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Chen H, White JF, Malik K, Li C. Molecular assessment of oat head blight fungus, including a new genus and species in a family of Nectriaceae. Int J Food Microbiol 2024; 417:110715. [PMID: 38657420 DOI: 10.1016/j.ijfoodmicro.2024.110715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/14/2024] [Accepted: 04/18/2024] [Indexed: 04/26/2024]
Abstract
Head blight (HB) of oat (Avena sativa) has caused significant production losses in oats growing areas of western China. A total of 314 isolates, associated with HB were collected from the major oat cultivating areas of Gansu, Qinghai, and Yunnan Provinces in western China. Based on morphological characters, the isolates were initially classified into three genera, as differentiation to species was a bit difficult. Taxonomic analysis of these isolates based on muti-gene phylogenetic analyses (ITS, TEF1, TUB2, and RPB2) revealed four known Fusarium species, F. proliferatum, F. avenaceum, F. poae, and F. sibiricum, and one Acremonium specie (A. sclerotigenum). In addition, a new genus Neonalanthamala gen. nov., similar to genus Nalanthamala was introduced herein with a new combination, Neonalanthamala graminearum sp. nov., to accommodate the HB fungus. The molecular clock analyses estimated the divergence time of the Neonalanthamala and Nalanthamala based on a dataset (ITS, TUB2, RPB2), and we recognized the mean stem ages of the two genera are 98.95 Mya, which showed that they evolved from the same ancestor. N. graminearum was the most prevalent throughout the surveyed provinces. Pathogenicity test was carried out by using two different methods: seed inoculation and head inoculation. Results showed that F. sibiricum isolates were the most aggressive on the seed and head. A. sclerotigenum isolates were not pathogenic to seeds, and were developed less symptoms to the head compared to other species. Data analyses showed that the correlation of the germination potential, germination index, and dry weight of seed inoculation and disease index of plant inoculation had a highly significant negative correlation (P < 0.001). These results showed that the development of HB might be predicted by seed tests for this species. A. sclerotigenum and N. graminearum causing HB are being firstly reported on oat in the world. Similarly, F. proliferatum, F. avenaceum, F. poae and F. sibiricum causing oat HB are firstly reported in China.
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Affiliation(s)
- Hao Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, Gansu Tech Innovation Center of Western China Grassland Industry, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - James F White
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901-8520, USA
| | - Kamran Malik
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, Gansu Tech Innovation Center of Western China Grassland Industry, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Chunjie Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, Gansu Tech Innovation Center of Western China Grassland Industry, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; Grassland Research Center of National Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing 100091, China.
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2
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Baroncelli R, Cobo-Díaz JF, Benocci T, Peng M, Battaglia E, Haridas S, Andreopoulos W, LaButti K, Pangilinan J, Lipzen A, Koriabine M, Bauer D, Le Floch G, Mäkelä MR, Drula E, Henrissat B, Grigoriev IV, Crouch JA, de Vries RP, Sukno SA, Thon MR. Genome evolution and transcriptome plasticity is associated with adaptation to monocot and dicot plants in Colletotrichum fungi. Gigascience 2024; 13:giae036. [PMID: 38940768 PMCID: PMC11212070 DOI: 10.1093/gigascience/giae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 04/05/2024] [Accepted: 05/25/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND Colletotrichum fungi infect a wide diversity of monocot and dicot hosts, causing diseases on almost all economically important plants worldwide. Colletotrichum is also a suitable model for studying gene family evolution on a fine scale to uncover events in the genome associated with biological changes. RESULTS Here we present the genome sequences of 30 Colletotrichum species covering the diversity within the genus. Evolutionary analyses revealed that the Colletotrichum ancestor diverged in the late Cretaceous in parallel with the diversification of flowering plants. We provide evidence of independent host jumps from dicots to monocots during the evolution of Colletotrichum, coinciding with a progressive shrinking of the plant cell wall degradative arsenal and expansions in lineage-specific gene families. Comparative transcriptomics of 4 species adapted to different hosts revealed similarity in gene content but high diversity in the modulation of their transcription profiles on different plant substrates. Combining genomics and transcriptomics, we identified a set of core genes such as specific transcription factors, putatively involved in plant cell wall degradation. CONCLUSIONS These results indicate that the ancestral Colletotrichum were associated with dicot plants and certain branches progressively adapted to different monocot hosts, reshaping the gene content and its regulation.
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Affiliation(s)
- Riccardo Baroncelli
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Viale Fanin 40-50, 40127 Bologna, Italy
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, Calle del Duero, 37185 Villamayor, Salamanca, Spain
| | - José F Cobo-Díaz
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, University of León, Campus Vegazana, 24007 León, Spain
| | - Tiziano Benocci
- Center for Health and Bioresources, Austrian Institute of Technology (AIT), Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
| | - Mao Peng
- Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Fungal Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Evy Battaglia
- Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Fungal Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Sajeet Haridas
- Joint Genome Institute, Lawrence Berkeley National Laboratory, United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
| | - William Andreopoulos
- Joint Genome Institute, Lawrence Berkeley National Laboratory, United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
| | - Kurt LaButti
- Joint Genome Institute, Lawrence Berkeley National Laboratory, United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
| | - Jasmyn Pangilinan
- Joint Genome Institute, Lawrence Berkeley National Laboratory, United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
| | - Anna Lipzen
- Joint Genome Institute, Lawrence Berkeley National Laboratory, United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
| | - Maxim Koriabine
- Joint Genome Institute, Lawrence Berkeley National Laboratory, United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
| | - Diane Bauer
- Joint Genome Institute, Lawrence Berkeley National Laboratory, United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
| | - Gaetan Le Floch
- Laboratory of Biodiversity and Microbial Ecology (LUBEM), IBSAM, ESIAB, EA 3882, University of Brest, Technopôle Brest-Iroise, Parv. Blaise Pascal, 29280 Plouzané, France
| | - Miia R Mäkelä
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Siltavuorenpenger 5, 00170 Helsinki, Finland
| | - Elodie Drula
- UMR 7257, Architecture et Fonction des Macromolécules Biologiques, The French National Centre for Scientific Research (CNRS), University of Aix-Marseille (AMU), 163 Avenue de Luminy, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France
- The French National Institute for Agricultural Research (INRA), USC 1408 AFMB, 163 Avenue de Luminy, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France
| | - Bernard Henrissat
- UMR 7257, Architecture et Fonction des Macromolécules Biologiques, The French National Centre for Scientific Research (CNRS), University of Aix-Marseille (AMU), 163 Avenue de Luminy, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France
- The French National Institute for Agricultural Research (INRA), USC 1408 AFMB, 163 Avenue de Luminy, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, 23453 Jeddah, Saudi Arabia
| | - Igor V Grigoriev
- Joint Genome Institute, Lawrence Berkeley National Laboratory, United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Jo Anne Crouch
- Mycology and Nematology Genetic Diversity and Biology Laboratory, Agricultural Research Service, United States Department of Agriculture, 10300 Baltimore Ave, MD 20705, Beltsville, USA
| | - Ronald P de Vries
- Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Fungal Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Serenella A Sukno
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, Calle del Duero, 37185 Villamayor, Salamanca, Spain
| | - Michael R Thon
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, Calle del Duero, 37185 Villamayor, Salamanca, Spain
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Strullu-Derrien C, Goral T, Spencer ART, Kenrick P, Catherine Aime M, Gaya E, Hawksworth DL. A fungal plant pathogen discovered in the Devonian Rhynie Chert. Nat Commun 2023; 14:7932. [PMID: 38040707 PMCID: PMC10692235 DOI: 10.1038/s41467-023-43276-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 11/03/2023] [Indexed: 12/03/2023] Open
Abstract
Fungi are integral to well-functioning ecosystems, and their broader impact on Earth systems is widely acknowledged. Fossil evidence from the Rhynie Chert (Scotland, UK) shows that Fungi were already diverse in terrestrial ecosystems over 407-million-years-ago, yet evidence for the occurrence of Dikarya (the subkingdom of Fungi that includes the phyla Ascomycota and Basidiomycota) in this site is scant. Here we describe a particularly well-preserved asexual fungus from the Rhynie Chert which we examined using brightfield and confocal microscopy. We document Potteromyces asteroxylicola gen. et sp. nov. that we attribute to Ascomycota incertae sedis (Dikarya). The fungus forms a stroma-like structure with conidiophores arising in tufts outside the cuticle on aerial axes and leaf-like appendages of the lycopsid plant Asteroxylon mackiei. It causes a reaction in the plant that gives rise to dome-shaped surface projections. This suite of features in the fungus together with the plant reaction tissues provides evidence of it being a plant pathogenic fungus. The fungus evidently belongs to an extinct lineage of ascomycetes that could serve as a minimum node age calibration point for the Ascomycota as a whole, or even the Dikarya crown group, along with some other Ascomycota previously documented in the Rhynie Chert.
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Affiliation(s)
- Christine Strullu-Derrien
- Science Group, The Natural History Museum, London, UK.
- Institut Systématique Évolution Biodiversité (UMR 7205), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, Paris, France.
| | - Tomasz Goral
- Imaging and Analysis Centre, The Natural History Museum, London, UK
- Center of New Technologies, University of Warsaw, Warsaw, Poland
| | - Alan R T Spencer
- Science Group, The Natural History Museum, London, UK
- Department of Earth Science & Engineering, Imperial College London, London, UK
| | - Paul Kenrick
- Science Group, The Natural History Museum, London, UK
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA
| | - Ester Gaya
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
| | - David L Hawksworth
- Science Group, The Natural History Museum, London, UK
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
- Jilin Agricultural University, Changchun, 130118, Jilin Province, China
- Geography and Environmental Science, University of Southampton, Southampton, UK
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4
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Zhao H, Vlasák J, Yuan Y. Outline, phylogenetic and divergence times analyses of the genus Haploporus (Polyporales, Basidiomycota): two new species are proposed. MycoKeys 2023; 98:233-252. [PMID: 37534305 PMCID: PMC10390986 DOI: 10.3897/mycokeys.98.105684] [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: 04/28/2023] [Accepted: 07/06/2023] [Indexed: 08/04/2023] Open
Abstract
Haploporus species have a worldwide distribution and 27 species have been accepted. In this study, two new species, Haploporuscrystallinus and H.dextrinoideus, are proposed from South America, based on the molecular fragments (ITS, LSU and mtSSU) and morphological evidence. Molecular clock analysis was performed and the result suggests that the ancestor of Polyporales originated between the Late Jurassic and Early Cretaceous period, with a mean stem of 159.8 Mya [95% higher posterior density (HPD) of 142.4-184.1 Mya] and the genus Haploporus occurred at a mean stem of 108.3 Mya (95% HPD of 88.5-128.2 Mya). In addition, most species of the genus are diversified between 60.5 Mya and 1.8 Mya, during the Paleogene to Neogene. A key to the accepted species of the genus Haploporus is provided.
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Affiliation(s)
- Heng Zhao
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, ChinaBeijing Forestry UniversityBeijingChina
| | - Josef Vlasák
- Biology Centre of the Academy of Sciences of the Czech Republic, Branišovská 31, CZ-370 05 České Budějovice, Czech RepublicBiology Centre of the Czech Academy of SciencesČeské BudějoviceCzech Republic
| | - Yuan Yuan
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, ChinaBeijing Forestry UniversityBeijingChina
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5
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Freire-Rallo S, Wedin M, Diederich P, Millanes AM. To explore strange new worlds - The diversification in Tremella caloplacae was linked to the adaptive radiation of the Teloschistaceae. Mol Phylogenet Evol 2023; 180:107680. [PMID: 36572164 DOI: 10.1016/j.ympev.2022.107680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 09/12/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Lichenicolous fungi are a heterogeneous group of organisms that grow exclusively on lichens, forming obligate associations with them. It has often been assumed that cospeciation has occurred between lichens and lichenicolous fungi, but this has been seldom analysed from a macroevolutionary perspective. Many lichenicolous species are rare or are rarely observed, which results in frequent and large gaps in the knowledge of the diversity of many groups. This, in turn, hampers evolutionary studies that necessarily are based on a reasonable knowledge of this diversity. Tremella caloplacae is a heterobasidiomycete growing on various hosts from the lichen-forming family Teloschistaceae, and evidence suggests that it may represent a species complex. We combine an exhaustive sampling with molecular and ecological data to study species delimitation, cophylogenetic events and temporal concordance of this association. Tremella caloplacae is here shown to include at least six distinct host-specific lineages (=putative species). Host switch is the dominant and most plausible event influencing diversification and explaining the coupled evolutionary history in this system, although cospeciation cannot be discarded. Speciation in T. caloplacae would therefore have occurred coinciding with the rapid diversification - by an adaptive radiation starting in the late Cretaceous - of their hosts. New species in T. caloplacae would have developed as a result of specialization on diversifying lichen hosts that suddenly offered abundant new ecological niches to explore or adapt to.
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Affiliation(s)
- Sandra Freire-Rallo
- Rey Juan Carlos University/Departamento de Biología y Geología, Física y Química Inorgánica, E-28933 Móstoles, Spain
| | - Mats Wedin
- Swedish Museum of Natural History/Botany Dept., PO Box 50007, SE-10405 Stockholm, Sweden.
| | - Paul Diederich
- Musée national d'histoire naturelle, 25 rue Munster, L-2160 Luxembourg, Luxembourg
| | - Ana M Millanes
- Rey Juan Carlos University/Departamento de Biología y Geología, Física y Química Inorgánica, E-28933 Móstoles, Spain
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Liu S, Zhou JL, Song J, Sun YF, Dai YC, Cui BK. Climacocystaceae fam. nov. and Gloeoporellaceae fam. nov., two new families of Polyporales (Basidiomycota). Front Microbiol 2023; 14:1115761. [PMID: 36819032 PMCID: PMC9935835 DOI: 10.3389/fmicb.2023.1115761] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 01/11/2023] [Indexed: 02/05/2023] Open
Abstract
Polyporales is a diverse group of Agaricomycetes including more than 2,500 species belonging to 255 genera and 18 families. Recently, many studies focused on the classification of Polyporales, but the familial placements of some taxa remain uncertain. In this study, two new families, Climacocystaceae and Gloeoporellaceae of Polyporales, are proposed based on morphological characters and molecular data. Phylogenetic analyses of the two new families are inferred from the DNA sequences of the internal transcribed spacer regions (ITS), the large subunit of nuclear ribosomal RNA gene (nLSU), the largest subunit of RNA polymerase II gene (RPB1), the second largest subunit of RNA polymerase II gene (RPB2), and the translation elongation factor 1-α gene (TEF1). Furthermore, the divergence time of Polyporales was estimated as an additional taxonomic criterion based on the conserved regions of five DNA fragments (5.8S, nLSU, RPB1, RPB2, and TEF1). Bayesian evolutionary analysis revealed that the ancestor of Polyporales splits with a mean stem age of 136.53 Mya with a 95% highest posterior density (HPD) of 118.08-158.06 Mya. The mean stem ages of the families within Polyporales originated between 66.02 and 119.22 Mya, of which Climacocystaceae occurred in a mean stem age of 77.49 Mya with a 95% HPD of 61.45-93.16 Mya, and Gloeoporellaceae occurred in a mean stem age of 88.06 Mya with a 95% HPD of 67.15-107.76 Mya.
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Affiliation(s)
- Shun Liu
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
| | - Jun-Liang Zhou
- International Exchange and Cooperation Department, Kunming University, Kunming, Yunnan, China
| | - Jie Song
- Department of Horticulture and Food, Guangdong Eco-Engineering Polytechnic, Guangzhou, China
| | - Yi-Fei Sun
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
| | - Yu-Cheng Dai
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
| | - Bao-Kai Cui
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China,*Correspondence: Bao-Kai Cui,
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7
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Zhang Z, Liu X, Tao M, Liu X, Xia J, Zhang X, Meng Z. Taxonomy, Phylogeny, Divergence Time Estimation, and Biogeography of the Family Pseudoplagiostomataceae ( Ascomycota, Diaporthales). J Fungi (Basel) 2023; 9:82. [PMID: 36675903 PMCID: PMC9860658 DOI: 10.3390/jof9010082] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/03/2023] [Accepted: 01/03/2023] [Indexed: 01/07/2023] Open
Abstract
Species of Pseudoplagiostomataceae were mainly introduced as endophytes, plant pathogens, or saprobes from various hosts. Based on multi-locus phylogenies from the internal transcribed spacers (ITS), the large subunit of nuclear ribosomal RNA gene (LSU), partial DNA-directed RNA polymerase II subunit two gene (rpb2), the partial translation elongation factor 1-alpha gene (tef1α), and the partial beta-tubulin gene (tub2), in conjunction with morphological characteristics, we describe three new species, viz. Pseudoplagiostoma alsophilae sp. nov., P. bambusae sp. nov., and P. machili sp. nov. Molecular clock analyses on the divergence times of Pseudoplagiostomataceae indicated that the conjoint ancestor of Pseudoplagiostomataceae and Apoharknessiaceae occurred in the Cretaceous period. and had a mean stem age of 104.1 Mya (95% HPD of 86.0-129.0 Mya, 1.0 PP), and most species emerged in the Paleogene and Neogene period. Historical biogeography was reconstructed for Pseudoplagiostomataceae by the RASP software with a S-DEC model, and suggested that Asia, specifically Southeast Asia, was probably the ancestral area.
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Affiliation(s)
- Zhaoxue Zhang
- College of Life Sciences, Shandong Normal University, Jinan 250358, China
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Xinye Liu
- College of Life Sciences, Shandong Normal University, Jinan 250358, China
| | - Mengfei Tao
- College of Life Sciences, Shandong Normal University, Jinan 250358, China
| | - Xiaoyong Liu
- College of Life Sciences, Shandong Normal University, Jinan 250358, China
| | - Jiwen Xia
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Xiuguo Zhang
- College of Life Sciences, Shandong Normal University, Jinan 250358, China
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Zhe Meng
- College of Life Sciences, Shandong Normal University, Jinan 250358, China
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8
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Meng Q, Xie Z, Xu H, Guo J, Tang Y, Ma T, Peng Q, Wang B, Mao Y, Yan S, Yang J, Dong D, Duan Y, Zhang F, Gao T. Out of the Qinghai-Tibetan plateau: Origin, evolution and historical biogeography of Morchella (both Elata and Esculenta clades). Front Microbiol 2022; 13:1078663. [PMID: 36643413 PMCID: PMC9832445 DOI: 10.3389/fmicb.2022.1078663] [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: 10/24/2022] [Accepted: 11/30/2022] [Indexed: 12/29/2022] Open
Abstract
Introduction Morchella has become a research hotspot because of its wide distribution, delicious taste, and phenotypic plasticity. The Qinghai-Tibet Plateau subkingdoms (QTPs) are known as the cradle of Ice age biodiversity. However, the diversity of Morchella in the QTPs has been poorly investigated, especially in phylogenetic diversity, origin, and biogeography. Methods The genealogical concordance phylogenetic species recognition (GCPSR, based on Bayesian evolutionary analysis using sequences from the internal transcribed spacer (ITS), nuclear large subunit rDNA (nrLSU), translation elongation factor 1-α (EF1-α), and the largest and second largest subunits of RNA polymerase II (RPB1 and RPB2)), differentiation time estimation, and ancestral region reconstruction were used to infer Morchella's phylogenetic relationships and historical biogeography in the QTPs. Results Firstly, a total of 18 Morchella phylogenetic species are recognized in the QTPs, including 10 Elata clades and 8 Esculenta clades of 216 individuals Secondly, the divergences of the 18 phylogenetic species were 50.24-4.20 Mya (Eocene-Pliocene), which was closely related to the geological activities in the QTPs. Furthermore, the ancestor of Morchella probably originated in the Northern regions (Qilian Shan, Elata cade) and southwestern regions (Shangri-La, Esculenta clade) of QTPs and might have migrated from North America (Rufobrunnea clade) via Beringian Land Bridge (BLB) and Long-Distance Dispersal (LDD) expansions during the Late Cretaceous. Moreover, as the cradle of species origin and diversity, the fungi species in the QTPs have spread out and diffused to Eurasia and South Africa starting in the Paleogene Period. Conclusion This is the first report that Esculenta and Elata clade of Morchella originated from the QTPs because of orogenic, and rapid differentiation of fungi is strongly linked to geological uplift movement and refuge in marginal areas of the QTPs. Our findings contribute to increasing the diversity of Morchella and offer more evidence for the origin theory of the QTPs.
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Affiliation(s)
- Qing Meng
- College of Ecological and Environment Engineering, Qinghai University, Xining, Qinghai, China
- State Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Qinghai University, Xining, Qinghai, China
| | - Zhanling Xie
- College of Ecological and Environment Engineering, Qinghai University, Xining, Qinghai, China
- State Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Qinghai University, Xining, Qinghai, China
| | - Hongyan Xu
- College of Ecological and Environment Engineering, Qinghai University, Xining, Qinghai, China
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, Qinghai, China
| | - Jing Guo
- College of Ecological and Environment Engineering, Qinghai University, Xining, Qinghai, China
- State Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Qinghai University, Xining, Qinghai, China
| | - Yongpeng Tang
- State-owned Forest Farm of Tianjun County, Delingha, Qinghai, China
| | - Ting Ma
- College of Ecological and Environment Engineering, Qinghai University, Xining, Qinghai, China
| | - Qingqing Peng
- College of Ecological and Environment Engineering, Qinghai University, Xining, Qinghai, China
| | - Bao Wang
- College of Ecological and Environment Engineering, Qinghai University, Xining, Qinghai, China
- State Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Qinghai University, Xining, Qinghai, China
| | - Yujing Mao
- College of Ecological and Environment Engineering, Qinghai University, Xining, Qinghai, China
- State Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Qinghai University, Xining, Qinghai, China
| | - Shangjin Yan
- College of Ecological and Environment Engineering, Qinghai University, Xining, Qinghai, China
| | - Jiabao Yang
- College of Ecological and Environment Engineering, Qinghai University, Xining, Qinghai, China
- State Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Qinghai University, Xining, Qinghai, China
| | - Deyu Dong
- College of Ecological and Environment Engineering, Qinghai University, Xining, Qinghai, China
- State Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Qinghai University, Xining, Qinghai, China
| | - Yingzhu Duan
- State-owned Forest Farm of Tianjun County, Delingha, Qinghai, China
| | - Fan Zhang
- Forestry and Grassland Station of Tianjun County, Delingha, Qinghai, China
| | - Taizhen Gao
- State-owned Forest Farm of Tianjun County, Delingha, Qinghai, China
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Zhao H, Zhou M, Liu XY, Wu F, Dai YC. Phylogeny, Divergence Time Estimation and Biogeography of the Genus Onnia (Basidiomycota, Hymenochaetaceae). Front Microbiol 2022; 13:907961. [PMID: 35875515 PMCID: PMC9301299 DOI: 10.3389/fmicb.2022.907961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/06/2022] [Indexed: 11/18/2022] Open
Abstract
Species of Onnia are important tree pathogens and play a crucial role in forest ecosystems. The species diversity and distribution of Onnia have been studied, however, its evolutionary history is poorly understood. In this study, we reconstructed the phylogeny of Onnia using internal transcribed spacers (ITS) and large subunit (LSU) rDNA sequence data. Molecular clock analyses developed the divergence times of Onnia based on a dataset (ITS + LSU rDNA + rpb1 + rpb2 + tef1α). Reconstruct Ancestral State in Phylogenies (RASP) was used to reconstruct the historical biogeography for the genus Onnia with a Dispersal Extinction Cladogenesis (DEC) model. Here, we provide a robust phylogeny of Onnia, with a description of a new species, Onnia himalayana from Yunnan Province, China. Molecular clock analyses suggested that the common ancestor of Onnia and Porodaedalea emerged in the Paleogene period with full support and a mean stem age of 56.9 Mya (95% highest posterior density of 35.9-81.6 Mya), and most species occurred in the Neogene period. Biogeographic studies suggest that Asia, especially in the Hengduan-Himalayan region, is probably the ancestral area. Five dispersals and two vicariances indicate that species of Onnia were rapidly diversified. Speciation occurred in the Old World and New World due to geographic separation. This study is the first inference of the divergence times, biogeography, and speciation of the genus Onnia.
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Affiliation(s)
- Heng Zhao
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
| | - Meng Zhou
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
| | - Xiao-Yong Liu
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Fang Wu
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
| | - Yu-Cheng Dai
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
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10
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Liu ZB, Wu YD, Zhao H, Lian YP, Wang YR, Wang CG, Mao WL, Yuan Y. Outline, Divergence Times, and Phylogenetic Analyses of Trechisporales (Agaricomycetes, Basidiomycota). Front Microbiol 2022; 13:818358. [PMID: 35547118 PMCID: PMC9083364 DOI: 10.3389/fmicb.2022.818358] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Phylogenetic analyses inferred from the nuc rDNA ITS1-5.8S-ITS2 (ITS) data set and the combined 2-locus data set [5.8S + nuc 28S rDNA (nLSU)] of taxa of Trechisporales around the world show that Sistotremastrum family forms a monophyletic lineage within Trechisporales. Bayesian evolutionary and divergence time analyses on two data sets of 5.8S and nLSU sequences indicate an ancient divergence of Sistotremastrum family from Hydnodontaceae during the Triassic period (224.25 Mya). Sistotremastrum family is characterized by resupinate and thin basidiomata, smooth, verruculose, or odontoid-semiporoid hymenophore, a monomitic hyphal structure, and generative hyphae bearing clamp connections, the presence of cystidia and hyphidia in some species, thin-walled, smooth, inamyloid, and acyanophilous basidiospores. In addition, four new species, namely, Trechispora dentata, Trechispora dimitiella, Trechispora fragilis, and Trechispora laevispora, are described and illustrated. In addition, three new combinations, namely, Brevicellicium daweishanense, Brevicellicium xanthum, and Sertulicium limonadense, are also proposed.
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Affiliation(s)
- Zhan-Bo Liu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Ying-Da Wu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China.,Key Laboratory of Forest and Grassland Fire Risk Prevention, Ministry of Emergency Management, China Fire and Rescue Institute, Beijing, China
| | - Heng Zhao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Ya-Ping Lian
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Ya-Rong Wang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Chao-Ge Wang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Wei-Lin Mao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yuan Yuan
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
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11
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Strullu-Derrien C, Philippe M, Kenrick P, Blanchette RA. Blue stain fungi infecting an 84-million-year-old conifer from South Africa. THE NEW PHYTOLOGIST 2022; 233:1032-1037. [PMID: 34743346 DOI: 10.1111/nph.17843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/28/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Christine Strullu-Derrien
- Institut Systématique Evolution Biodiversité, Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, 75005, Paris, France
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Marc Philippe
- CNRS, ENTPE, UMR 5023 LEHNA, Univ Lyon, Université Claude Bernard Lyon 1, F-69622, Villeurbanne, France
| | - Paul Kenrick
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Robert A Blanchette
- Department of Plant Pathology, University of Minnesota, St Paul, MN, 55126, USA
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12
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Wang C, Zeng ZQ, Zhuang WY. Comparative molecular evolution of chitinases in ascomycota with emphasis on mycoparasitism lifestyle. Microb Genom 2021; 7. [PMID: 34516366 PMCID: PMC8715425 DOI: 10.1099/mgen.0.000646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chitinases are involved in multiple aspects of fungal life cycle, such as cell wall remodelling, chitin degradation and mycoparasitism lifestyle. To improve our knowledge of the chitinase molecular evolution of Ascomycota, the gene family of 72 representatives of this phylum was identified and subjected to phylogenetic, evolution trajectory and selective pressure analyses. Phylogenetic analysis showed that the chitinase gene family size and enzyme types varied significantly, along with species evolution, especially for groups B and C. In addition, two new subgroups, C3 and C4, are recognized in group C chitinases. Random birth and death testing indicated that gene expansion and contraction occurred in most of the taxa, particularly for species in the order Hypocreales (class Sordariomycetes). From an enzyme function point of view, we speculate that group A chitinases are mainly involved in species growth and development, while the expansion of genes in group B chitinases is related to fungal mycoparasitic and entomopathogenic abilities, and, to a certain extent, the expansion of genes in group C chitinases seems to be correlated with the host range broadening of some plant-pathogenic fungi in Sordariomycetes. Further selection pressure testing revealed that chitinases and the related amino acid sites were under positive selection in the evolutionary history, especially at the nodes sharing common ancestors and the terminal branches of Hypocreales. These results give a reasonable explanation for the size and function differences of chitinase genes among ascomycetes, and provide a scientific basis for understanding the evolutionary trajectories of chitinases, particularly that towards a mycoparasitic lifestyle.
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Affiliation(s)
- Chao Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China.,Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, PR China
| | - Zhao-Qing Zeng
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Wen-Ying Zhuang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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13
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Derbyshire MC, Harper LA, Lopez-Ruiz FJ. Positive Selection of Transcription Factors Is a Prominent Feature of the Evolution of a Plant Pathogenic Genus Originating in the Miocene. Genome Biol Evol 2021; 13:6325025. [PMID: 34289036 PMCID: PMC8379374 DOI: 10.1093/gbe/evab167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2021] [Indexed: 01/18/2023] Open
Abstract
Tests based on the dN/dS statistic are used to identify positive selection of nonsynonymous polymorphisms. Using these tests on alignments of all orthologs from related species can provide insights into which gene categories have been most frequently positively selected. However, longer alignments have more power to detect positive selection, creating a detection bias that could create misleading results from functional enrichment tests. Most studies of positive selection in plant pathogens focus on genes with specific virulence functions, with little emphasis on broader molecular processes. Furthermore, no studies in plant pathogens have accounted for detection bias due to alignment length when performing functional enrichment tests. To address these research gaps, we analyze 12 genomes of the phytopathogenic fungal genus Botrytis, including two sequenced in this study. To establish a temporal context, we estimated fossil-calibrated divergence times for the genus. We find that Botrytis likely originated 16–18 Ma in the Miocene and underwent continuous radiation ending in the Pliocene. An untargeted scan of Botrytis single-copy orthologs for positive selection with three different statistical tests uncovered evidence for positive selection among proteases, signaling proteins, CAZymes, and secreted proteins. There was also a strong overrepresentation of transcription factors among positively selected genes. This overrepresentation was still apparent after two complementary controls for detection bias due to sequence length. Positively selected sites were depleted within DNA-binding domains, suggesting changes in transcriptional responses to internal and external cues or protein–protein interactions have undergone positive selection more frequently than changes in promoter fidelity.
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Affiliation(s)
- Mark C Derbyshire
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
| | - Lincoln A Harper
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
| | - Francisco J Lopez-Ruiz
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
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14
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Wang XW, May TW, Liu SL, Zhou LW. Towards a Natural Classification of Hyphodontia Sensu Lato and the Trait Evolution of Basidiocarps within Hymenochaetales ( Basidiomycota). J Fungi (Basel) 2021; 7:jof7060478. [PMID: 34204800 PMCID: PMC8231612 DOI: 10.3390/jof7060478] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 11/16/2022] Open
Abstract
Hyphodontia sensu lato, belonging to Hymenochaetales, accommodates corticioid wood-inhabiting basidiomycetous fungi with resupinate basidiocarps and diverse hymenophoral characters. Species diversity of Hyphodontia sensu lato has been extensively explored worldwide, but in previous studies the six accepted genera in Hyphodontia sensu lato, viz. Fasciodontia, Hastodontia, Hyphodontia, Kneiffiella, Lyomyces and Xylodon were not all strongly supported from a phylogenetic perspective. Moreover, the relationships among these six genera in Hyphodontia sensu lato and other lineages within Hymenochaetales are not clear. In this study, we performed comprehensive phylogenetic analyses on the basis of multiple loci. For the first time, the independence of each of the six genera receives strong phylogenetic support. The six genera are separated in four clades within Hymenochaetales: Fasciodontia, Lyomyces and Xylodon are accepted as members of a previously known family Schizoporaceae, Kneiffiella and Hyphodontia are, respectively, placed in two monotypic families, viz. a previous name Chaetoporellaceae and a newly introduced name Hyphodontiaceae, and Hastodontia is considered to be a genus with an uncertain taxonomic position at the family rank within Hymenochaetales. The three families emerged between 61.51 and 195.87 million years ago. Compared to other families in the Hymenochaetales, these ages are more or less similar to those of Coltriciaceae, Hymenochaetaceae and Oxyporaceae, but much older than those of the two families Neoantrodiellaceae and Nigrofomitaceae. In regard to species, two, one, three and 10 species are newly described from Hyphodontia, Kneiffiella, Lyomyces and Xylodon, respectively. The taxonomic status of additional 30 species names from these four genera is briefly discussed; an epitype is designated for X. australis. The resupinate habit and poroid hymenophoral configuration were evaluated as the ancestral state of basidiocarps within Hymenochaetales. The resupinate habit mainly remains, while the hymenophoral configuration mainly evolves to the grandinioid-odontioid state and also back to the poroid state at the family level. Generally, a taxonomic framework for Hymenochaetales with an emphasis on members belonging to Hyphodontia sensu lato is constructed, and trait evolution of basidiocarps within Hymenochaetales is revealed accordingly.
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Affiliation(s)
- Xue-Wei Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (X.-W.W.); (S.-L.L.)
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tom W. May
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne 3004, Australia;
| | - Shi-Liang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (X.-W.W.); (S.-L.L.)
| | - Li-Wei Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (X.-W.W.); (S.-L.L.)
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
- Correspondence:
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15
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Terranova ML. Radioactivity to Rethink the Earth's Energy Balance. GLOBAL CHALLENGES (HOBOKEN, NJ) 2021; 5:2000094. [PMID: 34141445 PMCID: PMC8182276 DOI: 10.1002/gch2.202000094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/09/2021] [Indexed: 05/27/2023]
Abstract
This contribution invites to re-examine the whole matter of radioactivity, reconsidering it from the point of view of a realistic source of energy. State-of-the-art and technical aspects are briefly illustrated in this note that aims to open a discussion on this challenging topic.
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Affiliation(s)
- Maria Letizia Terranova
- Tor Vergata University of RomaDepartment of Chemical Sciences and TechnologiesVia della Ricerca ScientificaRoma00133Italy
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16
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Haelewaters D, Blackwell M, Pfister DH. Laboulbeniomycetes: Intimate Fungal Associates of Arthropods. ANNUAL REVIEW OF ENTOMOLOGY 2021; 66:257-276. [PMID: 32867528 DOI: 10.1146/annurev-ento-013020-013553] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Arthropod-fungus interactions involving the Laboulbeniomycetes have been pondered for several hundred years. Early studies of Laboulbeniomycetes faced several uncertainties. Were they parasitic worms, red algal relatives, or fungi? If they were fungi, to which group did they belong? What was the nature of their interactions with their arthropod hosts? The historical misperceptions resulted from the extraordinary morphological features of these oddly constructed ectoparasitic fungi. More recently, molecular phylogenetic studies, in combination with a better understanding of life histories, have clearly placed these fungi among filamentous Ascomycota (subphylum Pezizomycotina). Species discovery and research on the classification of the group continue today as arthropods, and especially insects, are routinely collected and examined for the presence of Laboulbeniomycetes. Newly armed with molecular methods, mycologists are poisedto use Laboulbeniomycetes-insect associations as models for the study of a variety of basic evolutionary and ecological questions involving host-parasite relationships, modes of nutrient intake, population biology, host specificity, biological control, and invasion biology. Collaboration between mycologists and entomologists is essential to successfully advance knowledge of Laboulbeniomycetes and their intimate association with their hosts.
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Affiliation(s)
- Danny Haelewaters
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA;
- Department of Zoology, University of South Bohemia, 37005 České Budejovice, Czech Republic
- Department of Biology, Research Group Mycology, Ghent University, 9000 Ghent, Belgium
| | - Meredith Blackwell
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA;
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Donald H Pfister
- Farlow Reference Library and Herbarium of Cryptogamic Botany, Harvard University, Cambridge, Massachusetts 02138, USA;
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17
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Shen XX, Steenwyk JL, LaBella AL, Opulente DA, Zhou X, Kominek J, Li Y, Groenewald M, Hittinger CT, Rokas A. Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota. SCIENCE ADVANCES 2020; 6:eabd0079. [PMID: 33148650 PMCID: PMC7673691 DOI: 10.1126/sciadv.abd0079] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/21/2020] [Indexed: 05/14/2023]
Abstract
Ascomycota, the largest and most well-studied phylum of fungi, contains three subphyla: Saccharomycotina (budding yeasts), Pezizomycotina (filamentous fungi), and Taphrinomycotina (fission yeasts). Despite its importance, we lack a comprehensive genome-scale phylogeny or understanding of the similarities and differences in the mode of genome evolution within this phylum. By examining 1107 genomes from Saccharomycotina (332), Pezizomycotina (761), and Taphrinomycotina (14) species, we inferred a robust genome-wide phylogeny that resolves several contentious relationships and estimated that the Ascomycota last common ancestor likely originated in the Ediacaran period. Comparisons of genomic properties revealed that Saccharomycotina and Pezizomycotina differ greatly in their genome properties and enabled inference of the direction of evolutionary change. The Saccharomycotina typically have smaller genomes, lower guanine-cytosine contents, lower numbers of genes, and higher rates of molecular sequence evolution compared with Pezizomycotina. These results provide a robust evolutionary framework for understanding the diversity and ecological lifestyles of the largest fungal phylum.
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Affiliation(s)
- Xing-Xing Shen
- Institute of Insect Sciences, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Jacob L Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Abigail L LaBella
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Dana A Opulente
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, DOE Great Lakes Bioenergy Research Center, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Xiaofan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Jacek Kominek
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, DOE Great Lakes Bioenergy Research Center, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yuanning Li
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | | | - Chris T Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, DOE Great Lakes Bioenergy Research Center, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
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18
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Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits. Nat Commun 2020; 11:5125. [PMID: 33046698 PMCID: PMC7550596 DOI: 10.1038/s41467-020-18795-w] [Citation(s) in RCA: 189] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 09/16/2020] [Indexed: 12/25/2022] Open
Abstract
Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucoromycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present a combined analysis of 135 fungal genomes from 73 saprotrophic, endophytic and pathogenic species, and 62 mycorrhizal species, including 29 new mycorrhizal genomes. This study samples ecologically dominant fungal guilds for which there were previously no symbiotic genomes available, including ectomycorrhizal Russulales, Thelephorales and Cantharellales. Our analyses show that transitions from saprotrophy to symbiosis involve (1) widespread losses of degrading enzymes acting on lignin and cellulose, (2) co-option of genes present in saprotrophic ancestors to fulfill new symbiotic functions, (3) diversification of novel, lineage-specific symbiosis-induced genes, (4) proliferation of transposable elements and (5) divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild. Mycorrhizal symbioses have evolved repeatedly in diverse fungal lineages. A large phylogenomic analysis sheds light on genomic changes associated with transitions from saprotrophy to symbiosis, including divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.
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19
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20
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Genomic and fossil windows into the secret lives of the most ancient fungi. Nat Rev Microbiol 2020; 18:717-730. [PMID: 32908302 DOI: 10.1038/s41579-020-0426-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2020] [Indexed: 12/26/2022]
Abstract
Fungi have crucial roles in modern ecosystems as decomposers and pathogens, and they engage in various mutualistic associations with other organisms, especially plants. They have a lengthy geological history, and there is an emerging understanding of their impact on the evolution of Earth systems on a large scale. In this Review, we focus on the roles of fungi in the establishment and early evolution of land and freshwater ecosystems. Today, questions of evolution over deep time are informed by discoveries of new fossils and evolutionary analysis of new genomes. Inferences can be drawn from evolutionary analysis by comparing the genes and genomes of fungi with the biochemistry and development of their plant and algal hosts. We then contrast this emerging picture against evidence from the fossil record to develop a new, integrated perspective on the origin and early evolution of fungi.
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21
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Samarakoon MC, Hyde KD, Hongsanan S, McKenzie EHC, Ariyawansa HA, Promputtha I, Zeng XY, Tian Q, Liu JK(J. Divergence time calibrations for ancient lineages of Ascomycota classification based on a modern review of estimations. FUNGAL DIVERS 2019. [DOI: 10.1007/s13225-019-00423-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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22
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An Q, Wu XJ, Dai YC. Comparative genomics of 40 edible and medicinal mushrooms provide an insight into the evolution of lignocellulose decomposition mechanisms. 3 Biotech 2019; 9:157. [PMID: 30944804 DOI: 10.1007/s13205-019-1689-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/19/2019] [Indexed: 11/28/2022] Open
Abstract
Diversity comparison and phylogenetic analyses of carbohydrate-active enzymes (CAZymes), auxiliary activities (AAs) and cytochromes P450 among 40 fungi, which are based on different nutritional pathways, help clarify and explain their divergence and improvement of various life-styles. Molecular clock analyses allow us to understand the evolutionary and developmental rules in decomposition gene families. Our results suggested that fungi in different ecological types acquired an obvious preference on specific decomposing gene families during evolutionary selection. White rot and litter saprotrophic fungi possessed more complete types of varied degradation gene families and were superior in quantities. With evolution and development of lignocellulose decomposition mechanism, certain families (like CBM1, GH6, GH7, GH10, and CYP53) disappeared in brown rot fungi and symbiotic fungi. In addition, the earlier time of phylogenetic divergence determined the more integrated and larger decomposition families. And various gains and losses in gene quantity of varied decomposition families led in particularly phylogenetic clades or nodes, then accelerated in forming varied ecotypes of species.
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Affiliation(s)
- Qi An
- 1Institute of Microbiology, Beijing Forestry University, Beijing, 100083 People's Republic of China
- 2Edible and Medicinal Fungi Research and Development Center, Universities/Colleges in Hebei Province, Langfang Normal University, Langfang, 065000 Hebei People's Republic of China
| | - Xue-Jun Wu
- 1Institute of Microbiology, Beijing Forestry University, Beijing, 100083 People's Republic of China
| | - Yu-Cheng Dai
- 1Institute of Microbiology, Beijing Forestry University, Beijing, 100083 People's Republic of China
- 3Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Forestry University, 35 Qinghuadong Road, Haidian District, Beijing, 100083 People's Republic of China
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23
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Haelewaters D, Pfliegler WP, Gorczak M, Pfister DH. Birth of an order: Comprehensive molecular phylogenetic study excludes Herpomyces (Fungi, Laboulbeniomycetes) from Laboulbeniales. Mol Phylogenet Evol 2019; 133:286-301. [PMID: 30625361 DOI: 10.1016/j.ympev.2019.01.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/15/2018] [Accepted: 01/04/2019] [Indexed: 01/09/2023]
Abstract
The class Laboulbeniomycetes comprises biotrophic parasites associated with arthropods and fungi. Two orders are currently recognized, Pyxidiophorales and Laboulbeniales. Herpomyces is an isolated genus of Laboulbeniales, with species that exclusively parasitize cockroaches (Blattodea). Here, we evaluate 39 taxa of Laboulbeniomycetes with a three-locus phylogeny (nrSSU, ITS, nrLSU) and propose a new order in this class. Herpomycetales accommodates a single genus, Herpomyces, with currently 26 species, one of which is described here based on morphological and molecular data. Herpomyces shelfordellae is found on Shelfordella lateralis cockroaches from Hungary, Poland, and the USA. We also build on the six-locus dataset from the Ascomycota Tree of Life paper (Schoch and colleagues, 2009) to confirm that Laboulbeniomycetes and Sordariomycetes are sister classes, and we apply laboulbeniomyceta as a rankless taxon for the now well-resolved node that describes the most recent common ancestor of both classes.
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Affiliation(s)
- Danny Haelewaters
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA; Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic; Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA.
| | - Walter P Pfliegler
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, Debrecen, Hungary
| | - Michał Gorczak
- Department of Molecular Phylogenetics and Evolution, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Donald H Pfister
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
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Strullu-Derrien C, Selosse MA, Kenrick P, Martin FM. The origin and evolution of mycorrhizal symbioses: from palaeomycology to phylogenomics. THE NEW PHYTOLOGIST 2018; 220:1012-1030. [PMID: 29573278 DOI: 10.1111/nph.15076] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/14/2018] [Indexed: 05/05/2023]
Abstract
Contents Summary 1012 I. Introduction 1013 II. The mycorrhizal symbiosis at the dawn and rise of the land flora 1014 III. From early land plants to early trees: the origin of roots and true mycorrhizas 1016 IV. The diversification of the AM symbiosis 1019 V. The ECM symbiosis 1021 VI. The recently evolved ericoid and orchid mycorrhizas 1023 VII. Limits of paleontological vs genetic approaches and perspectives 1023 Acknowledgements 1025 References 1025 SUMMARY: The ability of fungi to form mycorrhizas with plants is one of the most remarkable and enduring adaptations to life on land. The occurrence of mycorrhizas is now well established in c. 85% of extant plants, yet the geological record of these associations is sparse. Fossils preserved under exceptional conditions provide tantalizing glimpses into the evolutionary history of mycorrhizas, showing the extent of their occurrence and aspects of their evolution in extinct plants. The fossil record has important roles to play in establishing a chronology of when key fungal associations evolved and in understanding their importance in ecosystems through time. Together with calibrated phylogenetic trees, these approaches extend our understanding of when and how groups evolved in the context of major environmental change on a global scale. Phylogenomics furthers this understanding into the evolution of different types of mycorrhizal associations, and genomic studies of both plants and fungi are shedding light on how the complex set of symbiotic traits evolved. Here we present a review of the main phases of the evolution of mycorrhizal interactions from palaeontological, phylogenetic and genomic perspectives, with the aim of highlighting the potential of fossil material and a geological perspective in a cross-disciplinary approach.
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Affiliation(s)
- Christine Strullu-Derrien
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
- Interactions Arbres/Microorganismes, Laboratoire d'excellence ARBRE, Centre INRA-Lorraine, Institut national de la recherche agronomique (INRA), Unité Mixte de Recherche 1136 INRA-Université de Lorraine, 54280, Champenoux, France
| | - Marc-André Selosse
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP39, 75005, Paris, France
- Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Paul Kenrick
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Francis M Martin
- Interactions Arbres/Microorganismes, Laboratoire d'excellence ARBRE, Centre INRA-Lorraine, Institut national de la recherche agronomique (INRA), Unité Mixte de Recherche 1136 INRA-Université de Lorraine, 54280, Champenoux, France
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25
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Wang XH, Halling RE, Hofstetter V, Lebel T, Buyck B. Phylogeny, biogeography and taxonomic re-assessment of Multifurca (Russulaceae, Russulales) using three-locus data. PLoS One 2018; 13:e0205840. [PMID: 30403698 PMCID: PMC6221288 DOI: 10.1371/journal.pone.0205840] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 10/01/2018] [Indexed: 11/19/2022] Open
Abstract
Multifurca is a small genus newly established to accommodate lactarioid and russuloid species with some characters reminiscent of corticoid members of Russulaceae. It shows an amphi-pacific distribution with strong preference for the tropical zone of the Northern Hemisphere and thus has particular significance for biogeographical study. Using worldwide samples and three loci (ITS, 28S rDNA and rpb2), we demonstrated that Multifurca is split into two highly supported major clades that are here recognized at the subgeneric level: subg. Furcata subg. nov. exclusively includes lactarioid species, while subg. Multifurca includes species with a russuloid habit. Using phylogenetic species recognition and comparison of genetic distances we recognize five new and six previously described species, almost double the known number of species before this study. Molecular dating using a Bayesian method suggested that Multifurca originated in early Paleocene and diversified in the Eocene. The most recent interspecific divergences occurred both in Asia and America, roughly at the same time around the Pliocene. Ancestral area reconstruction and comparisons of genetic distances and morphology suggested an early divergence within Australasia or tropical Asia. From the early Miocene to Pliocene, multiple dispersals/migrations to Australasia and North America by island hopping or land bridge likely happened. Vicariance at the late Tertiary might be the most likely mechanism accounting for the eastern Asia-southeastern North America and Australasia-tropical Asia disjunct distributions. The shared polymorphisms in the ITS alignment, numerous degenerated base pairs in the rpb2 sequences and weak conflict between the ITS and LSU genealogies of M. subg. Furcata suggest recent speciation. Host specificity of Multifurca species or species pairs is relatively low. Host shifts are believed to have aided establishment in new territories during the dispersals and migrations.
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Affiliation(s)
- Xiang-Hua Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, P. R. China
| | - Roy E. Halling
- New York Botanical Garden, Institute of Systematic Botany, Bronx, New York, United States of America
| | - Valérie Hofstetter
- Agroscope, Plant Protection, Mycology and Biotechnology Lab, Nyon, Switzerland
| | - Teresa Lebel
- National Herbarium of Victoria, Royal Botanic Gardens Victoria, Melbourne, Australia
| | - Bart Buyck
- Institut de Systématique, Ecologie, Biodiversité (ISYEB), Muséum national D’histoire naturelle, CNRS, Sorbonne Université, Paris, France
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Hibbett DS, Blackwell M, James TY, Spatafora JW, Taylor JW, Vilgalys R. Phylogenetic taxon definitions for Fungi, Dikarya, Ascomycota and Basidiomycota. IMA Fungus 2018; 9:291-298. [PMID: 30622884 PMCID: PMC6317587 DOI: 10.5598/imafungus.2018.09.02.05] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 09/11/2018] [Indexed: 11/02/2022] Open
Abstract
Phylogenetic taxon definitions (PTDs) are explicit, phylogeny-based statements that specify clades. PTDs are central to the system of rank-free classification that is governed by the PhyloCode, but they can also be used to clarify the meanings of ranked names. We present PTDs for four major groups: Fungi, Dikarya, Ascomycota, and Basidiomycota.
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Affiliation(s)
- David S Hibbett
- Biology Department, Clark University, Worcester, MA 01610, USA
| | - Meredith Blackwell
- Department of Biology, Louisiana State University, Baton Rouge, LA 70803 and Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - John W Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Rytas Vilgalys
- Biology Department, Duke University, Durham NC 27708, USA
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Animal origins and the Tonian Earth system. Emerg Top Life Sci 2018; 2:289-298. [PMID: 32412615 DOI: 10.1042/etls20170160] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/23/2018] [Accepted: 05/25/2018] [Indexed: 01/30/2023]
Abstract
The Neoproterozoic Era (1000-541 million years ago, Ma) was characterized by dramatic environmental and evolutionary change, including at least two episodes of extensive, low-latitude glaciation, potential changes in the redox structure of the global ocean, and the origin and diversification of animal life. How these different events related to one another remains an active area of research, particularly how these environmental changes influenced, and were influenced by, the earliest evolution of animals. Animal multicellularity is estimated to have evolved in the Tonian Period (1000-720 Ma) and represents one of at least six independent acquisitions of complex multicellularity, characterized by cellular differentiation, three-dimensional body plans, and active nutrient transport. Compared with the other instances of complex multicellularity, animals represent the only clade to have evolved from wall-less, phagotrophic flagellates, which likely placed unique cytological and trophic constraints on the evolution of animal multicellularity. Here, we compare recent molecular clock estimates with compilations of the chromium isotope, micropaleontological, and organic biomarker records, suggesting that, as of now, the origin of animals was not obviously correlated to any environmental-ecological change in the Tonian Period. This lack of correlation is consistent with the idea that the evolution of animal multicellularity was primarily dictated by internal, developmental constraints and occurred independently of the known environmental-ecological changes that characterized the Neoproterozoic Era.
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Edwards D, Kenrick P, Dolan L. History and contemporary significance of the Rhynie cherts-our earliest preserved terrestrial ecosystem. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2016.0489. [PMID: 29254954 DOI: 10.1098/rstb.2016.0489] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2017] [Indexed: 01/03/2023] Open
Abstract
The Rhynie cherts Unit is a 407 million-year old geological site in Scotland that preserves the most ancient known land plant ecosystem, including associated animals, fungi, algae and bacteria. The quality of preservation is astonishing, and the initial description of several plants 100 years ago had a huge impact on botany. Subsequent discoveries provided unparalleled insights into early life on land. These include the earliest records of plant life cycles and fungal symbioses, the nature of soil microorganisms and the diversity of arthropods. Today the Rhynie chert (here including the Rhynie and Windyfield cherts) takes on new relevance, especially in relation to advances in the fields of developmental genetics and Earth systems science. New methods and analytical techniques also contribute to a better understanding of the environment and its organisms. Key discoveries are reviewed, focusing on the geology of the site, the organisms and the palaeoenvironments. The plants and their symbionts are of particular relevance to understanding the early evolution of the plant life cycle and the origins of fundamental organs and tissue systems. The Rhynie chert provides remarkable insights into the structure and interactions of early terrestrial communities, and it has a significant role to play in developing our understanding of their broader impact on Earth systems.This article is part of a discussion meeting issue 'The Rhynie cherts: our earliest terrestrial ecosystem revisited'.
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Affiliation(s)
- Dianne Edwards
- School of Earth and Ocean Sciences, Cardiff University, Cardiff CF10 3AT, UK
| | - Paul Kenrick
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Liam Dolan
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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Nagy LG, Kovács GM, Krizsán K. Complex multicellularity in fungi: evolutionary convergence, single origin, or both? Biol Rev Camb Philos Soc 2018; 93:1778-1794. [DOI: 10.1111/brv.12418] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 03/23/2018] [Accepted: 03/28/2018] [Indexed: 12/22/2022]
Affiliation(s)
- László G. Nagy
- Synthetic and Systems Biology Unit; Institute of Biochemistry, BRC-HAS, 62 Temesvári krt; 6726 Szeged Hungary
| | - Gábor M. Kovács
- Department of Plant Anatomy; Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C; H-1117 Budapest Hungary
- Plant Protection Institute, Centre for Agricultural Research; Hungarian Academy of Sciences (MTA-ATK); PO Box 102, H-1525 Budapest Hungary
| | - Krisztina Krizsán
- Synthetic and Systems Biology Unit; Institute of Biochemistry, BRC-HAS, 62 Temesvári krt; 6726 Szeged Hungary
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30
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Strullu-Derrien C, Kenrick P. Thomas Norwood Taylor (1938–2016). Mycologia 2018; 110:448-452. [DOI: 10.1080/00275514.2018.1462080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Christine Strullu-Derrien
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
| | - Paul Kenrick
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
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31
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Aime MC, Bell CD, Wilson AW. Deconstructing the evolutionary complexity between rust fungi ( Pucciniales) and their plant hosts. Stud Mycol 2018; 89:143-152. [PMID: 29910520 PMCID: PMC6002339 DOI: 10.1016/j.simyco.2018.02.002] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The rust fungi (Pucciniales) are the most speciose natural group of plant pathogens, members of which possess the most complex lifecycles in Fungi. How natural selection works on the Pucciniales has been the subject of several hypotheses in mycology. This study uses molecular age estimation using sequence data from multiple loci, and cophylogeny reconciliation analyses to test hypotheses regarding how the aecial and telial stages in the lifecycle of rust fungi may have differentially impacted their diversification. Molecular age estimates show that the timing of diversification in the Pucciniales correlates with the diversification of their gymnosperm and angiosperm hosts. Host reconciliation analyses suggest that systematic relationships of hosts from the aecial stage of the Pucciniales lifecycle better reflect the systematic relationships among the Pucciniales. The results demonstrate the relative importance of this stage on the overall evolution of the Pucciniales and supports hypotheses made by Leppik over half a century ago. This study represents the first evaluation of how different life stages in the Pucciniales shape the evolution of these fungi.
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Affiliation(s)
- M C Aime
- Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - C D Bell
- Biology Department, University of New Orleans, New Orleans, LA 70148, USA
| | - A W Wilson
- Sam Mitchel Herbarium of Fungi, Denver Botanic Gardens, Denver, CO 80206, USA
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32
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Krings M, Harper CJ, Taylor EL. Fungi and fungal interactions in the Rhynie chert: a review of the evidence, with the description of Perexiflasca tayloriana gen. et sp. nov. †. Philos Trans R Soc Lond B Biol Sci 2018; 373:20160500. [PMID: 29254965 PMCID: PMC5745336 DOI: 10.1098/rstb.2016.0500] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2017] [Indexed: 12/11/2022] Open
Abstract
The Lower Devonian Rhynie chert is one of the most important rock deposits yielding comprehensive information on early continental plant, animal and microbial life. Fungi are especially abundant among the microbial remains, and include representatives of all major fungal lineages except Basidiomycota. This paper surveys the evidence assembled to date of fungal hyphae, mycelial cords and reproductive units (e.g. spores, sporangia, sporocarps), and presents examples of fungal associations and interactions with land plants, other fungi, algae, cyanobacteria and animals from the Rhynie chert. Moreover, a small, chytrid-like organism that occurs singly, in chain-like, linear arrangements, planar assemblages and three-dimensional aggregates of less than 10 to [Formula: see text] individuals in degrading land plant tissue in the Rhynie chert is formally described, and the name Perexiflasca tayloriana proposed for the organism. Perexiflasca tayloriana probably colonized senescent or atrophied plant parts and participated in the process of biological degradation. The fungal fossils described to date from the Rhynie chert constitute the largest body of structurally preserved evidence of fungi and fungal interactions from any rock deposit, and strongly suggest that fungi played important roles in the functioning of the Early Devonian Rhynie ecosystem.This article is part of a discussion meeting issue 'The Rhynie cherts: our earliest terrestrial ecosystem revisited'.
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Affiliation(s)
- Michael Krings
- Department für Geo- und Umweltwissenschaften, Paläontologie und Geobiologie, Ludwig-Maximilians-Universität, and SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Straße 10, 80333 Munich, Germany
- Department of Ecology and Evolutionary Biology, and Biodiversity Institute, The University of Kansas, Lawrence, KS 66045, USA
| | - Carla J Harper
- Department für Geo- und Umweltwissenschaften, Paläontologie und Geobiologie, Ludwig-Maximilians-Universität, and SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Straße 10, 80333 Munich, Germany
- Department of Ecology and Evolutionary Biology, and Biodiversity Institute, The University of Kansas, Lawrence, KS 66045, USA
| | - Edith L Taylor
- Department of Ecology and Evolutionary Biology, and Biodiversity Institute, The University of Kansas, Lawrence, KS 66045, USA
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Honegger R, Edwards D, Axe L, Strullu-Derrien C. Fertile Prototaxites taiti: a basal ascomycete with inoperculate, polysporous asci lacking croziers. Philos Trans R Soc Lond B Biol Sci 2018; 373:20170146. [PMID: 29254969 PMCID: PMC5745340 DOI: 10.1098/rstb.2017.0146] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2017] [Indexed: 12/30/2022] Open
Abstract
The affinities of Prototaxites have been debated ever since its fossils, some attaining tree-trunk proportions, were discovered in Canadian Lower Devonian rocks in 1859. Putative assignations include conifers, red and brown algae, liverworts and fungi (some lichenised). Detailed anatomical investigation led to the reconstruction of the type species, P. logani, as a giant sporophore (basidioma) of an agaricomycete (= holobasidiomycete), but evidence for its reproduction remained elusive. Tissues associated with P. taiti in the Rhynie chert plus charcoalified fragments from southern Britain are investigated here to describe the reproductive characters and hence affinities of Prototaxites Thin sections and peels (Pragian Rhynie chert, Aberdeenshire) were examined using light and confocal microscopy; Přídolí and Lochkovian charcoalified samples (Welsh Borderland) were liberated from the rock and examined with scanning electron microscopy. Prototaxites taiti possessed a superficial hymenium comprising an epihymenial layer, delicate septate paraphyses, inoperculate polysporic asci lacking croziers and a subhymenial layer composed predominantly of thin-walled hyphae and occasional larger hyphae. Prototaxites taiti combines features of extant Taphrinomycotina (Neolectomycetes lacking croziers) and Pezizomycotina (epihymenial layer secreted by paraphyses) but is not an ancestor of the latter. Brief consideration is given to its nutrition and potential position in the phylogeny of the Ascomycota.This article is part of a discussion meeting issue 'The Rhynie cherts: our earliest terrestrial ecosystem revisited'.
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Affiliation(s)
- Rosmarie Honegger
- Institute of Plant and Microbiology, University of Zürich, Zollikerstrasse 107, 8008 Zürich, Switzerland
| | - Dianne Edwards
- School of Earth and Ocean Sciences, Cardiff University, Park Place, Cardiff CF10 3AT, UK
| | - Lindsey Axe
- School of Earth and Ocean Sciences, Cardiff University, Park Place, Cardiff CF10 3AT, UK
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Awards and Personalia. IMA Fungus 2017. [DOI: 10.1007/bf03449462] [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] Open
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35
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Vanderpool D, Bracewell RR, McCutcheon JP. Know your farmer: Ancient origins and multiple independent domestications of ambrosia beetle fungal cultivars. Mol Ecol 2017; 27:2077-2094. [PMID: 29087025 DOI: 10.1111/mec.14394] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/05/2017] [Accepted: 10/11/2017] [Indexed: 12/27/2022]
Abstract
Bark and ambrosia beetles are highly specialized weevils (Curculionidae) that have established diverse symbioses with fungi, most often from the order Ophiostomatales (Ascomycota, Sordariomycetes). The two types of beetles are distinguished by their feeding habits and intimacy of interactions with their symbiotic fungi. The tree tissue diet of bark beetles is facilitated by fungi, while ambrosia beetles feed solely on fungi that they farm. The farming life history strategy requires domestication of a fungus, which the beetles consume as their sole food source. Ambrosia beetles in the subfamily Platypodinae originated in the mid-Cretaceous (119-88 Ma) and are the oldest known group of farming insects. However, attempts to resolve phylogenetic relationships and the timing of domestication events for fungal cultivars have been largely inconclusive. We sequenced the genomes of 12 ambrosia beetle fungal cultivars and bark beetle associates, including the devastating laurel wilt pathogen, Raffaelea lauricola, to estimate a robust phylogeny of the Ophiostomatales. We find evidence for contemporaneous diversification of the beetles and their associated fungi, followed by three independent domestication events of the ambrosia fungi genus Raffaelea. We estimate the first domestication of an Ophiostomatales fungus occurred ~86 Ma, 25 million years earlier than prior estimates and in close agreement with the estimated age of farming in the Platypodinae (96 Ma). Comparisons of the timing of fungal domestication events with the timing of beetle radiations support the hypothesis that the first large beetle radiations may have spread domesticated "ambrosia" fungi to other fungi-associated beetle groups, perhaps facilitating the evolution of new farming lineages.
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Affiliation(s)
- Dan Vanderpool
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Ryan R Bracewell
- Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, MT, USA
| | - John P McCutcheon
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
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Ekanayaka AH, Ariyawansa HA, Hyde KD, Jones EBG, Daranagama DA, Phillips AJL, Hongsanan S, Jayasiri SC, Zhao Q. DISCOMYCETES: the apothecial representatives of the phylum Ascomycota. FUNGAL DIVERS 2017. [DOI: 10.1007/s13225-017-0389-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Biedermann PH, Rohlfs M. Evolutionary feedbacks between insect sociality and microbial management. CURRENT OPINION IN INSECT SCIENCE 2017; 22:92-100. [PMID: 28805645 DOI: 10.1016/j.cois.2017.06.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/22/2017] [Accepted: 06/09/2017] [Indexed: 06/07/2023]
Abstract
Fitness-determining interactions with microbes-in particular fungi-have often been considered a by-product of social evolution in insects. Here, we take the view that both beneficial and harmful microbial consortia are major drivers of social behaviours in many insect systems-ranging from aggregation to eusociality. We propose evolutionary feedbacks between the insect sociality and microbial communities that strengthen mutualistic interactions with beneficial (dietary or defensive) microbes and simultaneously increase the capacity to defend against pathogens (i.e. social immunity). We identified variation in habitat stability-as determined by breeding site predictability and ephemerality-as a main ecological factor that constrains these feedbacks. To test this hypothesis we suggest following the evolution of insect social traits upon experimental manipulation of habitat stability and microbial consortia.
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Affiliation(s)
- Peter Hw Biedermann
- Department of Biochemistry, Max-Planck-Institute for Chemical Ecology, Jena, Germany; Institute for Animal Ecology and Tropical Biology, Julius-Maximilians-University of Würzburg, Germany.
| | - Marko Rohlfs
- University of Bremen, Institute of Ecology, Population- and Evolutionary Ecology Group, Germany; University of Goettingen, J.F. Blumenbach Institute of Zoology, Animal Ecology Group, Germany.
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38
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Heads SW, Miller AN, Crane JL, Thomas MJ, Ruffatto DM, Methven AS, Raudabaugh DB, Wang Y. The oldest fossil mushroom. PLoS One 2017; 12:e0178327. [PMID: 28591180 PMCID: PMC5462346 DOI: 10.1371/journal.pone.0178327] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 05/10/2017] [Indexed: 11/19/2022] Open
Abstract
A new fossil mushroom is described and illustrated from the Lower Cretaceous Crato Formation of northeast Brazil. Gondwanagaricites magnificus gen. et sp. nov. is remarkable for its exceptional preservation as a mineralized replacement in laminated limestone, as all other fossil mushrooms are known from amber inclusions. Gondwanagaricites represents the oldest fossil mushroom to date and the first fossil mushroom from Gondwana.
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Affiliation(s)
- Sam W. Heads
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
- * E-mail:
| | - Andrew N. Miller
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - J. Leland Crane
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - M. Jared Thomas
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Danielle M. Ruffatto
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Andrew S. Methven
- Department of Biology, Savannah State University, Savannah, Georgia, United States of America
| | - Daniel B. Raudabaugh
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Yinan Wang
- Independent Researcher, Arlington, Virginia, United States of America
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Worobiec G, Neumann FH, Worobiec E, Nitz V, Hartkopf-Fröder C. New fungal cephalothecoid-like fructifications from central European Neogene deposits. Fungal Biol 2017; 121:285-292. [PMID: 28215354 DOI: 10.1016/j.funbio.2016.12.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 11/10/2016] [Accepted: 12/29/2016] [Indexed: 11/25/2022]
Abstract
Fragments of cephalothecoid fructifications (peridia) were encountered during palynological investigations of Neogene deposits in Mizerna-Nowa/Poland and Adendorf/Germany. Isolated plates of cephalothecoid ascoma in shape and cellular structure similar to the extant members of the family Cephalothecaceae are described as Cephalothecoidomyces neogenicus fossil gen. et sp. nov. while remnants of fungal sporocarps with cephalothecoid walls with indistinct lines of dehiscence, similar in structure to peridia with cephalothecoid morphology of extant representatives the family Chaetomiaceae (mainly genus Chaetomidium) are assigned to Adendorfia miocenica fossil gen. et sp. nov. We also propose a new interpretation of some previously described fossil fungal taxa that we consider to be remnants of cephalothecoid ascomata.
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Affiliation(s)
- Grzegorz Worobiec
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, PL-31-512 Kraków, Poland.
| | - Frank Harald Neumann
- Forschungsstelle für Paläobotanik, University of Münster, Heisenbergstrasse 2, D-48149 Münster, Germany.
| | - Elżbieta Worobiec
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, PL-31-512 Kraków, Poland.
| | - Verena Nitz
- Forschungsstelle für Paläobotanik, University of Münster, Heisenbergstrasse 2, D-48149 Münster, Germany.
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Zhang N, Castlebury LA, Miller AN, Huhndorf SM, Schoch CL, Seifert KA, Rossman AY, Rogers JD, Kohlmeyer J, Volkmann-Kohlmeyer B, Sung GH. An overview of the systematics of the Sordariomycetes based on a four-gene phylogeny. Mycologia 2017. [DOI: 10.1080/15572536.2006.11832635] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ning Zhang
- Department of Plant Pathology, NYSAES, Cornell University, Geneva, New York 14456
| | - Lisa A. Castlebury
- Systematic Botany & Mycology Laboratory, USDA-ARS, Beltsville, Maryland 20705
| | - Andrew N. Miller
- Center for Biodiversity, Illinois Natural History Survey, Champaign, Illinois 61820
| | - Sabine M. Huhndorf
- Department of Botany, The Field Museum of Natural History, Chicago, Illinois 60605
| | - Conrad L. Schoch
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - Keith A. Seifert
- Biodiversity (Mycology and Botany), Agriculture and Agri-Food Canada, Ottawa, Ontario, K1A 0C6 Canada
| | - Amy Y. Rossman
- Systematic Botany & Mycology Laboratory, USDA-ARS, Beltsville, Maryland 20705
| | - Jack D. Rogers
- Department of Plant Pathology, Washington State University, Pullman, Washington 99164
| | | | - Brigitte Volkmann-Kohlmeyer
- Institute of Marine Sciences, University of North Carolina at Chapel Hill, Morehead City, North Carolina 28557
| | - Gi-Ho Sung
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
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41
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Affiliation(s)
- John W. Taylor
- Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, California 94720-3102
| | - Mary L. Berbee
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4 Canada
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Identification of differentially expressed genes from Trichoderma atroviride strain SS003 in the presence of cell wall of Cronartium ribicola. Genes Genomics 2017. [DOI: 10.1007/s13258-016-0512-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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43
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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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Barthlott W, Mail M, Neinhuis C. Superhydrophobic hierarchically structured surfaces in biology: evolution, structural principles and biomimetic applications. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:20160191. [PMID: 27354736 PMCID: PMC4928508 DOI: 10.1098/rsta.2016.0191] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/03/2016] [Indexed: 05/09/2023]
Abstract
A comprehensive survey of the construction principles and occurrences of superhydrophobic surfaces in plants, animals and other organisms is provided and is based on our own scanning electron microscopic examinations of almost 20 000 different species and the existing literature. Properties such as self-cleaning (lotus effect), fluid drag reduction (Salvinia effect) and the introduction of new functions (air layers as sensory systems) are described and biomimetic applications are discussed: self-cleaning is established, drag reduction becomes increasingly important, and novel air-retaining grid technology is introduced. Surprisingly, no evidence for lasting superhydrophobicity in non-biological surfaces exists (except technical materials). Phylogenetic trees indicate that superhydrophobicity evolved as a consequence of the conquest of land about 450 million years ago and may be a key innovation in the evolution of terrestrial life. The approximate 10 million extant species exhibit a stunning diversity of materials and structures, many of which are formed by self-assembly, and are solely based on a limited number of molecules. A short historical survey shows that bionics (today often called biomimetics) dates back more than 100 years. Statistical data illustrate that the interest in biomimetic surfaces is much younger still. Superhydrophobicity caught the attention of scientists only after the extreme superhydrophobicity of lotus leaves was published in 1997. Regrettably, parabionic products play an increasing role in marketing.This article is part of the themed issue 'Bioinspired hierarchically structured surfaces for green science'.
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Affiliation(s)
- W Barthlott
- Nees Institute for Biodiversity of Plants, University of Bonn, Venusbergweg 22, Bonn 53115, Germany
| | - M Mail
- Nees Institute for Biodiversity of Plants, University of Bonn, Venusbergweg 22, Bonn 53115, Germany Institute of Crop Science and Resource Conservation (INRES)-Horticultural Science, University of Bonn, Auf dem Hügel 6, Bonn 53121, Germany
| | - C Neinhuis
- Institute of Botany, Technische Universität Dresden, Zellescher Weg 20b, Dresden 01217, Germany B CUBE Innovation Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstrasse 18, Dresden 01217, Germany
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Karlsson M, Durling MB, Choi J, Kosawang C, Lackner G, Tzelepis GD, Nygren K, Dubey MK, Kamou N, Levasseur A, Zapparata A, Wang J, Amby DB, Jensen B, Sarrocco S, Panteris E, Lagopodi AL, Pöggeler S, Vannacci G, Collinge DB, Hoffmeister D, Henrissat B, Lee YH, Jensen DF. Insights on the evolution of mycoparasitism from the genome of Clonostachys rosea. Genome Biol Evol 2015; 7:465-80. [PMID: 25575496 PMCID: PMC4350171 DOI: 10.1093/gbe/evu292] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/27/2014] [Indexed: 11/14/2022] Open
Abstract
Clonostachys rosea is a mycoparasitic fungus that can control several important plant diseases. Here, we report on the genome sequencing of C. rosea and a comparative genome analysis, in order to resolve the phylogenetic placement of C. rosea and to study the evolution of mycoparasitism as a fungal lifestyle. The genome of C. rosea is estimated to 58.3 Mb, and contains 14,268 predicted genes. A phylogenomic analysis shows that C. rosea clusters as sister taxon to plant pathogenic Fusarium species, with mycoparasitic/saprotrophic Trichoderma species in an ancestral position. A comparative analysis of gene family evolution reveals several distinct differences between the included mycoparasites. Clonostachys rosea contains significantly more ATP-binding cassette (ABC) transporters, polyketide synthases, cytochrome P450 monooxygenases, pectin lyases, glucose-methanol-choline oxidoreductases, and lytic polysaccharide monooxygenases compared with other fungi in the Hypocreales. Interestingly, the increase of ABC transporter gene number in C. rosea is associated with phylogenetic subgroups B (multidrug resistance proteins) and G (pleiotropic drug resistance transporters), whereas an increase in subgroup C (multidrug resistance-associated proteins) is evident in Trichoderma virens. In contrast with mycoparasitic Trichoderma species, C. rosea contains very few chitinases. Expression of six group B and group G ABC transporter genes was induced in C. rosea during exposure to the Fusarium mycotoxin zearalenone, the fungicide Boscalid or metabolites from the biocontrol bacterium Pseudomonas chlororaphis. The data suggest that tolerance toward secondary metabolites is a prominent feature in the biology of C. rosea.
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Affiliation(s)
- Magnus Karlsson
- Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Jaeyoung Choi
- Department of Agricultural Biotechnology, Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
| | - Chatchai Kosawang
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Copenhagen, Denmark
| | - Gerald Lackner
- Department of Pharmaceutical Microbiology at the Hans-Knöll-Institute, Friedrich-Schiller-Universität, Jena, Germany
| | - Georgios D Tzelepis
- Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Kristiina Nygren
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mukesh K Dubey
- Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Nathalie Kamou
- Plant Pathology Laboratory, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Anthony Levasseur
- INRA and Aix-Marseille Université, Polytech Marseille, UMR1163 Biotechnologie des Champignons Filamenteux, Marseille, France
| | - Antonio Zapparata
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Jinhui Wang
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Daniel Buchvaldt Amby
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Copenhagen, Denmark
| | - Birgit Jensen
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Copenhagen, Denmark
| | - Sabrina Sarrocco
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Emmanuel Panteris
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Anastasia L Lagopodi
- Plant Pathology Laboratory, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Stefanie Pöggeler
- Department of Genetics of Eukaryotic Microorganisms, Institute of Microbiology and Genetics, Georg-August University, Göttingen, Germany
| | - Giovanni Vannacci
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - David B Collinge
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Copenhagen, Denmark
| | - Dirk Hoffmeister
- Department of Pharmaceutical Microbiology at the Hans-Knöll-Institute, Friedrich-Schiller-Universität, Jena, Germany
| | - Bernard Henrissat
- Centre National de la Recherche Scientifique (CNRS), UMR7257, Université Aix-Marseille, Marseille, France, and Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
| | - Dan Funck Jensen
- Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Identification of horizontally transferred genes in the genus Colletotrichum reveals a steady tempo of bacterial to fungal gene transfer. BMC Genomics 2015; 16:2. [PMID: 25555398 PMCID: PMC4320630 DOI: 10.1186/1471-2164-16-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 12/08/2014] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Horizontal gene transfer (HGT) is the stable transmission of genetic material between organisms by means other than vertical inheritance. HGT has an important role in the evolution of prokaryotes but is relatively rare in eukaryotes. HGT has been shown to contribute to virulence in eukaryotic pathogens. We studied the importance of HGT in plant pathogenic fungi by identifying horizontally transferred genes in the genomes of three members of the genus Colletotrichum. RESULTS We identified eleven HGT events from bacteria into members of the genus Colletotrichum or their ancestors. The HGT events include genes involved in amino acid, lipid and sugar metabolism as well as lytic enzymes. Additionally, the putative minimal dates of transference were calculated using a time calibrated phylogenetic tree. This analysis reveals a constant flux of genes from bacteria to fungi throughout the evolution of subphylum Pezizomycotina. CONCLUSIONS Genes that are typically transferred by HGT are those that are constantly subject to gene duplication and gene loss. The functions of some of these genes suggest roles in niche adaptation and virulence. We found no evidence of a burst of HGT events coinciding with major geological events. In contrast, HGT appears to be a constant, albeit rare phenomenon in the Pezizomycotina, occurring at a steady rate during their evolution.
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47
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Evolutionary History of Terrestrial Pathogens and Endoparasites as Revealed in Fossils and Subfossils. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/181353] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The present work uses fossils and subfossils to decipher the origin and evolution of terrestrial pathogens and endoparasites. Fossils, as interpreted by morphology or specific features of their hosts, furnish minimum dates for the origin of infectious agents, coevolution with hosts, and geographical locations. Subfossils, those that can be C14 dated (roughly under 50,000 years) and are identified by morphology as well as molecular and immunological techniques, provide time periods when humans became infected with various diseases. The pathogen groups surveyed include viruses, bacteria, protozoa, fungi, and select multicellular endoparasites including nematodes, trematodes, cestodes, and insect parasitoids in the terrestrial environment.
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48
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Kubicek CP, Herrera-Estrella A, Seidl-Seiboth V, Martinez DA, Druzhinina IS, Thon M, Zeilinger S, Casas-Flores S, Horwitz BA, Mukherjee PK, Mukherjee M, Kredics L, Alcaraz LD, Aerts A, Antal Z, Atanasova L, Cervantes-Badillo MG, Challacombe J, Chertkov O, McCluskey K, Coulpier F, Deshpande N, von Döhren H, Ebbole DJ, Esquivel-Naranjo EU, Fekete E, Flipphi M, Glaser F, Gómez-Rodríguez EY, Gruber S, Han C, Henrissat B, Hermosa R, Hernández-Oñate M, Karaffa L, Kosti I, Le Crom S, Lindquist E, Lucas S, Lübeck M, Lübeck PS, Margeot A, Metz B, Misra M, Nevalainen H, Omann M, Packer N, Perrone G, Uresti-Rivera EE, Salamov A, Schmoll M, Seiboth B, Shapiro H, Sukno S, Tamayo-Ramos JA, Tisch D, Wiest A, Wilkinson HH, Zhang M, Coutinho PM, Kenerley CM, Monte E, Baker SE, Grigoriev IV. Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. Genome Biol 2011; 12:R40. [PMID: 21501500 PMCID: PMC3218866 DOI: 10.1186/gb-2011-12-4-r40] [Citation(s) in RCA: 383] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Revised: 03/28/2011] [Accepted: 04/18/2011] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea/Trichoderma. RESULTS Here we report an analysis of the genome sequences of the two biocontrol species Trichoderma atroviride (teleomorph Hypocrea atroviridis) and Trichoderma virens (formerly Gliocladium virens, teleomorph Hypocrea virens), and a comparison with Trichoderma reesei (teleomorph Hypocrea jecorina). These three Trichoderma species display a remarkable conservation of gene order (78 to 96%), and a lack of active mobile elements probably due to repeat-induced point mutation. Several gene families are expanded in the two mycoparasitic species relative to T. reesei or other ascomycetes, and are overrepresented in non-syntenic genome regions. A phylogenetic analysis shows that T. reesei and T. virens are derived relative to T. atroviride. The mycoparasitism-specific genes thus arose in a common Trichoderma ancestor but were subsequently lost in T. reesei. CONCLUSIONS The data offer a better understanding of mycoparasitism, and thus enforce the development of improved biocontrol strains for efficient and environmentally friendly protection of plants.
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Affiliation(s)
- Christian P Kubicek
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Campus Guanajuato, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Mexico
| | - Verena Seidl-Seiboth
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Diego A Martinez
- Broad Institute of MIT and Harvard, 301 Binney St, Cambridge, MA 02142, USA
| | - Irina S Druzhinina
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Michael Thon
- Centro Hispanoluso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, Calle Del Duero, 12, Villamayor 37185, Spain
| | - Susanne Zeilinger
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Sergio Casas-Flores
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, No. 2055, Colonia Lomas 4a Sección, San Luis Potosí, SLP., 78216, México
| | - Benjamin A Horwitz
- Department of Biology, Technion - Israel Institute of Technology, Neve Shaanan Campus, Technion City, Haifa, 32000, Israel
| | - Prasun K Mukherjee
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Mala Mukherjee
- Department of Biology, Technion - Israel Institute of Technology, Neve Shaanan Campus, Technion City, Haifa, 32000, Israel
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, H-6726, Hungary
| | - Luis D Alcaraz
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Campus Guanajuato, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Mexico
| | - Andrea Aerts
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Zsuzsanna Antal
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, H-6726, Hungary
| | - Lea Atanasova
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Mayte G Cervantes-Badillo
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, No. 2055, Colonia Lomas 4a Sección, San Luis Potosí, SLP., 78216, México
| | - Jean Challacombe
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Olga Chertkov
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Kevin McCluskey
- School of Biological Sciences, University of Missouri- Kansas City, 5007 Rockhill Road, Kansas City, MO 64110, USA
| | - Fanny Coulpier
- Institut de Biologie de l'École normale supérieure (IBENS), Institut National de la Santé et de la Recherche Médicale U1024, Centre National de la Recherche Scientifique UMR8197, 46, rue d'Ulm, Paris 75005, France
| | - Nandan Deshpande
- Chemistry and Biomolecular Sciences, Macquarie University, Research Park Drive Building F7B, North Ryde, Sydney, NSW 2109, Australia
| | - Hans von Döhren
- TU Berlin, Institut für Chemie, FG Biochemie und Molekulare Biologie OE2, Franklinstr. 29, 10587 Berlin, Germany
| | - Daniel J Ebbole
- Department of Plant Pathology and Microbiology Building 0444, Nagle Street, Texas A&M University College Station, TX 77843, USA
| | - Edgardo U Esquivel-Naranjo
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Campus Guanajuato, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Mexico
| | - Erzsébet Fekete
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, Debrecen, H-4010, Hungary
| | - Michel Flipphi
- Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas, Apartado de Correos 73, Burjassot (Valencia) E-46100, Spain
| | - Fabian Glaser
- Department of Biology, Technion - Israel Institute of Technology, Neve Shaanan Campus, Technion City, Haifa, 32000, Israel
| | - Elida Y Gómez-Rodríguez
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, No. 2055, Colonia Lomas 4a Sección, San Luis Potosí, SLP., 78216, México
| | - Sabine Gruber
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Cliff Han
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Université de la Méditerranée, Case 932, 163 Avenue de Luminy, 13288 Marseille 13288, France
| | - Rosa Hermosa
- Centro Hispanoluso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, Calle Del Duero, 12, Villamayor 37185, Spain
| | - Miguel Hernández-Oñate
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Campus Guanajuato, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Mexico
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, Debrecen, H-4010, Hungary
| | - Idit Kosti
- Department of Biology, Technion - Israel Institute of Technology, Neve Shaanan Campus, Technion City, Haifa, 32000, Israel
| | - Stéphane Le Crom
- Institut de Biologie de l'École normale supérieure (IBENS), Institut National de la Santé et de la Recherche Médicale U1024, Centre National de la Recherche Scientifique UMR8197, 46, rue d'Ulm, Paris 75005, France
| | - Erika Lindquist
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Susan Lucas
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Mette Lübeck
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Lautrupvang 15, DK-2750 Ballerup, Denmark
| | - Peter S Lübeck
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Lautrupvang 15, DK-2750 Ballerup, Denmark
| | - Antoine Margeot
- Biotechnology Department, IFP Energies nouvelles, 1-4 avenue de Bois Préau, Rueil-Malmaison, 92852, France
| | - Benjamin Metz
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Monica Misra
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Helena Nevalainen
- Chemistry and Biomolecular Sciences, Macquarie University, Research Park Drive Building F7B, North Ryde, Sydney, NSW 2109, Australia
| | - Markus Omann
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Nicolle Packer
- Chemistry and Biomolecular Sciences, Macquarie University, Research Park Drive Building F7B, North Ryde, Sydney, NSW 2109, Australia
| | - Giancarlo Perrone
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Edith E Uresti-Rivera
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, No. 2055, Colonia Lomas 4a Sección, San Luis Potosí, SLP., 78216, México
| | - Asaf Salamov
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Monika Schmoll
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Bernhard Seiboth
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Harris Shapiro
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Serenella Sukno
- Centro Hispanoluso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, Calle Del Duero, 12, Villamayor 37185, Spain
| | - Juan Antonio Tamayo-Ramos
- Wageningen University, Systems and Synthetic Biology, Fungal Systems Biology Group, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | - Doris Tisch
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Aric Wiest
- School of Biological Sciences, University of Missouri- Kansas City, 5007 Rockhill Road, Kansas City, MO 64110, USA
| | - Heather H Wilkinson
- Department of Plant Pathology and Microbiology Building 0444, Nagle Street, Texas A&M University College Station, TX 77843, USA
| | - Michael Zhang
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Pedro M Coutinho
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Université de la Méditerranée, Case 932, 163 Avenue de Luminy, 13288 Marseille 13288, France
| | - Charles M Kenerley
- Department of Plant Pathology and Microbiology Building 0444, Nagle Street, Texas A&M University College Station, TX 77843, USA
| | - Enrique Monte
- Centro Hispanoluso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, Calle Del Duero, 12, Villamayor 37185, Spain
| | - Scott E Baker
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
- Chemical and Biological Process Development Group, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352, USA
| | - Igor V Grigoriev
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
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Evolutionary Trends in Remarkable Fossil Preservation Across the Ediacaran–Cambrian Transition and the Impact of Metazoan Mixing. TOPICS IN GEOBIOLOGY 2010. [DOI: 10.1007/978-90-481-8643-3_15] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Lücking R, Huhndorf S, Pfister DH, Plata ER, Lumbsch HT. Fungi evolved right on track. Mycologia 2009; 101:810-22. [PMID: 19927746 DOI: 10.3852/09-016] [Citation(s) in RCA: 184] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Dating of fungal divergences with molecular clocks thus far has yielded highly inconsistent results. The origin of fungi was estimated at between 660 million and up to 2.15 billion y ago, and the divergence of the two major lineages of higher fungi, Ascomycota and Basidiomycota, at between 390 million y and up to 1.5 billion y ago. Assuming that these inconsistencies stem from various causes, we reassessed the systematic placement of the most important fungal fossil, Paleopyrenomycites, and recalibrated internally unconstrained, published molecular clock trees by applying uniform calibration points. As a result the origin of fungi was re-estimated at between 760 million and 1.06 billion y ago and the origin of the Ascomycota at 500-650 million y ago. These dates are much more consistent than previous estimates, even if based on the same phylogenies and molecular clock trees, and they are also much better in line with the fossil record of fungi and plants and the ecological interdependence between filamentous fungi and land plants. Our results do not provide evidence to suggest the existence of ancient protolichens as an alternative to explain the ecology of early terrestrial fungi in the absence of land plants.
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Affiliation(s)
- Robert Lücking
- Department of Botany, The Field Museum, 1400 South Lake Shore Drive, Chicago, Illinois 60605-2496, USA.
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