Full Text Is a Publisher's Version
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Diversification of Fungal Chitinases and Their Functional Differentiation in 2 Histoplasma Capsulatum 3
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.09.137125; this version posted June 16, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 1 Diversification of fungal chitinases and their functional differentiation in 2 Histoplasma capsulatum 3 4 Kristie D. Goughenour1*, Janice Whalin1, 5 Jason C. Slot2, Chad A. Rappleye1# 6 7 1 Department of Microbiology, Ohio State University 8 2 Department of Plant Pathology, Ohio State University 9 10 11 #corresponding author: 12 [email protected] 13 614-247-2718 14 15 *current affiliation: 16 Division of Pulmonary and Critical Care Medicine 17 University of Michigan 18 VA Ann Arbor Healthcare System, Research Service 19 Ann Arbor, Michigan, USA 20 21 22 running title: Fungal chitinases 23 24 keywords: chitinase, GH18, fungi, Histoplasma 25 bioRxiv preprint doi: https://doi.org/10.1101/2020.06.09.137125; this version posted June 16, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 26 ABSTRACT 27 Chitinases enzymatically hydrolyze chitin, a highly abundant biomolecule with many potential 28 industrial and medical uses in addition to their natural biological roles. Fungi are a rich source of 29 chitinases, however the phylogenetic and functional diversity of fungal chitinases are not well 30 understood. -
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, -
Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes
University of Rhode Island DigitalCommons@URI Biological Sciences Faculty Publications Biological Sciences 9-26-2018 Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes Christopher E. Lane Et Al Follow this and additional works at: https://digitalcommons.uri.edu/bio_facpubs Journal of Eukaryotic Microbiology ISSN 1066-5234 ORIGINAL ARTICLE Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes Sina M. Adla,* , David Bassb,c , Christopher E. Laned, Julius Lukese,f , Conrad L. Schochg, Alexey Smirnovh, Sabine Agathai, Cedric Berneyj , Matthew W. Brownk,l, Fabien Burkim,PacoCardenas n , Ivan Cepi cka o, Lyudmila Chistyakovap, Javier del Campoq, Micah Dunthornr,s , Bente Edvardsent , Yana Eglitu, Laure Guillouv, Vladimır Hamplw, Aaron A. Heissx, Mona Hoppenrathy, Timothy Y. Jamesz, Anna Karn- kowskaaa, Sergey Karpovh,ab, Eunsoo Kimx, Martin Koliskoe, Alexander Kudryavtsevh,ab, Daniel J.G. Lahrac, Enrique Laraad,ae , Line Le Gallaf , Denis H. Lynnag,ah , David G. Mannai,aj, Ramon Massanaq, Edward A.D. Mitchellad,ak , Christine Morrowal, Jong Soo Parkam , Jan W. Pawlowskian, Martha J. Powellao, Daniel J. Richterap, Sonja Rueckertaq, Lora Shadwickar, Satoshi Shimanoas, Frederick W. Spiegelar, Guifre Torruellaat , Noha Youssefau, Vasily Zlatogurskyh,av & Qianqian Zhangaw a Department of Soil Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, S7N 5A8, SK, Canada b Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom -
BMC Evolutionary Biology Biomed Central
BMC Evolutionary Biology BioMed Central Research article Open Access A fungal phylogeny based on 82 complete genomes using the composition vector method Hao Wang1, Zhao Xu1, Lei Gao2 and Bailin Hao*1,3,4 Address: 1T-life Research Center, Department of Physics, Fudan University, Shanghai 200433, PR China, 2Department of Botany & Plant Sciences, University of California, Riverside, CA(92521), USA, 3Institute of Theoretical Physics, Academia Sinica, Beijing 100190, PR China and 4Santa Fe Institute, Santa Fe, NM(87501), USA Email: Hao Wang - [email protected]; Zhao Xu - [email protected]; Lei Gao - [email protected]; Bailin Hao* - [email protected] * Corresponding author Published: 10 August 2009 Received: 30 September 2008 Accepted: 10 August 2009 BMC Evolutionary Biology 2009, 9:195 doi:10.1186/1471-2148-9-195 This article is available from: http://www.biomedcentral.com/1471-2148/9/195 © 2009 Wang et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Molecular phylogenetics and phylogenomics have greatly revised and enriched the fungal systematics in the last two decades. Most of the analyses have been performed by comparing single or multiple orthologous gene regions. Sequence alignment has always been an essential element in tree construction. These alignment-based methods (to be called the standard methods hereafter) need independent verification in order to put the fungal Tree of Life (TOL) on a secure footing. -
Performance of Four Ribosomal DNA Regions to Infer Higher-Level Phylogenetic Relationships of Inoperculate Euascomycetes (Leotiomyceta)
Molecular Phylogenetics and Evolution 34 (2005) 512–524 www.elsevier.com/locate/ympev Performance of four ribosomal DNA regions to infer higher-level phylogenetic relationships of inoperculate euascomycetes (Leotiomyceta) H. Thorsten Lumbscha,¤, Imke Schmitta, Ralf Lindemuthb, Andrew Millerc, Armin Mangolda,b, Fernando Fernandeza, Sabine Huhndorfa a Department of Botany, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA b Universität Duisburg-Essen, Campus Essen, 45117 Essen, Germany c Center for Biodiversity, Illinois Natural History Survey, 607 E. Peabody Drive, Champaign, IL 61820, USA Received 9 June 2004; revised 14 October 2004 Available online 1 January 2005 Abstract The inoperculate euascomycetes are Wlamentous fungi that form saprobic, parasitic, and symbiotic associations with a wide vari- ety of animals, plants, cyanobacteria, and other fungi. The higher-level relationships of this economically important group have been unsettled for over 100 years. A data set of 55 species was assembled including sequence data from nuclear and mitochondrial small and large subunit rDNAs for each taxon; 83 new sequences were obtained for this study. Parsimony and Bayesian analyses were per- formed using the four-region data set and all 14 possible subpartitions of the data. The mitochondrial LSU rDNA was used for the Wrst time in a higher-level phylogenetic study of ascomycetes and its use in concatenated analyses is supported. The classes that were recognized in Leotiomyceta ( D inoperculate euascomycetes) in a classiWcation by Eriksson and Winka [Myconet 1 (1997) 1] are strongly supported as monophyletic. The following classes formed strongly supported sister-groups: Arthoniomycetes and Doth- ideomycetes, Chaetothyriomycetes and Eurotiomycetes, and Leotiomycetes and Sordariomycetes. -
Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their Mrna Targets
RESEARCH ARTICLE Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets Gregory J. Hogan1,2¤a, Patrick O. Brown1,2¤b*, Daniel Herschlag1,3,4,5* 1 Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America, 2 Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America, 3 Department of Chemistry, Stanford University, Stanford, California, United States of America, 4 Department of Chemical Engineering, Stanford University, Stanford, California, United States of America, 5 ChEM-H Institute, Stanford University, Stanford, California, United States of America ¤a Current address: Counsyl, South San Francisco, California, United States of America ¤b Current address: Impossible Foods, Redwood City, California, United States of America * [email protected] (POB); [email protected] (DH) Abstract OPEN ACCESS Reprogramming of a gene’s expression pattern by acquisition and loss of sequences recog- Citation: Hogan GJ, Brown PO, Herschlag D (2015) Evolutionary Conservation and Diversification of Puf nized by specific regulatory RNA binding proteins may be a major mechanism in the evolu- RNA Binding Proteins and Their mRNA Targets. tion of biological regulatory programs. We identified that RNA targets of Puf3 orthologs PLoS Biol 13(11): e1002307. doi:10.1371/journal. have been conserved over 100–500 million years of evolution in five eukaryotic lineages. pbio.1002307 Focusing on Puf proteins -
Toward a Fully Resolved Fungal Tree of Life
Annual Review of Microbiology Toward a Fully Resolved Fungal Tree of Life Timothy Y. James,1 Jason E. Stajich,2 Chris Todd Hittinger,3 and Antonis Rokas4 1Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA; email: [email protected] 2Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, California 92521, USA; email: [email protected] 3Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Center for Genomic Science and Innovation, J.F. Crow Institute for the Study of Evolution, University of Wisconsin–Madison, Madison, Wisconsin 53726, USA; email: [email protected] 4Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, USA; email: [email protected] Annu. Rev. Microbiol. 2020. 74:291–313 Keywords First published as a Review in Advance on deep phylogeny, phylogenomic inference, uncultured majority, July 13, 2020 classification, systematics The Annual Review of Microbiology is online at micro.annualreviews.org Abstract https://doi.org/10.1146/annurev-micro-022020- Access provided by Vanderbilt University on 06/28/21. For personal use only. In this review, we discuss the current status and future challenges for fully 051835 Annu. Rev. Microbiol. 2020.74:291-313. Downloaded from www.annualreviews.org elucidating the fungal tree of life. In the last 15 years, advances in genomic Copyright © 2020 by Annual Reviews. technologies have revolutionized fungal systematics, ushering the field into All rights reserved the phylogenomic era. This has made the unthinkable possible, namely ac- cess to the entire genetic record of all known extant taxa. -
Molecular Taxonomy, Origins and Evolution of Freshwater Ascomycetes
Fungal Diversity Molecular taxonomy, origins and evolution of freshwater ascomycetes Dhanasekaran Vijaykrishna*#, Rajesh Jeewon and Kevin D. Hyde* Centre for Research in Fungal Diversity, Department of Ecology & Biodiversity, University of Hong Kong, Pokfulam Road, Hong Kong SAR, PR China Vijaykrishna, D., Jeewon, R. and Hyde, K.D. (2006). Molecular taxonomy, origins and evolution of freshwater ascomycetes. Fungal Diversity 23: 351-390. Fungi are the most diverse and ecologically important group of eukaryotes with the majority occurring in terrestrial habitats. Even though fewer numbers have been isolated from freshwater habitats, fungi growing on submerged substrates exhibit great diversity, belonging to widely differing lineages. Fungal biodiversity surveys in the tropics have resulted in a marked increase in the numbers of fungi known from aquatic habitats. Furthermore, dominant fungi from aquatic habitats have been isolated only from this milieu. This paper reviews research that has been carried out on tropical lignicolous freshwater ascomycetes over the past decade. It illustrates their diversity and discusses their role in freshwater habitats. This review also questions, why certain ascomycetes are better adapted to freshwater habitats. Their ability to degrade waterlogged wood and superior dispersal/ attachment strategies give freshwater ascomycetes a competitive advantage in freshwater environments over their terrestrial counterparts. Theories regarding the origin of freshwater ascomycetes have largely been based on ecological findings. In this study, phylogenetic analysis is used to establish their evolutionary origins. Phylogenetic analysis of the small subunit ribosomal DNA (18S rDNA) sequences coupled with bayesian relaxed-clock methods are used to date the origin of freshwater fungi and also test their relationships with their terrestrial counterparts. -
EVALUATING the ENDOPHYTIC FUNGAL COMMUNITY in PLANTED and WILD RUBBER TREES (Hevea Brasiliensis)
ABSTRACT Title of Document: EVALUATING THE ENDOPHYTIC FUNGAL COMMUNITY IN PLANTED AND WILD RUBBER TREES (Hevea brasiliensis) Romina O. Gazis, Ph.D., 2012 Directed By: Assistant Professor, Priscila Chaverri, Plant Science and Landscape Architecture The main objectives of this dissertation project were to characterize and compare the fungal endophytic communities associated with rubber trees (Hevea brasiliensis) distributed in wild habitats and under plantations. This study recovered an extensive number of isolates (more than 2,500) from a large sample size (190 individual trees) distributed in diverse regions (various locations in Peru, Cameroon, and Mexico). Molecular and classic taxonomic tools were used to identify, quantify, describe, and compare the diversity of the different assemblages. Innovative phylogenetic analyses for species delimitation were superimposed with ecological data to recognize operational taxonomic units (OTUs) or ―putative species‖ within commonly found species complexes, helping in the detection of meaningful differences between tree populations. Sapwood and leaf fragments showed high infection frequency, but sapwood was inhabited by a significantly higher number of species. More than 700 OTUs were recovered, supporting the hypothesis that tropical fungal endophytes are highly diverse. Furthermore, this study shows that not only leaf tissue can harbor a high diversity of endophytes, but also that sapwood can contain an even more diverse assemblage. Wild and managed habitats presented high species richness of comparable complexity (phylogenetic diversity). Nevertheless, main differences were found in the assemblage‘s taxonomic composition and frequency of specific strains. Trees growing within their native range were dominated by strains belonging to Trichoderma and even though they were also present in managed trees, plantations trees were dominated by strains of Colletotrichum. -
Elsevier Editorial System(Tm) for Mycological Research
Elsevier Editorial System(tm) for Mycological Research Manuscript Draft Manuscript Number: MYCRES-D-07-00031R2 Title: A Higher-Level Phylogenetic Classification of the Fungi Article Type: Original Research Keywords: AFTOL, Eumycota, Lichens, Molecular phylogenetics, Mycota, Nomenclature, Systematics Corresponding Author: David S. Hibbett, Corresponding Author's Institution: Clark University First Author: David S Hibbett, PhD Order of Authors: David S Hibbett, PhD; David S. Hibbett Manuscript Region of Origin: UNITED STATES Abstract: A comprehensive phylogenetic classification of the kingdom Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from diverse members of the fungal taxonomic community. The classification includes 195 taxa, down to the level of order, of which 19 are described or validated here: Dikarya subkingdom nov.; Chytridiomycota, Neocallimastigomycota phyla nov.; Agaricomycetes, Dacrymycetes, Monoblepharidomycetes, Neocallimastigomycetes, Tremellomycetes class. nov.; Eurotiomycetidae, Lecanoromycetidae, Mycocaliciomycetidae subclass. nov.; Acarosporales, Corticiales, Baeomycetales, Candelariales, Gloeophyllales, Melanosporales, Trechisporales, Umbilicariales ords. nov. The clade containing Ascomycota and Basidiomycota is classified as subkingdom Dikarya, reflecting the putative synapomorphy of dikaryotic hyphae. The most dramatic shifts in the classification relative to previous works concern the groups that have traditionally been included in the Chytridiomycota and Zygomycota. -
Emergence and Loss of Spliceosomal Twin Introns
Flipphi et al. Fungal Biol Biotechnol (2017) 4:7 DOI 10.1186/s40694-017-0037-y Fungal Biology and Biotechnology RESEARCH Open Access Emergence and loss of spliceosomal twin introns Michel Flipphi1, Norbert Ág1, Levente Karafa1, Napsugár Kavalecz1, Gustavo Cerqueira2, Claudio Scazzocchio3,4 and Erzsébet Fekete1* Abstract Background: In the primary transcript of nuclear genes, coding sequences—exons—usually alternate with non- coding sequences—introns. In the evolution of spliceosomal intron–exon structure, extant intron positions can be abandoned and new intron positions can be occupied. Spliceosomal twin introns (“stwintrons”) are unconventional intervening sequences where a standard “internal” intron interrupts a canonical splicing motif of a second, “external” intron. The availability of genome sequences of more than a thousand species of fungi provides a unique opportunity to study spliceosomal intron evolution throughout a whole kingdom by means of molecular phylogenetics. Results: A new stwintron was encountered in Aspergillus nidulans and Aspergillus niger. It is present across three classes of Leotiomyceta in the transcript of a well-conserved gene encoding a putative lipase (lipS). It occupies the same position as a standard intron in the orthologue gene in species of the early divergent classes of the Pezizomy- cetes and the Orbiliomycetes, suggesting that an internal intron has appeared within a pre-extant intron. On the other hand, the stwintron has been lost from certain taxa in Leotiomycetes and Eurotiomycetes at several occa- sions, most likely by a mechanism involving reverse transcription and homologous recombination. Another ancient stwintron present across whole Pezizomycotina orders—in the transcript of the bifunctional biotin biosynthesis gene bioDA—occurs at the same position as a standard intron in many species of non-Dikarya. -
Evolution of Lichens H
Evolution of Lichens H. Thorsten Lumbsch and Jouko Rikkinen 1 INTRODUCTION—THE DIVERSITY OF FUNGAL LIFESTYLES Fungi represent one of the three major crown lineages of eukaryotes, besides plants and animals. For their nutrition, fungi either decompose organic material or form symbiotic associations with other organisms. These symbiotic relationships vary from parasitic lifestyle, such as the rice blight fungus (Partida-Martinez and Hertweck 2005), which causes damage to rice seedlings and uses endosymbiotic bacteria for toxin production, to mutualistic relationships, such as endomycorrhizal relationships, the origin of which coincides with the early evolution of land plants (Simon et al. 1993). There is a continuum among symbiotic associations, from mutualistic to parasitic lifestyles, and some fungal species are known to exhibit different kinds of relationships with different hosts, such as species in the genus Colletotrichum, which can form mutualistic relationships with some plants and have parasitic relationship with other hosts (Redman, Dunigan, and Rodriguez 2001). In addition, at an evolutionary scale, changes of nutritional modes (parasitism versus mutualism) and inter-kingdom host switches have been shown to be common in fungi (Spatafora et al. 2007; Arnold et al. 2009). Given that all fungi are heterotrophic, it is not surprising that many of them have developed symbiotic relationships with photoautotrophic organisms, such as cyanobacteria, algae, and land plants. Fungal relationships with vascular plants are mostly in form of mycorrhiza, such as ectomycorrhizal (Agerer 1991; Wiemken and Boller 2002), endomycorrhizal (Bonfantefasolo and Spanu 1992), and the unique orchid mycorrhizal associations, in which plant seedlings are, from the very beginning, dependent on symbiotic fungi as carbohydrate source (Rasmussen 2002; Dearnaley 2007; Rasmussen and Rasmussen 2009).