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Harder CB, Hesling E, Botnen SS, Lorberau KE, Dima B, von Bonsdorff-Salminen T, Niskanen T, Jarvis SG, Ouimette A, Hester A, Hobbie EA, Taylor AFS, Kauserud H. Mycena species can be opportunist-generalist plant root invaders. Environ Microbiol 2023; 25:1875-1893. [PMID: 37188366 DOI: 10.1111/1462-2920.16398] [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: 02/13/2023] [Accepted: 04/27/2023] [Indexed: 05/17/2023]
Abstract
Traditional strict separation of fungi into ecological niches as mutualist, parasite or saprotroph is increasingly called into question. Sequences of assumed saprotrophs have been amplified from plant root interiors, and several saprotrophic genera can invade and interact with host plants in laboratory growth experiments. However, it is uncertain if root invasion by saprotrophic fungi is a widespread phenomenon and if laboratory interactions mirror field conditions. Here, we focused on the widespread and speciose saprotrophic genus Mycena and performed (1) a systematic survey of their occurrences (in ITS1/ITS2 datasets) in mycorrhizal roots of 10 plant species, and (2) an analysis of natural abundances of 13 C/15 N stable isotope signatures of Mycena basidiocarps from five field locations to examine their trophic status. We found that Mycena was the only saprotrophic genus consistently found in 9 out of 10 plant host roots, with no indication that the host roots were senescent or otherwise vulnerable. Furthermore, Mycena basidiocarps displayed isotopic signatures consistent with published 13 C/15 N profiles of both saprotrophic and mutualistic lifestyles, supporting earlier laboratory-based studies. We argue that Mycena are widespread latent invaders of healthy plant roots and that Mycena species may form a spectrum of interactions besides saprotrophy also in the field.
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Affiliation(s)
- Christoffer Bugge Harder
- Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Microbial Ecology, Lund University, Lund, Sweden
- Department of Biology, Section of Terrestrial Ecology, University of Copenhagen, Copenhagen, Denmark
| | - Emily Hesling
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Synnøve S Botnen
- Department of Biosciences, University of Oslo, Oslo, Norway
- Oslo Metropolitan University, Oslo, Norway
| | - Kelsey E Lorberau
- Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Arctic and Marine Biology, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Bálint Dima
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
- Botany Unit, Finnish Museum of Natural History LUOMUS, University of Helsinki, Helsinki, Finland
| | | | - Tuula Niskanen
- Botany Unit, Finnish Museum of Natural History LUOMUS, University of Helsinki, Helsinki, Finland
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Surrey, UK
| | | | - Andrew Ouimette
- Earth Systems Research Center, University of New Hampshire, Durham, New Hampshire, USA
| | | | - Erik A Hobbie
- Earth Systems Research Center, University of New Hampshire, Durham, New Hampshire, USA
| | - Andy F S Taylor
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
- The James Hutton Institute, Aberdeen, UK
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Wang Y, Wang LY, Dai D, Qi ZX, Zhang ZH, Liu YJ, Hu JJ, Zhang P, Li Y, Zhang B. Boletaceae in China: Taxonomy and phylogeny reveal a new genus, two new species, and a new record. Front Microbiol 2023; 13:1052948. [PMID: 36817106 PMCID: PMC9932287 DOI: 10.3389/fmicb.2022.1052948] [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: 09/24/2022] [Accepted: 12/08/2022] [Indexed: 02/05/2023] Open
Abstract
Boletaceae, the largest family in Boletales, has been attracted by mycologists in the world due to its diverse morphology and complex history of evolution. Although considerable work has been done in the past decades, novel taxa are continually described. The current study aimed to introduce three new taxa and one new record of Boletaceae from China. The morphological descriptions, color photographs, phylogenetic trees to show the positions of the taxa, and comparisons with allied taxa are provided. The new genus Hemilanmaoa is unique in the Pulveroboletus group, and Hemilanmaoa retistipitatus was introduced as the type species. It can be distinguished by its bluing basidioma when injured, a decurrent hymenophore, a stipe covered with distinct reticulations, and a fertile stipitipellis. Porphyrellus pseudocyaneotinctus is characterized by its pileipellis consisting of broadly concatenated cells and thin-walled caulocystidia in Porphyrellus. In Phylloporus, Phylloporus biyangensis can be distinguished by its hymenophores that change to blue when injured and yellow basal mycelium. Lanmaoa angustispora, as a new record, is first reported in Northern China. Internal transcribed spacer (ITS), 28S rDNA (28S), translation elongation factor 1-alpha (tef1-α), RNA polymerase II subunit 1 (rpb1), and RNA polymerase II subunit 2 (rpb2) were employed to execute phylogenetic analyses.
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Affiliation(s)
- Yang Wang
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun, China,College of Plant Protection, Shenyang Agricultural University, Shenyang, China,Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, College of Plant Protection, Jilin Agricultural University, Changchun, China
| | - Li-Ying Wang
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun, China,Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, College of Plant Protection, Jilin Agricultural University, Changchun, China
| | - Dan Dai
- Institute of Agricultural Applied Microbiology, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Zheng-Xiang Qi
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, College of Plant Protection, Jilin Agricultural University, Changchun, China
| | - Zhen-Hao Zhang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, College of Plant Protection, Jilin Agricultural University, Changchun, China
| | - Ya-Jie Liu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, College of Plant Protection, Jilin Agricultural University, Changchun, China
| | - Jia-Jun Hu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, College of Plant Protection, Jilin Agricultural University, Changchun, China
| | - Peng Zhang
- Mudanjiang Sub-Academy, Heilongjiang Academy of Agricultural Sciences, Mudanjiang, Heilongjiang, China
| | - Yu Li
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun, China,College of Plant Protection, Shenyang Agricultural University, Shenyang, China,Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, College of Plant Protection, Jilin Agricultural University, Changchun, China,*Correspondence: Yu Li,
| | - Bo Zhang
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun, China,Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, College of Plant Protection, Jilin Agricultural University, Changchun, China,Bo Zhang,
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3
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Grupe II A, Smith M, Weier A, Healy R, Caiafa M, Pfister D, Haelewaters D, Quandt C. Two new species of Phaeohelotium ( Leotiomycetes: Helotiaceae) from Chile and their putative ectomycorrhizal status. Fungal Syst Evol 2022; 10:231-249. [PMID: 36741556 PMCID: PMC9875694 DOI: 10.3114/fuse.2022.10.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
Species of the genus Phaeohelotium (Leotiomycetes: Helotiaceae) are cup fungi that grow on decaying wood, leaves, litter, and directly on soil. Northern Hemisphere species are primarily found on litter and wood, whereas in the Southern Hemisphere the genus includes a mix of saprotrophs as well as taxa that grow on soil in association with ectomycorrhizal trees. The diversity of this genus has not been fully explored in southern South America. Here we describe two species from Chile, Phaeohelotium maiusaurantium sp. nov. and Ph. pallidum sp. nov., found on soil in Patagonian Nothofagaceae-dominated forests. We present macro- and micromorphological descriptions, illustrations, and molecular phylogenetic analyses. The two new species are placed in Phaeohelotium with high support in our 15-locus phylogeny as well as phylogenetic reconstructions based on the internal transcribed spacer (ITS) region of the nuclear ribosomal RNA gene. Our ITS phylogeny places both Ph. maiusaurantium and Ph. pallidum in a well-supported subclade that includes ectomycorrhizal root tip samples from Australasia. Similar species can be separated from these new taxa based on morphological characteristics, biogeography, substrate, and sequence data. In addition, two unnamed species from Chilean Nothofagaceae forests (Phaeohelotium sp. 1 and Phaeohelotium sp. 2) are documented from scant collections and sequence data and await description until more material becomes available. Citation: Grupe II AC, Smith ME, Weier A, Healy R, Caiafa MV, Pfister DH, Haelewaters D, Quandt CA (2022). Two new species of Phaeohelotium (Leotiomycetes: Helotiaceae) from Chile and their putative ectomycorrhizal status. Fungal Systematics and Evolution 10: 231-249. doi: 10.3114/fuse.2022.10.10.
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Affiliation(s)
- A.C. Grupe II
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - M.E. Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - A. Weier
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - R. Healy
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - M.V. Caiafa
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA 92521, USA
| | - D.H. Pfister
- Department of Organismic and Evolutionary Biology & Farlow Reference Library and Herbarium of Cryptogamic Botany, Harvard University, Cambridge MA 20138, USA
| | - D. Haelewaters
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
- Research Group Mycology, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - C.A. Quandt
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA
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Corrales A, Koch RA, Vasco-Palacios AM, Smith ME, Ge ZW, Henkel TW. Diversity and distribution of tropical ectomycorrhizal fungi. Mycologia 2022; 114:919-933. [PMID: 36194092 DOI: 10.1080/00275514.2022.2115284] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2022]
Abstract
The tropics were long considered to have few ectomycorrhizal fungi, presumably due to a paucity of ectomycorrhizal host plants relative to higher-latitude ecosystems. However, an increase in research in tropical regions over the past 30 years has greatly expanded knowledge about the occurrence of tropical ectomycorrhizal fungi. To assess their broad biogeographic and diversity patterns, we conducted a comprehensive review and quantitative data analysis of 49 studies with 80 individual data sets along with additional data from GlobalFungi to elucidate tropical diversity patterns and biogeography of ectomycorrhizal fungi across the four main tropical regions: the Afrotropics, the Neotropics, Southeast Asia, and Oceania. Generalized linear models were used to explore biotic and abiotic influences on the relative abundance of the 10 most frequently occurring lineages. We also reviewed the available literature and synthesized current knowledge about responses of fungi to anthropogenic disturbances, and their conservation status and threats. We found that /russula-lactarius and /tomentella-thelephora were the most abundant lineages in the Afrotropics, the Neotropics, and Southeast Asia, whereas /cortinarius was the most abundant lineage in Oceania, and that /russula-lactarius, /inocybe, and /tomentella-thelephora were the most species-rich lineages across all of the tropical regions. Based on these analyses, we highlight knowledge gaps for each tropical region. Increased sampling of tropical regions, collaborative efforts, and use of molecular methodologies are needed for a more comprehensive view of the ecology and diversity of tropical ectomycorrhizal fungi.
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Affiliation(s)
- Adriana Corrales
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Carrera 26 # 63B - 48, Bogotá 111221, Colombia
| | - Rachel A Koch
- Department of Plant Science and Landscape Architecture, University of Connecticut, 1376 Storrs Rd., Storrs, Connecticut 06269, USA
| | - Aída M Vasco-Palacios
- Grupo BioMicro y de Microbiología Ambiental, Escuela de Microbiología, Universidad de Antioquia UdeA, Calle 70 No. 52-2, Medellín, Colombia. Asociación Colombiana de Micología, ASCOLMIC
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, 2550 Hull Road, Gainesville, Florida 32611, USA
| | - Zai-Wei Ge
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, Kunming 650201, China
| | - Terry W Henkel
- Department of Biological Sciences, California State Polytechnic University, Humboldt, 1 Harpst St., Arcata, California 95521, USA
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5
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Menolli N, Sánchez-Ramírez S, Sánchez-García M, Wang C, Patev S, Ishikawa NK, Mata JL, Lenz AR, Vargas-Isla R, Liderman L, Lamb M, Nuhn M, Hughes KW, Xiao Y, Hibbett DS. Global phylogeny of the Shiitake mushroom and related Lentinula species uncovers novel diversity and suggests an origin in the Neotropics. Mol Phylogenet Evol 2022; 173:107494. [PMID: 35490968 DOI: 10.1016/j.ympev.2022.107494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 01/18/2023]
Abstract
Lentinula (Basidiomycota, Agaricales) includes the most widely cultivated mushroom in the world, Lentinula edodes, also known as shiitake (Japanese) or xiang-gu (Chinese). At present, nine species are recognized in the genus, based on morphology, mating criteria, and geographic distributions. However, analyses of internal transcribed spacers (ITS) of ribosomal RNA genes have suggested that there are cryptic lineages. We analyzed a global-scale phylogenetic dataset from 325 Lentinula individuals from 24 countries in Asia-Australasia and the Americas plus Madagascar, with 325 sequences of ITS, 80 LSU sequences, and 111 sequences of translation elongation factor (tef1-α) genes. We recovered 15 independent lineages (Groups 1-15) that may correspond to species. Lineages in Asia-Australasia (Groups 1-5) and the Americas plus Madagascar (Groups 6-15) formed sister clades. Four lineages are represented only by sequences from single individuals and require further molecular sampling, including L. aff. raphanica (Group 7), L. ixodes (Group 8), L. boryana (Group 12), and L. aff. aciculospora (Group 14). Groups 1 and 5 are here referred to L. edodes and L. aff. edodes, respectively. However, these groups most likely represent the same species and are only recognized as (unsupported) monophyletic lineages by maximum likelihood analyses of ITS alone. Other putative species resolved here include L. lateritia (Group 2), L. novae-zelandieae (Group 3), L. aff. lateritia (Group 4), L. raphanica (Group 6), L. aff. detonsa (Group 9), L. detonsa (Group 10), L. guzmanii sp. nov. (Group 11), L. aciculospora (Group 13), and L. madagasikarensis (Group 15). Groups 9-12 represent the "L. boryana complex". Molecular clock and historical biogeographic analyses suggest that the most recent common ancestor (MRCA) of Lentinula can be placed in the middle Oligocene, ca. 30 million years ago (Ma), and had a likely presence in neotropical America. The MRCA of Lentinula in the Americas and Madagascar lived ca. 22 Ma in the Neotropics and the MRCA of Lentinula in Asia-Australasia lived ca. 6 Ma in Oceania. Given the current knowledge about plate tectonics and paleoclimatic models of the last 30 Myr, our phylogenetic hypothesis suggests that the extant distribution of Lentinula is likely to have arisen, in large part, due to long-distance dispersal. Lentinula collections include at least four dubious taxa that need further taxonomic studies: L. reticeps from the USA (Ohio); L. guarapiensis from Paraguay; Lentinus puiggarii from Brazil (São Paulo); and "L. platinedodes" from Vietnam. Approximately ten of the fifteen Groups are reported on Fagaceae, which appears to be the ancestral substrate of Lentinula.
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Affiliation(s)
- Nelson Menolli
- IFungiLab, Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), Câmpus São Paulo (SPO), Departamento de Ciências da Natureza e Matemática (DCM) / Subárea de Biologia (SAB), Rua Pedro Vicente 625, São Paulo, SP 01109-010, Brazil.
| | - Santiago Sánchez-Ramírez
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario M5S 3B2, Canada
| | - Marisol Sánchez-García
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-75005, Sweden
| | - Chaoqun Wang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Science, Guangzhou 510070, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sean Patev
- Biology Department, Clark University, Worcester, MA 01610, USA
| | - Noemia Kazue Ishikawa
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo, 2936, Petrópolis, Manaus, AM 69067-375, Brazil
| | - Juan L Mata
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Alexandre Rafael Lenz
- Departamento de Ciências Exatas e da Terra, Colegiado de Sistemas de Informação, Campus I, Universidade do Estado da Bahia (UNEB), Salvador, BA, Brazil
| | - Ruby Vargas-Isla
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo, 2936, Petrópolis, Manaus, AM 69067-375, Brazil
| | - Lauren Liderman
- Biology Department, Clark University, Worcester, MA 01610, USA
| | - Meriel Lamb
- Biology Department, Clark University, Worcester, MA 01610, USA
| | - Mitchell Nuhn
- Biology Department, Clark University, Worcester, MA 01610, USA
| | - Karen W Hughes
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Yang Xiao
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - David S Hibbett
- Biology Department, Clark University, Worcester, MA 01610, USA
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Cytochrome P450 Complement May Contribute to Niche Adaptation in Serpula Wood-Decay Fungi. J Fungi (Basel) 2022; 8:jof8030283. [PMID: 35330285 PMCID: PMC8949155 DOI: 10.3390/jof8030283] [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: 01/19/2022] [Revised: 03/06/2022] [Accepted: 03/07/2022] [Indexed: 02/04/2023] Open
Abstract
Serpula wood-decay fungi occupy a diverse range of natural and man-made ecological niches. Serpula himantioides is a forest-floor generalist with global coverage and strong antagonistic ability, while closely related species Serpula lacrymans contains specialist sister strains with widely differing ecologies. Serpula lacrymans var. shastensis is a forest-floor specialist in terms of resource preference and geographic coverage, while Serpula lacrymans var. lacrymans has successfully invaded the built environment and occupies a building-timber niche. To increase understanding of the cellular machinery required for niche adaptation, a detailed study of the P450 complement of these three strains was undertaken. Cytochrome P450 monooxygenases are present in all fungi and typically seen in high numbers in wood decay species, with putative roles in breakdown of plant extractives and lignocellulose metabolism. Investigating the genomes of these related yet ecologically diverse fungi revealed a high level of concordance in P450 complement, but with key differences in P450 family representation and expression during growth on wood, suggesting P450 proteins may play a role in niche adaptation. Gene expansion of certain key P450 families was noted, further supporting an important role for these proteins during wood decay. The generalist species S. himantioides was found to have the most P450 genes with the greatest family diversity and the highest number of P450 protein families expressed during wood decay.
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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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Hess J, Balasundaram SV, Bakkemo RI, Drula E, Henrissat B, Högberg N, Eastwood D, Skrede I. Niche differentiation and evolution of the wood decay machinery in the invasive fungus Serpula lacrymans. THE ISME JOURNAL 2021; 15:592-604. [PMID: 33077886 PMCID: PMC8027034 DOI: 10.1038/s41396-020-00799-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/26/2020] [Accepted: 09/25/2020] [Indexed: 11/21/2022]
Abstract
Ecological niche breadth and the mechanisms facilitating its evolution are fundamental to understanding adaptation to changing environments, persistence of generalist and specialist lineages and the formation of new species. Woody substrates are structurally complex resources utilized by organisms with specialized decay machinery. Wood-decaying fungi represent ideal model systems to study evolution of niche breadth, as they vary greatly in their host range and preferred decay stage of the substrate. In order to dissect the genetic basis for niche specialization in the invasive brown rot fungus Serpula lacrymans, we used phenotyping and integrative analysis of phylogenomic and transcriptomic data to compare this species to wild relatives in the Serpulaceae with a range of specialist to generalist decay strategies. Our results indicate specialist species have rewired regulatory networks active during wood decay towards decreased reliance on enzymatic machinery, and therefore nitrogen-intensive decay components. This shift was likely accompanied with adaptation to a narrow tree line habitat and switch to a pioneer decomposer strategy, both requiring rapid colonization of a nitrogen-limited substrate. Among substrate specialists with narrow niches, we also found evidence for pathways facilitating reversal to generalism, highlighting how evolution may move along different axes of niche space.
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Affiliation(s)
- Jaqueline Hess
- Department of Biosciences, University of Oslo, Oslo, Norway.
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.
- Department of Soil Ecology, Helmholtz Centre for Environmental Research, UFZ, Halle (Saale), Germany.
| | | | | | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille University, Marseille, France
- INRA, USC1408 AFMB, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille University, Marseille, France
- INRA, USC1408 AFMB, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nils Högberg
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Daniel Eastwood
- Department of Biosciences, University of Swansea, Swansea, UK
| | - Inger Skrede
- Department of Biosciences, University of Oslo, Oslo, Norway
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9
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Thoen E, Harder CB, Kauserud H, Botnen SS, Vik U, Taylor AFS, Menkis A, Skrede I. In vitro evidence of root colonization suggests ecological versatility in the genus Mycena. THE NEW PHYTOLOGIST 2020; 227:601-612. [PMID: 32171021 DOI: 10.1111/nph.16545] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 03/03/2020] [Indexed: 06/10/2023]
Abstract
The root-associated habit has evolved on numerous occasions in different fungal lineages, suggesting a strong evolutionary pressure for saprotrophic fungi to switch to symbiotic associations with plants. Species within the ubiquitous, saprotrophic genus Mycena are frequently major components in molecular studies of root-associated fungal communities, suggesting that an evaluation of their trophic status is warranted. Here, we report on interactions between a range of Mycena species and the plant Betula pendula. In all, 17 Mycena species were inoculated onto B. pendula seedlings. Physical interactions between hyphae and fine roots were examined using differential staining and fluorescence microscopy. Physiological interactions were investigated using 14 C and 32 P to show potential transfer between symbionts. All Mycena species associated closely with fine roots, showing hyphal penetration into the roots, which in some cases were intracellular. Seven species formed mantle-like structures around root tips, but none formed a Hartig net. Mycena pura and Mycena galopus both enhanced seedling growth, with M. pura showing significant transfer of 32 P to the seedlings. Our results support the view that several Mycena species can associate closely with plant roots and some may potentially occupy a transitional state between saprotrophy and biotrophy.
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Affiliation(s)
- Ella Thoen
- Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316, Oslo, Norway
| | - Christoffer Bugge Harder
- Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316, Oslo, Norway
- Department of Plant and Soil Science, Texas Tech University, PO Box 42122, Lubbock, TX, 79409, USA
| | - Håvard Kauserud
- Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316, Oslo, Norway
| | - Synnøve S Botnen
- Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316, Oslo, Norway
| | - Unni Vik
- Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316, Oslo, Norway
| | - Andy F S Taylor
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
- The James Hutton Institute, Craigiebuckler, Aberdeen, AB15 8QH, UK
| | - Audrius Menkis
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, PO Box 7026, SE-75007, Uppsala, Sweden
| | - Inger Skrede
- Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316, Oslo, Norway
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The saprotrophic Pleurotus ostreatus species complex: late Eocene origin in East Asia, multiple dispersal, and complex speciation. IMA Fungus 2020; 11:10. [PMID: 32617259 PMCID: PMC7325090 DOI: 10.1186/s43008-020-00031-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/31/2020] [Indexed: 12/02/2022] Open
Abstract
The Pleurotus ostreatus species complex is saprotrophic and of significant economic and ecological importance. However, species delimitation has long been problematic because of phenotypic plasticity and morphological stasis. In addition, the evolutionary history is poorly understood due to limited sampling and insufficient gene fragments employed for phylogenetic analyses. Comprehensive sampling from Asia, Europe, North and South America and Africa was used to run phylogenetic analyses of the P. ostreatus species complex based on 40 nuclear single-copy orthologous genes using maximum likelihood and Bayesian inference analyses. Here, we present a robust phylogeny of the P. ostreatus species complex, fully resolved from the deepest nodes to species level. The P. ostreatus species complex was strongly supported as monophyletic, and 20 phylogenetic species were recognized, with seven putatively new species. Data from our molecular clock analyses suggested that divergence of the genus Pleurotus probably occurred in the late Jurassic, while the most recent common ancestor of the P. ostreatus species complex diversified about 39 Ma in East Asia. Species of the P. ostreatus complex might migrate from the East Asia into North America across the North Atlantic Land Bridge or the Bering Land Bridge at different times during the late Oligocene, late Miocene and late Pliocene, and then diversified in the Old and New Worlds simultaneously through multiple dispersal and vicariance events. The dispersal from East Asia to South America in the middle Oligocene was probably achieved by a long-distance dispersal event. Intensification of aridity and climate cooling events in the late Miocene and Quaternary glacial cycling probably had a significant influence on diversification patterns of the complex. The disjunctions among East Asia, Europe, North America and Africa within Clade IIc are hypothesized to be a result of allopatric speciation. Substrate transitions to Apiaceae probably occurred no earlier than 6 Ma. Biogeographic analyses suggested that the global cooling of the late Eocene, intensification of aridity caused by rapid uplift of the QTP and retreat of the Tethys Sea in the late Miocene, climate cooling events in Quaternary glacial cycling, and substrate transitions have contributed jointly to diversification of the species complex.
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Teste FP, Jones MD, Dickie IA. Dual-mycorrhizal plants: their ecology and relevance. THE NEW PHYTOLOGIST 2020; 225:1835-1851. [PMID: 31514244 DOI: 10.1111/nph.16190] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/17/2019] [Indexed: 06/10/2023]
Abstract
Dual-mycorrhizal plants are capable of associating with fungi that form characteristic arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) structures. Here, we address the following questions: (1) How many dual-mycorrhizal plant species are there? (2) What are the advantages for a plant to host two, rather than one, mycorrhizal types? (3) Which factors can provoke shifts in mycorrhizal dominance (i.e. mycorrhizal switching)? We identify a large number (89 genera within 32 families) of confirmed dual-mycorrhizal plants based on observing arbuscules or coils for AM status and Hartig net or similar structures for EM status within the same plant species. We then review the possible nutritional benefits and discuss the possible mechanisms leading to net costs and benefits. Cost and benefits of dual-mycorrhizal status appear to be context dependent, particularly with respect to the life stage of the host plant. Mycorrhizal switching occurs under a wide range of abiotic and biotic factors, including soil moisture and nutrient status. The relevance of dual-mycorrhizal plants in the ecological restoration of adverse sites where plants are not carbon limited is discussed. We conclude that dual-mycorrhizal plants are underutilized in ecophysiological-based experiments, yet are powerful model plant-fungal systems to better understand mycorrhizal symbioses without confounding host effects.
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Affiliation(s)
- François P Teste
- Grupo de Estudios Ambientales, IMASL-CONICET & Universidad Nacional de San Luis, Av. Ejercito de los Andes 950 (5700), San Luis, Argentina
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley (Perth), WA, 6009, Australia
| | - Melanie D Jones
- Department of Biology, University of British Columbia, Okanagan Campus, Kelowna, BC, V1V 1V7, Canada
| | - Ian A Dickie
- Bio-Protection Research Centre, School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
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12
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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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Matheny PB, Fordyce JA. Not all ectomycorrhizal fungal lineages are equal. THE NEW PHYTOLOGIST 2019; 222:1670-1672. [PMID: 30942910 DOI: 10.1111/nph.15811] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- P Brandon Matheny
- Department of Ecology and Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, TN, 37996-1610, USA
| | - James A Fordyce
- Department of Ecology and Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, TN, 37996-1610, USA
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Sato H, Toju H. Timing of evolutionary innovation: scenarios of evolutionary diversification in a species-rich fungal clade, Boletales. THE NEW PHYTOLOGIST 2019; 222:1924-1935. [PMID: 30664238 DOI: 10.1111/nph.15698] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 01/14/2019] [Indexed: 06/09/2023]
Abstract
Acquisition of mutualistic symbiosis could provide hosts and/or symbionts with novel ecological opportunities for evolutionary diversification. Such a mechanism is one of the major components of coevolutionary diversification. However, whether the origin of mycorrhizal symbiosis promotes diversification in fungi still requires clarification. Here, we aimed to reveal evolutionary diversification in a clade comprising ectomycorrhizal (ECM) fungi. Based on a phylogenic tree inferred from the sequences of 87 single-copy genes, we reconstructed the origins of ECM symbiosis in a species-rich basidiomycetous order, Boletales. High-resolution phylogeny of Boletales revealed that ECM symbiosis independently evolved from non-ECM states at least four times in the group. Among them, only the second most recent event, occurring in the clade of Boletaceae, was inferred to involve an almost synchronous rapid diversification and rapid transition from non-ECM to ECM symbiosis. Our results contradict the hypothesis of evolutionary priority effect, which postulates the greatest ecological opportunities in the oldest lineages. Therefore, the novel resources that had not been pre-empted by the old ECM fungal lineages - supposedly the coevolving angiosperm hosts - could be available for the young ECM fungal lineages, which resulted in evolutionary diversification occurring only in the young ECM fungal lineages.
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Affiliation(s)
- Hirotoshi Sato
- Graduate School of Human and Environmental Studies, Kyoto University, Sakyo, Kyoto, 606-8501, Japan
| | - Hirokazu Toju
- Center for Ecological Research, Kyoto University, 509-3, 2-chome, Hirano, Otsu, Shiga, 520-2113, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
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Mujic AB, Zheng N, Kim K, Spatafora JW, Castellano MA, Smith ME. The Cedrus-associated truffle Trappeindia himalayensis is a morphologically unique and phylogenetically divergent species of Rhizopogon. Mycologia 2019; 111:225-234. [PMID: 30753119 DOI: 10.1080/00275514.2018.1542864] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In the northwestern Himalayan mountains of India, the hypogeous sequestrate fungus Trappeindia himalayensis is harvested from forests dominated by the ectomycorrhizal tree Cedrus deodara (Himalayan cedar). This truffle has basidiospores that are ornamented with raised reticulation. The original description of Trappeindia himalayensis suggested that the gleba of this species is similar to young specimens of Scleroderma (Boletales), whereas its basidiospores are ornamented with raised reticulation, suggesting a morphological affinity to Leucogaster (Russulales) or Strobilomyces (Boletales). Given this systematic ambiguity, we have generated DNA sequence data from type material and other herbarium specimens and present the first molecular phylogenetic analysis of this unusual Cedrus-associated truffle. Despite the irregular ornamented basidiospore morphology, T. himalayensis is resolved within the genus Rhizopogon (Suillineae, Boletales) and represents a unique lineage that has not been previously detected. All known Rhizopogon species possess an ectomycorrhizal trophic mode, and because of its placement in this lineage, it is likely that Trappeindia himalayensis is an ectomycorrhizal partner of Cedrus deodara. This study highlights the importance of generating sequence data from herbarium specimens in order to identify fungal biodiversity and clarify the systematic relationships of poorly documented fungi.
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Affiliation(s)
- Alija B Mujic
- a Department of Plant Pathology , University of Florida , Gainesville , Florida 32611
| | - Nan Zheng
- a Department of Plant Pathology , University of Florida , Gainesville , Florida 32611
| | - Kristy Kim
- a Department of Plant Pathology , University of Florida , Gainesville , Florida 32611
| | - Joseph W Spatafora
- b Department of Botany and Plant Pathology , Oregon State University , Corvallis , Oregon 97331
| | - Michael A Castellano
- c US Department of Agriculture, Forest Service , Northern Research Station , 3200 SW Jefferson Way, Corvallis , Oregon 97331
| | - Matthew E Smith
- a Department of Plant Pathology , University of Florida , Gainesville , Florida 32611
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16
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Ectomycorrhizal Fungi in South America: Their Diversity in Past, Present and Future Research. Fungal Biol 2019. [DOI: 10.1007/978-3-030-15228-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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17
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Feng B, Yang Z. Studies on diversity of higher fungi in Yunnan, southwestern China: A review. PLANT DIVERSITY 2018; 40:165-171. [PMID: 30740561 PMCID: PMC6137262 DOI: 10.1016/j.pld.2018.07.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/02/2018] [Accepted: 07/05/2018] [Indexed: 06/02/2023]
Abstract
Yunnan is exceedingly rich in higher fungi (Ascomycota and Basidiomycota). Given that the number of fungi (including lichens) occurring in a given area is, as Hawksworth suggested, roughly six times that of local vascular plants, a total of approximately 104,000 fungal species would be expected in Yunnan. However, to date only about 6000 fungal species, including roughly 3000 species of higher fungi, have been reported from the province. Although studies on Yunnan's fungi started in the late nineteenth century, significant progress has been made only in the last forty-five years. Over the first twenty-five years of this period, studies on fungal diversity in this area have largely been about taxonomy based on morphological characters and partially on geographical distribution. Over the past twenty years, the combination of both morphological and molecular phylogenetic approaches has become the preferred method to help understand the diversity and evolution of higher fungi. This review focuses on our current knowledge of how geological, geographical, and ecological factors may have contributed to the diversity patterns of higher fungi in Yunnan. Based on this knowledge, three aspects for future studies are suggested.
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Affiliation(s)
| | - Zhuliang Yang
- Corresponding author. Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road #132, Kunming 650201, Yunnan, China.
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18
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Qin J, Horak E, Popa F, Rexer KH, Kost G, Li F, Yang ZL. Species diversity, distribution patterns, and substrate specificity of Strobilurus. Mycologia 2018; 110:584-604. [PMID: 29913116 DOI: 10.1080/00275514.2018.1463064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The fungal genus Strobilurus belongs to Physalacriaceae and contains approximately 11 species worldwide. Species of this genus grow and reproduce on cones of various conifers, seed pods or fruits of Magnolia and Liquidambar, and branches and wood of conifers. Previous studies focused mainly on samples from Europe and North America. And no genus-specific phylogenetic analysis has been carried out to date. The monophyly, degree of species diversity and substrate specificity, and overall distribution patterns are addressed here using morphological and molecular evidence. The authors collected samples of Strobilurus from much of its known distribution ranges and carried out morphological observations and multilocus phylogenetic analyses using five molecular markers. The results show that Strobilurus is a monophyletic group but may exclude one species, S. ohshimae. A total of 13 species was identified, with two, S. orientalis and S. pachycystidiatus, described as new from China. Several species were shown to be specific to certain substrates, whereas a few less so. Biogeographic analyses indicated that historical exchanges of species between East Asia, Europe, and North America, later vicariance events, and substrate specificity have contributed jointly to diversification of Strobilurus.
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Affiliation(s)
- Jiao Qin
- a Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201 , China.,b Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201 , China
| | - Egon Horak
- c Schlossfeld 17, AT-6020 Innsbruck , Austria
| | - Flavius Popa
- d Department of Ecosystem Monitoring , Research and Conservation , Black Forest National Park, Kniebisstr. 67, 77740 Bad Peterstal-Griesbach , Germany
| | - Karl-Heinz Rexer
- e Systematic Botany and Mycology, FB17, Philipps University Marburg , 35032 Marburg , Germany
| | - Gerhard Kost
- e Systematic Botany and Mycology, FB17, Philipps University Marburg , 35032 Marburg , Germany
| | - Fang Li
- f School of Life Sciences , Sun Yat-sen University , Guangzhou 510275 , China
| | - Zhu L Yang
- a Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201 , China
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The fungus that came in from the cold: dry rot's pre-adapted ability to invade buildings. ISME JOURNAL 2018; 12:791-801. [PMID: 29305577 DOI: 10.1038/s41396-017-0006-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 10/17/2017] [Indexed: 01/24/2023]
Abstract
Many organisms benefit from being pre-adapted to niches shaped by human activity, and have successfully invaded man-made habitats. One such species is the dry rot fungus Serpula lacrymans, which has a wide distribution in buildings in temperate and boreal regions, where it decomposes coniferous construction wood. Comparative genomic analyses and growth experiments using this species and its wild relatives revealed that S. lacrymans evolved a very effective brown rot decay compared to its wild relatives, enabling an extremely rapid decay in buildings under suitable conditions. Adaptations in intracellular transport machineries promoting hyphal growth, and nutrient and water transport may explain why it is has become a successful invader of timber in houses. Further, we demonstrate that S. lacrymans has poor combative ability in our experimental setup, compared to other brown rot fungi. In sheltered indoor conditions, the dry rot fungus may have limited encounters with other wood decay fungi compared to its wild relatives. Overall, our analyses indicate that the dry rot fungus is an ecological specialist with poor combative ability against other fungi.
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20
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Hyde KD, Maharachchikumbura SSN, Hongsanan S, Samarakoon MC, Lücking R, Pem D, Harishchandra D, Jeewon R, Zhao RL, Xu JC, Liu JK, Al-Sadi AM, Bahkali AH, Elgorban AM. The ranking of fungi: a tribute to David L. Hawksworth on his 70th birthday. FUNGAL DIVERS 2017. [DOI: 10.1007/s13225-017-0383-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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21
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Zhao RL, Li GJ, Sánchez-Ramírez S, Stata M, Yang ZL, Wu G, Dai YC, He SH, Cui BK, Zhou JL, Wu F, He MQ, Moncalvo JM, Hyde KD. A six-gene phylogenetic overview of Basidiomycota and allied phyla with estimated divergence times of higher taxa and a phyloproteomics perspective. FUNGAL DIVERS 2017. [DOI: 10.1007/s13225-017-0381-5] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Truong C, Sánchez-Ramírez S, Kuhar F, Kaplan Z, Smith ME. The Gondwanan connection - Southern temperate Amanita lineages and the description of the first sequestrate species from the Americas. Fungal Biol 2017; 121:638-651. [PMID: 28705393 DOI: 10.1016/j.funbio.2017.04.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 03/16/2017] [Accepted: 04/18/2017] [Indexed: 02/04/2023]
Abstract
Amanita is a diverse and cosmopolitan genus of ectomycorrhizal fungi. We describe Amanita nouhrae sp. nov., a new hypogeous ('truffle-like') species associated with Nothofagus antarctica in northern Patagonia. This constitutes the first report of a sequestrate Amanita from the Americas. Thick-walled basidiospores ornamented on the interior spore wall ('crassospores') were observed consistently in A. nouhrae and its sister epigeous taxon Amanita morenoi, a rarely collected but apparently common species from northern Patagonia that has sometimes been misidentified as the Australian taxon Amanita umbrinella. Nuclear 18S and 28S ribosomal DNA and mitochondrial 16S and 26S DNA placed these two species in a southern temperate clade within subgenus Amanita, together with other South American and Australian species. Based on a dated genus-level phylogeny, we estimate that the southern temperate clade may have originated near the Eocene/Oligocene boundary (ca. 35 Ma ± 10 Ma). This date suggests a broadly distributed ancestor in the Southern Hemisphere, which probably diversified as a result of continental drift, as well as the initiation of the Antarctic glaciation. By comparison, we show that this clade follows an exceptional biogeographic pattern within a genus otherwise seemingly dominated by Northern Hemisphere dispersal.
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Affiliation(s)
- Camille Truong
- University of Florida, Department of Plant Pathology, 2523 Fifield Hall, Gainesville FL 32611, USA.
| | - Santiago Sánchez-Ramírez
- Department of Ecology and Evolutionary Biology, University of Toronto, 100 Queen's Park, Toronto, ON, M5S 2C6, Canada
| | - Francisco Kuhar
- Centro de Investigación y Extensión Forestal Andino Patagónico (CONICET), Ruta 259, Km 4, Esquel 9200, Chubut, Argentina
| | - Zachary Kaplan
- University of Florida, Department of Plant Pathology, 2523 Fifield Hall, Gainesville FL 32611, USA
| | - Matthew E Smith
- University of Florida, Department of Plant Pathology, 2523 Fifield Hall, Gainesville FL 32611, USA
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23
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Truong C, Mujic AB, Healy R, Kuhar F, Furci G, Torres D, Niskanen T, Sandoval-Leiva PA, Fernández N, Escobar JM, Moretto A, Palfner G, Pfister D, Nouhra E, Swenie R, Sánchez-García M, Matheny PB, Smith ME. How to know the fungi: combining field inventories and DNA-barcoding to document fungal diversity. THE NEW PHYTOLOGIST 2017; 214:913-919. [PMID: 28272801 DOI: 10.1111/nph.14509] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- Camille Truong
- Department of Plant Pathology, University of Florida, PO Box 110680, Gainesville, FL, 32611, USA
| | - Alija B Mujic
- Department of Plant Pathology, University of Florida, PO Box 110680, Gainesville, FL, 32611, USA
| | - Rosanne Healy
- Department of Plant Pathology, University of Florida, PO Box 110680, Gainesville, FL, 32611, USA
| | - Francisco Kuhar
- Centro de Investigación y Extensión Forestal Andino Patagónico (CONICET), Ruta 259, Km 4, Esquel, 9200, Chubut, Argentina
| | - Giuliana Furci
- Fundación Fungi, José Zapiola 8240 E, La Reina, Santiago, Chile
| | - Daniela Torres
- Fundación Fungi, José Zapiola 8240 E, La Reina, Santiago, Chile
| | - Tuula Niskanen
- The Jodrell Laboratory, Royal Botanic Gardens, Kew, Surrey, TW9 3AB, UK
| | | | - Natalia Fernández
- Laboratorio de Microbiología Aplicada y Biotecnología (CONICET), Universidad Nacional del Comahue, IPATEC, Quintral 1250, San Carlos de Bariloche, 8400, Río Negro, Argentina
| | - Julio M Escobar
- Centro Austral de Investigaciones Científicas (CONICET), Bernardo Houssay 200, Ushuaia, 9410, Tierra del Fuego, Argentina
| | - Alicia Moretto
- Centro Austral de Investigaciones Científicas (CONICET), Bernardo Houssay 200, Ushuaia, 9410, Tierra del Fuego, Argentina
- Universidad Nacional de Tierra del Fuego, Onas 450, Ushuaia, 9410, Tierra del Fuego, Argentina
| | - Götz Palfner
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Donald Pfister
- Farlow Herbarium of Cryptogamic Botany and Department of Organismic and Evolutionary Biology, Harvard University, 22 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Eduardo Nouhra
- Instituto Multidisciplinario de Biología Vegetal (CONICET), FCEFyN, Universidad Nacional de Córdoba, Casilla de correo 495, Córdoba, 5000, Argentina
| | - Rachel Swenie
- Department of Ecology and Evolutionary Biology, University of Tennessee, 334 Hesler Biology Building, Knoxville, TN, 37996, USA
| | - Marisol Sánchez-García
- Department of Ecology and Evolutionary Biology, University of Tennessee, 334 Hesler Biology Building, Knoxville, TN, 37996, USA
| | - P Brandon Matheny
- Department of Ecology and Evolutionary Biology, University of Tennessee, 334 Hesler Biology Building, Knoxville, TN, 37996, USA
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, PO Box 110680, Gainesville, FL, 32611, USA
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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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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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Trappe MJ, Smith ME, Hobbie EA. Exploring the phylogenetic affiliations and the trophic mode of Sedecula pulvinata (Sedeculaceae). Mycologia 2017; 107:688-96. [DOI: 10.3852/14-110] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 02/02/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Matthew J. Trappe
- Department of Forest Ecosystems and Society, 321 Richardson Hall, Oregon State University, Corvallis, Oregon 97331
| | - Matthew E. Smith
- Department of Plant Pathology, University of Florida, 2517 Fifield Hall, Gainesville, Florida 32611
| | - Erik A. Hobbie
- Earth Systems Research Center, University of New Hampshire, Durham, New Hampshire 03824
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Overview of Phylogenetic Approaches to Mycorrhizal Biogeography, Diversity and Evolution. BIOGEOGRAPHY OF MYCORRHIZAL SYMBIOSIS 2017. [DOI: 10.1007/978-3-319-56363-3_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Martin F, Kohler A, Murat C, Veneault-Fourrey C, Hibbett DS. Unearthing the roots of ectomycorrhizal symbioses. Nat Rev Microbiol 2016; 14:760-773. [PMID: 27795567 DOI: 10.1038/nrmicro.2016.149] [Citation(s) in RCA: 185] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
During the diversification of Fungi and the rise of conifer-dominated and angiosperm- dominated forests, mutualistic symbioses developed between certain trees and ectomycorrhizal fungi that enabled these trees to colonize boreal and temperate regions. The evolutionary success of these symbioses is evident from phylogenomic analyses that suggest that ectomycorrhizal fungi have arisen in approximately 60 independent saprotrophic lineages, which has led to the wide range of ectomycorrhizal associations that exist today. In this Review, we discuss recent genomic studies that have revealed the adaptations that seem to be fundamental to the convergent evolution of ectomycorrhizal fungi, including the loss of some metabolic functions and the acquisition of effectors that facilitate mutualistic interactions with host plants. Finally, we consider how these insights can be integrated into a model of the development of ectomycorrhizal symbioses.
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Affiliation(s)
- Francis Martin
- Institut national de la recherche agronomique (INRA), Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (ARBRE), Centre INRA-Lorraine, 54280 Champenoux, France
| | - Annegret Kohler
- Institut national de la recherche agronomique (INRA), Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (ARBRE), Centre INRA-Lorraine, 54280 Champenoux, France
| | - Claude Murat
- Institut national de la recherche agronomique (INRA), Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (ARBRE), Centre INRA-Lorraine, 54280 Champenoux, France
| | - Claire Veneault-Fourrey
- Université de Lorraine, Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Laboratoire d'excellence Recherches Avancées sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (ARBRE), 54500 Vandoeuvre-lès-Nancy, France
| | - David S Hibbett
- Biology Department, Clark University, Lasry Center for Bioscience, 950 Main Street, Worcester, Massachusetts 01610, USA
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Garnica S, Riess K, Schön ME, Oberwinkler F, Setaro SD. Divergence Times and Phylogenetic Patterns of Sebacinales, a Highly Diverse and Widespread Fungal Lineage. PLoS One 2016; 11:e0149531. [PMID: 26938104 PMCID: PMC4795679 DOI: 10.1371/journal.pone.0149531] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 02/02/2016] [Indexed: 01/03/2023] Open
Abstract
Patterns of geographic distribution and composition of fungal communities are still poorly understood. Widespread occurrence in terrestrial ecosystems and the unique richness of interactions of Sebacinales with plants make them a target group to study evolutionary events in the light of nutritional lifestyle. We inferred diversity patterns, phylogenetic structures and divergence times of Sebacinales with respect to their nutritional lifestyles by integrating data from fossil-calibrated phylogenetic analyses. Relaxed molecular clock analyses indicated that Sebacinales originated late Permian within Basidiomycota, and their split into Sebacinaceae and Serendipitaceae nom. prov. likely occurred during the late Jurassic and the early Cretaceous, coinciding with major diversifications of land plants. In Sebacinaceae, diversification of species with ectomycorrhizal lifestyle presumably started during the Paleocene. Lineage radiations of the core group of ericoid and cavendishioid mycorrhizal Sebacinales started probably in the Eocene, coinciding with diversification events of their hosts. The diversification of Sebacinales with jungermannioid interactions started during the Oligocene, and occurred much later than the diversification of their hosts. Sebacinales communities associated either with ectomycorrhizal plants, achlorophyllous orchids, ericoid and cavendishioid Ericaceae or liverworts were phylogenetically clustered and globally distributed. Major Sebacinales lineage diversifications started after the continents had drifted apart. We also briefly discuss dispersal patterns of extant Sebacinales.
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Affiliation(s)
- Sigisfredo Garnica
- University of Tübingen, Institute of Evolution and Ecology, Plant Evolutionary Ecology, Auf der Morgenstelle 1, 72076, Tübingen, Germany
| | - Kai Riess
- University of Tübingen, Institute of Evolution and Ecology, Plant Evolutionary Ecology, Auf der Morgenstelle 1, 72076, Tübingen, Germany
| | - Max E. Schön
- University of Tübingen, Institute of Evolution and Ecology, Plant Evolutionary Ecology, Auf der Morgenstelle 1, 72076, Tübingen, Germany
| | - Franz Oberwinkler
- University of Tübingen, Institute of Evolution and Ecology, Plant Evolutionary Ecology, Auf der Morgenstelle 1, 72076, Tübingen, Germany
| | - Sabrina D. Setaro
- Wake Forest University, Department of Biology, 205 Winston Hall, 1834 Wake Forest Road, Winston-Salem, North Carolina, 27106, United States of America
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Looney BP, Ryberg M, Hampe F, Sánchez-García M, Matheny PB. Into and out of the tropics: global diversification patterns in a hyperdiverse clade of ectomycorrhizal fungi. Mol Ecol 2016; 25:630-47. [PMID: 26642189 DOI: 10.1111/mec.13506] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 11/10/2015] [Accepted: 11/22/2015] [Indexed: 01/30/2023]
Abstract
Ectomycorrhizal (ECM) fungi, symbiotic mutualists of many dominant tree and shrub species, exhibit a biogeographic pattern counter to the established latitudinal diversity gradient of most macroflora and fauna. However, an evolutionary basis for this pattern has not been explicitly tested in a diverse lineage. In this study, we reconstructed a mega-phylogeny of a cosmopolitan and hyperdiverse genus of ECM fungi, Russula, sampling from annotated collections and utilizing publically available sequences deposited in GenBank. Metadata from molecular operational taxonomic unit cluster sets were examined to infer the distribution and plant association of the genus. This allowed us to test for differences in patterns of diversification between tropical and extratropical taxa, as well as how their associations with different plant lineages may be a driver of diversification. Results show that Russula is most species-rich at temperate latitudes and ancestral state reconstruction shows that the genus initially diversified in temperate areas. Migration into and out of the tropics characterizes the early evolution of the genus, and these transitions have been frequent since this time. We propose the 'generalized diversification rate' hypothesis to explain the reversed latitudinal diversity gradient pattern in Russula as we detect a higher net diversification rate in extratropical lineages. Patterns of diversification with plant associates support host switching and host expansion as driving diversification, with a higher diversification rate in lineages associated with Pinaceae and frequent transitions to association with angiosperms.
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Affiliation(s)
- Brian P Looney
- Department of Ecology and Evolutionary Biology, University of Tennessee, 332 Hesler Biology Building, Knoxville, TN, 37996-1610, USA
| | - Martin Ryberg
- Department of Organismal Biology, Uppsala University, Evolutionsbiologiskt Centrum, Norbyv. 18D, 75236, Uppsala, Sweden
| | - Felix Hampe
- Department of Biology, Gent University, K.L. Ledeganckstraat 35, 9000, Gent, Belgium
| | - Marisol Sánchez-García
- Department of Ecology and Evolutionary Biology, University of Tennessee, 332 Hesler Biology Building, Knoxville, TN, 37996-1610, USA
| | - P Brandon Matheny
- Department of Ecology and Evolutionary Biology, University of Tennessee, 332 Hesler Biology Building, Knoxville, TN, 37996-1610, USA
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31
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Balasundaram SV, Engh IB, Skrede I, Kauserud H. How many DNA markers are needed to reveal cryptic fungal species? Fungal Biol 2015; 119:940-945. [DOI: 10.1016/j.funbio.2015.07.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 06/17/2015] [Accepted: 07/14/2015] [Indexed: 10/23/2022]
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32
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Harrower E, Bougher NL, Henkel TW, Horak E, Matheny PB. Long-distance dispersal and speciation of Australasian and American species of Cortinarius sect. Cortinarius. Mycologia 2015; 107:697-709. [PMID: 25911703 DOI: 10.3852/14-182] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 02/28/2015] [Indexed: 11/10/2022]
Abstract
We present a multigene phylogeny (partial nuc rDNA and RPB2) of Cortinarius sect. Cortinarius (i.e. the C. violaceus group), which reveals eight species distributed in Europe, Australasia, South America, Central America and North America. Relaxed molecular clock analyses suggested that diversification began during the Miocene, thus rejecting more ancient Gondwanan origin scenarios among the taxa currently occurring in the northern and southern hemispheres. There was strong support for an Australasian origin of the C. violaceus group with initial dispersal to the Neotropics, followed by migration into North America and Europe. A dispersal-extinction cladogenesis model that includes a parameter for founder effects was the most highly supported biogeographic model in the program BioGeoBEARS. A maximum likelihood analysis showed the most recent common ancestor of sect. Cortinarius was an angiosperm ectomycorrhizal associate. Ancestral associations at the plant family level, however, were ambiguous. Of eight recovered species-level lineages, C. violaceus is the only one that associates with Pinaceae and the only species to associate with both Pinaceae and angiosperms. This analysis showed that long-distance dispersal and founder event speciation have been important factors during evolution of the C. violaceus group.
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Affiliation(s)
- Emma Harrower
- Department of Ecology and Evolutionary Biology, 569 Dabney Hall, University of Tennessee, Knoxville, Tennessee 37996
| | - Neale L Bougher
- Department of Parks and Wildlife, Science and Conservation Division, Western Australian Herbarium, Bentley Delivery Centre, Kensington, WA 6151, Australia
| | - Terry W Henkel
- Department of Biological Sciences, Humboldt State University, Arcata, California 95521
| | - Egon Horak
- Schlossfeld 17, A-6020 Innsbruck, Austria
| | - P Brandon Matheny
- Department of Ecology and Evolutionary Biology, 569 Dabney Hall, University of Tennessee, Knoxville, Tennessee 37996
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33
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Chen JJ, Cui BK, Zhou LW, Korhonen K, Dai YC. Phylogeny, divergence time estimation, and biogeography of the genus Heterobasidion (Basidiomycota, Russulales). FUNGAL DIVERS 2015. [DOI: 10.1007/s13225-014-0317-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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34
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Lebel T, Castellano MA, Beever RE. Cryptic diversity in the sequestrate genus Stephanospora (Stephanosporaceae: Agaricales) in Australasia. Fungal Biol 2014; 119:201-28. [PMID: 25813509 DOI: 10.1016/j.funbio.2014.12.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 12/02/2014] [Accepted: 12/08/2014] [Indexed: 11/27/2022]
Abstract
Historically a single name, Stephanospora flava, was applied to all collections of Stephanospora in Australasia. We used morphological characters with molecular support to differentiate and describe nine novel cryptic species, and refine the circumscription of S. flava. Stephanospora flava is herein restricted to bispored collections from Tasmania, and the quadrisporic Stephanospora tetraspora is raised to species level. Six species (four new) are endemic to Australia, S. flava s.s, S. tetraspora comb. nov., Stephanospora sheoak, Stephanospora cribbae, Stephanospora hystrispora, and Stephanospora occidentiaustralis. Three species Stephanospora poropingao, Stephanospora pounamu, and Stephanospora kanuka are endemic to New Zealand; and one species, Stephanospora aorangi occurs in both Australia and New Zealand. Two other new species, Stephanospora novae-caledoniae and Stephanospora papua, are endemic to New Caledonia or Papua New Guinea, respectively. Analyses of three nuclear gene regions (ITS, ef-1, and LSU) are consistent with current classifications of the family Stephanosporaceae. Athelidium aurantiacum is an outlier, with a strongly supported core of Cristinia (Clade I), Lindtneria (Clade II), Stephanospora, Mayamontana, and Lindtneria trachyspora (Clade III), and a novel lineage of environmental and sporocarp sequences (Clade IV). Taxonomic and nomenclatural issues raised by the presence of both type species of Stephanospora (Stephanospora caroticolor) and Lindtneria (L. trachyspora) in the same clade are discussed.
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Affiliation(s)
- Teresa Lebel
- Manaaki Whenua - Landcare Research, Private Bag 92170, Auckland 1142, New Zealand; National Herbarium of Victoria, Royal Botanic Gardens Melbourne, Private Bag 2000, Melbourne, Victoria 3141, Australia.
| | - Michael A Castellano
- U.S. Department of Agriculture, Forest Service, Northern Research Station, Forest Sciences Laboratory, 3200 Jefferson Way, Corvallis, OR 97331, USA
| | - Ross E Beever
- Manaaki Whenua - Landcare Research, Private Bag 92170, Auckland 1142, New Zealand
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Multigene molecular phylogeny and biogeographic diversification of the earth tongue fungi in the genera Cudonia and Spathularia (Rhytismatales, Ascomycota). PLoS One 2014; 9:e103457. [PMID: 25084276 PMCID: PMC4118880 DOI: 10.1371/journal.pone.0103457] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Accepted: 06/30/2014] [Indexed: 11/19/2022] Open
Abstract
The family Cudoniaceae (Rhytismatales, Ascomycota) was erected to accommodate the "earth tongue fungi" in the genera Cudonia and Spathularia. There have been no recent taxonomic studies of these genera, and the evolutionary relationships within and among these fungi are largely unknown. Here we explore the molecular phylogenetic relationships within Cudonia and Spathularia using maximum likelihood and Bayesian inference analyses based on 111 collections from across the Northern Hemisphere. Phylogenies based on the combined data from ITS, nrLSU, rpb2 and tef-1α sequences support the monophyly of three main clades, the /flavida, /velutipes, and /cudonia clades. The genus Cudonia and the family Cudoniaceae are supported as monophyletic groups, while the genus Spathularia is not monophyletic. Although Cudoniaceae is monophyletic, our analyses agree with previous studies that this family is nested within the Rhytismataceae. Our phylogenetic analyses circumscribes 32 species-level clades, including the putative recognition of 23 undescribed phylogenetic species. Our molecular phylogeny also revealed an unexpectedly high species diversity of Cudonia and Spathularia in eastern Asia, with 16 (out of 21) species-level clades of Cudonia and 8 (out of 11) species-level clades of Spathularia. We estimate that the divergence time of the Cudoniaceae was in the Paleogene approximately 28 Million years ago (Mya) and that the ancestral area for this group of fungi was in Eastern Asia based on the current data. We hypothesize that the large-scale geological and climatic events in Oligocene (e.g. the global cooling and the uplift of the Tibetan plateau) may have triggered evolutionary radiations in this group of fungi in East Asia. This work provides a foundation for future studies on the phylogeny, diversity, and evolution of Cudonia and Spathularia and highlights the need for more molecular studies on collections from Europe and North America.
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Tedersoo L, Bahram M, Ryberg M, Otsing E, Kõljalg U, Abarenkov K. Global biogeography of the ectomycorrhizal /sebacina lineage (Fungi, Sebacinales) as revealed from comparative phylogenetic analyses. Mol Ecol 2014; 23:4168-83. [PMID: 24981058 DOI: 10.1111/mec.12849] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 06/18/2014] [Accepted: 06/20/2014] [Indexed: 01/26/2023]
Abstract
Compared with plants and animals, large-scale biogeographic patterns of microbes including fungi are poorly understood. By the use of a comparative phylogenetic approach and ancestral state reconstructions, we addressed the global biogeography, rate of evolution and evolutionary origin of the widely distributed ectomycorrhizal (EcM) /sebacina lineage that forms a large proportion of the Sebacinales order. We downloaded all publicly available internal transcribed spacer (ITS) sequences and metadata and supplemented sequence information from three genes to construct dated phylogenies and test biogeographic hypotheses. The /sebacina lineage evolved 45-57 Myr ago that groups it with relatively young EcM taxa in other studies. The most parsimonious origin for /sebacina is inferred to be North American temperate coniferous forests. Among biogeographic traits, region and biome exhibited stronger phylogenetic signal than host family. Consistent with the resource availability (environmental energy) hypothesis, the ITS region is evolving at a faster rate in tropical than nontropical regions. Most biogeographic regions exhibited substantial phylogenetic clustering suggesting a strong impact of dispersal limitation over a large geographic scale. In northern Holarctic regions, however, phylogenetic distances and phylogenetic grouping of isolates indicate multiple recent dispersal events.
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Affiliation(s)
- Leho Tedersoo
- Natural History Museum of Tartu University, 14A Ravila, Tartu, 50411, Estonia
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Dillenberger MS, Kadereit JW. The phylogeny of the European high mountain genus Adenostyles (Asteraceae-Senecioneae) reveals that edaphic shifts coincide with dispersal events. AMERICAN JOURNAL OF BOTANY 2013; 100:1171-1183. [PMID: 23709635 DOI: 10.3732/ajb.1300060] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
PREMISE OF THE STUDY Heterogeneity of edaphic conditions plays a large role in driving the diversification of many plant groups. In the Alps and other European high mountains, many closely related calcicole and calcifuge plant taxa exist. To better understand patterns and processes of edaphic differentiation, the phylogeny of the edaphically variable genus Adenostyles was studied. The genus contains three species, of which A. alpina has five subspecies. Each species and subspecies is largely confined to either calcareous or noncalcareous substrates. • METHODS We analyzed the phylogeny of Adenostyles using DNA sequences of nrITS, nrETS, nuclear chalcone synthase, and three plastid markers (rpl32-trnL, psbA-trnH, and ndhF-rpl32) from 45 in-group and five out-group samples. The phylogeny was used to reconstruct ancestral edaphic associations and distribution areas. • KEY RESULTS Within Adenostyles alpina, the shifts of edaphic association from calcicole to calcifuge in subsp. briquetii (Corsica) and in a clade of subsp. macrocephala (southernmost Italy) plus subsp. pyrenaica (Pyrenees) coincide with dispersal events. • CONCLUSIONS We conclude that colonization of areas with novel edaphic conditions via dispersal can trigger shifts of edaphic association. Accordingly, edaphic niche shifts can result from chance events.
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Affiliation(s)
- Markus S Dillenberger
- Institut für Spezielle Botanik, Johannes Gutenberg-Universität Mainz, Bentzelweg 9a, 55099 Mainz, Germany.
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Da Lage JL, Binder M, Hua-Van A, Janeček S, Casane D. Gene make-up: rapid and massive intron gains after horizontal transfer of a bacterial α-amylase gene to Basidiomycetes. BMC Evol Biol 2013; 13:40. [PMID: 23405862 PMCID: PMC3584928 DOI: 10.1186/1471-2148-13-40] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 01/30/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Increasing genome data show that introns, a hallmark of eukaryotes, already existed at a high density in the last common ancestor of extant eukaryotes. However, intron content is highly variable among species. The tempo of intron gains and losses has been irregular and several factors may explain why some genomes are intron-poor whereas other are intron-rich. RESULTS We studied the dynamics of intron gains and losses in an α-amylase gene, whose product breaks down starch and other polysaccharides. It was transferred from an Actinobacterium to an ancestor of Agaricomycotina. This gene underwent further duplications in several species. The results indicate a high rate of intron insertions soon after the gene settled in the fungal genome. A number of these oldest introns, regularly scattered along the gene, remained conserved. Subsequent gains and losses were lineage dependent, with a majority of losses. Moreover, a few species exhibited a high number of both specific intron gains and losses in recent periods. There was little sequence conservation around insertion sites, then probably little information for splicing, whereas splicing sites, inside introns, showed typical and conserved patterns. There was little variation of intron size. CONCLUSIONS Since most Basidiomycetes have intron-rich genomes and this richness was ancestral in Fungi, long before the transfer event, we suggest that the new gene was shaped to comply with requirements of the splicing machinery, such as short exon and intron sizes, in order to be correctly processed.
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Affiliation(s)
- Jean-Luc Da Lage
- Laboratoire Evolution, génomes et spéciation UPR 9034 CNRS, 91198 Gif-sur-Yvette, and Université Paris-Sud, Orsay, 91405, France.
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Evolutionary origin, worldwide dispersal, and population genetics of the dry rot fungus Serpula lacrymans. FUNGAL BIOL REV 2012. [DOI: 10.1016/j.fbr.2012.08.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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40
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Wilson AW, Binder M, Hibbett DS. Diversity and evolution of ectomycorrhizal host associations in the Sclerodermatineae (Boletales, Basidiomycota). THE NEW PHYTOLOGIST 2012; 194:1079-1095. [PMID: 22471405 DOI: 10.1111/j.1469-8137.2012.04109.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
This study uses phylogenetic analysis of the Sclerodermatineae to reconstruct the evolution of ectomycorrhizal host associations in the group using divergence dating, ancestral range and ancestral state reconstructions. Supermatrix and supertree analysis were used to create the most inclusive phylogeny for the Sclerodermatineae. Divergence dates were estimated in BEAST. Lagrange was used to reconstruct ancestral ranges. BayesTraits was used to reconstruct ectomycorrhizal host associations using extant host associations with data derived from literature sources. The supermatrix data set was combined with internal transcribed spacer (ITS) data sets for Astraeus, Calostoma, and Pisolithus to produce a 168 operational taxonomic unit (OTU) supertree. The ensuing analysis estimated that basal Sclerodermatineae originated in the late Cretaceous while major genera diversified near the mid Cenozoic. Asia and North America are the most probable ancestral areas for all Sclerodermatineae, and angiosperms, primarily rosids, are the most probable ancestral hosts. Evolution in the Sclerodermatineae follows the biogeographic history of disjunct plant communities associated with early Cenozoic mesophytic forests and a boreotropical history. Broad geographic distributions are observed in the most promiscuous Sclerodermatineae (those with broad host ranges), while those with relatively limited distribution have fewer documented ectomycorrhizal associations. This suggests that ectomycorrhizal generalists have greater dispersal capabilities than specialists.
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Affiliation(s)
- Andrew W Wilson
- Department of Biology, Clark University, 950 Main St., Worcester, MA 01610, USA
| | - Manfred Binder
- Department of Biology, Clark University, 950 Main St., Worcester, MA 01610, USA
| | - David S Hibbett
- Department of Biology, Clark University, 950 Main St., Worcester, MA 01610, USA
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DNA sequence analyses reveal abundant diversity, endemism and evidence for Asian origin of the porcini mushrooms. PLoS One 2012; 7:e37567. [PMID: 22629418 PMCID: PMC3356339 DOI: 10.1371/journal.pone.0037567] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 04/20/2012] [Indexed: 11/19/2022] Open
Abstract
The wild gourmet mushroom Boletus edulis and its close allies are of significant ecological and economic importance. They are found throughout the Northern Hemisphere, but despite their ubiquity there are still many unresolved issues with regard to the taxonomy, systematics and biogeography of this group of mushrooms. Most phylogenetic studies of Boletus so far have characterized samples from North America and Europe and little information is available on samples from other areas, including the ecologically and geographically diverse regions of China. Here we analyzed DNA sequence variation in three gene markers from samples of these mushrooms from across China and compared our findings with those from other representative regions. Our results revealed fifteen novel phylogenetic species (about one-third of the known species) and a newly identified lineage represented by Boletus sp. HKAS71346 from tropical Asia. The phylogenetic analyses support eastern Asia as the center of diversity for the porcini sensu stricto clade. Within this clade, B. edulis is the only known holarctic species. The majority of the other phylogenetic species are geographically restricted in their distributions. Furthermore, molecular dating and geological evidence suggest that this group of mushrooms originated during the Eocene in eastern Asia, followed by dispersal to and subsequent speciation in other parts of Asia, Europe, and the Americas from the middle Miocene through the early Pliocene. In contrast to the ancient dispersal of porcini in the strict sense in the Northern Hemisphere, the occurrence of B. reticulatus and B. edulis sensu lato in the Southern Hemisphere was probably due to recent human-mediated introductions.
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Du XH, Zhao Q, O'Donnell K, Rooney AP, Yang ZL. Multigene molecular phylogenetics reveals true morels (Morchella) are especially species-rich in China. Fungal Genet Biol 2012; 49:455-69. [PMID: 22503770 DOI: 10.1016/j.fgb.2012.03.006] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 03/18/2012] [Accepted: 03/23/2012] [Indexed: 10/28/2022]
Abstract
The phylogenetic diversity of true morels (Morchella) in China was estimated by initially analyzing nuclear ribosomal internal transcribed spacer (ITS) rDNA sequences from 361 specimens collected in 21 provinces during the 2003-2011 growing seasons, together with six collections obtained on loan from three Chinese herbaria. Based on the results of this preliminary screen, 40 Esculenta Clade (yellow morels) and 30 Elata Clade (black morels) were chosen to represent the full range of phylogenetic diversity sampled. To investigate their species limits, we generated DNA sequences from portions of three protein-coding genes (RPB1, RPB2 and EF-1α) and domains D1 and D2 of the nuclear large subunit (LSU) rDNA for all 70 collections. To fully assess evolutionary relationships, previously published multilocus DNA sequence data representing all known Morchella species was included in this study. Phylogenetic analyses employing maximum parsimony and maximum likelihood frameworks resolved 30 species in China compared with 22 in Europe and 19 within North America. Eleven novel phylogenetically distinct species were discovered in China, including two species within the Elata Clade and nine within the Esculenta Clade. Of the 30 species in China, 20 appear to be endemic, nine were also represented in Europe, and four putatively fire-adapted species have disjunct distributions in China, Europe and western North America. Although the diversification time estimates place the Esculenta Clade in China as early as the late Cretaceous and the Elata Clade by the early Oligocene, 27 of the 30 species evolved between the middle Miocene 12Mya and present.
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Affiliation(s)
- Xi-Hui Du
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road, No. 132, Kunming, 650201 Yunnan Province, PR China
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Watkinson S, Eastwood D. Serpula lacrymans, Wood and Buildings. ADVANCES IN APPLIED MICROBIOLOGY 2012; 78:121-49. [PMID: 22305095 DOI: 10.1016/b978-0-12-394805-2.00005-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Serpula lacrymans, the causative agent of dry rot timber decay in buildings, is a Basidiomycete fungus in the Boletales clade. It owes its destructiveness to a uniquely well-developed capacity to colonize by rapid mycelial spread from sites of initial spore infection, coupled with aggressive degradation of wood cellulose. Genomic methods have recently elucidated the evolution and enzymic repertoire of the fungus, suggesting that it has a distinctive mode of brown rot wood decay. Using novel methods to image nutrient translocation, its mycelium has been modeled as a highly responsive resource-supply network. Dry rot is preventable by keeping timber dry. However, in established outbreaks, further mycelial spread can be arrested by inhibitors of translocation.
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