J Fungi (Basel) 2022; 8:jof8030278. [PMID: 35330280 PMCID: PMC8955211 DOI: 10.3390/jof8030278] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 12/10/2022] Open
Abstract
Rubinosporus, a new bolete genus from tropical forests of Thailand is introduced with R. auriporus as the type species. The genus is unique among Xerocomoideae in producing dark ruby spore deposits. It can be differentiated from all other Boletaceae genera by the following combination of characters: pileus surface evenly covered with matted tomentum; stipe surface with evenly scattered minute squamules; golden yellow tubular hymenophore, which is relatively thin especially when young; unchanging surfaces and context when bruised or cut; smooth, broadly ellipsoid basidiospores; and dark ruby spore deposits. The Boletaceae-wide and Xerocomoideae-wide phylogenetic analyses based on four-gene data sets (atp6, cox3, rpb2, and tef1) support Rubinosporus as monophyletic and places it in Boletaceae subfamily Xerocomoideae. Full descriptions and illustrations of the new genus and species are presented.
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Raghoonundon B, Davoodian N, Phonemany M, Raspé O. Tylocinum is no longer monotypic: Tylocinumbrevisporum sp. nov. (Boletales, Boletaceae) from northern Thailand. Biodivers Data J 2021; 9:e75907. [PMID: 34975279 PMCID: PMC8716511 DOI: 10.3897/bdj.9.e75907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/16/2021] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Tylocinum Y.C. Li & Zhu L. Yang 2016 is a Boletaceae genus belonging in subfamily Leccinoideae. It was described in 2016 from China and, prior to this study, it contained only one species, T.griseolum Y.C. Li & Zhu L. Yang 2016. During our survey of Boletaceae from Thailand, we collected some specimens that could be identified as a Tylocinum species, different from T.griseolum. NEW INFORMATION The bolete specimens, collected in forests dominated by Dipterocarpaceae and Fagaceae in northern Thailand, are described as Tylocinumbrevisporum Raghoonundon & Raspé sp. nov. Macroscopic and microscopic descriptions with illustrations are provided, as well as a 3-gene phylogeny, which confirms the new taxon's position in Tylocinum. Tylocinumbrevisporum differs from the only other known Tylocinum species (T.griseolum) by its brownish-grey colour, greyish-orange to brownish-orange colour change in the hymenophore when bruised, smaller pores (≤ 0.5 mm), longer tubes (up to 6 mm long), shorter and narrower basidiospores, longer and broader basidia and longer pleurocystidia relative to cheilocystidia. T.brevisporum is the second species from the genus Tylocinum and the only one to be found outside China thus far.
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Affiliation(s)
- Bhavesh Raghoonundon
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, ThailandCenter of Excellence in Fungal Research, Mae Fah Luang UniversityChiang RaiThailand
- School of Science, Mae Fah Luang University, Chiang Rai, ThailandSchool of Science, Mae Fah Luang UniversityChiang RaiThailand
| | - Naveed Davoodian
- National Herbarium of Victoria, Royal Botanic Gardens Victoria, Melbourne, Victoria, AustraliaNational Herbarium of Victoria, Royal Botanic Gardens VictoriaMelbourne, VictoriaAustralia
| | - Monthien Phonemany
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, ThailandCenter of Excellence in Fungal Research, Mae Fah Luang UniversityChiang RaiThailand
- School of Science, Mae Fah Luang University, Chiang Rai, ThailandSchool of Science, Mae Fah Luang UniversityChiang RaiThailand
| | - Olivier Raspé
- School of Science, Mae Fah Luang University, Chiang Rai, ThailandSchool of Science, Mae Fah Luang UniversityChiang RaiThailand
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He MQ, Zhao RL, Hyde KD, Begerow D, Kemler M, Yurkov A, McKenzie EHC, Raspé O, Kakishima M, Sánchez-Ramírez S, Vellinga EC, Halling R, Papp V, Zmitrovich IV, Buyck B, Ertz D, Wijayawardene NN, Cui BK, Schoutteten N, Liu XZ, Li TH, Yao YJ, Zhu XY, Liu AQ, Li GJ, Zhang MZ, Ling ZL, Cao B, Antonín V, Boekhout T, da Silva BDB, De Crop E, Decock C, Dima B, Dutta AK, Fell JW, Geml J, Ghobad-Nejhad M, Giachini AJ, Gibertoni TB, Gorjón SP, Haelewaters D, He SH, Hodkinson BP, Horak E, Hoshino T, Justo A, Lim YW, Menolli N, Mešić A, Moncalvo JM, Mueller GM, Nagy LG, Nilsson RH, Noordeloos M, Nuytinck J, Orihara T, Ratchadawan C, Rajchenberg M, Silva-Filho AGS, Sulzbacher MA, Tkalčec Z, Valenzuela R, Verbeken A, Vizzini A, Wartchow F, Wei TZ, Weiß M, Zhao CL, Kirk PM. Notes, outline and divergence times of Basidiomycota. FUNGAL DIVERS 2019. [DOI: 10.1007/s13225-019-00435-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AbstractThe Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.
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Vadthanarat S, Lumyong S, Raspé O. Cacaoporus, a new Boletaceae genus, with two new species from Thailand. MycoKeys 2019; 54:1-29. [PMID: 31231163 PMCID: PMC6579793 DOI: 10.3897/mycokeys.54.35018] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 04/26/2019] [Indexed: 11/18/2022] Open
Abstract
We introduce a new genus, Cacaoporus, characterised by chocolate brown to dark brown basidiomata and hymenophore, tubes not separable from the pileus context, white to off-white basal mycelium, reddening when bruised, amygdaliform to ovoid spores and dark brown spore deposit. Phylogenetic analyses of a four-gene dataset (atp6, tef1, rpb2 and cox3) with a wide selection of Boletaceae showed that the new genus is monophyletic and sister to the genera Cupreoboletus and Cyanoboletus in the Pulveroboletus group. Two new species in the genus, C.pallidicarneus and C.tenebrosus are described from northern Thailand. Full descriptions and illustrations of the new genus and species are presented. The phylogeny also confirmed the reciprocal monophyly of Neoboletus and Sutorius, which further support the separation of these two genera.
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Affiliation(s)
- Santhiti Vadthanarat
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand Department of Biology, Faculty of Science, Chiang Mai University Chiang Mai Thailand.,PhD's Degree Program in Biodiversity and Ethnobiology, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand Botanic Garden Meise Meise Belgium.,Center of Excellence in Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand Department of Biology, Faculty of Science, Chiang Mai University Chiang Mai Thailand
| | - Saisamorn Lumyong
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand Department of Biology, Faculty of Science, Chiang Mai University Chiang Mai Thailand.,Center of Excellence in Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand Department of Biology, Faculty of Science, Chiang Mai University Chiang Mai Thailand.,Academy of Science, The Royal Society of Thailand, Bangkok, 10300, Thailand Botanic Garden Meise Meise Belgium
| | - Olivier Raspé
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium Botanic Garden Meise Meise Belgium.,Fédération Wallonie-Bruxelles, Service général de l'Enseignement universitaire et de la Recherche scientifique, Rue A. Lavallée 1, 1080 Bruxelles, Belgium Department of Biology, Faculty of Science, Chiang Mai University Chiang Mai Thailand
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Vadthanarat S, Raspé O, Lumyong S. Phylogenetic affinities of the sequestrate genus Rhodactina (Boletaceae), with a new species, R. rostratispora from Thailand. MycoKeys 2018:63-80. [PMID: 29559826 PMCID: PMC5804118 DOI: 10.3897/mycokeys.29.22572] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 01/15/2018] [Indexed: 11/23/2022] Open
Abstract
Rhodactina is a small sequestrate genus in Boletaceae with two described species, R.himalayensis and R.incarnata. Phylogenetic analyses of a three-gene dataset including atp6, tef1 and rpb2 of Rhodactina species along with selected Boletaceae species showed that all Rhodactina species formed a monophyletic clade, sister to the genera Spongiforma and Borofutus in subfamily Leccinoideae with high support. All of the taxa in the clade have a similar chemical reaction in which basidiospores turn purplish, purplish red to violet or violet grey when in contact with potassium hydroxide. The molecular analyses also showed that all Rhodactina specimens collected from Ubon Ratchathani province, northeastern Thailand, belong to a new species. Morphologically, the new species is different from others by having a markedly prominent hilar appendage and a terminal hilum on its basidiospores. Thus, the new species, Rhodactinarostratispora, is introduced with detailed macroscopic and microscopic descriptions and illustrations.
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Affiliation(s)
- Santhiti Vadthanarat
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Olivier Raspé
- Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium.,Fédération Wallonie-Bruxelles, Service général de l'Enseignement universitaire et de la Recherche scientifique, Rue A. Lavallée 1, 1080 Bruxelles, Belgium
| | - Saisamorn Lumyong
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
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Casale M, Bagnasco L, Zotti M, Di Piazza S, Sitta N, Oliveri P. A NIR spectroscopy-based efficient approach to detect fraudulent additions within mixtures of dried porcini mushrooms. Talanta 2016; 160:729-734. [PMID: 27591669 DOI: 10.1016/j.talanta.2016.08.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/28/2016] [Accepted: 08/01/2016] [Indexed: 10/21/2022]
Abstract
Boletus edulis and allied species (BEAS), known as "porcini mushrooms", represent almost the totality of wild mushrooms placed on the Italian market, both fresh and dehydrated. Furthermore, considerable amounts of these dried fungi are imported from China. The presence of Tylopilus spp. and other extraneous species (i.e., species edible but not belonging to BEAS) within dried porcini mushrooms - mainly from those imported from China and sold in Italy - may represent an evaluable problem from a commercial point of view. The purpose of the present study is to evaluate near-infrared spectroscopy (NIRS) as a rapid and effective alternative to classical methods for identifying extraneous species within dried porcini batches and detecting related commercial frauds. To this goal, 80 dried fungi including BEAS, Tylopilus spp., and Boletus violaceofuscus were analysed by NIRS. For each sample, 3 different parts of the pileus (pileipellis, flesh and hymenium) were analysed and a low-level strategy for data fusion, consisting of combining the signals obtained by the different parts before data processing, was applied. Then, NIR spectra were used to develop reliable and efficient class-models using a novel method, partial least squares density modelling (PLS-DM), and the two most commonly used class-modelling techniques, UNEQ and SIMCA. The results showed that NIR spectroscopy coupled with chemometric class-modelling technique can be suggested as an effective analytical strategy to check the authenticity of dried BEAS mushrooms.
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Affiliation(s)
- Monica Casale
- Department of Pharmacy, University of Genoa, Viale Cembrano, 4, Genoa, I-16148 Italy
| | - Lucia Bagnasco
- Department of Pharmacy, University of Genoa, Viale Cembrano, 4, Genoa, I-16148 Italy
| | - Mirca Zotti
- Department of Earth, Environment and Life Sciences - Laboratory of Mycology, University of Genoa, Corso Europa, 26, Genoa, I-16132 Italy
| | - Simone Di Piazza
- Department of Earth, Environment and Life Sciences - Laboratory of Mycology, University of Genoa, Corso Europa, 26, Genoa, I-16132 Italy
| | - Nicola Sitta
- Professional Consulting Mycologist, Loc. Farné, 32, Lizzano in Belvedere, I-40042 Italy
| | - Paolo Oliveri
- Department of Pharmacy, University of Genoa, Viale Cembrano, 4, Genoa, I-16148 Italy.
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