DOCSLIB.ORG

Sequence-Based Classification and Identification of Fungi

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Sequence-Based Classification and Identification of Fungi Mycologia ISSN: 0027-5514 (Print) 1557-2536 (Online) Journal homepage: http://www.tandfonline.com/loi/umyc20 Sequence-based classification and identification of Fungi David Hibbett, Kessy Abarenkov, Urmas Kõljalg, Maarja Öpik, Benli Chai, James Cole, Qiong Wang, Pedro Crous, Vincent Robert, Thorunn Helgason, Joshua R. Herr, Paul Kirk, Shiloh Lueschow, Kerry O’Donnell, R. Henrik Nilsson, Ryoko Oono, Conrad Schoch, Christopher Smyth, Donald M. Walker, Andrea Porras-Alfaro, John W. Taylor & David M. Geiser To cite this article: David Hibbett, Kessy Abarenkov, Urmas Kõljalg, Maarja Öpik, Benli Chai, James Cole, Qiong Wang, Pedro Crous, Vincent Robert, Thorunn Helgason, Joshua R. Herr, Paul Kirk, Shiloh Lueschow, Kerry O’Donnell, R. Henrik Nilsson, Ryoko Oono, Conrad Schoch, Christopher Smyth, Donald M. Walker, Andrea Porras-Alfaro, John W. Taylor & David M. Geiser (2016) Sequence-based classification and identification of Fungi, Mycologia, 108:6, 1049-1068 To link to this article: https://doi.org/10.3852/16-130 © 2016 by The Mycological Society of America Published online: 30 Jan 2017. Submit your article to this journal Article views: 9271 View Crossmark data Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=umyc20 Mycologia, 108(6), 2016, pp. 1049–1068. DOI: 10.3852/16-130 # 2016 by The Mycological Society of America, Lawrence, KS 66044-8897 Issued 25 January 2017 Sequence-based classification and identification of Fungi David Hibbett1 Christopher Smyth Biology Department, Clark University, Worcester, Department of Plant Pathology and Environmental Massachusetts 01610 Microbiology, 121 Buckhout Laboratory, Penn State University, University Park, Pennsylvania 16802 Kessy Abarenkov Urmas Kõljalg Donald M. Walker Maarja Öpik Department of Biology, Tennessee Technological University, Institute of Ecology and Earth Sciences, 1100 N. Dixie Ave., Cookeville, Tennessee 38505 University of Tartu, 40 Lai St, Tartu 51005, Estonia Andrea Porras-Alfaro Benli Chai Department of Biological Sciences, Western Illinois University, James Cole Waggoner Hall 372, 1 University Circle Macomb, Illinois 61455 Qiong Wang Department of Plant, Soil, and Microbial Sciences, John W. Taylor Michigan State University, Plant and Soil Sciences University of California, Department of Plant and Microbial Building, 1066 Bogue St. Room 540, East Lansing, Biology, 111 Koshland Hall, Berkeley, California 94720 Michigan 48824 David M. Geiser Pedro Crous Department of Plant Pathology and Environmental Vincent Robert Microbiology, 121 Buckhout Laboratory, Penn State Centraalbureau voor Schimmelcultures Fungal Biodiversity University, University Park, Pennsylvania 16802 Centre (CBS-KNAW), 3508 AD, Utrecht, the Netherlands Abstract: Thorunn Helgason Fungal taxonomy and ecology have been Department of Biology, University of York, revolutionized by the application of molecular meth- York YO10 5DD, United Kingdom ods and both have increasing connections to genomics and functional biology. However, data streams from Joshua R. Herr traditional specimen- and culture-based systematics Department of Plant Pathology and Center for Plant Science Innovation, University of Nebraska, are not yet fully integrated with those from metage- Lincoln, Nebraska 68503 nomic and metatranscriptomic studies, which limits understanding of the taxonomic diversity and meta‐ Paul Kirk bolic properties of fungal communities. This article Biodiversity Informatics and Spatial Analysis, Royal Botanic Gardens, Kew, Surrey TW9 3AF, United Kingdom reviews current resources, needs, and opportunities for sequence-based classification and identification Shiloh Lueschow (SBCI) in fungi as well as related efforts in prokaryotes. Kerry O’Donnell To realize the full potential of fungal SBCI it will be NCAUR ARS USDA, 1815 N. University St., Peoria, necessary to make advances in multiple areas. Improve- Illinois 61604 ments in sequencing methods, including long-read and R. Henrik Nilsson single-cell technologies, will empower fungal molecu- University of Gothenburg, Department of Biological and lar ecologists to look beyond ITS and current shotgun Environmental Sciences, Box 461, 405 30 Göteborg, metagenomics approaches. Data quality and accessibil- Sweden ity will be enhanced by attention to data and metadata Ryoko Oono standards and rigorous enforcement of policies for Department of Ecology, Evolution, and Marine Biology, deposition of data and workflows. Taxonomic commu- University of California Santa Barbara, Santa Barbara, nities will need to develop best practices for molecular California 93106 characterization in their focal clades, while also con- Conrad Schoch tributing to globally useful datasets including ITS. National Center for Biotechnology Information, National Changes to nomenclatural rules are needed to enable Library of Medicine, National Institutes of Health, Bethesda, valid publication of sequence-based taxon descriptions. Maryland 20892 Finally, cultural shifts are necessary to promote adop- tion of SBCI and to accord professional credit to indivi- duals who contribute to community resources. Submitted 25 Jun 2016; accepted for publication 29 Sep 2016. Key words: biodiversity informatics, metagenomics, 1 Corresponding author. E-mail: [email protected] molecular ecology, nomenclature, systematics, taxonomy 1049 Published online 30 Jan 2017 1050 MYCOLOGIA TABLE I. Terms and concepts for sequence-based classification and identification Candidatus A provisional taxonomic category for prokaryotes that lack a type culture Environmental nucleic acid species (ENAS) A species recognized solely with environmental molecular sequences Environmental sequence A DNA or RNA sequence obtained directly from a microbial community using amplicon or shotgun methods Molecular operational taxonomic unit (MOTU) An unranked taxonomic entity recognized with environmental sequences Nomenclature The set of rules detailed in the ICNAFP that determine the correct name for algae, fungi, and plants Sequence-based classification (SBC) The process by which species are discovered, named, and classified according to their phylogenetic relationships. Sequence-based identification (SBI) The process by which the products of taxonomy are used to identify individuals and determine the composition of communities with reference to existing classifications Species hypotheses (SH) A term coined to describe taxa whose ITS rRNA gene sequences cluster at user-defined cutoff levels i.e. 97–99% Taxonomy The branch of science focused on naming, describing, and classifying all forms of life Virtual taxa (VT) Phylogenetically defined sequence groups that roughly correspond to species INTRODUCTION Analyses of environmental DNA and RNA sequences may involve two complementary but distinct activities: Fungi make up an underdescribed, poorly documen- Sequence-based classification (SBC) and sequence-based ted clade of eukaryotes that have immense ecological identification (SBI) (Herr et al. 2015). The goals of SBC and economic impacts. Many fungi are microscopic are to discover, name, and classify fungal species accord- or have cryptic life cycles that make detection difficult. ing to their phylogenetic relationships. In contrast, SBI Approximately 135 000 species of fungi have been uses the products of taxonomy to identify individuals described, but the actual diversity of the group is likely and determine the composition of fungal communities to be in the millions of species (Blackwell 2011, Taylor with reference to existing classifications. SBI is a central et al. 2014). Investigations into fungal diversity have element of ecological studies, including metatranscrip- traditionally been based on fruiting bodies or cultures, tomic studies of community-level metabolic processes. but an increasing number of studies that obtain DNA Collectively, sequence-based classification and identifica- “ ” and RNA sequences directly from environmental tion (SBCI) denotes the full range of activities required — sources such as soil, water, air, or tissues of other to detect and characterize fungi in the environment — organisms are revealing potentially new fungal spe- based on nucleic acid sequences (TABLE I). cies at dramatically accelerated rates (Hibbett et al. New resources for SBCI are required to fully 2011, Lindahl et al. 2013). For example, the Cryptomy- exploit the staggering volume of data flowing from fun- cota (Rozellomycota, rozellida) (Lara et al. 2010, Jones gal molecular ecology studies using high-throughput et al. 2011, Corsaro et al. 2014) and Archaeorhizomy- sequencing technologies. Huge numbers of undescribed cetes are major clades of Fungi that are known almost taxa known only from environmental sequences need to entirely from environmental DNA sequences (Rosling be classified and linked to phenotypic, ecological, and et al. 2011, James and Berbee 2012). Many environmen- functional traits. This article aims to: (i) envision the tal sequences can only be identified to the level of a potential of SBCI and identify its conceptual challenges; phylum or simply “fungi” (Nilsson et al. 2016), even in (ii) survey current resources for SBCI in fungi and sophisticated analyses that use rigorous phylogenetic assess their strengths, limitations, and opportunities for methods and that consider ribosomal RNA (rRNA) sec- enhancement; and (iii) consider options for integrating ondary structure (Glass et al. 2013). Thus, it is likely sequence-based fungal species into taxonomic systems
Load more

Recommended publications
  • Taxonomy and Phylogenetic Relationships of Nine Species of Hypocrea with Anamorphs Assignable to Trichoderma Section Hypocreanum
    STUDIES IN MYCOLOGY 56: 39–65. 2006. doi:10.3114/sim.2006.56.02 Taxonomy and phylogenetic relationships of nine species of Hypocrea with anamorphs assignable to Trichoderma section Hypocreanum Barrie E. Overton1*, Elwin L. Stewart2 and David M. Geiser2 1The Pennsylvania State University, Department of Plant Pathology, Buckhout Laboratory, University Park, Pennsylvania 16802, U.S.A.: Current address: Lock Haven University of Pennsylvania, Department of Biology, 119 Ulmer Hall, Lock Haven PA, 17745, U.S.A.; 2The Pennsylvania State University, Department of Plant Pathology, Buckhout Laboratory, University Park, Pennsylvania 16802, U.S.A. *Correspondence: Barrie E. Overton, [email protected] Abstract: Morphological studies and phylogenetic analyses of DNA sequences from the internal transcribed spacer (ITS) regions of the nuclear ribosomal gene repeat, a partial sequence of RNA polymerase II subunit (rpb2), and a partial sequence of the large exon of tef1 (LEtef1) were used to investigate the taxonomy and systematics of nine Hypocrea species with anamorphs assignable to Trichoderma sect. Hypocreanum. Hypocrea corticioides and H. sulphurea are reevaluated. Their Trichoderma anamorphs are described and the phylogenetic positions of these species are determined. Hypocrea sulphurea and H. subcitrina are distinct species based on studies of the type specimens. Hypocrea egmontensis is a facultative synonym of the older name H. subcitrina. Hypocrea with anamorphs assignable to Trichoderma sect. Hypocreanum formed a well-supported clade. Five species with anamorphs morphologically similar to sect. Hypocreanum, H. avellanea, H. parmastoi, H. megalocitrina, H. alcalifuscescens, and H. pezizoides, are not located in this clade. Protocrea farinosa belongs to Hypocrea s.s. Taxonomic novelties: Hypocrea eucorticioides Overton, nom.
    [Show full text]
  • Development and Evaluation of Rrna Targeted in Situ Probes and Phylogenetic Relationships of Freshwater Fungi
    Development and evaluation of rRNA targeted in situ probes and phylogenetic relationships of freshwater fungi vorgelegt von Diplom-Biologin Christiane Baschien aus Berlin Von der Fakultät III - Prozesswissenschaften der Technischen Universität Berlin zur Erlangung des akademischen Grades Doktorin der Naturwissenschaften - Dr. rer. nat. - genehmigte Dissertation Promotionsausschuss: Vorsitzender: Prof. Dr. sc. techn. Lutz-Günter Fleischer Berichter: Prof. Dr. rer. nat. Ulrich Szewzyk Berichter: Prof. Dr. rer. nat. Felix Bärlocher Berichter: Dr. habil. Werner Manz Tag der wissenschaftlichen Aussprache: 19.05.2003 Berlin 2003 D83 Table of contents INTRODUCTION ..................................................................................................................................... 1 MATERIAL AND METHODS .................................................................................................................. 8 1. Used organisms ............................................................................................................................. 8 2. Media, culture conditions, maintenance of cultures and harvest procedure.................................. 9 2.1. Culture media........................................................................................................................... 9 2.2. Culture conditions .................................................................................................................. 10 2.3. Maintenance of cultures.........................................................................................................10
    [Show full text]
  • Hydrolysis of Untreated Lignocellulosic Feedstock Is Independent of S-Lignin
    Hooker et al. Biotechnol Biofuels (2018) 11:293 https://doi.org/10.1186/s13068-018-1292-8 Biotechnology for Biofuels RESEARCH Open Access Hydrolysis of untreated lignocellulosic feedstock is independent of S‑lignin composition in newly classifed anaerobic fungal isolate, Piromyces sp. UH3‑1 Casey A. Hooker1,2, Ethan T. Hillman1,3, Jonathan C. Overton1,2, Adrian Ortiz‑Velez1, Makayla Schacht4, Abigail Hunnicutt1, Nathan S. Mosier1,2 and Kevin V. Solomon1,2,3* Abstract Background: Plant biomass is an abundant but underused feedstock for bioenergy production due to its complex and variable composition, which resists breakdown into fermentable sugars. These feedstocks, however, are routinely degraded by many uncommercialized microbes such as anaerobic gut fungi. These gut fungi express a broad range of carbohydrate active enzymes and are native to the digestive tracts of ruminants and hindgut fermenters. In this study, we examine gut fungal performance on these substrates as a function of composition, and the ability of this isolate to degrade inhibitory high syringyl lignin-containing forestry residues. Results: We isolated a novel fungal specimen from a donkey in Independence, Indiana, United States. Phylogenetic analysis of the Internal Transcribed Spacer 1 sequence classifed the isolate as a member of the genus Piromyces within the phylum Neocallimastigomycota (Piromyces sp. UH3-1, strain UH3-1). The isolate penetrates the substrate with an extensive rhizomycelial network and secretes many cellulose-binding enzymes, which are active on various components of lignocellulose. These activities enable the fungus to hydrolyze at least 58% of the glucan and 28% of the available xylan in untreated corn stover within 168 h and support growth on crude agricultural residues, food waste, and energy crops.
    [Show full text]
  • Taxonomy and Phylogeny of Gliocladium Analysed from Nuclear Large Subunit Ribosomal DNA Sequences
    Mycol. Res. 98 (6):625-634 (1994) Printed in Great Britain 625 Taxonomy and phylogeny of Gliocladium analysed from nuclear large subunit ribosomal DNA sequences STEPHEN A. REHNER AND GARY J. SAMUELS USDA, ARS, Systematic Botany and Mycology Laboratory Room 304, Building OIIA, Beltsville, BARC-W, Maryland 20705, U.SA. The phylogenetic distribution of Gliocladium within the Hypocreales was investigated by parsimony analysis of partial sequences from the nuclear large subunit ribosomal DNA (28s rDNA). Two principal monophyletic groups were resolved that included species with anarnorphs classified in Gliocladium. The first clade includes elements of the genera Hypocrea (H. gelatinosa, H. lutea) plus Trichodema, Hypocrea pallida, Hypomyces and Sphaerostilbella, which are each shown to be monophyletic but whose sister group relationships are unresolved with the present data set. Gliocladium anamorphs in this clade include Gliocladium penicillioides, the type species of Gliocladium and anamorph of Sphaerostilbella aureonitens, and Trichodema virens (= G. virens) which is a member of the clade containing Hypocrea and Trichodema. A second clade, consisting of species with pallid perithecia, is grouped around Nectria ochroleuca, whose anamorph is Gliocladium roseum. Other species in this clade having Gliocladium-like anamorphs are Nectriopsis sporangiicola and Roumeguericlla rufula. The species of Nectria represented in this study are polyphyletic and resolved as four separate groups: (1)N. cinnabarina the type species, (2) three species with Fusarium anamorphs including N. albosuccinea, N. haematococca and Gibberella fujikoroi, (3) N. purtonii a species whose anamorph is classified in Fwarium sect. Eupionnofes, and (4) N. ochroleuca, which is representative of species with pallid perithecia. The results indicate that Gliocladium is polyphyletic and that G.
    [Show full text]
  • Mini-Paper – the Use of Microbial Biocontrol Agents Against Soil-Borne Diseases
    Focus Group SOIL-BORNE DISEASES Mini-paper – The use of microbial biocontrol agents against soil-borne diseases Ilaria Pertot; Claude Alabouvette; Estefanía Hinarejos Esteve; Soraya Franca INTRODUCTION The value of the global biopesticide market is expected to reach $4,556.37 Million by 2019, at a compound annual growth rate of 15.30% from 2014 to 2019 (source: Marketsandmarkets.com, 2014; last access 31/03/2015). The reasons for such growth can be found in: the increasing concerns on the impact of residues and overuse of synthetic chemical pesticides and the increasing relevance of pests and pathogens due to growth in food demand, the withdrawal of several chemical pesticides including soil fumigants, the appearance of new invasive species and pesticide resistant strains of pests, the effect of climate change and the specialised monoculture. The decrease of the cost of several biopesticides, the introduction of technologically advanced products, the increase knowledge of farmers and the strict thresholds in pesticides residues set by many food retailers are also promoting the switch form chemical to biopesticides. In addition in EU the Directive on the Sustainable Use of Pesticides (2009/128/EC) is also expected to stimulate the biopesticide market positively. Some active ingredients have been included in Annex 1 according Regulation EC 1107/2009 and several new others are most probably under development by multinational agrochemical companies following recent acquisitions. According the present regulation if a microorganism has fungicide activity should be registered in order to be applied for such use. The high cost of registration prevents a large number of potential biocontrol agents to reach the market.
    [Show full text]
  • Biodiversity of Trichoderma in Neotropics
    13 Biodiversity of Trichoderma in Neotropics Lilliana Hoyos-Carvajal1 and John Bissett2 1Universidad Nacional de Colombia, Sede Bogotá 2Agriculture and Agri-Food Canada, Eastern Cereal and Oilseed Research Centre, Ottawa 1Colombia 2Canada 1. Introduction Trichoderma species frequently are predominant over wide geographic regions in all climatic zones, where they are significant decomposers of woody and herbaceous materials. They are characterized by rapid growth, an ability to assimilate a diverse array of substrates, and by their production of an range of antimicrobials. Strains have been exploited for production of enzymes and antibiotics, bioremediation of xenobiotic substances, and as biological control agents against plant pathogenic fungi and nematodes. The main use of Trichoderma in global trade is derived from its high production of enzymes. Trichoderma reesei (teleomorph: Hypocrea jecorina) is the most widely employed cellulolytic organism in the world, although high levels of cellulase production are also seen in other species of this genus (Baig et al., 2003, Watanabe et al., 2006). Worldwide sales of enzymes had reached the figure of $ 1.6 billion by the year 2000 (Demain 2000, cited by Karmakar and Ray, 2011), with an annual growth of 6.5 to 10% not including pharmaceutical enzymes (Stagehands, 2008). Of these, cellulases comprise approximately 20% of the enzymes marketed worldwide (Tramoy et al., 2009). Cellulases of microbial origin are used to process food and animal feed, biofuel production, baking, textiles, detergents, paper pulp, agriculture and research areas at all levels (Karmakar and Ray, 2011). Most cellulases are derived from Trichoderma (section Longibrachiatum in particular) and Aspergillus (Begum et al., 2009).
    [Show full text]
  • Protistology Molecular Phylogeny of Aphelidium Arduennense Sp. Nov
    Protistology 13 (4), 192–198 (2019) Protistology Molecular phylogeny of Aphelidium arduennense sp. nov. – new representative of Aphelida (Opis- thosporidia) Victoria S. Tcvetkova1, Natalia A. Zorina1, Maria A. Mamkaeva1 and Sergey A. Karpov1,2 1 St. Petersburg State University, St. Petersburg 199034, Russia 2 Zoological Institute, Russian Academy of Sciences, St. Petersburg 199034, Russia | Submitted November 14, 2019 | Accepted December 2, 2019 | Summary Aphelids (Aphelida) are poorly known parasitoids of algae that have raised considerable interest because of their phylogenetic position as phagotrophic protists sister to Fungi. Together with Rozellida and Microsporidia they have been classified in the Opisthosporidia but seem to be more closely related to the Fungi rather than to the Cryptomycota and Microsporidia, the other members of the Opisthosporidia. Molecular environmental studies have revealed high genetic diversity within the aphelids, but only four genera have been described: Aphelidium, Amoeboaphelidium, Paraphelidium and Pseudaphelidium. Here, we describe the life cycle of a new species of Aphelidium, Aph. arduennense. Molecular phylogenetic analysis of its 18S rRNA indicates that Aph. arduennense is sister to Aph. tribonematis, and together with Aph. melosirae they form a monophyletic cluster. Within the aphelids, this cluster is distantly related to Paraphelidium and Amoeboaphelidium. Key words: aphelids, Holomycota, Opisthosporidia, Rozellosporidia, taxonomy Introduction Rozellosporidia (Cryptomycota) formed the super- phylum Opisthosporidia, the deepest branch Aphelids are a divergent group of intracellular of the Holomycota lineage, separated from the parasitoids of green, yellow-green and diatom algae Fungi (Karpov et al., 2014a; Letcher et al., 2015; (Gromov, 2000; Karpov et al., 2014a). The four 2017; Torruella et al., 2015). Several biological known genera have different ecological preferences: peculiarities of the aphelids do not conform the Aphelidium, Amoeboaphelidium and Paraphelidium classical definition of the Fungi.
    [Show full text]
  • Tracing the Origin of Planktonic Protists in an Ancient Lake
    microorganisms Article Tracing the Origin of Planktonic Protists in an Ancient Lake Nataliia V. Annenkova 1,* , Caterina R. Giner 2,3 and Ramiro Logares 2,* 1 Limnological Institute Siberian Branch of the Russian Academy of Sciences 3, Ulan-Batorskaya St., 664033 Irkutsk, Russia 2 Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, ES08003 Barcelona, Spain; [email protected] 3 Institute for the Oceans and Fisheries, University of British Columbia, 2202 Main Mall, Vancouver, BC V6T 1Z4, Canada * Correspondence: [email protected] (N.V.A.); [email protected] (R.L.) Received: 26 February 2020; Accepted: 7 April 2020; Published: 9 April 2020 Abstract: Ancient lakes are among the most interesting models for evolution studies because their biodiversity is the result of a complex combination of migration and speciation. Here, we investigate the origin of single celled planktonic eukaryotes from the oldest lake in the world—Lake Baikal (Russia). By using 18S rDNA metabarcoding, we recovered 1414 Operational Taxonomic Units (OTUs) belonging to protists populating surface waters (1–50 m) and representing pico/nano-sized cells. The recovered communities resembled other lacustrine freshwater assemblages found elsewhere, especially the taxonomically unclassified protists. However, our results suggest that a fraction of Baikal protists could belong to glacial relicts and have close relationships with marine/brackish species. Moreover, our results suggest that rapid radiation may have occurred among some protist taxa, partially mirroring what was already shown for multicellular organisms in Lake Baikal. We found 16% of the OTUs belonging to potential species flocks in Stramenopiles, Alveolata, Opisthokonta, Archaeplastida, Rhizaria, and Hacrobia.
    [Show full text]
  • S41467-021-25308-W.Pdf
    ARTICLE https://doi.org/10.1038/s41467-021-25308-w OPEN Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota ✉ ✉ Luis Javier Galindo 1 , Purificación López-García 1, Guifré Torruella1, Sergey Karpov2,3 & David Moreira 1 Compared to multicellular fungi and unicellular yeasts, unicellular fungi with free-living fla- gellated stages (zoospores) remain poorly known and their phylogenetic position is often 1234567890():,; unresolved. Recently, rRNA gene phylogenetic analyses of two atypical parasitic fungi with amoeboid zoospores and long kinetosomes, the sanchytrids Amoeboradix gromovi and San- chytrium tribonematis, showed that they formed a monophyletic group without close affinity with known fungal clades. Here, we sequence single-cell genomes for both species to assess their phylogenetic position and evolution. Phylogenomic analyses using different protein datasets and a comprehensive taxon sampling result in an almost fully-resolved fungal tree, with Chytridiomycota as sister to all other fungi, and sanchytrids forming a well-supported, fast-evolving clade sister to Blastocladiomycota. Comparative genomic analyses across fungi and their allies (Holomycota) reveal an atypically reduced metabolic repertoire for sanchy- trids. We infer three main independent flagellum losses from the distribution of over 60 flagellum-specific proteins across Holomycota. Based on sanchytrids’ phylogenetic position and unique traits, we propose the designation of a novel phylum, Sanchytriomycota. In addition, our results indicate that most of the hyphal morphogenesis gene repertoire of multicellular fungi had already evolved in early holomycotan lineages. 1 Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France. 2 Zoological Institute, Russian Academy of Sciences, St. ✉ Petersburg, Russia. 3 St.
    [Show full text]
  • Complex Communities of Small Protists and Unexpected Occurrence Of
    Complex communities of small protists and unexpected occurrence of typical marine lineages in shallow freshwater systems Marianne Simon, Ludwig Jardillier, Philippe Deschamps, David Moreira, Gwendal Restoux, Paola Bertolino, Purificación López-García To cite this version: Marianne Simon, Ludwig Jardillier, Philippe Deschamps, David Moreira, Gwendal Restoux, et al.. Complex communities of small protists and unexpected occurrence of typical marine lineages in shal- low freshwater systems. Environmental Microbiology, Society for Applied Microbiology and Wiley- Blackwell, 2015, 17 (10), pp.3610-3627. 10.1111/1462-2920.12591. hal-03022575 HAL Id: hal-03022575 https://hal.archives-ouvertes.fr/hal-03022575 Submitted on 24 Nov 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Europe PMC Funders Group Author Manuscript Environ Microbiol. Author manuscript; available in PMC 2015 October 26. Published in final edited form as: Environ Microbiol. 2015 October ; 17(10): 3610–3627. doi:10.1111/1462-2920.12591. Europe PMC Funders Author Manuscripts Complex communities of small protists and unexpected occurrence of typical marine lineages in shallow freshwater systems Marianne Simon, Ludwig Jardillier, Philippe Deschamps, David Moreira, Gwendal Restoux, Paola Bertolino, and Purificación López-García* Unité d’Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, 91405 Orsay, France Summary Although inland water bodies are more heterogeneous and sensitive to environmental variation than oceans, the diversity of small protists in these ecosystems is much less well-known.
    [Show full text]
  • Proposal for Practical Multi-Kingdom Classification of Eukaryotes Based on Monophyly 2 and Comparable Divergence Time Criteria
    bioRxiv preprint doi: https://doi.org/10.1101/240929; this version posted December 29, 2017. 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 4.0 International license. 1 Proposal for practical multi-kingdom classification of eukaryotes based on monophyly 2 and comparable divergence time criteria 3 Leho Tedersoo 4 Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia 5 Contact: email: [email protected], tel: +372 56654986, twitter: @tedersoo 6 7 Key words: Taxonomy, Eukaryotes, subdomain, phylum, phylogenetic classification, 8 monophyletic groups, divergence time 9 Summary 10 Much of the ecological, taxonomic and biodiversity research relies on understanding of 11 phylogenetic relationships among organisms. There are multiple available classification 12 systems that all suffer from differences in naming, incompleteness, presence of multiple non- 13 monophyletic entities and poor correspondence of divergence times. These issues render 14 taxonomic comparisons across the main groups of eukaryotes and all life in general difficult 15 at best. By using the monophyly criterion, roughly comparable time of divergence and 16 information from multiple phylogenetic reconstructions, I propose an alternative 17 classification system for the domain Eukarya to improve hierarchical taxonomical 18 comparability for animals, plants, fungi and multiple protist groups. Following this rationale, 19 I propose 32 kingdoms of eukaryotes that are treated in 10 subdomains. These kingdoms are 20 further separated into 43, 115, 140 and 353 taxa at the level of subkingdom, phylum, 21 subphylum and class, respectively (http://dx.doi.org/10.15156/BIO/587483).
    [Show full text]
  • University of Groningen Multiple Origins of Hydrogenosomes
    University of Groningen Multiple origins of hydrogenosomes Voncken, F; Boxma, B; Tjaden, J; Akhmanova, A; Huynen, M; Tielens, AGM; Haferkamp, [No Value]; Neuhaus, HE; Vogels, G; Veenhuis, M Published in: Molecular Microbiology DOI: 10.1046/j.1365-2958.2002.02959.x IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2002 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Voncken, F., Boxma, B., Tjaden, J., Akhmanova, A., Huynen, M., Tielens, AGM., Haferkamp, N. V., Neuhaus, HE., Vogels, G., Veenhuis, M., Hackstein, JHP., Tielens, A. G. M., Haferkamp, I., & Hackstein, J. H. P. (2002). Multiple origins of hydrogenosomes: functional and phylogenetic evidence from the ADP/ATP carrier of the anaerobic chytrid Neocallimastix sp. Molecular Microbiology, 44(6), 1441-1454. https://doi.org/10.1046/j.1365-2958.2002.02959.x Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum.
    [Show full text]