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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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Sahin E, Edis G, Keskin E, Akata I. Molecular characterization of the complete genome of a novel ormycovirus infecting the ectomycorrhizal fungus Hortiboletus rubellus. Arch Virol 2024; 169:110. [PMID: 38664287 DOI: 10.1007/s00705-024-06027-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 03/11/2024] [Indexed: 05/24/2024]
Abstract
Advancements in high-throughput sequencing and the development of new bioinformatics tools for large-scale data analysis play a crucial role in uncovering virus diversity and enhancing our understanding of virus evolution. The discovery of the ormycovirus clades, a group of RNA viruses that are phylogenetically distinct from all known Riboviria members and are found in fungi, highlights the value of these tools for the discovery of novel viruses. The aim of this study was to examine viral populations in fungal hosts to gain insights into the diversity, evolution, and classification of these viruses. Here, we report the molecular characterization of a newly discovered ormycovirus, which we have named "Hortiboletus rubellus ormycovirus 1" (HrOMV1), that was found in the ectomycorrhizal fungus Hortiboletus rubellus. The bipartite genome of HrOMV1, whose nucleotide sequence was determined by HTS and RLM-RACE, consists of two RNA segments (RNA1 and RNA2) that exhibit similarity to those of previously studied ormycoviruses in their organization and the proteins they encode. The presence of upstream, in-frame AUG triplets in the 5' termini of both RNA segments suggests that HrOMV1, like certain other ormycoviruses, employs a non-canonical translation initiation strategy. Phylogenetic analysis showed that HrOMV1 is positioned within the gammaormycovirus clade. Its putative RNA-dependent RNA polymerase (RdRp) exhibits sequence similarity to those of other gammaormycovirus members, the most similarity to that of Termitomyces ormycovirus 1, with 33.05% sequence identity. This protein was found to contain conserved motifs that are crucial for RNA replication, including the distinctive GDQ catalytic triad observed in gammaormycovirus RdRps. The results of this study underscore the significance of investigating the ecological role of mycoviruses in mycorrhizal fungi. This is the first report of an ormycovirus infecting a member of the ectomycorrhizal genus Hortiboletus.
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Affiliation(s)
- Ergin Sahin
- Faculty of Science, Department of Biology, Dokuz Eylul University, Buca, Izmir, 35390, Turkey.
- Fauna and Flora Research and Application Center, Dokuz Eylul University, Buca, Izmir, 35390, Turkey.
| | - Gulce Edis
- Graduate School of Natural and Applied Sciences, Ankara University, Dışkapı, Ankara, 06110, Turkey
| | - Emre Keskin
- Evolutionary Genetics Laboratory (eGL), Faculty of Agriculture Department of Fisheries and Aquaculture, Ankara University, Dışkapı, Ankara, 06110, Turkey
| | - Ilgaz Akata
- Faculty of Science Department of Biology, Ankara University, Tandogan, Ankara, 06100, Turkey
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Das K, Ghosh A, Datta S, Singh U, Chakraborty D, Tudu D, Vizzini A. Concordance of multigene genealogy along with morphological evidence unveils five novel species and two new records of boletoid mushrooms (fungi) from India. Sci Rep 2024; 14:9298. [PMID: 38654032 DOI: 10.1038/s41598-024-59781-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/15/2024] [Indexed: 04/25/2024] Open
Abstract
Agaricales, Russulales and Boletales are dominant orders among the wild mushrooms in Basidiomycota. Boletaceae, one of the major functional elements in terrestrial ecosystem and mostly represented by ectomycorrhizal symbionts of trees in Indian Himalaya and adjoining hills, are extraordinarily diverse and represented by numerous genera and species which are unexplored or poorly known. Therefore, their hidden diversity is yet to be revealed. Extensive macrofungal exploration by the authors to different parts of Himalaya and surroundings, followed by through morphological studies and multigene molecular phylogeny lead to the discovery of five new species of wild mushrooms: Leccinellum bothii sp. nov., Phylloporus himalayanus sp. nov., Phylloporus smithii sp. nov., Porphyrellus uttarakhandae sp. nov., and Retiboletus pseudoater sp. nov. Present communication deals with morphological details coupled with illustrations and phylogenetic inferences. Besides, Leccinellum sinoaurantiacum and Xerocomus rugosellus are also reported for the first time from this country.
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Affiliation(s)
- Kanad Das
- Central National Herbarium, Botanical Survey of India, P.O.-B. Garden, Howrah, 711103, India
| | - Aniket Ghosh
- Central National Herbarium, Botanical Survey of India, P.O.-B. Garden, Howrah, 711103, India
| | - Sudeshna Datta
- Central National Herbarium, Botanical Survey of India, P.O.-B. Garden, Howrah, 711103, India
| | - Upendra Singh
- Department of Botany and Microbiology, H.N.B. Garhwal University, Srinagar Garhwal, Uttarakhand, 246174, India
| | | | - Debala Tudu
- Eastern Regional Centre, Botanical Survey of India, Shillong, Meghalaya, 793003, India
| | - Alfredo Vizzini
- Department of Life Sciences and Systems Biology, University of Torino, 10125, Turin, Italy.
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Das K, Ghosh A, Chakraborty D, Datta S, Bera I, Layola Mr R, Banu F, Vizzini A, Wisitrassameewong K. Four Novel Species and Two New Records of Boletes from India. J Fungi (Basel) 2023; 9:754. [PMID: 37504742 PMCID: PMC10381181 DOI: 10.3390/jof9070754] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 07/29/2023] Open
Abstract
Repeated macrofungal explorations, followed by thorough examination of species through morphology and molecular phylogeny, have made it clear that European and American names of wild mushrooms were inadvertently misapplied quite often to Asian lookalikes by mycologists/taxonomists in the past. Therefore, in order to reveal this mushroom treasure, in recent years, taxonomical research on wild mushrooms has been intensified in Asian countries, including India, by undertaking a combined approach of morpho-taxonomy and multigene molecular phylogeny. Boletoid mushrooms (Boletaceae) are no exception. While working on boletoid mushrooms of the Indian Himalayas, authors recently came across six interesting species of boletoid mushrooms. In the present communication, four novel species, namely Leccinellum binderi, Cyanoboletus paurianus, Xerocomus uttarakhandae, and Xerocomellus himalayanus, are established based on morphology and molecular phylogenetic estimations. Moreover, Cyanoboletus macroporus and Xerocomus fraternus are also reported here for the first time in India.
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Affiliation(s)
- Kanad Das
- Central National Herbarium, Botanical Survey of India, Howrah 711103, India
| | - Aniket Ghosh
- Central National Herbarium, Botanical Survey of India, Howrah 711103, India
| | | | - Sudeshna Datta
- Central National Herbarium, Botanical Survey of India, Howrah 711103, India
| | - Ishika Bera
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Ranjith Layola Mr
- Central National Herbarium, Botanical Survey of India, Howrah 711103, India
| | - Farheen Banu
- Central National Herbarium, Botanical Survey of India, Howrah 711103, India
| | - Alfredo Vizzini
- Department of Life Sciences and Systems Biology, University of Torino, 10124 Torino, Italy
| | - Komsit Wisitrassameewong
- National Biobank of Thailand, National Science and Technology Development Agency, Pathum Thani 12120, Thailand
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B Patil P, Gunasekaran S, K Singh S, Vaidya S. Parvixerocomus matheranensis ( Boletaceae), a new species from India. MYCOSCIENCE 2021; 62:244-249. [PMID: 37092172 PMCID: PMC9721517 DOI: 10.47371/mycosci.2021.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 11/16/2022]
Abstract
A new species of Parvixerocomus, P. matheranensis belonging to Boletoideae of Boletaceae is described and illustrated from tropical region of Maharashtra, India. P. matheranensis is morphologically distinguished by small basidiomes having ruby red pileus with concolorous stipe, yellow hymenophore that stains blue to blackish blue on bruising, elongate ellipsoid to cylindrical basidiospores with inconspicuous suprahilar depression, ventricose to clavate cheilocystidia, ventricose to lageniform pleurocystidia. Further, extensive phylogenetic analyses based on five gene markers (nrITS, nrLSU, rpb1, rpb2, tef1-α) confirmed that P. matheranensis is distinct from its closest taxa P. aokii and P. pseudoaokii and also from other members of Boletoideae.
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Affiliation(s)
- Prashant B Patil
- Department of Botany, Smt. Chandibai Himathmal Mansukhani College
| | | | - Sanjay K Singh
- MACS’Agharkar Research Institute, Biodiversity and Palaeobiology Group, National Fungal Culture Collection of India (NFCCI)
| | - Sharda Vaidya
- Department of Botany, Smt. Chandibai Himathmal Mansukhani College
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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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Parihar A, Hembrom ME, Vizzini A, Das K. Indoporus shoreae gen. et sp. nov. (Boletaceae) from Tropical India. CRYPTOGAMIE MYCOL 2018. [DOI: 10.7872/crym/v39.iss4.2018.447] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Arvind Parihar
- Cryptogamic Unit, Botanical Survey of India, P.O. Botanic Garden, Howrah – 711103, India, emails: ar
| | - Manoj E. Hembrom
- Central National Herbarium, Botanical Survey of India, P.O. Botanic Garden, Howrah – 711103, India,
| | - Alfredo Vizzini
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, I-101
| | - Kanad Das
- Cryptogamic Unit, Botanical Survey of India, P.O. Botanic Garden, Howrah – 711103, India, emails: ar
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Das K, Ghosh A, Chakraborty D, Li J, Qiu L, Baghela A, Halama M, Hembrom ME, Mehmood T, Parihar A, Pencakowski B, Bielecka M, Reczyńska K, Sasiela D, Singh U, Song Y, Świerkosz K, Szczęśniak K, Uniyal P, Zhang J, Buyck B. Fungal Biodiversity Profiles 31–40. CRYPTOGAMIE MYCOL 2017. [DOI: 10.7872/crym/v38.iss3.2017.353] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kanad Das
- Cryptogamic Unit, Botanical Survey of India, P.O. Botanic Garden, Howrah 711103, India,, ,
| | - Aniket Ghosh
- Department of Botany & Microbiology, H.N.B. Garhwal University (A Central University), Srinagar, Garhwal, 246174, Uttarakhand, India,, , ,
| | - Dyutiparna Chakraborty
- Cryptogamic Unit, Botanical Survey of India, P.O. Botanic Garden, Howrah 711103, India,, ,
| | - Jingwei Li
- State Key Lab of Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou 510275, China,
| | - Lihong Qiu
- State Key Lab of Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou 510275, China,
| | - Abhishek Baghela
- MACS' Agharkar Research Institute, Biodiversity and Palaeobiology Group, National Fungal Culture Collection of India (NFCCI), G.G. Agarkar Road, Pune - 411004, India,
| | - Marek Halama
- Museum of Natural History, University of Wrocław, ul. Sienkiewicza 21, 50-335 Wrocław, Poland
| | - Manoj E. Hembrom
- Central National Herbarium, Botanical Survey of India, P.O. Botanic Garden, Howrah 711103, India,
| | - Tahir Mehmood
- Department of Botany & Microbiology, H.N.B. Garhwal University (A Central University), Srinagar, Garhwal, 246174, Uttarakhand, India,, , ,
| | - Arvind Parihar
- Cryptogamic Unit, Botanical Survey of India, P.O. Botanic Garden, Howrah 711103, India,, ,
| | - Bartosz Pencakowski
- Department of Pharmaceutical Biotechnology, Wrocław Medical University, ul. Borowska 211a, 50-556 Wrocław, Poland
| | - Monika Bielecka
- Department of Pharmaceutical Biotechnology, Wrocław Medical University, ul. Borowska 211a, 50-556 Wrocław, Poland
| | - Kamila Reczyńska
- Department of Botany, University of Wrocław, ul. Kanonia 6/8, 50-328 Wrocław, Poland
| | - Dorota Sasiela
- Museum of Natural History, University of Wrocław, ul. Sienkiewicza 21, 50-335 Wrocław, Poland
| | - Upendra Singh
- Department of Botany & Microbiology, H.N.B. Garhwal University (A Central University), Srinagar, Garhwal, 246174, Uttarakhand, India,, , ,
| | - Yu Song
- State Key Lab of Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou 510275, China,
| | - Krzysztof Świerkosz
- Museum of Natural History, University of Wrocław, ul. Sienkiewicza 21, 50-335 Wrocław, Poland
| | - Katarzyna Szczęśniak
- Museum of Natural History, University of Wrocław, ul. Sienkiewicza 21, 50-335 Wrocław, Poland
| | - Priyanka Uniyal
- Department of Botany & Microbiology, H.N.B. Garhwal University (A Central University), Srinagar, Garhwal, 246174, Uttarakhand, India,, , ,
| | - Jianbin Zhang
- State Key Lab of Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou 510275, China,
| | - Bart Buyck
- Museum National d'Histoire Naturelle, Institut de Systematique, Evolution, Biodiversité - UMR 7205 CNRS MNHN UPMC EPHE, CP 39, 12 rue Buffon, F-75005 Paris, France
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