1
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Schultz TR, Sosa-Calvo J, Kweskin MP, Lloyd MW, Dentinger B, Kooij PW, Vellinga EC, Rehner SA, Rodrigues A, Montoya QV, Fernández-Marín H, Ješovnik A, Niskanen T, Liimatainen K, Leal-Dutra CA, Solomon SE, Gerardo NM, Currie CR, Bacci M, Vasconcelos HL, Rabeling C, Faircloth BC, Doyle VP. The coevolution of fungus-ant agriculture. Science 2024; 386:105-110. [PMID: 39361762 DOI: 10.1126/science.adn7179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 09/05/2024] [Indexed: 10/05/2024]
Abstract
Fungus-farming ants cultivate multiple lineages of fungi for food, but, because fungal cultivar relationships are largely unresolved, the history of fungus-ant coevolution remains poorly known. We designed probes targeting >2000 gene regions to generate a dated evolutionary tree for 475 fungi and combined it with a similarly generated tree for 276 ants. We found that fungus-ant agriculture originated ~66 million years ago when the end-of-Cretaceous asteroid impact temporarily interrupted photosynthesis, causing global mass extinctions but favoring the proliferation of fungi. Subsequently, ~27 million years ago, one ancestral fungal cultivar population became domesticated, i.e., obligately mutualistic, when seasonally dry habitats expanded in South America, likely isolating the cultivar population from its free-living, wet forest-dwelling conspecifics. By revealing these and other major transitions in fungus-ant coevolution, our results clarify the historical processes that shaped a model system for nonhuman agriculture.
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Affiliation(s)
- Ted R Schultz
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Jeffrey Sosa-Calvo
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Matthew P Kweskin
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Michael W Lloyd
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Bryn Dentinger
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Pepijn W Kooij
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Surrey, UK
- Institute of Biosciences, Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
| | - Else C Vellinga
- University Herbarium, University of California at Berkeley, Berkeley, CA, USA
| | - Stephen A Rehner
- Mycology and Nematology Genetic Diversity and Biology Laboratory, US Department of Agriculture Agricultural Research Center, Beltsville, MD, USA
| | - Andre Rodrigues
- Institute of Biosciences, Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
| | - Quimi V Montoya
- Institute of Biosciences, Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
| | - Hermógenes Fernández-Marín
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Clayton, Panama
- Smithsonian Tropical Research Institute (STRI), Ancon, Panama
| | - Ana Ješovnik
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Tuula Niskanen
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Surrey, UK
| | | | - Caio A Leal-Dutra
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Scott E Solomon
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | | | - Cameron R Currie
- Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | - Mauricio Bacci
- Institute of Biosciences, Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
| | - Heraldo L Vasconcelos
- Instituto de Biologia, Universidade Federal de Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Christian Rabeling
- Social Insect Research Group, School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Department of Integrative Taxonomy of Insects, Institute of Biology, and KomBioTa - Center for Biodiversity and Integrative Taxonomy; University of Hohenheim, Stuttgart, Germany
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - Vinson P Doyle
- Department of Plant Pathology and Crop Physiology, Louisiana State University AgCenter, Baton Rouge, LA, USA
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2
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Gallone B, Kuyper TW, Nuytinck J. The genus Cortinarius should not (yet) be split. IMA Fungus 2024; 15:24. [PMID: 39138570 PMCID: PMC11321212 DOI: 10.1186/s43008-024-00159-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 07/25/2024] [Indexed: 08/15/2024] Open
Abstract
The genus Cortinarius (Agaricales, Basidiomycota) is one of the most species-rich fungal genera, with thousands of species reported. Cortinarius species are important ectomycorrhizal fungi and form associations with many vascular plants globally. Until recently Cortinarius was the single genus of the family Cortinariaceae, despite several attempts to provide a workable, lower-rank hierarchical structure based on subgenera and sections. The first phylogenomic study for this group elevated the old genus Cortinarius to family level and the family was split into ten genera, of which seven were described as new. Here, by careful re-examination of the recently published phylogenomic dataset, we detected extensive gene-tree/species-tree conflicts using both concatenation and multispecies coalescent approaches. Our analyses demonstrate that the Cortinarius phylogeny remains unresolved and the resulting phylogenomic hypotheses suffer from very short and unsupported branches in the backbone. We can confirm monophyly of only four out of ten suggested new genera, leaving uncertain the relationships between each other and the general branching order. Thorough exploration of the tree space demonstrated that the topology on which Cortinarius revised classification relies on does not represent the best phylogenetic hypothesis and should not be used as constrained topology to include additional species. For this reason, we argue that based on available evidence the genus Cortinarius should not (yet) be split. Moreover, considering that phylogenetic uncertainty translates to taxonomic uncertainty, we advise for careful evaluation of phylogenomic datasets before proposing radical taxonomic and nomenclatural changes.
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Affiliation(s)
- Brigida Gallone
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands.
| | - Thomas W Kuyper
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
- Soil Biology Group, Wageningen University, 6700 AA, Wageningen, The Netherlands
| | - Jorinde Nuytinck
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
- Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
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3
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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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4
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Kraisitudomsook N, Ahrendt S, Riley R, LaButti K, Lipzen A, Daum C, Barry K, Grigoriev IV, Rämä T, Martin F, Smith ME. On the origin of bird's nest fungi: Phylogenomic analyses of fungi in the Nidulariaceae (Agaricales, Basidiomycota). Mol Phylogenet Evol 2024; 193:108010. [PMID: 38195011 DOI: 10.1016/j.ympev.2024.108010] [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: 11/08/2022] [Revised: 11/15/2023] [Accepted: 01/06/2024] [Indexed: 01/11/2024]
Abstract
Nidulariaceae, also known as bird's nest fungi, is an understudied group of mushroom-forming fungi. The common name is derived from their nest-like morphology. Bird's nest fungi are ubiquitous wood decomposers or saprobes on dung. Recent studies showed that species in the Nidulariaceae form a monophyletic group with five sub-clades. However, phylogenetic relationships among genera and placement of Nidulariaceae are still unclear. We present phylogenomic analyses of bird's nest fungi and related Agaricales fungi to gain insight into the evolution of Nidulariaceae. A species tree with 17 newly generated genomes of bird's nest fungi and representatives from all major clades of Agaricales was constructed using 1044 single-copy genes to explore the intergeneric relationships and pinpoint the placement of Nidulariaceae within Agaricales. We corroborated the hypothesis that bird's nest fungi are sister to Squamanitaceae, which includes mushroom-shaped fungi with a stipe and pileus that are saprobes and mycoparasites. Lastly, stochastic character mapping of discrete traits on phylogenies (SIMMAP) suggests that the ancestor of bird's nest fungi likely possessed an evanescent, globose peridium without strings attaching to the spore packets (funiculi). This analysis suggests that the funiculus was gained twice and that the persistent, cupulate peridium form was gained at least four times and lost once. However, alternative coding schemes and datasets with a wider array of Agaricales produced conflicting results during ancestral state reconstruction, indicating that there is some uncertainty in the number of peridium transitions and that taxon sampling may significantly alter ancestral state reconstructions. Overall, our results suggest that several key morphological characters of Nidulariaceae have been subject to homoplasy.
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Affiliation(s)
- Nattapol Kraisitudomsook
- Plant Pathology Department, Institute of Food and Agricultural Sciences (UF-IFAS), University of Florida, Gainesville, FL 32607, USA; Department of Biology, Faculty of Science and Technology, Muban Chombueng Rajabhat University, Ratchaburi 70150, Thailand.
| | - Steven Ahrendt
- U.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Robert Riley
- U.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Kurt LaButti
- U.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Anna Lipzen
- U.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Chris Daum
- U.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Kerrie Barry
- U.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Igor V Grigoriev
- U.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California Berkeley, 110 Koshland Hall, Berkeley, CA 94720, USA
| | - Teppo Rämä
- The Norwegian College of Fishery Science, UiT the Arctic University of Norway, Tromsø N-9037, Norway
| | - Francis Martin
- University of Lorraine, National Research Institute for Agriculture, Food, and Environment (INRAE), Tree-Microbe Interactions Department, Champenoux 54280, France.
| | - Matthew E Smith
- Plant Pathology Department, Institute of Food and Agricultural Sciences (UF-IFAS), University of Florida, Gainesville, FL 32607, USA.
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5
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Vizzini A, Alvarado P, Consiglio G, Marchetti M, Xu J. Family matters inside the order Agaricales: systematic reorganization and classification of incertae sedis clitocyboid, pleurotoid and tricholomatoid taxa based on an updated 6-gene phylogeny. Stud Mycol 2024; 107:67-148. [PMID: 38600959 PMCID: PMC11003440 DOI: 10.3114/sim.2024.107.02] [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: 07/28/2023] [Accepted: 12/17/2023] [Indexed: 04/12/2024] Open
Abstract
The phylogenetic position of several clitocyboid/pleurotoid/tricholomatoid genera previously considered incertae sedis is here resolved using an updated 6-gene dataset of Agaricales including newly sequenced lineages and more complete data from those already analyzed before. Results allowed to infer new phylogenetic relationships, and propose taxonomic novelties to accommodate them, including up to ten new families and a new suborder. Giacomia (for which a new species from China is here described) forms a monophyletic clade with Melanoleuca (Melanoleucaceae) nested inside suborder Pluteineae, together with the families Pluteaceae, Amanitaceae (including Leucocortinarius), Limnoperdaceae and Volvariellaceae. The recently described family Asproinocybaceae is shown to be a later synonym of Lyophyllaceae (which includes also Omphaliaster and Trichocybe) within suborder Tricholomatineae. The families Biannulariaceae, Callistosporiaceae, Clitocybaceae, Fayodiaceae, Macrocystidiaceae (which includes Pseudoclitopilus), Entolomataceae, Pseudoclitocybaceae (which includes Aspropaxillus), Omphalinaceae (Infundibulicybe and Omphalina) and the new families Paralepistaceae and Pseudoomphalinaceae belong also to Tricholomatineae. The delimitation of the suborder Pleurotineae (= Schizophyllineae) is discussed and revised, accepting five distinct families within it, viz. Pleurotaceae, Cyphellopsidaceae, Fistulinaceae, Resupinataceae and Schizophyllaceae. The recently proposed suborder Phyllotopsidineae (= Sarcomyxineae) is found to encompass the families Aphroditeolaceae, Pterulaceae, Phyllotopsidaceae, Radulomycetaceae, Sarcomyxaceae (which includes Tectella), and Stephanosporaceae, all of them unrelated to Pleurotaceae (suborder Pleurotineae) or Typhulaceae (suborder Typhulineae). The new family Xeromphalinaceae, encompassing the genera Xeromphalina and Heimiomyces, is proposed within Marasmiineae. The suborder Hygrophorineae is here reorganized into the families Hygrophoraceae, Cantharellulaceae, Cuphophyllaceae, Hygrocybaceae and Lichenomphaliaceae, to homogenize the taxonomic rank of the main clades inside all suborders of Agaricales. Finally, the genus Hygrophorocybe is shown to represent a distinct clade inside Cuphophyllaceae, and the new combination H. carolinensis is proposed. Taxonomic novelties: New suborder: Typhulineae Vizzini, Consiglio & P. Alvarado. New families: Aphroditeolaceae Vizzini, Consiglio & P. Alvarado, Melanoleucaceae Locq. ex Vizzini, Consiglio & P. Alvarado, Paralepistaceae Vizzini, Consiglio & P. Alvarado, Pseudoomphalinaceae Vizzini, Consiglio & P. Alvarado, Volvariellaceae Vizzini, Consiglio & P. Alvarado, Xeromphalinaceae Vizzini, Consiglio & P. Alvarado. New species: Giacomia sinensis J.Z. Xu. Stat. nov.: Cantharellulaceae (Lodge, Redhead, Norvell & Desjardin) Vizzini, Consiglio & P. Alvarado, Cuphophyllaceae (Z.M. He & Zhu L. Yang) Vizzini, Consiglio & P. Alvarado, Hygrocybaceae (Padamsee & Lodge) Vizzini, Consiglio & P. Alvarado, Lichenomphaliaceae (Lücking & Redhead) Vizzini, Consiglio & P. Alvarado. New combination: Hygrophorocybe carolinensis (H.E. Bigelow & Hesler) Vizzini, Consiglio & P. Alvarado. New synonyms: Sarcomyxineae Zhu L. Yang & G.S. Wang, Schizophyllineae Aime, Dentinger & Gaya, Asproinocybaceae T. Bau & G.F. Mou. Incertae sedis taxa placed at family level: Aphroditeola Redhead & Manfr. Binder, Giacomia Vizzini & Contu, Hygrophorocybe Vizzini & Contu, Leucocortinarius (J.E. Lange) Singer, Omphaliaster Lamoure, Pseudoclitopilus Vizzini & Contu, Resupinatus Nees ex Gray, Tectella Earle, Trichocybe Vizzini. New delimitations of taxa: Hygrophorineae Aime, Dentinger & Gaya, Phyllotopsidineae Zhu L. Yang & G.S. Wang, Pleurotineae Aime, Dentinger & Gaya, Pluteineae Aime, Dentinger & Gaya, Tricholomatineae Aime, Dentinger & Gaya. Resurrected taxa: Fayodiaceae Jülich, Resupinataceae Jülich. Citation: Vizzini A, Alvarado P, Consiglio G, Marchetti M, Xu J (2024). Family matters inside the order Agaricales: systematic reorganization and classification of incertae sedis clitocyboid, pleurotoid and tricholomatoid taxa based on an updated 6-gene phylogeny. Studies in Mycology 107: 67-148. doi: 10.3114/sim.2024.107.02.
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Affiliation(s)
- A. Vizzini
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, 10125 Turin, Italy
- Institute for Sustainable Plant Protection (IPSP-SS Turin), C.N.R., Viale P.A. Mattioli, 25, 10125 Turin, Italy
| | - P. Alvarado
- ALVALAB, Dr. Fernando Bongera st., Severo Ochoa bldg. S1.04, 33006 Oviedo, Spain
| | - G. Consiglio
- Via Ronzani 61, Casalecchio di Reno, 40033 Bologna, Italy
| | | | - J. Xu
- Agricultural College, Jilin Agriculture Science and Technology University, Jilin 132101, Jilin Province, P. R. China
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6
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Bradshaw AJ, Ramírez-Cruz V, Awan AR, Furci G, Guzmán-Dávalos L, Dentinger BTM. Phylogenomics of the psychoactive mushroom genus Psilocybe and evolution of the psilocybin biosynthetic gene cluster. Proc Natl Acad Sci U S A 2024; 121:e2311245121. [PMID: 38194448 PMCID: PMC10801892 DOI: 10.1073/pnas.2311245121] [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: 07/20/2023] [Accepted: 11/28/2023] [Indexed: 01/11/2024] Open
Abstract
Psychoactive mushrooms in the genus Psilocybe have immense cultural value and have been used for centuries in Mesoamerica. Despite the recent surge of interest in these mushrooms due to the psychotherapeutic potential of their natural alkaloid psilocybin, their phylogeny and taxonomy remain substantially incomplete. Moreover, the recent elucidation of the psilocybin biosynthetic gene cluster is known for only five of ~165 species of Psilocybe, four of which belong to only one of two major clades. We set out to improve the phylogeny of Psilocybe using shotgun sequencing of fungarium specimens, from which we obtained 71 metagenomes including from 23 types, and conducting phylogenomic analysis of 2,983 single-copy gene families to generate a fully supported phylogeny. Molecular clock analysis suggests the stem lineage of Psilocybe arose ~67 mya and diversified ~56 mya. We also show that psilocybin biosynthesis first arose in Psilocybe, with 4 to 5 possible horizontal transfers to other mushrooms between 40 and 9 mya. Moreover, predicted orthologs of the psilocybin biosynthetic genes revealed two distinct gene orders within the biosynthetic gene cluster that corresponds to a deep split within the genus, possibly a signature of two independent acquisitions of the cluster within Psilocybe.
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Affiliation(s)
- Alexander J. Bradshaw
- School of Biological Sciences, University of Utah, Salt Lake City, UT84112
- Natural History Museum of Utah, Collections and Research, University of Utah, Salt Lake City, UT84108
| | - Virginia Ramírez-Cruz
- Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT), Departamento de Botánica y Zoología, Universidad de Guadalajara, Zapopan45147, Mexico
| | - Ali R. Awan
- Genomics Innovation Unit, Guy’s and St.Thomas’ NHS Foundation Trust, St Thomas’ Hospital, LondonSE1 7EH, United Kingdom
| | | | - Laura Guzmán-Dávalos
- Departamento de Botánica y Zoología, Universidad de Guadalajara, Zapopan45147, Mexico
| | - Bryn T. M. Dentinger
- School of Biological Sciences, University of Utah, Salt Lake City, UT84112
- Natural History Museum of Utah, Collections and Research, University of Utah, Salt Lake City, UT84108
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7
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Wang GS, Cai Q, Hao YJ, Bau T, Chen ZH, Li MX, David N, Kraisitudomsook N, Yang ZL. Phylogenetic and taxonomic updates of Agaricales, with an emphasis on Tricholomopsis. Mycology 2023; 15:180-209. [PMID: 38813470 PMCID: PMC11133883 DOI: 10.1080/21501203.2023.2263031] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/20/2023] [Indexed: 05/31/2024] Open
Abstract
The order Agaricales was divided into eight suborders. However, the phylogenetic relationships among some suborders are largely unresolved, and the phylogenetic positions and delimitations of some taxa, such as Sarcomyxaceae and Tricholomopsis, remain unsettled. In this study, sequence data of 38 genomes were generated through genome skimming on an Illumina sequencing system. To anchor the systematic position of Sarcomyxaceae and Tricholomopsis, a phylogenetic analysis based on 555 single-copy orthologous genes from the aforementioned genomes and 126 publicly accessible genomes was performed. The results fully supported the clustering of Tricholomopsis with Phyllotopsis and Pleurocybella within Phyllotopsidaceae, which formed a divergent monophyletic major lineage together with Pterulaceae, Radulomycetaceae, and Macrotyphula in Agaricales. The analysis also revealed that Sarcomyxaceae formed a unique major clade. Therefore, two new suborders, Phyllotopsidineae and Sarcomyxineae, are proposed for the two major lineages. Analyses of 450 single-copy orthologous genes and four loci suggested that Tricholomopsis consisted of at least four clades. Tricholomopsis is subsequently subdivided into four distinct sections. Seventeen Tricholomopsis species in China, including six new species, are reported. Conoloma is established to accommodate T. mucronata. The substrate preference of Tricholomopsis species and the transitions of the pileate ornamentations among the species within the genus are discussed.
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Affiliation(s)
- Geng-Shen Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany Chinese Academy of Sciences, Kunming, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qing Cai
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany Chinese Academy of Sciences, Kunming, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yan-Jia Hao
- School of Horticulture, Anhui Agricultural University, Hefei, China
| | - Tolgor Bau
- Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Zuo-Hong Chen
- Life Science College, Hunan Normal University, Changsha, China
| | - Mei-Xiang Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Navarro David
- INRAE, Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, Marseille, France
- INRAE, Aix Marseille Université, CIRM-CF, Marseille, France
| | - Nattapol Kraisitudomsook
- Department of Biology, Faculty of Science and Technology, Muban Chombueng Rajabhat University, Ratchaburi, Thailand
| | - Zhu-Liang Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany Chinese Academy of Sciences, Kunming, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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8
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Ferrari G, Esselens L, Hart ML, Janssens S, Kidner C, Mascarello M, Peñalba JV, Pezzini F, von Rintelen T, Sonet G, Vangestel C, Virgilio M, Hollingsworth PM. Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections. Biodivers Data J 2023; 11:e102317. [PMID: 38327316 PMCID: PMC10848826 DOI: 10.3897/bdj.11.e102317] [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: 02/21/2023] [Accepted: 08/04/2023] [Indexed: 02/09/2024] Open
Abstract
Intentionally preserved biological material in natural history collections represents a vast repository of biodiversity. Advances in laboratory and sequencing technologies have made these specimens increasingly accessible for genomic analyses, offering a window into the genetic past of species and often permitting access to information that can no longer be sampled in the wild. Due to their age, preparation and storage conditions, DNA retrieved from museum and herbarium specimens is often poor in yield, heavily fragmented and biochemically modified. This not only poses methodological challenges in recovering nucleotide sequences, but also makes such investigations susceptible to environmental and laboratory contamination. In this paper, we review the practical challenges associated with making the recovery of DNA sequence data from museum collections more routine. We first review key operational principles and issues to address, to guide the decision-making process and dialogue between researchers and curators about when and how to sample museum specimens for genomic analyses. We then outline the range of steps that can be taken to reduce the likelihood of contamination including laboratory set-ups, workflows and working practices. We finish by presenting a series of case studies, each focusing on protocol practicalities for the application of different mainstream methodologies to museum specimens including: (i) shotgun sequencing of insect mitogenomes, (ii) whole genome sequencing of insects, (iii) genome skimming to recover plant plastid genomes from herbarium specimens, (iv) target capture of multi-locus nuclear sequences from herbarium specimens, (v) RAD-sequencing of bird specimens and (vi) shotgun sequencing of ancient bovid bone samples.
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Affiliation(s)
- Giada Ferrari
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Lore Esselens
- Royal Museum for Central Africa, Tervuren, BelgiumRoyal Museum for Central AfricaTervurenBelgium
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Michelle L Hart
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Steven Janssens
- Meise Botanic Garden, Meise, BelgiumMeise Botanic GardenMeiseBelgium
- Leuven Plant Institute, Department of Biology, Leuven, BelgiumLeuven Plant Institute, Department of BiologyLeuvenBelgium
| | - Catherine Kidner
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | | | - Joshua V Peñalba
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, GermanyMuseum für Naturkunde, Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Flávia Pezzini
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Thomas von Rintelen
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, GermanyMuseum für Naturkunde, Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Gontran Sonet
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Carl Vangestel
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Massimiliano Virgilio
- Royal Museum for Central Africa, Department of African Zoology, Tervuren, BelgiumRoyal Museum for Central Africa, Department of African ZoologyTervurenBelgium
| | - Peter M Hollingsworth
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
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9
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Peng L, Zhang Y, Druzhinina IS, Kubicek CP, Wang Y, Zhu Z, Zhang Y, Wang K, Liu Z, Zhang X, Martin F, Yuan Z. A facultative ectomycorrhizal association is triggered by organic nitrogen. Curr Biol 2022; 32:5235-5249.e7. [PMID: 36402137 DOI: 10.1016/j.cub.2022.10.054] [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: 05/20/2022] [Revised: 09/19/2022] [Accepted: 10/25/2022] [Indexed: 11/19/2022]
Abstract
Increasing nitrogen (N) deposition often tends to negatively impact the functions of belowground ectomycorrhizal networks, although the exact molecular mechanisms underlying this trait are still unclear. Here, we assess how the root-associated fungus Clitopilus hobsonii establishes an ectomycorrhiza-like association with its host tree Populus tomentosa and how this interaction is favored by organic N over mineral N. The establishment of a functional symbiosis in the presence of organic N promotes plant growth and the transfer of 15N from the fungus to above ground plant tissues. Genomic traits and in planta transcriptional signatures suggest that C. hobsonii may have a dual lifestyle with saprotrophic and mutualistic traits. For example, several genes involved in the digestion of cellulose and hemicellulose are highly expressed during the interaction, whereas the expression of multiple copies of pectin-digesting genes is tightly controlled. Conversely, the nutritional mutualism is dampened in the presence of ammonium (NH4+) or nitrate (NO3-). Increasing levels of NH4+ led to a higher expression of pectin-digesting genes and a continuous increase in hydrogen peroxide production in roots, whereas the presence of NO3- resulted in toxin production. In summary, our results suggest that C. hobsonii is a facultative ectomycorrhizal fungus. Access to various forms of N acts as an on/off switch for mutualism caused by large-scale fungal physiological remodeling. Furthermore, the abundance of pectin-degrading enzymes with distinct expression patterns during functional divergence after exposure to NH4+ or organic N is likely to be central to the transition from parasitism to mutualism.
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Affiliation(s)
- Long Peng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Dongxiaofu 1, Beijing 10091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Daqiao Road 73, Hangzhou 311400, China
| | - Yan Zhang
- Liaoning Provincial Institute of Poplar, Gaizhou 115213, China
| | | | - Christian P Kubicek
- Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna A1060, Austria
| | - Yuchen Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Dongxiaofu 1, Beijing 10091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Daqiao Road 73, Hangzhou 311400, China
| | - Zhiyong Zhu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Daqiao Road 73, Hangzhou 311400, China
| | - Yuwei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Dongxiaofu 1, Beijing 10091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Daqiao Road 73, Hangzhou 311400, China
| | - Kexuan Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Dongxiaofu 1, Beijing 10091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Daqiao Road 73, Hangzhou 311400, China
| | - Zhuo Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Dongxiaofu 1, Beijing 10091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Daqiao Road 73, Hangzhou 311400, China
| | - Xiaoguo Zhang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Daqiao Road 73, Hangzhou 311400, China
| | - Francis Martin
- Université de Lorraine, INRAE, UMR 1136 "Interactions Arbres/Microorganismes," Centre INRAE Grand Est - Nancy, Champenoux 54280, France.
| | - Zhilin Yuan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Dongxiaofu 1, Beijing 10091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Daqiao Road 73, Hangzhou 311400, China.
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10
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Miller AN, Karakehian J, Raudabaugh DB. Next-Generation Sequencing of Ancient and Recent Fungarium Specimens. J Fungi (Basel) 2022; 8:932. [PMID: 36135657 PMCID: PMC9503353 DOI: 10.3390/jof8090932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 01/04/2023] Open
Abstract
Fungaria are an unmatched resource for providing genetic data from authoritative, taxonomically-correct fungal species, especially type specimens. These specimens serve to anchor species hypotheses by enabling the correct taxonomic placement of taxa in systematic studies. The DNA from ancient specimens older than 30 years is commonly fragmented, and sometimes highly contaminated by exogenous, non-target fungal DNA, making conventional PCR amplification and Sanger sequencing difficult or impossible. Here, we present the results of DNA extraction, PCR amplification of the ITS2 region, and Illumina MiSeq Nano sequencing of nine recent and 11 ancient specimens, including seven type specimens. The taxa sampled included a range of large and fleshy, to small and tough, or small, melanized specimens of Discina, Gyromitra, Propolis, Stictis, and Xerotrema, with a culture of Lasiosphaeria serving as a positive control. DNA was highly fragmented and in very low quantity for most samples, resulting in inconclusive or incorrect results for all but five samples. Taxonomically-correct sequences were generated from the holotype specimens of G. arctica, G. korshinskii, and G. leucoxantha, from the neotype of G. ussuriensis, and from the positive control. Taxonomic assignments were confirmed through morphology, top BLASTn hits, and maximum likelihood phylogenetic analyses. Though this study was not cost-effective due to the small number of samples submitted and few generating correct sequences, it did produce short DNA barcode fragments for four type specimens that are essential for their correct taxonomic placement in our ongoing systematic studies.
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Affiliation(s)
- Andrew N. Miller
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, 1816 South Oak Street, Champaign, IL 61820, USA
| | - Jason Karakehian
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, 1816 South Oak Street, Champaign, IL 61820, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 505 South Avenue, Urbana, IL 61801, USA
| | - Daniel B. Raudabaugh
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, 1816 South Oak Street, Champaign, IL 61820, USA
- Department of Botany and Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN 47907, USA
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11
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New data in Porotheleaceae and Cyphellaceae: epitypification of Prunulus scabripes Murrill, the status of Mycopan Redhead, Moncalvo & Vilgalys and a new combination in Pleurella Horak emend. Mycol Prog 2022. [DOI: 10.1007/s11557-022-01795-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
AbstractMycopan is a genus established for Hydropus scabripes by Redhead, Moncalvo & Vilgalys (in Redhead 2013). They considered the genus to be distinct based on morphology and the phylogenetic analysis by Moncalvo et al. (2002) which included a sequence of Hydropus scabripes (AF042635, DAOM 192847) unrelated to the type species of Hydropus (H. fuliginarius). Subsequent sequences of material identified as Hydropus scabripes are not conspecific with the sequence of DAOM 192847. We consider this sequence (obtained from a mycelium culture) to be misidentified. We investigated the true phylogenetic position of authentic Mycopan including genera previously included in Cyphellaceae and Porotheleaceae. Sixteen collections of M. scabripes from Europe and North America were studied on morphological and molecular basis (nrITS and nrLSU sequences). No sequences were obtained from the holotype of Mycopan scabripes, and we designate an epitype to fix the interpretation of this species and the genus Mycopan. Mycopan is maintained as a good genus nested within Cyphellaceae as sister to the mycenoid genus Atheniella. The misidentified Hydropus scabripes AF042635 (DAOM 192847) represents a different species that is closely related to the holotype (and a new Italian collection) of Hebelomina microspora and the monospecific genus Pleurella described from New Zealand. Consequently, Hebelomina microspora is transferred to the emended genus Pleurella, which is sister to Baeospora within the Cyphellaceae. Additionally, based on these phylogenetic results, an updated taxonomic arrangement of Cyphellaceae and Porotheleaceae is proposed, emphasizing once again the polyphyletic nature of Hydropus and Gerronema.
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12
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Cazabonne J, Bartrop L, Dierickx G, Gafforov Y, Hofmann TA, Martin TE, Piepenbring M, Rivas-Ferreiro M, Haelewaters D. Molecular-Based Diversity Studies and Field Surveys Are Not Mutually Exclusive: On the Importance of Integrated Methodologies in Mycological Research. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:860777. [PMID: 37746218 PMCID: PMC10512293 DOI: 10.3389/ffunb.2022.860777] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 02/21/2022] [Indexed: 09/26/2023]
Abstract
Understanding and describing the diversity of living organisms is a great challenge. Fungi have for a long time been, and unfortunately still are, underestimated when it comes to taxonomic research. The foundations were laid by the first mycologists through field observations. These important fundamental works have been and remain vital reference works. Nevertheless, a non-negligible part of the studied funga escaped their attention. Thanks to modern developments in molecular techniques, the study of fungal diversity has been revolutionized in terms of tools and knowledge. Despite a number of disadvantages inherent to these techniques, traditional field-based inventory work has been increasingly superseded and neglected. This perspective aims to demonstrate the central importance of field-based research in fungal diversity studies, and encourages researchers not to be blinded by the sole use of molecular methods.
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Affiliation(s)
- Jonathan Cazabonne
- Groupe de Recherche en Écologie de la MRC Abitibi (GREMA), Institut de Recherche sur les Forêts (IRF), Université du Québec en Abitibi-Témiscamingue, Amos, QC, Canada
| | | | - Glen Dierickx
- Research Group Mycology, Department of Biology, Ghent University, Ghent, Belgium
- Research Institute for Nature and Forest (INBO), Brussels, Belgium
| | - Yusufjon Gafforov
- Laboratory of Mycology, Institute of Botany, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Goethe-Universität Frankfurt am Main, Frankfurt am Main, Germany
| | - Tina A. Hofmann
- Centro de Investigaciones Micológicas (CIMi), Herbario UCH, Universidad Autónoma de Chiriquí, David, Panama
| | - Thomas E. Martin
- Operation Wallacea Ltd, Wallace House, Old Bolingbroke, United Kingdom
| | - Meike Piepenbring
- Mycology Working Group, Goethe-Universität Frankfurt am Main, Frankfurt am Main, Germany
| | - Mauro Rivas-Ferreiro
- Population Genetics and Cytogenetics Group, Facultade de Bioloxía, Universidade de Vigo, Vigo, Spain
| | - Danny Haelewaters
- Research Group Mycology, Department of Biology, Ghent University, Ghent, Belgium
- Centro de Investigaciones Micológicas (CIMi), Herbario UCH, Universidad Autónoma de Chiriquí, David, Panama
- Operation Wallacea Ltd, Wallace House, Old Bolingbroke, United Kingdom
- Faculty of Science, University of South Bohemia, Ceské Budějovice, Czechia
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13
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Infundibulicybe trachyspora, a New Species from Northeastern China Based on Morphology and Molecular Phylogeny. Curr Microbiol 2022; 79:130. [PMID: 35286493 DOI: 10.1007/s00284-022-02808-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 02/11/2022] [Indexed: 11/03/2022]
Abstract
Infundibulicybe trachyspora is described as a new species from northeastern China. The species is characterized by clitocyboid to omphalioid habit, carneous, greyish-yellow to brownish pileus, brown to dark reddish-brown, longitudinally fibrillose-striate stipe, non-amyloid, non-smooth spores, the absence of cystidia and the presence of clamp connections. A comprehensive description of the species is provided together with photo-illustrations and comparisons with phenotypically similar and phylogenetically related species. The nuclear ribosomal internal transcribed spacer (ITS) region and the nuclear, large subunit rDNA (nrLSU) region of the new species was sequenced and analyzed. The phylogenetic analysis supported the novelty of the species and its placement within the genus. Furthermore, a discussion on the proposal to establish a new section is made, and a key is provided for the Infundibulicybe species reported from China.
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14
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Van Dam AR, Covas Orizondo JO, Lam AW, McKenna DD, Van Dam MH. Metagenomic clustering reveals microbial contamination as an essential consideration in ultraconserved element design for phylogenomics with insect museum specimens. Ecol Evol 2022; 12:e8625. [PMID: 35342556 PMCID: PMC8932080 DOI: 10.1002/ece3.8625] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 01/03/2022] [Accepted: 01/17/2022] [Indexed: 11/30/2022] Open
Abstract
Phylogenomics via ultraconserved elements (UCEs) has led to improved phylogenetic reconstructions across the tree of life. However, inadvertently incorporating non-targeted DNA into the UCE marker design will lead to misinformation being incorporated into subsequent analyses. To date, the effectiveness of basic metagenomic filtering strategies has not been assessed in arthropods. Designing markers from museum specimens requires careful consideration of methods due to the high levels of microbial contamination typically found in such specimens. We investigate if contaminant sequences are carried forward into a UCE marker set we developed from insect museum specimens using a standard bioinformatics pipeline. We find that the methods currently employed by most researchers do not exclude contamination from the final set of targets. Lastly, we highlight several paths forward for reducing contamination in UCE marker design.
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Affiliation(s)
- Alex R. Van Dam
- Department of BiologyUniversity of Puerto Rico MayagüezMayagüezPuerto Rico
| | | | - Athena W. Lam
- Department of EntomologyCalifornia Academy of SciencesSan FranciscoCaliforniaUSA
| | - Duane D. McKenna
- Department of Biological SciencesUniversity of MemphisMemphisTennesseeUSA
- Center for Biodiversity ResearchUniversity of MemphisMemphisTennesseeUSA
| | - Matthew H. Van Dam
- Department of EntomologyCalifornia Academy of SciencesSan FranciscoCaliforniaUSA
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15
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Liimatainen K, Kim JT, Pokorny L, Kirk PM, Dentinger B, Niskanen T. Taming the beast: a revised classification of Cortinariaceae based on genomic data. FUNGAL DIVERS 2022. [DOI: 10.1007/s13225-022-00499-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
AbstractFamily Cortinariaceae currently includes only one genus, Cortinarius, which is the largest Agaricales genus, with thousands of species worldwide. The species are important ectomycorrhizal fungi and form associations with many vascular plant genera from tropicals to arctic regions. Genus Cortinarius contains a lot of morphological variation, and its complexity has led many taxonomists to specialize in particular on infrageneric groups. The previous attempts to divide Cortinarius have been shown to be unnatural and the phylogenetic studies done to date have not been able to resolve the higher-level classification of the group above section level. Genomic approaches have revolutionized our view on fungal relationships and provide a way to tackle difficult groups. We used both targeted capture sequencing and shallow whole genome sequencing to produce data and to perform phylogenomic analyses of 75 single-copy genes from 19 species. In addition, a wider 5-locus analysis of 245 species, from the Northern and Southern Hemispheres, was also done. Based on our results, a classification of the family Cortinariaceae into ten genera—Cortinarius, Phlegmacium, Thaxterogaster, Calonarius, Aureonarius, Cystinarius, Volvanarius, Hygronarius, Mystinarius, and Austrocortinarius—is proposed. Seven genera, 10 subgenera, and four sections are described as new to science and five subgenera are introduced as new combinations in a new rank. In addition, 41 section names and 514 species names are combined in new genera and four lecto- and epitypes designated. The position of Stephanopus in suborder Agaricineae remains to be studied. Targeted capture sequencing is used for the first time in fungal taxonomy in Basidiomycetes. It provides a cost-efficient way to produce -omics data in species-rich groups. The -omics data was produced from fungarium specimens up to 21 years old, demonstrating the value of museum specimens in the study of the fungal tree of life. This study is the first family revision in Agaricales based on genomics data and hopefully many others will soon follow.
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16
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Genome Sequencing of Hericium coralloides by a Combination of PacBio RS II and Next-Generation Sequencing Platforms. Int J Genomics 2022; 2022:4017654. [PMID: 35141329 PMCID: PMC8820905 DOI: 10.1155/2022/4017654] [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: 08/27/2021] [Revised: 12/07/2021] [Accepted: 01/09/2022] [Indexed: 11/17/2022] Open
Abstract
The fruiting bodies or mycelia of Hericium coralloides (H. coralloides) contain many physiologically active compounds that are used to treat various diseases, including cardiovascular disorders and cancers. However, the genome of H. coralloides has not been sequenced, which hinders further investigations into aspects, such as bioactivity or evolutionary events. The present study is aimed at (i) performing de novo sequencing of the assembled genome; (ii) mapping the reads from PE400 DNA into the assembled genome; (iii) identifying the full length of all the repeated sequences; and (iv) annotating protein-coding genes using GO, eggNOG, and KEGG databases. The assembled genome comprised 5,59,05,675 bp, including 307 contigs. The mapping rate of reads obtained from PE400 DNA in the assembled genome was 92.46%. We identified 2,525 repeated sequences of 14,23,274 bp length. We predicted ncRNAs of 48,895 bp and 11,736 genes encoding proteins that were annotated in the GO, eggNOG, and KEGG databases. We are the first to sequence the entire H. coralloides genome (NCBI; Assembly: ASM367540v1), which will serve as a reference for studying the evolutionary diversification of edible and medicinal mushrooms and facilitate the application of bioactivity in H. coralloides.
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17
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Xu J, Yu X, Suwannarach N, Jiang Y, Zhao W, Li Y. Additions to Lyophyllaceae s.l. from China. J Fungi (Basel) 2021; 7:jof7121101. [PMID: 34947083 PMCID: PMC8704695 DOI: 10.3390/jof7121101] [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: 11/03/2021] [Revised: 12/01/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
Four new species, viz. Calocybe coacta, C. fulvipes, C. vinacea and Clitolyophyllum umbilicatum, are described in northern China. Comparisons are made of macro- and micromorphological features among the new species and closely related species within the genus. The new species feature unique morphological characteristics that separate them from the previously described species. Calocybe coacta is characterized by medium- to large-sized basidiocarps, greyish cream, felty pileus and non-cellular epicutis. The key characteristics of C. fulvipes are rose-brown to greyish-brown pileus, stone-brown stipe and non-cellular epicutis. The unique morphological characteristics of C. vinacea that distinguish it from its closely related species are pastel red to dull-red pileus and stipe surface with densely white pruina. The main characteristics of Clitolyophyllum umbilicatum are deeply depressed dark orange to light-brown pileus, central stipe and subglobose-ellipsoid spores. Phylogenetic analyses based on the ITS and 28S regions indicated that the four new species are distinct and monophyletic. Full descriptions, color images, illustrations and a phylogenetic tree that show the placement of the four new species are provided. A key to the Calocybe species reported from China is also given.
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Affiliation(s)
- Jize Xu
- Department of Applied Biological Science, Faculty of Agriculture, Jilin Agriculture Science and Technology University, Jilin 132101, China; (Y.J.); (W.Z.)
- Correspondence:
| | - Xiaodong Yu
- Department of Protection and Utilization of Wild Animals and Plants, Faculty of Chinese Herbal Medicine, Jilin Agricultural University, Changchun 130118, China;
| | - Nakarin Suwannarach
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Yi Jiang
- Department of Applied Biological Science, Faculty of Agriculture, Jilin Agriculture Science and Technology University, Jilin 132101, China; (Y.J.); (W.Z.)
| | - Wei Zhao
- Department of Applied Biological Science, Faculty of Agriculture, Jilin Agriculture Science and Technology University, Jilin 132101, China; (Y.J.); (W.Z.)
| | - Yu Li
- Faculty of Plant Protection, Jilin Agricultural University, Changchun 130118, China;
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18
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Oliveira JJ, Vargas-Isla R, Cabral TS, Cardoso JS, Andriolli FS, Rodrigues DP, Ikeda T, Clement CR, Ishikawa NK. The Amazonian luminescent Mycena cristinae sp. nov. from Brazil. MYCOSCIENCE 2021; 62:395-405. [PMID: 37090179 PMCID: PMC9721513 DOI: 10.47371/mycosci.2021.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 11/16/2022]
Abstract
A new luminescent lignicolous fungal species, Mycena cristinae sp. nov., is proposed from the Central Amazon forest. This is unique and supported by morphological evaluation along with LSU- and ITS-based phylogenetic analyses. The basidiomata have mostly fuscous olivaceous brown pileus, adnate to subdecurrent and distant lamellae, and stipe with slightly bulbous base (basal mycelium absent). It also has inamyloid and/or weakly amyloid basidiospores, ramose cheilocystidia and a pileipellis composed of an aerated tangle of slender, diverticulate hyphae forming a coralloid pellicle overlaying the hypodermium. The luminescence is evident in the basidiomata (especially the stipe) and in the mycelium on the substrate. The LSU phylogenetic trees reveal that M. cristinae is sister to M. coralliformis within the Mycenaceae clade. In the ITS trees, it forms a unique lineage grouping with undetermined Mycena taxa. Morphological data support M. cristinae as a different species compared to previously described taxa.
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Affiliation(s)
- Jadson J.S. Oliveira
- Divisão de Pós-graduação em Botânica, Instituto Nacional de Pesquisas da Amazônia
| | - Ruby Vargas-Isla
- Coordenação de Tecnologia e Inovação, Instituto Nacional de Pesquisas da Amazônia
| | - Tiara S. Cabral
- Divisão de Pós-graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia
| | - Julia S. Cardoso
- Divisão de Pós-graduação em Botânica, Instituto Nacional de Pesquisas da Amazônia
| | | | - Doriane P. Rodrigues
- Laboratório de Evolução Aplicada, Divisão de Biotecnologia, Instituto de Ciências Biológicas, Universidade Federal do Amazonas
| | | | - Charles R. Clement
- Coordenação de Tecnologia e Inovação, Instituto Nacional de Pesquisas da Amazônia
| | - Noemia K. Ishikawa
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia
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Transcriptomics Reveals the Putative Mycoparasitic Strategy of the Mushroom Entoloma abortivum on Species of the Mushroom Genus Armillaria. mSystems 2021; 6:e0054421. [PMID: 34636668 PMCID: PMC8510539 DOI: 10.1128/msystems.00544-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
During mycoparasitism, a fungus—the host—is parasitized by another fungus—the mycoparasite. The genetic underpinnings of these relationships have been best characterized in ascomycete fungi. However, within basidiomycete fungi, there are rare instances of mushroom-forming species parasitizing the reproductive structures, or sporocarps, of other mushroom-forming species, which have been rarely investigated on a genetic level. One of the most enigmatic of these occurs between Entoloma abortivum and species of Armillaria, where hyphae of E. abortivum are hypothesized to disrupt the development of Armillaria sporocarps, resulting in the formation of carpophoroids. However, it remains unknown whether carpophoroids are the direct result of a mycoparasitic relationship. To address the nature of this unique interaction, we analyzed gene expression of field-collected Armillaria and E. abortivum sporocarps and carpophoroids. Transcripts in the carpophoroids are primarily from E. abortivum, supporting the hypothesis that this species is parasitizing Armillaria. Most notably, we identified differentially upregulated E. abortivum β-trefoil-type lectins in the carpophoroid, which we hypothesize bind to Armillaria cell wall galactomannoproteins, thereby mediating recognition between the mycoparasite and the host. The most differentially upregulated E. abortivum transcripts in the carpophoroid code for oxalate decarboxylases—enzymes that degrade oxalic acid. Oxalic acid is a virulence factor in many plant pathogens, including Armillaria species; however, E. abortivum has evolved a sophisticated strategy to overcome this defense mechanism. The number of gene models and genes that code for carbohydrate-active enzymes in the E. abortivum transcriptome was reduced compared to other closely related species, perhaps as a result of the specialized nature of this interaction. IMPORTANCE By studying fungi that parasitize other fungi, we can understand the basic biology of these unique interactions. Studies focused on the genetic mechanisms regulating mycoparasitism between host and parasite have thus far concentrated on a single fungal lineage within the Ascomycota. The work presented here expands our understanding of mycoparasitic relationships to the Basidiomycota and represents the first transcriptomic study to our knowledge that examines fungal-fungal relationships in their natural setting. The results presented here suggest that even distantly related mycoparasites utilize similar mechanisms to parasitize their host. Given that species of the mushroom-forming pathogen Armillaria cause plant root-rot diseases in many agroecosystems, an enhanced understanding of this interaction may contribute to better control of these diseases through biocontrol applications.
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Lofgren LA, Stajich JE. Fungal biodiversity and conservation mycology in light of new technology, big data, and changing attitudes. Curr Biol 2021; 31:R1312-R1325. [PMID: 34637742 PMCID: PMC8516061 DOI: 10.1016/j.cub.2021.06.083] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Fungi have successfully established themselves across seemingly every possible niche, substrate, and biome. They are fundamental to biogeochemical cycling, interspecies interactions, food production, and drug bioprocessing, as well as playing less heroic roles as difficult to treat human infections and devastating plant pathogens. Despite community efforts to estimate and catalog fungal diversity, we have only named and described a minute fraction of the fungal world. The identification, characterization, and conservation of fungal diversity is paramount to preserving fungal bioresources, and to understanding and predicting ecosystem cycling and the evolution and epidemiology of fungal disease. Although species and ecosystem conservation are necessarily the foundation of preserving this diversity, there is value in expanding our definition of conservation to include the protection of biological collections, ecological metadata, genetic and genomic data, and the methods and code used for our analyses. These definitions of conservation are interdependent. For example, we need metadata on host specificity and biogeography to understand rarity and set priorities for conservation. To aid in these efforts, we need to draw expertise from diverse fields to tie traditional taxonomic knowledge to data obtained from modern -omics-based approaches, and support the advancement of diverse research perspectives. We also need new tools, including an updated framework for describing and tracking species known only from DNA, and the continued integration of functional predictions to link genetic diversity to functional and ecological diversity. Here, we review the state of fungal diversity research as shaped by recent technological advancements, and how changing viewpoints in taxonomy, -omics, and systematics can be integrated to advance mycological research and preserve fungal biodiversity.
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Affiliation(s)
- Lotus A Lofgren
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA 92521, USA.
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA 92521, USA
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21
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Kooij PW, Pellicer J. Genome Size Versus Genome Assemblies: Are the Genomes Truly Expanded in Polyploid Fungal Symbionts? Genome Biol Evol 2021; 12:2384-2390. [PMID: 33283863 PMCID: PMC7719231 DOI: 10.1093/gbe/evaa217] [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] [Accepted: 10/10/2020] [Indexed: 12/21/2022] Open
Abstract
Each day, as the amount of genomic data and bioinformatics resources grows, researchers are increasingly challenged with selecting the most appropriate approach to analyze their data. In addition, the opportunity to undertake comparative genomic analyses is growing rapidly. This is especially true for fungi due to their small genome sizes (i.e., mean 1C = 44.2 Mb). Given these opportunities and aiming to gain novel insights into the evolution of mutualisms, we focus on comparing the quality of whole genome assemblies for fungus-growing ants cultivars (Hymenoptera: Formicidae: Attini) and a free-living relative. Our analyses reveal that currently available methodologies and pipelines for analyzing whole-genome sequence data need refining. By using different genome assemblers, we show that the genome assembly size depends on what software is used. This, in turn, impacts gene number predictions, with higher gene numbers correlating positively with genome assembly size. Furthermore, the majority of fungal genome size data currently available are based on estimates derived from whole-genome assemblies generated from short-read genome data, rather than from the more accurate technique of flow cytometry. Here, we estimated the haploid genome sizes of three ant fungal symbionts by flow cytometry using the fungus Pleurotus ostreatus (Jacq.) P. Kumm. (1871) as a calibration standard. We found that published genome sizes based on genome assemblies are 2.5- to 3-fold larger than our estimates based on flow cytometry. We, therefore, recommend that flow cytometry is used to precalibrate genome assembly pipelines, to avoid incorrect estimates of genome sizes and ensure robust assemblies.
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Affiliation(s)
- Pepijn W Kooij
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom.,Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, Sao Paulo, Brazil
| | - Jaume Pellicer
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom.,Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain
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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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23
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Boekhout T, Aime MC, Begerow D, Gabaldón T, Heitman J, Kemler M, Khayhan K, Lachance MA, Louis EJ, Sun S, Vu D, Yurkov A. The evolving species concepts used for yeasts: from phenotypes and genomes to speciation networks. FUNGAL DIVERS 2021; 109:27-55. [PMID: 34720775 PMCID: PMC8550739 DOI: 10.1007/s13225-021-00475-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/31/2021] [Indexed: 12/12/2022]
Abstract
Here we review how evolving species concepts have been applied to understand yeast diversity. Initially, a phenotypic species concept was utilized taking into consideration morphological aspects of colonies and cells, and growth profiles. Later the biological species concept was added, which applied data from mating experiments. Biophysical measurements of DNA similarity between isolates were an early measure that became more broadly applied with the advent of sequencing technology, leading to a sequence-based species concept using comparisons of parts of the ribosomal DNA. At present phylogenetic species concepts that employ sequence data of rDNA and other genes are universally applied in fungal taxonomy, including yeasts, because various studies revealed a relatively good correlation between the biological species concept and sequence divergence. The application of genome information is becoming increasingly common, and we strongly recommend the use of complete, rather than draft genomes to improve our understanding of species and their genome and genetic dynamics. Complete genomes allow in-depth comparisons on the evolvability of genomes and, consequently, of the species to which they belong. Hybridization seems a relatively common phenomenon and has been observed in all major fungal lineages that contain yeasts. Note that hybrids may greatly differ in their post-hybridization development. Future in-depth studies, initially using some model species or complexes may shift the traditional species concept as isolated clusters of genetically compatible isolates to a cohesive speciation network in which such clusters are interconnected by genetic processes, such as hybridization.
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Affiliation(s)
- Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - M. Catherine Aime
- Dept Botany and Plant Pathology, College of Agriculture, Purdue University, West Lafayette, IN 47907 USA
| | - Dominik Begerow
- Evolution of Plants and Fungi, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC–CNS), Jordi Girona, 29, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710 USA
| | - Martin Kemler
- Evolution of Plants and Fungi, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Kantarawee Khayhan
- Department of Microbiology and Parasitology, Faculty of Medical Sciences, University of Phayao, Phayao, 56000 Thailand
| | - Marc-André Lachance
- Department of Biology, University of Western Ontario, London, ON N6A 5B7 Canada
| | - Edward J. Louis
- Department of Genetics and Genome Biology, Genetic Architecture of Complex Traits, University of Leicester, Leicester, LE1 7RH UK
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710 USA
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Andrey Yurkov
- German Collection of Microorganisms and Cell Cultures, Leibniz Institute DSMZ, Brunswick, Germany
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Hill R, Llewellyn T, Downes E, Oddy J, MacIntosh C, Kallow S, Panis B, Dickie JB, Gaya E. Seed Banks as Incidental Fungi Banks: Fungal Endophyte Diversity in Stored Seeds of Banana Wild Relatives. Front Microbiol 2021; 12:643731. [PMID: 33841366 PMCID: PMC8024981 DOI: 10.3389/fmicb.2021.643731] [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: 12/18/2020] [Accepted: 02/19/2021] [Indexed: 01/19/2023] Open
Abstract
Seed banks were first established to conserve crop genetic diversity, but seed banking has more recently been extended to wild plants, particularly crop wild relatives (CWRs) (e.g., by the Millennium Seed Bank (MSB), Royal Botanic Gardens Kew). CWRs have been recognised as potential reservoirs of beneficial traits for our domesticated crops, and with mounting evidence of the importance of the microbiome to organismal health, it follows that the microbial communities of wild relatives could also be a valuable resource for crop resilience to environmental and pathogenic threats. Endophytic fungi reside asymptomatically inside all plant tissues and have been found to confer advantages to their plant host. Preserving the natural microbial diversity of plants could therefore represent an important secondary conservation role of seed banks. At the same time, species that are reported as endophytes may also be latent pathogens. We explored the potential of the MSB as an incidental fungal endophyte bank by assessing diversity of fungi inside stored seeds. Using banana CWRs in the genus Musa as a case-study, we sequenced an extended ITS-LSU fragment in order to delimit operational taxonomic units (OTUs) and used a similarity and phylogenetics approach for classification. Fungi were successfully detected inside just under one third of the seeds, with a few genera accounting for most of the OTUs-primarily Lasiodiplodia, Fusarium, and Aspergillus-while a large variety of rare OTUs from across the Ascomycota were isolated only once. Fusarium species were notably abundant-of significance in light of Fusarium wilt, a disease threatening global banana crops-and so were targeted for additional sequencing with the marker EF1α in order to delimit species and place them in a phylogeny of the genus. Endophyte community composition, diversity and abundance was significantly different across habitats, and we explored the relationship between community differences and seed germination/viability. Our results show that there is a previously neglected invisible fungal dimension to seed banking that could well have implications for the seed collection and storage procedures, and that collections such as the MSB are indeed a novel source of potentially useful fungal strains.
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Affiliation(s)
- Rowena Hill
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
- School of Biological and Chemical Sciences, Faculty of Science and Engineering, Queen Mary University of London, London, United Kingdom
| | - Theo Llewellyn
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Elizabeth Downes
- Department for Environment, Food and Rural Affairs, London, United Kingdom
| | - Joseph Oddy
- Department of Plant Science, Rothamsted Research, Harpenden, United Kingdom
| | - Catriona MacIntosh
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
- School of Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Simon Kallow
- Collections Department, Royal Botanic Gardens, Kew, Millennium Seed Bank, Ardingly, United Kingdom
- Division of Crop Biotechnics, Department of Biosystems, Faculty of Bioscience Engineering, University of Leuven, Leuven, Belgium
| | - Bart Panis
- Bioversity International, Montpellier, France
| | - John B. Dickie
- Collections Department, Royal Botanic Gardens, Kew, Millennium Seed Bank, Ardingly, United Kingdom
| | - Ester Gaya
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
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Gómez-Zapata PA, Haelewaters D, Quijada L, Pfister DH, Aime MC. Notes on Trochila (Ascomycota, Leotiomycetes), with new species and combinations. MycoKeys 2021; 78:21-47. [PMID: 36761369 PMCID: PMC9849072 DOI: 10.3897/mycokeys.78.62046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/07/2021] [Indexed: 12/25/2022] Open
Abstract
Studies of Trochila (Leotiomycetes, Helotiales, Cenangiaceae) are scarce. Here, we describe two new species based on molecular phylogenetic data and morphology. Trochilabostonensis was collected at the Boston Harbor Islands National Recreation Area, Massachusetts. It was found on the stem of Asclepiassyriaca, representing the first report of any Trochila species from a plant host in the family Apocynaceae. Trochilaurediniophila is associated with the uredinia of the rust fungus Ceroteliumfici. It was discovered during a survey for rust hyperparasites conducted at the Arthur Fungarium, in a single sample from 1912 collected in Trinidad. Macro- and micromorphological descriptions, illustrations, and molecular phylogenetic analyses are presented. The two new species are placed in Trochila with high support in both our six-locus (SSU, ITS, LSU, rpb1, rpb2, tef1) and two-locus (ITS, LSU) phylogenetic reconstructions. In addition, two species are combined in Trochila: Trochilacolensoi (formerly placed in Pseudopeziza) and T.xishuangbanna (originally described as the only species in Calycellinopsis). This study reveals new host plant families, a new ecological strategy, and a new country record for the genus Trochila. Finally, our work emphasizes the importance of specimens deposited in biological collections such as fungaria.
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Affiliation(s)
- Paula Andrea Gómez-Zapata
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USAPurdue UniversityWest LafayetteUnited States of America
| | - Danny Haelewaters
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USAPurdue UniversityWest LafayetteUnited States of America
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USAHarvard UniversityCambridgeUnited States of America
- Farlow Herbarium and Reference Library of Cryptogamic Botany, Harvard University Herbaria, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, USAHarvard University HerbariaCambridgeUnited States of America
- Faculty of Science, University of South Bohemia, České Budějovice, Czech RepublicUniversity of South BohemiaČeské BudějoviceCzech Republic
| | - Luis Quijada
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USAHarvard UniversityCambridgeUnited States of America
- Farlow Herbarium and Reference Library of Cryptogamic Botany, Harvard University Herbaria, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, USAHarvard University HerbariaCambridgeUnited States of America
| | - Donald H. Pfister
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USAHarvard UniversityCambridgeUnited States of America
- Farlow Herbarium and Reference Library of Cryptogamic Botany, Harvard University Herbaria, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, USAHarvard University HerbariaCambridgeUnited States of America
| | - M. Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USAPurdue UniversityWest LafayetteUnited States of America
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Vizzini A, Consiglio G, Setti L. Testing spore amyloidity in Agaricales under light microscope: the case study of Tricholoma. IMA Fungus 2020; 11:24. [PMID: 33292837 PMCID: PMC7656700 DOI: 10.1186/s43008-020-00046-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 10/15/2020] [Indexed: 11/10/2022] Open
Abstract
Although species of the genus Tricholoma are currently considered to produce inamyloid spores, a novel standardized method to test sporal amyloidity (which involves heating the sample in Melzer's reagent) showed evidence that in the tested species of this genus, which belong in all 10 sections currently recognized from Europe, the spores are amyloid. In two species, T. josserandii and T. terreum, the spores are also partly dextrinoid. This result provides strong indication that a positive reaction of the spores in Melzer's reagent could be a character shared by all genera in Tricholomataceae s. str.
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Affiliation(s)
- Alfredo Vizzini
- Department of Life Sciences and Systems Biology, University of Torino and Institute for Sustainable Plant Protection (IPSP-SS Turin), C.N.R, Viale P.A. Mattioli, 25, I-10125, Torino, Italy.
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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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Olariaga I, Huhtinen S, Læssøe T, Petersen JH, Hansen K. Phylogenetic origins and family classification of typhuloid fungi, with emphasis on Ceratellopsis, Macrotyphula and Typhula ( Basidiomycota). Stud Mycol 2020; 96:155-184. [PMID: 32774511 PMCID: PMC7388190 DOI: 10.1016/j.simyco.2020.05.003] [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] [Indexed: 11/07/2022] Open
Abstract
Typhuloid fungi are a very poorly known group of tiny clavarioid homobasidiomycetes. The phylogenetic position and family classification of the genera targeted here, Ceratellopsis, Macrotyphula, Pterula sensu lato and Typhula, are controversial and based on unresolved phylogenies. Our six-gene phylogeny with an expanded taxon sampling shows that typhuloid fungi evolved at least twice in the Agaricales (Pleurotineae, Clavariineae) and once in the Hymenochaetales. Macrotyphula, Pterulicium and Typhula are nested within the Pleurotineae. The type of Typhula (1818) and Sclerotium (1790), T. phacorrhiza and S. complanatum (synonym T. phacorrhiza), are encompassed in the Macrotyphula clade that is distantly related to a monophyletic group formed by species usually assigned to Typhula. Thus, the correct name for Macrotyphula (1972) and Typhula is Sclerotium and all Typhula species but those in the T. phacorrhiza group need to be transferred to Pistillaria (1821). To avoid undesirable nomenclatural changes, we suggest to conserve Typhula with T. incarnata as type. Clavariaceae is supported as a separate, early diverging lineage within Agaricales, with Hygrophoraceae as a successive sister taxon to the rest of the Agaricales. Ceratellopsis s. auct. is polyphyletic because C. acuminata nests in Clavariaceae and C. sagittiformis in the Hymenochaetales. Ceratellopsis is found to be an earlier name for Pterulicium, because the type, C. queletii, represents Pterulicium gracile (synonym Pterula gracilis), deeply nested in the Pterulicium clade. To avoid re-combining a large number of names in Ceratellopsis we suggest to conserve it with C. acuminata as type. The new genus Bryopistillaria is created to include C. sagittiformis. The families Sarcomyxaceae and Phyllotopsidaceae, and the suborder Clavariineae, are described as new. Six new combinations are proposed and 15 names typified.
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Key Words
- Agaricomycetes
- Bryopistillaria Olariaga, Huhtinen, Læssøe, J.H. Petersen & K. Hansen
- Bryopistillaria sagittiformis (Pat.) Olariaga, Huhtinen, Læssøe, J.H. Petersen & K. Hansen
- Ceratella ferryi Quél. & Fautrey
- Clavaria aculina Quél.
- Clavaria microscopica Malbr. & Sacc.
- Clavariaceae
- Clavariineae Olariaga, Huhtinen, Læssøe, J.H. Petersen & K. Hansen
- Macrotyphula megasperma (Berthier) Olariaga, Huhtinen, Læssøe, J.H. Petersen & K. Hansen
- Macrotyphula phacorrhiza (Reichard: Fr.) Olariaga, Huhtinen, Læssøe, J.H. Petersen & K. Hansen
- Phyllotopsidaceae Locquin ex Olariaga, Huhtinen, Læssøe, J.H. Petersen & K. Hansen
- Pistillaria aciculata Durieu & Lév. ex Sacc.
- Pistillaria aculeata Pat.
- Pistillaria acuminata Fuckel
- Pistillaria attenuata Syd. & P. Syd.
- Pistillaria carestiae Ces. in Bres. & Sacc.
- Pistillaria equiseticola Boud.
- Pistillaria helenae Pat.
- Pistillaria juncicola Bourdot & Galzin
- Pistillaria queletii Pat.
- Pistillaria sagittiformis Pat.
- Pleurotineae
- Sarcomyxaceae Olariaga, Huhtinen, Læssøe, J.H. Petersen & K. Hansen
- Sclerotium
- Sclerotium complanatum Tode
- Typhula brunaudii Quél.
- Typhula podocarpi (Crous) Olariaga, Huhtinen, Læssøe, J.H. Petersen & K. Hansen
- Typhulaceae
- basidioma evolution
- clavarioid fungi
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Affiliation(s)
- I Olariaga
- Department of Botany, Swedish Museum of Natural History, P.O. Box 50007, SE-10405, Stockholm, Sweden.,Biology and Geology, Physics and Inorganic Chemistry department, Rey Juan Carlos University, C/ Tulipán s/n, Móstoles, 28933, Madrid, Spain
| | - S Huhtinen
- Biodiversity Unit, Herbarium, University of Turku, FI-20014, Turku, Finland
| | - T Læssøe
- Department of Biology/Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, 2100, København Ø, Denmark
| | - J H Petersen
- MycoKey, Nøruplundvej 2, 8400, Ebeltoft, Denmark
| | - K Hansen
- Department of Botany, Swedish Museum of Natural History, P.O. Box 50007, SE-10405, Stockholm, Sweden
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Menolli N, Sánchez-García M. Brazilian fungal diversity represented by DNA markers generated over 20 years. Braz J Microbiol 2020; 51:729-749. [PMID: 31828716 PMCID: PMC7203393 DOI: 10.1007/s42770-019-00206-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 12/01/2019] [Indexed: 10/25/2022] Open
Abstract
Molecular techniques using fungal DNA barcoding (ITS) and other markers have been key to identifying the biodiversity of different geographic areas, mainly in megadiverse countries. Here, we provide an overview of the fungal diversity in Brazil based on DNA markers of phylogenetic importance generated since 1996. We retrieved fungal sequences of ITS, LSU, SSU, tef1-α, β-tubulin, rpb1, rpb2, actin, chitin synthase, and ATP6 from GenBank using different field keywords that indicated their origin in Brazil. A total of 19,440 sequences were recovered. ITS is the most representative marker (11,209 sequences), with 70.1% belonging to Ascomycota, 18.6% Basidiomycota, 10.2% unidentified, 1.1% Mucoromycota, two sequences of Olpidium bornovanus (Fungi incertae sedis), one sequence of Blastocladiomycota (Allomyces arbusculus), and one sequence of Chytridiomycota (Batrachochytrium dendrobatidis). Considering the sequences of all selected markers, only the phyla Cryptomycota and Entorrhizomycota were not represented. Based on ITS, using a cutoff of 98%, all sequences comprise 3047 OTUs, with the majority being Ascomycota (2088 OTUs) and Basidiomycota (681 OTUs). Previous numbers based mainly on morphological and bibliographical data revealed 5264 fungal species from Brazil, with a predominance of Basidiomycota (2741 spp.) and Ascomycota (1881 spp.). The unidentified ITS sequences not assigned to a higher taxonomic level represent 1.61% of all ITS sequences sampled and correspond to 38 unknown class-level lineages (75% cutoff). A maximum likelihood phylogeny based on LSU illustrates the fungal classes occurring in Brazil.
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Affiliation(s)
- Nelson Menolli
- Departamento de Ciências da Natureza e Matemática (DCM), Subárea de Biologia (SAB), Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), Câmpus São Paulo, Rua Pedro Vicente 625, São Paulo, SP, 01109-010, Brazil.
- Núcleo de Pesquisa em Micologia, Instituto de Botânica, Av. Miguel Stefano 3687, Água Funda, São Paulo, SP, 04301-012, Brazil.
| | - Marisol Sánchez-García
- Biology Department, Clark University, Worcester, MA, 01610, USA
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, SE-75005, Sweden
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Hyde KD, Dong Y, Phookamsak R, Jeewon R, Bhat DJ, Jones EBG, Liu NG, Abeywickrama PD, Mapook A, Wei D, Perera RH, Manawasinghe IS, Pem D, Bundhun D, Karunarathna A, Ekanayaka AH, Bao DF, Li J, Samarakoon MC, Chaiwan N, Lin CG, Phutthacharoen K, Zhang SN, Senanayake IC, Goonasekara ID, Thambugala KM, Phukhamsakda C, Tennakoon DS, Jiang HB, Yang J, Zeng M, Huanraluek N, Liu JK(J, Wijesinghe SN, Tian Q, Tibpromma S, Brahmanage RS, Boonmee S, Huang SK, Thiyagaraja V, Lu YZ, Jayawardena RS, Dong W, Yang EF, Singh SK, Singh SM, Rana S, Lad SS, Anand G, Devadatha B, Niranjan M, Sarma VV, Liimatainen K, Aguirre-Hudson B, Niskanen T, Overall A, Alvarenga RLM, Gibertoni TB, Pfliegler WP, Horváth E, Imre A, Alves AL, da Silva Santos AC, Tiago PV, Bulgakov TS, Wanasinghe DN, Bahkali AH, Doilom M, Elgorban AM, Maharachchikumbura SSN, Rajeshkumar KC, Haelewaters D, Mortimer PE, Zhao Q, Lumyong S, Xu J, Sheng J. Fungal diversity notes 1151–1276: taxonomic and phylogenetic contributions on genera and species of fungal taxa. FUNGAL DIVERS 2020. [DOI: 10.1007/s13225-020-00439-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Abstract
Fungal diversity notes is one of the important journal series of fungal taxonomy that provide detailed descriptions and illustrations of new fungal taxa, as well as providing new information of fungal taxa worldwide. This article is the 11th contribution to the fungal diversity notes series, in which 126 taxa distributed in two phyla, six classes, 24 orders and 55 families are described and illustrated. Taxa in this study were mainly collected from Italy by Erio Camporesi and also collected from China, India and Thailand, as well as in some other European, North American and South American countries. Taxa described in the present study include two new families, 12 new genera, 82 new species, five new combinations and 25 new records on new hosts and new geographical distributions as well as sexual-asexual reports. The two new families are Eriomycetaceae (Dothideomycetes, family incertae sedis) and Fasciatisporaceae (Xylariales, Sordariomycetes). The twelve new genera comprise Bhagirathimyces (Phaeosphaeriaceae), Camporesiomyces (Tubeufiaceae), Eriocamporesia (Cryphonectriaceae), Eriomyces (Eriomycetaceae), Neomonodictys (Pleurotheciaceae), Paraloratospora (Phaeosphaeriaceae), Paramonodictys (Parabambusicolaceae), Pseudoconlarium (Diaporthomycetidae, genus incertae sedis), Pseudomurilentithecium (Lentitheciaceae), Setoapiospora (Muyocopronaceae), Srinivasanomyces (Vibrisseaceae) and Xenoanthostomella (Xylariales, genera incertae sedis). The 82 new species comprise Acremonium chiangraiense, Adustochaete nivea, Angustimassarina camporesii, Bhagirathimyces himalayensis, Brunneoclavispora camporesii, Camarosporidiella camporesii, Camporesiomyces mali, Camposporium appendiculatum, Camposporium multiseptatum, Camposporium septatum, Canalisporium aquaticium, Clonostachys eriocamporesiana, Clonostachys eriocamporesii, Colletotrichum hederiicola, Coniochaeta vineae, Conioscypha verrucosa, Cortinarius ainsworthii, Cortinarius aurae, Cortinarius britannicus, Cortinarius heatherae, Cortinarius scoticus, Cortinarius subsaniosus, Cytospora fusispora, Cytospora rosigena, Diaporthe camporesii, Diaporthe nigra, Diatrypella yunnanensis, Dictyosporium muriformis, Didymella camporesii, Diutina bernali, Diutina sipiczkii, Eriocamporesia aurantia, Eriomyces heveae, Ernakulamia tanakae, Falciformispora uttaraditensis, Fasciatispora cocoes, Foliophoma camporesii, Fuscostagonospora camporesii, Helvella subtinta, Kalmusia erioi, Keissleriella camporesiana, Keissleriella camporesii, Lanspora cylindrospora, Loratospora arezzoensis, Mariannaea atlantica, Melanographium phoenicis, Montagnula camporesii, Neodidymelliopsis camporesii, Neokalmusia kunmingensis, Neoleptosporella camporesiana, Neomonodictys muriformis, Neomyrmecridium guizhouense, Neosetophoma camporesii, Paraloratospora camporesii, Paramonodictys solitarius, Periconia palmicola, Plenodomus triseptatus, Pseudocamarosporium camporesii, Pseudocercospora maetaengensis, Pseudochaetosphaeronema kunmingense, Pseudoconlarium punctiforme, Pseudodactylaria camporesiana, Pseudomurilentithecium camporesii, Pseudotetraploa rajmachiensis, Pseudotruncatella camporesii, Rhexocercosporidium senecionis, Rhytidhysteron camporesii, Rhytidhysteron erioi, Septoriella camporesii, Setoapiospora thailandica, Srinivasanomyces kangrensis, Tetraploa dwibahubeeja, Tetraploa pseudoaristata, Tetraploa thrayabahubeeja, Torula camporesii, Tremateia camporesii, Tremateia lamiacearum, Uzbekistanica pruni, Verruconis mangrovei, Wilcoxina verruculosa, Xenoanthostomella chromolaenae and Xenodidymella camporesii. The five new combinations are Camporesiomyces patagoniensis, Camporesiomyces vaccinia, Camposporium lycopodiellae, Paraloratospora gahniae and Rhexocercosporidium microsporum. The 22 new records on host and geographical distribution comprise Arthrinium marii, Ascochyta medicaginicola, Ascochyta pisi, Astrocystis bambusicola, Camposporium pellucidum, Dendryphiella phitsanulokensis, Diaporthe foeniculina, Didymella macrostoma, Diplodia mutila, Diplodia seriata, Heterosphaeria patella, Hysterobrevium constrictum, Neodidymelliopsis ranunculi, Neovaginatispora fuckelii, Nothophoma quercina, Occultibambusa bambusae, Phaeosphaeria chinensis, Pseudopestalotiopsis theae, Pyxine berteriana, Tetraploa sasicola, Torula gaodangensis and Wojnowiciella dactylidis. In addition, the sexual morphs of Dissoconium eucalypti and Phaeosphaeriopsis pseudoagavacearum are reported from Laurus nobilis and Yucca gloriosa in Italy, respectively. The holomorph of Diaporthe cynaroidis is also reported for the first time.
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Insights into the Tricholomatineae (Agaricales, Agaricomycetes): a new arrangement of Biannulariaceae and Callistosporium, Callistosporiaceae fam. nov., Xerophorus stat. nov., and Pleurocollybia incorporated into Callistosporium. FUNGAL DIVERS 2020. [DOI: 10.1007/s13225-020-00441-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Leal-Dutra CA, Griffith GW, Neves MA, McLaughlin DJ, McLaughlin EG, Clasen LA, Dentinger BTM. Reclassification of Pterulaceae Corner (Basidiomycota: Agaricales) introducing the ant-associated genus Myrmecopterula gen. nov., Phaeopterula Henn. and the corticioid Radulomycetaceae fam. nov. IMA Fungus 2020; 11:2. [PMID: 32617254 PMCID: PMC7325140 DOI: 10.1186/s43008-019-0022-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/08/2019] [Indexed: 11/10/2022] Open
Abstract
Pterulaceae was formally proposed to group six coralloid and dimitic genera: Actiniceps (=Dimorphocystis), Allantula, Deflexula, Parapterulicium, Pterula, and Pterulicium. Recent molecular studies have shown that some of the characters currently used in Pterulaceae do not distinguish the genera. Actiniceps and Parapterulicium have been removed, and a few other resupinate genera were added to the family. However, none of these studies intended to investigate the relationship between Pterulaceae genera. In this study, we generated 278 sequences from both newly collected and fungarium samples. Phylogenetic analyses supported with morphological data allowed a reclassification of Pterulaceae where we propose the introduction of Myrmecopterula gen. nov. and Radulomycetaceae fam. nov., the reintroduction of Phaeopterula, the synonymisation of Deflexula in Pterulicium, and 53 new combinations. Pterula is rendered polyphyletic requiring a reclassification; thus, it is split into Pterula, Myrmecopterula gen. nov., Pterulicium and Phaeopterula. Deflexula is recovered as paraphyletic alongside several Pterula species and Pterulicium, and is sunk into the latter genus. Phaeopterula is reintroduced to accommodate species with darker basidiomes. The neotropical Myrmecopterula gen. nov. forms a distinct clade adjacent to Pterula, and most members of this clade are associated with active or inactive attine ant nests. The resupinate genera Coronicium and Merulicium are recovered in a strongly supported clade close to Pterulicium. The other resupinate genera previously included in Pterulaceae, and which form basidiomes lacking cystidia and with monomitic hyphal structure (Radulomyces, Radulotubus and Aphanobasidium), are reclassified into Radulomycetaceae fam. nov. Allantula is still an enigmatic piece in this puzzle known only from the type specimen that requires molecular investigation. A key for the genera of Pterulaceae and Radulomycetaceae fam. nov. is also provided here.
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Affiliation(s)
- Caio A Leal-Dutra
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth,, Ceredigion, SY23 3DD UK.,CAPES Foundation, Ministry of Education of Brazil, P.O. Box 250, Brasília, DF 70040-020 Brazil
| | - Gareth W Griffith
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth,, Ceredigion, SY23 3DD UK
| | - Maria Alice Neves
- Micolab, Departamento de Botânica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina Brazil
| | - David J McLaughlin
- Department of Plant and Microbial Biology, University of Minnesota, 1445 Gortner Avenue, St Paul, MN 55108 USA
| | - Esther G McLaughlin
- Department of Plant and Microbial Biology, University of Minnesota, 1445 Gortner Avenue, St Paul, MN 55108 USA
| | - Lina A Clasen
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth,, Ceredigion, SY23 3DD UK
| | - Bryn T M Dentinger
- Natural History Museum of Utah & Biology Department, University of Utah, 301 Wakara Way, Salt Lake City, UT 84108 USA
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Prasanna AN, Gerber D, Kijpornyongpan T, Aime MC, Doyle VP, Nagy LG. Model Choice, Missing Data, and Taxon Sampling Impact Phylogenomic Inference of Deep Basidiomycota Relationships. Syst Biol 2020; 69:17-37. [PMID: 31062852 DOI: 10.1093/sysbio/syz029] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 04/21/2019] [Accepted: 04/26/2019] [Indexed: 11/12/2022] Open
Abstract
Resolving deep divergences in the tree of life is challenging even for analyses of genome-scale phylogenetic data sets. Relationships between Basidiomycota subphyla, the rusts and allies (Pucciniomycotina), smuts and allies (Ustilaginomycotina), and mushroom-forming fungi and allies (Agaricomycotina) were found particularly recalcitrant both to traditional multigene and genome-scale phylogenetics. Here, we address basal Basidiomycota relationships using concatenated and gene tree-based analyses of various phylogenomic data sets to examine the contribution of several potential sources of bias. We evaluate the contribution of biological causes (hard polytomy, incomplete lineage sorting) versus unmodeled evolutionary processes and factors that exacerbate their effects (e.g., fast-evolving sites and long-branch taxa) to inferences of basal Basidiomycota relationships. Bayesian Markov Chain Monte Carlo and likelihood mapping analyses reject the hard polytomy with confidence. In concatenated analyses, fast-evolving sites and oversimplified models of amino acid substitution favored the grouping of smuts with mushroom-forming fungi, often leading to maximal bootstrap support in both concatenation and coalescent analyses. On the contrary, the most conserved data subsets grouped rusts and allies with mushroom-forming fungi, although this relationship proved labile, sensitive to model choice, to different data subsets and to missing data. Excluding putative long-branch taxa, genes with high proportions of missing data and/or with strong signal failed to reveal a consistent trend toward one or the other topology, suggesting that additional sources of conflict are at play. While concatenated analyses yielded strong but conflicting support, individual gene trees mostly provided poor support for any resolution of rusts, smuts, and mushroom-forming fungi, suggesting that the true Basidiomycota tree might be in a part of tree space that is difficult to access using both concatenation and gene tree-based approaches. Inference-based assessments of absolute model fit strongly reject best-fit models for the vast majority of genes, indicating a poor fit of even the most commonly used models. While this is consistent with previous assessments of site-homogenous models of amino acid evolution, this does not appear to be the sole source of confounding signal. Our analyses suggest that topologies uniting smuts with mushroom-forming fungi can arise as a result of inappropriate modeling of amino acid sites that might be prone to systematic bias. We speculate that improved models of sequence evolution could shed more light on basal splits in the Basidiomycota, which, for now, remain unresolved despite the use of whole genome data.
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Affiliation(s)
- Arun N Prasanna
- Synthetic and Systems Biology Unit, Institute of Biochemistry, BRC-HAS, Szeged 6726, Hungary
| | - Daniel Gerber
- Synthetic and Systems Biology Unit, Institute of Biochemistry, BRC-HAS, Szeged 6726, Hungary.,Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
| | | | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Vinson P Doyle
- Department of Plant Pathology and Crop Physiology, Louisiana State University AgCenter, Baton Rouge, LA 70803, USA
| | - Laszlo G Nagy
- Synthetic and Systems Biology Unit, Institute of Biochemistry, BRC-HAS, Szeged 6726, Hungary
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Abstract
A six-gene phylogeny of the Inocybaceae is presented to address classification of major clades within the family. Seven genera are recognized that establish a global overview of phylogenetic relationships in the Inocybaceae. Two genera-Nothocybe and Pseudosperma-are described as new. Two subgenera of Inocybe-subg. Inosperma and subg. Mallocybe-are elevated to generic rank. These four new genera, together with the previously described Auritella, Tubariomyces, and now Inocybe sensu stricto, constitute the Inocybaceae, an ectomycorrhizal lineage of Agaricales that associates with at least 23 plant families worldwide. Pseudosperma, Nothocybe, and Inocybe are recovered as a strongly supported inclusive clade within the family. The genus Nothocybe, represented by a single species from tropical India, is strongly supported as the sister lineage to Inocybe, a hyperdiverse genus containing hundreds of species and global distribution. Two additional inclusive clades, including Inosperma, Tubariomyces, Auritella, and Mallocybe, and a nested grouping of Auritella, Mallocybe, and Tubariomyces, are recovered but with marginal statistical support. Overall, the six-gene data set provides a more robust phylogenetic estimate of relationships within the family than do single-gene and single-gene-region estimates. In addition, Africa, India, and Australia are characterized by the most genera in the family, with South America containing the fewest number of genera. A total of 180 names are recombined or proposed as new in Inosperma, Mallocybe, and Pseudosperma. A key to genera of Inocybaceae is provided.
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Affiliation(s)
- P Brandon Matheny
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - Alicia M Hobbs
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - Fernando Esteve-Raventós
- Departamento de Ciencias de la Vida (Area de Botánica), Universidad de Alcalá, 28805 Alcalá de Henares, Spain
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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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Viruel J, Conejero M, Hidalgo O, Pokorny L, Powell RF, Forest F, Kantar MB, Soto Gomez M, Graham SW, Gravendeel B, Wilkin P, Leitch IJ. A Target Capture-Based Method to Estimate Ploidy From Herbarium Specimens. FRONTIERS IN PLANT SCIENCE 2019; 10:937. [PMID: 31396248 PMCID: PMC6667659 DOI: 10.3389/fpls.2019.00937] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 07/04/2019] [Indexed: 05/24/2023]
Abstract
Whole genome duplication (WGD) events are common in many plant lineages, but the ploidy status and possible occurrence of intraspecific ploidy variation are unknown for most species. Standard methods for ploidy determination are chromosome counting and flow cytometry approaches. While flow cytometry approaches typically use fresh tissue, an increasing number of studies have shown that recently dried specimens can be used to yield ploidy data. Recent studies have started to explore whether high-throughput sequencing (HTS) data can be used to assess ploidy levels by analyzing allelic frequencies from single copy nuclear genes. Here, we compare different approaches using a range of yam (Dioscorea) tissues of varying ages, drying methods and quality, including herbarium tissue. Our aims were to: (1) explore the limits of flow cytometry in estimating ploidy level from dried samples, including herbarium vouchers collected between 1831 and 2011, and (2) optimize a HTS-based method to estimate ploidy by considering allelic frequencies from nuclear genes obtained using a target-capture method. We show that, although flow cytometry can be used to estimate ploidy levels from herbarium specimens collected up to fifteen years ago, success rate is low (5.9%). We validated our HTS-based estimates of ploidy using 260 genes by benchmarking with dried samples of species of known ploidy (Dioscorea alata, D. communis, and D. sylvatica). Subsequently, we successfully applied the method to the 85 herbarium samples analyzed with flow cytometry, and successfully provided results for 91.7% of them, comprising species across the phylogenetic tree of Dioscorea. We also explored the limits of using this HTS-based approach for identifying high ploidy levels in herbarium material and the effects of heterozygosity and sequence coverage. Overall, we demonstrated that ploidy diversity within and between species may be ascertained from historical collections, allowing the determination of polyploidization events from samples collected up to two centuries ago. This approach has the potential to provide insights into the drivers and dynamics of ploidy level changes during plant evolution and crop domestication.
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Affiliation(s)
- Juan Viruel
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Oriane Hidalgo
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Laboratori de Botànica, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Barcelona, Spain
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Michael B. Kantar
- Department of Tropical Plant and Soil Sciences, University of Hawai’i at Mânoa, Honolulu, HI, United States
| | - Marybel Soto Gomez
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, BC, Canada
| | - Sean W. Graham
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, BC, Canada
| | - Barbara Gravendeel
- Naturalis Biodiversity Center, Endless Forms, Leiden, Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, Netherlands
- Science and Technology Faculty, University of Applied Sciences Leiden, Leiden, Netherlands
| | - Paul Wilkin
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
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Oliveira JJS, Vargas-Isla R, Cabral TS, Rodrigues DP, Ishikawa NK. Progress on the phylogeny of the Omphalotaceae: Gymnopus s. str., Marasmiellus s. str., Paragymnopus gen. nov. and Pusillomyces gen. nov. Mycol Prog 2019. [DOI: 10.1007/s11557-019-01483-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Andrew C, Diez J, James TY, Kauserud H. Fungarium specimens: a largely untapped source in global change biology and beyond. Philos Trans R Soc Lond B Biol Sci 2018; 374:20170392. [PMID: 30455210 PMCID: PMC6282084 DOI: 10.1098/rstb.2017.0392] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2018] [Indexed: 11/12/2022] Open
Abstract
For several hundred years, millions of fungal sporocarps have been collected and deposited in worldwide collections (fungaria) to support fungal taxonomy. Owing to large-scale digitization programs, metadata associated with the records are now becoming publicly available, including information on taxonomy, sampling location, collection date and habitat/substrate information. This metadata, as well as data extracted from the physical fungarium specimens themselves, such as DNA sequences and biochemical characteristics, provide a rich source of information not only for taxonomy but also for other lines of biological inquiry. Here, we highlight and discuss how this information can be used to investigate emerging topics in fungal global change biology and beyond. Fungarium data are a prime source of knowledge on fungal distributions and richness patterns, and for assessing red-listed and invasive species. Information on collection dates has been used to investigate shifts in fungal distributions as well as phenology of sporocarp emergence in response to climate change. In addition to providing material for taxonomy and systematics, DNA sequences derived from the physical specimens provide information about fungal demography, dispersal patterns, and are emerging as a source of genomic data. As DNA analysis technologies develop further, the importance of fungarium specimens as easily accessible sources of information will likely continue to grow.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.
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Affiliation(s)
- Carrie Andrew
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
| | - Jeffrey Diez
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316 Oslo, Norway
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Villaverde T, Pokorny L, Olsson S, Rincón-Barrado M, Johnson MG, Gardner EM, Wickett NJ, Molero J, Riina R, Sanmartín I. Bridging the micro- and macroevolutionary levels in phylogenomics: Hyb-Seq solves relationships from populations to species and above. THE NEW PHYTOLOGIST 2018; 220:636-650. [PMID: 30016546 DOI: 10.1111/nph.15312] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/04/2018] [Indexed: 05/20/2023]
Abstract
Reconstructing phylogenetic relationships at the micro- and macroevoutionary levels within the same tree is problematic because of the need to use different data types and analytical frameworks. We test the power of target enrichment to provide phylogenetic resolution based on DNA sequences from above species to within populations, using a large herbarium sampling and Euphorbia balsamifera (Euphorbiaceae) as a case study. Target enrichment with custom probes was combined with genome skimming (Hyb-Seq) to sequence 431 low-copy nuclear genes and partial plastome DNA. We used supermatrix, multispecies-coalescent approaches, and Bayesian dating to estimate phylogenetic relationships and divergence times. Euphorbia balsamifera, with a disjunct Rand Flora-type distribution at opposite sides of Africa, comprises three well-supported subspecies: western Sahelian sepium is sister to eastern African-southern Arabian adenensis and Macaronesian-southwest Moroccan balsamifera. Lineage divergence times support Late Miocene to Pleistocene diversification and climate-driven vicariance to explain the Rand Flora pattern. We show that probes designed using genomic resources from taxa not directly related to the focal group are effective in providing phylogenetic resolution at deep and shallow evolutionary levels. Low capture efficiency in herbarium samples increased the proportion of missing data but did not bias estimation of phylogenetic relationships or branch lengths.
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Affiliation(s)
- Tamara Villaverde
- Real Jardín Botánico (RJB-CSIC), Plaza de Murillo 2, 28014, Madrid, Spain
| | - Lisa Pokorny
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, TW9 3DS, UK
| | - Sanna Olsson
- Department of Forest Ecology and Genetics, INIA Forest Research Centre (INIA-CIFOR), Ctra. de la Coruña km. 7.5, 28040, Madrid, Spain
| | | | - Matthew G Johnson
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX, 79409-43131, USA
- Department of Plant Science and Conservation, Chicago Botanical Garden, 1000 Lake Cook Road, Glencoe, IL, 60022, USA
| | | | - Norman J Wickett
- Department of Plant Science and Conservation, Chicago Botanical Garden, 1000 Lake Cook Road, Glencoe, IL, 60022, USA
- Program in Plant Biology and Conservation, Northwestern University, 2205 Tech Drive, Evanston, IL, 60208, USA
| | - Julià Molero
- Laboratori de Botànica, Departament de Biologia, Sanitat i Medi Ambient, Facultat de Farmàcia, Universitat de Barcelona, 08028, Barcelona, Spain
| | - Ricarda Riina
- Real Jardín Botánico (RJB-CSIC), Plaza de Murillo 2, 28014, Madrid, Spain
| | - Isabel Sanmartín
- Real Jardín Botánico (RJB-CSIC), Plaza de Murillo 2, 28014, Madrid, Spain
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Wang CQ, Zhang M, Li TH, Liang XS, Shen YH. Additions to tribe Chromosereae (Basidiomycota, Hygrophoraceae) from China, including Sinohygrocybe gen. nov. and a first report of Gloioxanthomycesnitidus. MycoKeys 2018:59-76. [PMID: 30275740 PMCID: PMC6160846 DOI: 10.3897/mycokeys.38.25427] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 08/02/2018] [Indexed: 11/12/2022] Open
Abstract
Sinohygrocybe gen. nov., typified by S.tomentosipes sp. nov., is described upon morphological and molecular evidence. The new genus is characterised by its sinuate to subdecurrent or short deccurent, usually furcate and interveined and relatively distant lamellae, dry and whitish tomentose stipe, thin-walled ellipsoid to oviod, non-constricted basidiospores and particularly elongated basidia and a ratio of basidiospore to basidium length of >5 to 8; it is close to genera Chromosera and Gloioxanthomyces of the tribe Chromosereae, but morphologically differs from Chromosera in less umbilicate basidiomata, tomentose stipe and usually longer basidia and differs from Gloioxanthomyces in more robust basidioma and less glutinous pileus and/or stipe surface. Phylogenetic analyses, with ITS-LSU-RPB2 data, also indicate that Sinohygrocybe forms a very distinct and independent clade at the generic level. In addition, a Chinese new record G.nitidus is described here.
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Affiliation(s)
- 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 Guangdong Institute of Microbiology Guangzhou China
| | - 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 Guangdong Institute of Microbiology Guangzhou China
| | - 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 Guangdong Institute of Microbiology Guangzhou China
| | - Xi-Shen Liang
- 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 Guangdong Institute of Microbiology Guangzhou China
| | - Ya-Heng Shen
- 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 Guangdong Institute of Microbiology Guangzhou China
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41
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Tying up loose threads: revised taxonomy and phylogeny of an avian-dispersed Neotropical rhizomorph-forming fungus. Mycol Prog 2018. [DOI: 10.1007/s11557-018-1411-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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42
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Koch RA, Aime MC. Population structure of
Guyanagaster necrorhizus
supports termite dispersal for this enigmatic fungus. Mol Ecol 2018; 27:2667-2679. [PMID: 29729049 DOI: 10.1111/mec.14710] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 04/07/2018] [Indexed: 02/02/2023]
Affiliation(s)
- Rachel A. Koch
- Department of Botany and Plant Pathology Purdue University West Lafayette Indiana
| | - M. Catherine Aime
- Department of Botany and Plant Pathology Purdue University West Lafayette Indiana
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43
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Alvarado P, Moreau PA, Dima B, Vizzini A, Consiglio G, Moreno G, Setti L, Kekki T, Huhtinen S, Liimatainen K, Niskanen T. Pseudoclitocybaceae fam. nov. (Agaricales, Tricholomatineae), a new arrangement at family, genus and species level. FUNGAL DIVERS 2018. [DOI: 10.1007/s13225-018-0400-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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44
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Matheny PB, Baroni TJ, Simoni A, Rojas MEH, Sánchez-García M, Gates GM. The Wild Edible MushroomPleurocollybia cibariafrom Peru is a Species ofGerhardtiain the Lyophyllaceae (Agaricales). CRYPTOGAMIE MYCOL 2017. [DOI: 10.7872/crym/v38.iss2.2017.205] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Patrick Brandon Matheny
- Department of Ecology and Evolutionary Biology, University of Tennessee, Dabney 569, Knoxville, Tennessee, 37996-1610 U.S.A
| | - Timothy J. Baroni
- Department of Biological Sciences, 340 Bowers Hall, State University of New York-College at Cortland, Cortland, New York 14054 U.S.A
| | - Adriana Simoni
- Hudbay Minerals, Av. El Derby 055, Torre 3, Piso 4, Santiago de Surco, Lima, Peru
| | - María E. Holgado Rojas
- Centro de Investigación y Producción de Hongos Alimenticiois y Medicinales — CIPHAM, Universidad Nacional de San Antonia Abad del Cusco, Peru
| | - Marisol Sánchez-García
- Department of Ecology and Evolutionary Biology, University of Tennessee, Dabney 569, Knoxville, Tennessee, 37996-1610 U.S.A
| | - Genevieve M. Gates
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 54, Hobart, Tasmania 7001 Australia
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45
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Tedersoo L, Bahram M, Puusepp R, Nilsson RH, James TY. Novel soil-inhabiting clades fill gaps in the fungal tree of life. MICROBIOME 2017; 5:42. [PMID: 28388929 PMCID: PMC5385062 DOI: 10.1186/s40168-017-0259-5] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 03/20/2017] [Indexed: 05/12/2023]
Abstract
BACKGROUND Fungi are a diverse eukaryotic group of degraders, pathogens, and symbionts, with many lineages known only from DNA sequences in soil, sediments, air, and water. RESULTS We provide rough phylogenetic placement and principal niche analysis for >40 previously unrecognized fungal groups at the order and class level from global soil samples based on combined 18S (nSSU) and 28S (nLSU) rRNA gene sequences. Especially, Rozellomycota (Cryptomycota), Zygomycota s.lat, Ascomycota, and Basidiomycota are rich in novel fungal lineages, most of which exhibit distinct preferences for climate and soil pH. CONCLUSIONS This study uncovers the great phylogenetic richness of previously unrecognized order- to phylum-level fungal lineages. Most of these rare groups are distributed in different ecosystems of the world but exhibit distinct ecological preferences for climate or soil pH. Across the fungal kingdom, tropical and non-tropical habitats are equally likely to harbor novel groups. We advocate that a combination of traditional and high-throughput sequencing methods enable efficient recovery and phylogenetic placement of such unknown taxonomic groups.
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Affiliation(s)
- Leho Tedersoo
- Natural History Museum, University of Tartu, 14a Ravila, 50411, Tartu, Estonia.
| | - Mohammad Bahram
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411, Tartu, Estonia
- Systematic Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Rasmus Puusepp
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411, Tartu, Estonia
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30, Göteborg, Sweden
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
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46
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Wilson AW, Hosaka K, Mueller GM. Evolution of ectomycorrhizas as a driver of diversification and biogeographic patterns in the model mycorrhizal mushroom genus Laccaria. THE NEW PHYTOLOGIST 2017; 213:1862-1873. [PMID: 28164331 PMCID: PMC5324586 DOI: 10.1111/nph.14270] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/15/2016] [Indexed: 05/03/2023]
Abstract
A systematic and evolutionary ecology study of the model ectomycorrhizal (ECM) genus Laccaria was performed using herbarium material and field collections from over 30 countries covering its known geographic range. A four-gene (nrITS, 28S, RPB2, EF1α) nucleotide sequence dataset consisting of 232 Laccaria specimens was analyzed phylogenetically. The resulting Global Laccaria dataset was used for molecular dating and estimating diversification rates in the genus. Stable isotope analysis of carbon and nitrogen was used to evaluate the origin of Laccaria's ECM ecology. In all, 116 Laccaria molecular species were identified, resulting in a near 50% increase in its known diversity, including the new species described herein: Laccaria ambigua. Molecular dating indicates that the most recent common ancestor to Laccaria existed in the early Paleocene (56-66 million yr ago), probably in Australasia. At this time, Laccaria split into two lineages: one represented by the new species L. ambigua, and the other reflecting a large shift in diversification that resulted in the remainder of Laccaria. L. ambigua shows a different isotopic profile than all other Laccaria species. Isotopes and diversification results suggest that the evolution of the ECM ecology was a key innovation in the evolution of Laccaria. Diversification shifts associated with Laccaria's dispersal to the northern hemisphere are attributed to adaptations to new ecological niches.
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Affiliation(s)
- Andrew W. Wilson
- Chicago Botanic GardenPlant Science and Conservation1000 Lake Cook RoadGlencoeIL60022USA
- Sam Mitchel Herbarium of FungiDenver Botanic Gardens909 York StreetDenverCO80206USA
| | - Kentaro Hosaka
- Department of BotanyNational Museum of Nature and ScienceTsukubaIbaraki305‐0005Japan
| | - Gregory M. Mueller
- Chicago Botanic GardenPlant Science and Conservation1000 Lake Cook RoadGlencoeIL60022USA
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47
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Chloroplast and ITS phylogenies to understand the evolutionary history of southern South American Azorella, Laretia and Mulinum (Azorelloideae, Apiaceae). Mol Phylogenet Evol 2017; 108:1-21. [DOI: 10.1016/j.ympev.2017.01.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 01/27/2017] [Accepted: 01/29/2017] [Indexed: 12/30/2022]
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48
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Koch RA, Wilson AW, Séné O, Henkel TW, Aime MC. Resolved phylogeny and biogeography of the root pathogen Armillaria and its gasteroid relative, Guyanagaster. BMC Evol Biol 2017; 17:33. [PMID: 28122504 PMCID: PMC5264464 DOI: 10.1186/s12862-017-0877-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 01/10/2017] [Indexed: 11/18/2022] Open
Abstract
Background Armillaria is a globally distributed mushroom-forming genus composed primarily of plant pathogens. Species in this genus are prolific producers of rhizomorphs, or vegetative structures, which, when found, are often associated with infection. Because of their importance as plant pathogens, understanding the evolutionary origins of this genus and how it gained a worldwide distribution is of interest. The first gasteroid fungus with close affinities to Armillaria—Guyanagaster necrorhizus—was described from the Neotropical rainforests of Guyana. In this study, we conducted phylogenetic analyses to fully resolve the relationship of G. necrorhizus with Armillaria. Data sets containing Guyanagaster from two collecting localities, along with a global sampling of 21 Armillaria species—including newly collected specimens from Guyana and Africa—at six loci (28S, EF1α, RPB2, TUB, actin-1 and gpd) were used. Three loci—28S, EF1α and RPB2—were analyzed in a partitioned nucleotide data set to infer divergence dates and ancestral range estimations for well-supported, monophyletic lineages. Results The six-locus phylogenetic analysis resolves Guyanagaster as the earliest diverging lineage in the armillarioid clade. The next lineage to diverge is that composed of species in Armillaria subgenus Desarmillaria. This subgenus is elevated to genus level to accommodate the exannulate mushroom-forming armillarioid species. The final lineage to diverge is that composed of annulate mushroom-forming armillarioid species, in what is now Armillaria sensu stricto. The molecular clock analysis and ancestral range estimation suggest the most recent common ancestor to the armillarioid lineage arose 51 million years ago in Eurasia. A new species, Guyanagaster lucianii sp. nov. from Guyana, is described. Conclusions The armillarioid lineage evolved in Eurasia during the height of tropical rainforest expansion about 51 million years ago, a time marked by a warm and wet global climate. Species of Guyanagaster and Desarmillaria represent extant taxa of these early diverging lineages. Desarmillaria represents an armillarioid lineage that was likely much more widespread in the past. Guyanagaster likely evolved from a gilled mushroom ancestor and could represent a highly specialized endemic in the Guiana Shield. Armillaria species represent those that evolved after the shift in climate from warm and tropical to cool and arid during the late Eocene. No species in either Desarmillaria or Guyanagaster are known to produce melanized rhizomorphs in nature, whereas almost all Armillaria species are known to produce them. The production of rhizomorphs is an adaptation to harsh environments, and could be a driver of diversification in Armillaria by conferring a competitive advantage to the species that produce them. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0877-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rachel A Koch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Andrew W Wilson
- Sam Mitchel Herbarium of Fungi, Denver Botanic Gardens, Denver, CO, 80206, USA
| | - Olivier Séné
- Institute of Agricultural Research for Development (IRAD), National Herbarium of Cameroon (MINRESI), PO Box 1601, Yaoundé, Cameroon
| | - Terry W Henkel
- Department of Biological Sciences, Humboldt State University, Arcata, CA, 95521, USA
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA.
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Phylogenetics and Phylogenomics of Rust Fungi. FUNGAL PHYLOGENETICS AND PHYLOGENOMICS 2017; 100:267-307. [DOI: 10.1016/bs.adgen.2017.09.011] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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50
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Uniting species- and community-oriented approaches to understand arbuscular mycorrhizal fungal diversity. FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2016.07.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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