Mediterranean Forested Wetlands Are Yeast Hotspots for Bioremediation: A
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Genome Sequence Analysis of Auricularia Heimuer Combined with Genetic Linkage Map
Journal of Fungi Article Genome Sequence Analysis of Auricularia heimuer Combined with Genetic Linkage Map Ming Fang 1, Xiaoe Wang 2, Ying Chen 2, Peng Wang 2, Lixin Lu 2, Jia Lu 2, Fangjie Yao 1,2,* and Youmin Zhang 1,* 1 Lab of genetic breeding of edible mushromm, Horticultural, College of Horticulture, Jilin Agricultural University, Changchun 130118, China; [email protected] 2 Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China; [email protected] (X.W.); [email protected] (Y.C.); [email protected] (P.W.); [email protected] (L.L.); [email protected] (J.L.) * Correspondence: [email protected] (F.Y.); [email protected] (Y.Z.) Received: 3 March 2020; Accepted: 12 March 2020; Published: 16 March 2020 Abstract: Auricularia heimuer is one of the most popular edible fungi in China. In this study, the whole genome of A. heimuer was sequenced on the Illumina HiSeq X system and compared with other mushrooms genomes. As a wood-rotting fungus, a total of 509 carbohydrate-active enzymes (CAZymes) were annotated in order to explore its potential capabilities on wood degradation. The glycoside hydrolases (GH) family genes in the A. heimuer genome were more abundant than the genes in the other 11 mushrooms genomes. The A. heimuer genome contained 102 genes encoding class III, IV, and V ethanol dehydrogenases. Evolutionary analysis based on 562 orthologous single-copy genes from 15 mushrooms showed that Auricularia formed an early independent branch of Agaricomycetes. The mating-type locus of A. heimuer was located on linkage group 8 by genetic linkage analysis. -
Increased Organic Fertilizer and Reduced Chemical Fertilizer Increased Fungal Diversity and the Abundance of Beneficial Fungi on the Grape Berry Surface in Arid Areas
ORIGINAL RESEARCH published: 07 May 2021 doi: 10.3389/fmicb.2021.628503 Increased Organic Fertilizer and Reduced Chemical Fertilizer Increased Fungal Diversity and the Abundance of Beneficial Fungi on the Grape Berry Surface in Arid Areas Linnan Wu 1†, Zhiqiang Li 2†, Fengyun Zhao 1, Benzhou Zhao 1, Fesobi Olumide Phillip 1, Jianrong Feng 1, Huaifeng Liu 1 and Kun Yu 1* 1 Department of Horticulture, College of Agriculture, The Key Laboratory of Characteristics of Fruit and Vegetable Cultivation and Utilization of Germoplasm Resources of the Xinjiang Production and Construction Crops, Shihezi University, Shihezi, China, 2 Shihezi Academy of Agricultural Sciences, Shihezi, China Edited by: Jia Liu, Chongqing University of Arts and Fertilizer practices can significantly impact the fruit quality and microbial diversity of the Sciences, China orchards. The fungi on the surface of fruits are essential for fruit storability and safety. However, Reviewed by: it is not clear whether fertilization affects the fungal diversity and community structure on the Asha Janadaree Dissanayake, surface of grape berries. Here, grape quality and the fungal diversity on the surface of grapes University of Electronic Science and Technology of China, China harvested from three fertilizer treatments were analyzed shortly after grape picking (T0) and Yanfang Wang, following 8 days of storage (T1). The study involved three treatments: (1) common chemical Shandong Agricultural University, China fertilizer for 2 years (CH); (2) increased organic fertilizer and reduced chemical fertilizer for *Correspondence: 1 year (A.O); and (3) increased organic fertilizer and reduced chemical fertilizer for 2 years Kun Yu (B.O). The application of increased organic fertilizer and reduced chemical fertilizer increased [email protected] the soluble solids content (SSC) of the grape berries and decreased the pH of the grape † These authors have contributed juice. -
The Flora Mycologica Iberica Project Fungi Occurrence Dataset
A peer-reviewed open-access journal MycoKeys 15: 59–72 (2016)The Flora Mycologica Iberica Project fungi occurrence dataset 59 doi: 10.3897/mycokeys.15.9765 DATA PAPER MycoKeys http://mycokeys.pensoft.net Launched to accelerate biodiversity research The Flora Mycologica Iberica Project fungi occurrence dataset Francisco Pando1, Margarita Dueñas1, Carlos Lado1, María Teresa Telleria1 1 Real Jardín Botánico-CSIC, Claudio Moyano 1, 28014, Madrid, Spain Corresponding author: Francisco Pando ([email protected]) Academic editor: C. Gueidan | Received 5 July 2016 | Accepted 25 August 2016 | Published 13 September 2016 Citation: Pando F, Dueñas M, Lado C, Telleria MT (2016) The Flora Mycologica Iberica Project fungi occurrence dataset. MycoKeys 15: 59–72. doi: 10.3897/mycokeys.15.9765 Resource citation: Pando F, Dueñas M, Lado C, Telleria MT (2016) Flora Mycologica Iberica Project fungi occurrence dataset. v1.18. Real Jardín Botánico (CSIC). Dataset/Occurrence. http://www.gbif.es/ipt/resource?r=floramicologicaiberi ca&v=1.18, http://doi.org/10.15468/sssx1e Abstract The dataset contains detailed distribution information on several fungal groups. The information has been revised, and in many times compiled, by expert mycologist(s) working on the monographs for the Flora Mycologica Iberica Project (FMI). Records comprise both collection and observational data, obtained from a variety of sources including field work, herbaria, and the literature. The dataset contains 59,235 records, of which 21,393 are georeferenced. These correspond to 2,445 species, grouped in 18 classes. The geographical scope of the dataset is Iberian Peninsula (Continental Portugal and Spain, and Andorra) and Balearic Islands. The complete dataset is available in Darwin Core Archive format via the Global Biodi- versity Information Facility (GBIF). -
A Metagenomic Approach to Understand Stand Failure in Bromus Tectorum
Brigham Young University BYU ScholarsArchive Theses and Dissertations 2019-06-01 A Metagenomic Approach to Understand Stand Failure in Bromus tectorum Nathan Joseph Ricks Brigham Young University Follow this and additional works at: https://scholarsarchive.byu.edu/etd BYU ScholarsArchive Citation Ricks, Nathan Joseph, "A Metagenomic Approach to Understand Stand Failure in Bromus tectorum" (2019). Theses and Dissertations. 8549. https://scholarsarchive.byu.edu/etd/8549 This Thesis is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. A Metagenomic Approach to Understand Stand Failure in Bromus tectorum Nathan Joseph Ricks A thesis submitted to the faculty of Brigham Young University in partial fulfillment of the requirements for the degree of Master of Science Craig Coleman, Chair John Chaston Susan Meyer Department of Plant and Wildlife Sciences Brigham Young University Copyright © 2019 Nathan Joseph Ricks All Rights Reserved ABSTACT A Metagenomic Approach to Understand Stand Failure in Bromus tectorum Nathan Joseph Ricks Department of Plant and Wildlife Sciences, BYU Master of Science Bromus tectorum (cheatgrass) is an invasive annual grass that has colonized large portions of the Intermountain west. Cheatgrass stand failures have been observed throughout the invaded region, the cause of which may be related to the presence of several species of pathogenic fungi in the soil or surface litter. In this study, metagenomics was used to better understand and compare the fungal communities between sites that have and have not experienced stand failure. -
Crittendenia Gen. Nov., a New Lichenicolous Lineage in the Agaricostilbomycetes (Pucciniomycotina), and a Review of the Biology
The Lichenologist (2021), 53, 103–116 doi:10.1017/S002428292000033X Standard Paper Crittendenia gen. nov., a new lichenicolous lineage in the Agaricostilbomycetes (Pucciniomycotina), and a review of the biology, phylogeny and classification of lichenicolous heterobasidiomycetes Ana M. Millanes1, Paul Diederich2, Martin Westberg3 and Mats Wedin4 1Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, E-28933 Móstoles, Spain; 2Musée national d’histoire naturelle, 25 rue Munster, L-2160 Luxembourg; 3Museum of Evolution, Norbyvägen 16, SE-75236 Uppsala, Sweden and 4Department of Botany, Swedish Museum of Natural History, P.O. Box 50007, SE-10405 Stockholm, Sweden Abstract The lichenicolous ‘heterobasidiomycetes’ belong in the Tremellomycetes (Agaricomycotina) and in the Pucciniomycotina. In this paper, we provide an introduction and review of these lichenicolous taxa, focusing on recent studies and novelties of their classification, phylogeny and evolution. Lichen-inhabiting fungi in the Pucciniomycotina are represented by only a small number of species included in the genera Chionosphaera, Cyphobasidium and Lichenozyma. The phylogenetic position of the lichenicolous representatives of Chionosphaera has, however, never been investigated by molecular methods. Phylogenetic analyses using the nuclear SSU, ITS, and LSU ribosomal DNA mar- kers reveal that the lichenicolous members of Chionosphaera form a monophyletic group in the Pucciniomycotina, distinct from Chionosphaera and outside the Chionosphaeraceae. The new genus Crittendenia is described to accommodate these lichen-inhabiting spe- cies. Crittendenia is characterized by minute synnemata-like basidiomata, the presence of clamp connections and aseptate tubular basidia from which 4–7 spores discharge passively, often in groups. Crittendenia, Cyphobasidium and Lichenozyma are the only lichenicolous lineages known so far in the Pucciniomycotina, whereas Chionosphaera does not include any lichenicolous taxa. -
A Higher-Level Phylogenetic Classification of the Fungi
mycological research 111 (2007) 509–547 available at www.sciencedirect.com journal homepage: www.elsevier.com/locate/mycres A higher-level phylogenetic classification of the Fungi David S. HIBBETTa,*, Manfred BINDERa, Joseph F. BISCHOFFb, Meredith BLACKWELLc, Paul F. CANNONd, Ove E. ERIKSSONe, Sabine HUHNDORFf, Timothy JAMESg, Paul M. KIRKd, Robert LU¨ CKINGf, H. THORSTEN LUMBSCHf, Franc¸ois LUTZONIg, P. Brandon MATHENYa, David J. MCLAUGHLINh, Martha J. POWELLi, Scott REDHEAD j, Conrad L. SCHOCHk, Joseph W. SPATAFORAk, Joost A. STALPERSl, Rytas VILGALYSg, M. Catherine AIMEm, Andre´ APTROOTn, Robert BAUERo, Dominik BEGEROWp, Gerald L. BENNYq, Lisa A. CASTLEBURYm, Pedro W. CROUSl, Yu-Cheng DAIr, Walter GAMSl, David M. GEISERs, Gareth W. GRIFFITHt,Ce´cile GUEIDANg, David L. HAWKSWORTHu, Geir HESTMARKv, Kentaro HOSAKAw, Richard A. HUMBERx, Kevin D. HYDEy, Joseph E. IRONSIDEt, Urmas KO˜ LJALGz, Cletus P. KURTZMANaa, Karl-Henrik LARSSONab, Robert LICHTWARDTac, Joyce LONGCOREad, Jolanta MIA˛ DLIKOWSKAg, Andrew MILLERae, Jean-Marc MONCALVOaf, Sharon MOZLEY-STANDRIDGEag, Franz OBERWINKLERo, Erast PARMASTOah, Vale´rie REEBg, Jack D. ROGERSai, Claude ROUXaj, Leif RYVARDENak, Jose´ Paulo SAMPAIOal, Arthur SCHU¨ ßLERam, Junta SUGIYAMAan, R. Greg THORNao, Leif TIBELLap, Wendy A. UNTEREINERaq, Christopher WALKERar, Zheng WANGa, Alex WEIRas, Michael WEISSo, Merlin M. WHITEat, Katarina WINKAe, Yi-Jian YAOau, Ning ZHANGav aBiology Department, Clark University, Worcester, MA 01610, USA bNational Library of Medicine, National Center for Biotechnology Information, -
Structure, Bioactivities and Applications of the Polysaccharides from Tremella Fuciformis Mushroom: a Review
International Journal of Biological Macromolecules 121 (2019) 1005–1010 Contents lists available at ScienceDirect International Journal of Biological Macromolecules journal homepage: http://www.elsevier.com/locate/ijbiomac Review Structure, bioactivities and applications of the polysaccharides from Tremella fuciformis mushroom: A review Yu-ji Wu a, Zheng-xun Wei a, Fu-ming Zhang b,RobertJ.Linhardtb,c, Pei-long Sun a,An-qiangZhanga,⁎ a Department of Food Science and Technology, Zhejiang University of Technology, Hangzhou 310014, China b Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA c Departments of Chemistry and Chemical Biology and Biomedical Engineering, Biological Science, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA article info abstract Article history: Tremella fuciformis is an important edible mushroom that has been widely cultivated and used as food and me- Received 8 August 2018 dicinal ingredient in traditional Chinese medicine. In the past decades, many researchers have reported that T. Received in revised form 12 September 2018 fuciformis polysaccharides (TPS) possess various bioactivities, including anti-tumor, immunomodulatory, anti- Accepted 14 October 2018 oxidation, anti-aging, repairing brain memory impairment, anti-inflammatory, hypoglycemic and Available online 18 October 2018 hypocholesterolemic. The structural characteristic of TPS has also been extensively investigated using advanced modern analytical technologies such as NMR, GC–MS, LC-MS and FT-IR to dissect the structure-activity relation- Keywords: fi Tremella fuciformis ship (SAR) of the TPS biomacromolecule. This article reviews the recent progress in the extraction, puri cation, Polysaccharide structural characterization and applications of TPS. -
Diversity and Roles of Mycorrhizal Fungi in the Bee Orchid Ophrys Apifera
Diversity and Roles of Mycorrhizal Fungi in the Bee Orchid Ophrys apifera By Wazeera Rashid Abdullah April 2018 A Thesis submitted to the University of Liverpool in fulfilment of the requirement for the degree of Doctor in Philosophy Table of Contents Page No. Acknowledgements ............................................................................................................. xiv Abbreviations ............................................................................ Error! Bookmark not defined. Abstract ................................................................................................................................... 2 1 Chapter one: Literature review: ........................................................................................ 3 1.1 Mycorrhiza: .................................................................................................................... 3 1.1.1Arbuscular mycorrhiza (AM) or Vesicular-arbuscular mycorrhiza (VAM): ........... 5 1.1.2 Ectomycorrhiza: ...................................................................................................... 5 1.1.3 Ectendomycorrhiza: ................................................................................................ 6 1.1.4 Ericoid mycorrhiza, Arbutoid mycorrhiza, and Monotropoid mycorrhiza: ............ 6 1.1.5 Orchid mycorrhiza: ................................................................................................. 7 1.1.5.1 Orchid mycorrhizal interaction: ...................................................................... -
Review on Cryptococcus Disease Aden Giro* College of Veterinary Medicine and Agriculture, Addis Ababa University, Ethiopia
iseas al D es OPEN ACCESS Freely available online ic & p P ro u T b l f i c o l H a e n a r l t u h o J Journal of Tropical Disease and Public Health ISSN: 2329-891X Review Article Review on Cryptococcus Disease Aden Giro* College of Veterinary Medicine and Agriculture, Addis Ababa University, Ethiopia ABSTRACT Fungal disease is the most important disease found in many part of the world. Cryptococcosis is one of important mycozoonosis that affecting human and animals. It is primarily caused by Cryptococcus neoformans and Cryptococcus gattii, which are mainly affecting human and animal. Agent is found in soil contaminated with avian droppings or eucalyptus trees and decaying woods. Cryptococcus neoformans can survive in pigeon drop for about 20 years. The inhalation is principal mode of entry of the pathogen. Cryptococcosis occurs in sporadic and epidemic form in susceptible hosts. The disease is most often found in cats but has also been reported in cattle, dogs, horses, sheep, goat and other animals. Cryptococcosis is the first manifestation of HIV infected patients to potentiate HIV infection. Diagnosis is application of Pal’s sunflower seed medium and Narayan stain help in the study of this enigmatic mycosis in humans as well as in animals. Keywords: Cryptococcus gattii; Cryptococcus neoformans; Cryptococcosis; Animals; Human INTRODUCTION with AIDS. On the contrary, C. gattii causes 70% to 80% infections in immunocompetent hosts [6]. Cryptococcosis is a fungal disease found worldwide in human and animal populations mainly caused by Cryptococcus neoformans Man and animal acquire the infection from environment where and Cryptococcus gattii. -
Reference Guide to the Classification of Fungi and Fungal-Like Protists, with Emphasis on the Fungal Genera with Medical Importance (Circa 2009)
Reference Guide to the Classification of Fungi and Fungal-like Protists, with Emphasis on the Fungal Genera with Medical Importance (circa 2009) This outline lists some common genera of fungi and fungal-like protists, which are classified into a number of phyla, subphyla, classes, subclasses and in most cases orders and families. The classification is patterned after the broad schemes of Hawksworth et al. (1), Kirk et al. (2), Eriksson et al. (3), Alexopoulos et al. (4), and Blackwell et al (5) and was devised by PJS to reflect his perception of the relationships of the various organisms traditionally studied by mycologists and included in textbooks and manuals dealing with mycology. The classification ranks below class reflect interpretations of Alexopoulos et al. (7), and PJS. It should be noted that different biologists until recently have had varying opinions on which organisms to include in the Kingdom Fungi and on what rank should be accorded each major group. This classification outline distributes the fungi and fungal-like organisms often dealt with in traditional mycology among the three kingdoms, Protozoa, Chromista and Fungi. With only a relatively few exceptions, the genera listed are very common or are of medical importance. However, not all genera of the Kingdom Fungi involved in human and animal medical mycology are listed. Kingdom: Protozoa/Amebozoa/Eumycetozoa (collection of numerous phyla of eukaryotic, generally wall- less, unicellular, plasmodial, or colonial phagotrophic microorganisms, which includes at least four fungal-like phyla that are no longer considered to be part of the Kingdom Fungi). These have all been reclassified and renamed to reflect their nonfungal nature (see for example Reading Sz 5, which discusses the reclassification of Rhinosporidium seeberi into the additional new Phylum Mezomycetozoea). -
Notes, Outline and Divergence Times of Basidiomycota
Fungal Diversity (2019) 99:105–367 https://doi.org/10.1007/s13225-019-00435-4 (0123456789().,-volV)(0123456789().,- volV) Notes, outline and divergence times of Basidiomycota 1,2,3 1,4 3 5 5 Mao-Qiang He • Rui-Lin Zhao • Kevin D. Hyde • Dominik Begerow • Martin Kemler • 6 7 8,9 10 11 Andrey Yurkov • Eric H. C. McKenzie • Olivier Raspe´ • Makoto Kakishima • Santiago Sa´nchez-Ramı´rez • 12 13 14 15 16 Else C. Vellinga • Roy Halling • Viktor Papp • Ivan V. Zmitrovich • Bart Buyck • 8,9 3 17 18 1 Damien Ertz • Nalin N. Wijayawardene • Bao-Kai Cui • Nathan Schoutteten • Xin-Zhan Liu • 19 1 1,3 1 1 1 Tai-Hui Li • Yi-Jian Yao • Xin-Yu Zhu • An-Qi Liu • Guo-Jie Li • Ming-Zhe Zhang • 1 1 20 21,22 23 Zhi-Lin Ling • Bin Cao • Vladimı´r Antonı´n • Teun Boekhout • Bianca Denise Barbosa da Silva • 18 24 25 26 27 Eske De Crop • Cony Decock • Ba´lint Dima • Arun Kumar Dutta • Jack W. Fell • 28 29 30 31 Jo´ zsef Geml • Masoomeh Ghobad-Nejhad • Admir J. Giachini • Tatiana B. Gibertoni • 32 33,34 17 35 Sergio P. Gorjo´ n • Danny Haelewaters • Shuang-Hui He • Brendan P. Hodkinson • 36 37 38 39 40,41 Egon Horak • Tamotsu Hoshino • Alfredo Justo • Young Woon Lim • Nelson Menolli Jr. • 42 43,44 45 46 47 Armin Mesˇic´ • Jean-Marc Moncalvo • Gregory M. Mueller • La´szlo´ G. Nagy • R. Henrik Nilsson • 48 48 49 2 Machiel Noordeloos • Jorinde Nuytinck • Takamichi Orihara • Cheewangkoon Ratchadawan • 50,51 52 53 Mario Rajchenberg • Alexandre G. -
Towards an Integrated Phylogenetic Classification of the Tremellomycetes
http://www.diva-portal.org This is the published version of a paper published in Studies in mycology. Citation for the original published paper (version of record): Liu, X., Wang, Q., Göker, M., Groenewald, M., Kachalkin, A. et al. (2016) Towards an integrated phylogenetic classification of the Tremellomycetes. Studies in mycology, 81: 85 http://dx.doi.org/10.1016/j.simyco.2015.12.001 Access to the published version may require subscription. N.B. When citing this work, cite the original published paper. Permanent link to this version: http://urn.kb.se/resolve?urn=urn:nbn:se:nrm:diva-1703 available online at www.studiesinmycology.org STUDIES IN MYCOLOGY 81: 85–147. Towards an integrated phylogenetic classification of the Tremellomycetes X.-Z. Liu1,2, Q.-M. Wang1,2, M. Göker3, M. Groenewald2, A.V. Kachalkin4, H.T. Lumbsch5, A.M. Millanes6, M. Wedin7, A.M. Yurkov3, T. Boekhout1,2,8*, and F.-Y. Bai1,2* 1State Key Laboratory for Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; 2CBS Fungal Biodiversity Centre (CBS-KNAW), Uppsalalaan 8, Utrecht, The Netherlands; 3Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig 38124, Germany; 4Faculty of Soil Science, Lomonosov Moscow State University, Moscow 119991, Russia; 5Science & Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA; 6Departamento de Biología y Geología, Física y Química Inorganica, Universidad Rey Juan Carlos, E-28933 Mostoles, Spain; 7Department of Botany, Swedish Museum of Natural History, P.O. Box 50007, SE-10405 Stockholm, Sweden; 8Shanghai Key Laboratory of Molecular Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, PR China *Correspondence: F.-Y.