CHAPTER 25. Phylogeny and Evolution
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Division II: Eumycota Subdivision: Mastigomycotina, Class: Chytridiomycetes (Chytridiales), Oomycetes (Peronosporales)
Division II: Eumycota Subdivision: Mastigomycotina, class: Chytridiomycetes (Chytridiales), Oomycetes (Peronosporales) General characters Members of the class Oomycetes are mostly aquatic but some are facultative or obligate parasites of vascular plants. Majority of them are with filamentous hyaline coenocytic mycelium. Cell wall contains cellulose. They produce asexual spores called zoospores. Oospore is the sexual spores. Class: Oomycetes Zoospores biflagellate (posterior flagellum whiplash-type; anterior tinsel-type); cell wall cellulosic. 1. Members of the class comycetes are mostly aquatic but some are facultative or obligate parasites of vascular plants. 2. They are distinguished by the presence of well-developed holocarpic or eucarpic mycelium or rhizomycelium and zoospores bearing two flagella, one whiplash type and the other tinsel type. In some members, Zoospores are not formed and the zoosporangia function as conidia. The cell wall does not contain chitin, small amounts of cellulose are detected but the principal components are glucans. 3. In sexual reproduction the union of antheridia and oogonia produces oospores. Order: Peronosporales This order includes highly economically important plant pathogens. The members cause downy mildew and white rust diseases. Hyphae are well developed and aseptate. Cell wall is composed of glucan-cellulose complex and hydroxyproline. Parasites produce haustoria, which may be knob-like, elongated or branched and are found within the host cells. Asexual reproduction is by well-defined sporangia. Sexual reproduction is by means of well- differentiated sex organs, antheridia (male) and oogonia (female). Oospores germinate directly or by producing a sporangium. Families Pythiaceae Sporangiophores similar to the vegetative hyphae or if different then of indeterminate growth. Pythiaceae contains genera like Pythium and Phytophthora Albuginaceae Sporangiophores strikingly different from vegetative hyphae, slender or thick, variously club-shaped, arranged in a layer, and bear sporangia in chain at the tip. -
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. -
Biological Classification Chapter 2
16 BIOLOGY CHAPTER 2 BIOLOGICAL CLASSIFICATION 2.1 Kingdom Monera Since the dawn of civilisation, there have been many attempts to classify living organisms. It was done instinctively not using criteria that were 2.2 Kingdom Protista scientific but borne out of a need to use organisms for our own use – for 2.3 Kingdom Fungi food, shelter and clothing. Aristotle was the earliest to attempt a more 2.4 Kingdom Plantae scientific basis for classification. He used simple morphological characters to classify plants into trees, shrubs and herbs. He also divided animals 2.5 Kingdom into two groups, those which had red blood and those that did not. Animalia In Linnaeus' time a Two Kingdom system of classification with 2.6 Viruses, Viroids Plantae and Animalia kingdoms was developed that included all plants and Lichens and animals respectively. This system was used till very recently. This system did not distinguish between the eukaryotes and prokaryotes, unicellular and multicellular organisms and photosynthetic (green algae) and non-photosynthetic (fungi) organisms. Classification of organisms into plants and animals was easily done and was easy to understand, inspite, a large number of organisms did not fall into either category. Hence the two kingdom classification used for a long time was found inadequate. A need was also felt for including, besides gross morphology, other characteristics like cell structure, nature of wall, mode of nutrition, habitat, methods of reproduction, evolutionary relationships, etc. Classification systems for the living organisms have hence, undergone several changes over time. Though plant and animal kingdoms have been a constant under all different systems, the understanding of what groups/organisms be included under these kingdoms have been changing; the number and nature of other kingdoms have also been understood differently by different scientists over time. -
1. in Whittaker's System of Classification, Prokaryotes Are Placed in the Kingdom (A) Protista (B) Monera (C) Plantae (D) Animal
1. In Whittaker's system of classification, prokaryotes are placed 12. An organism having cytoplasm i.e. DNA and RNA but no in the kingdom cell wall is (a) Protista (b) Monera (a) Cyanobacterium (b) Mycoplasma (c) Plantae (d) Animalia (c) Bacterium (d) Virus 2. In the five kingdom system of classification, which single 13. Kingdom monera comprises the – kingdom out of the following can include blue-green algae, (a) Plants of economic importance nitrogen fixing bacteria and methanogenic archaebacteria ? (b) All the plants studied in botany (a) Monera (b) Fungi (c) Prokaryotic organisms (c) Plantae (d) Protista (d) Plants of Thallophyta group 3. Which of the following kingdom does not have nuclear 14. The cell wall of green plants is made up of membrane? (a) Pectin (b) Suberin (a) Protista (b) Fungi (c) Cellulose (d) Chitin (c) Monera (d) Plantae 15. Which of the following is not a blue-green algae ? 4. What type of mode of nutrition is found in the kingdom (a) Nostoc (b) Anabaena Animalia? (c) Lichen (d) Aulosiras (a) Autotrophic and heterotrophic 16. During rainy seasons, the ground becomes slippery due to (b) Chemosynthetic and photosynthetic dense growth of (c) Saprophytic and parasitic (a) Lichens (b) Bacteria (d) Holozoic and saprophytic (c) Green algae (d) Cyanobacteria 5. The separation of living beings into five kingdoms is based 17. Paramecium is a on – (a) Protozoan (b) Bacterium (a) Complexity of cell structure (c) Virus (d) Annelid (b) Complexity of organism's body 18. Protists are (c) Mode of obtaining nutrition (a) single-celled eukaryotes (b) multicellular eukaryotes (d) All of the above (c) single-celled prokaryotes (d) single-celled akaryote 6. -
Intracellular Eukaryotic Pathogens in Brown Macroalgae in the Eastern Mediterranean, Including LSU Rrna Data for the Oomycete Eurychasma Dicksonii
Vol. 104: 1–11, 2013 DISEASES OF AQUATIC ORGANISMS Published April 29 doi: 10.3354/dao02583 Dis Aquat Org Intracellular eukaryotic pathogens in brown macroalgae in the Eastern Mediterranean, including LSU rRNA data for the oomycete Eurychasma dicksonii Martina Strittmatter1,2,6, Claire M. M. Gachon1, Dieter G. Müller3, Julia Kleinteich3, Svenja Heesch1,7, Amerssa Tsirigoti4, Christos Katsaros4, Maria Kostopoulou2, Frithjof C. Küpper1,5,* 1Scottish Association for Marine Science, Scottish Marine Institute, Oban, Argyll PA37 1QA, UK 2University of the Aegean, Department of Marine Sciences, University Hill, 81 100 Mytilene, Greece 3Universität Konstanz, FB Biologie, 78457 Konstanz, Germany 4University of Athens, Faculty of Biology, Athens 157 84, Greece 5Oceanlab, University of Aberdeen, Main Street, Newburgh AB41 6AA, UK 6Present address: CNRS and UPMC University Paris 06, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Place Georges Teissier, CS 90074, 29688 Roscoff Cedex, France 7Present address: Irish Seaweed Research Group, Ryan Institute, National University of Ireland Galway, University Road, Galway, Ireland ABSTRACT: For the Mediterranean Sea, and indeed most of the world’s oceans, the biodiversity and biogeography of eukaryotic pathogens infecting marine macroalgae remains poorly known, yet their ecological impact is probably significant. Based on 2 sampling campaigns on the Greek island of Lesvos in 2009 and 1 in northern Greece in 2012, this study provides first records of 3 intracellular eukaryotic pathogens infecting filamentous brown algae at these locations: Eury - chas ma dicksonii, Anisolpidium sphacellarum, and A. ectocarpii. Field and microscopic observa- tions of the 3 pathogens are complemented by the first E. dicksonii large subunit ribosomal RNA (LSU rRNA) gene sequence analyses of isolates from Lesvos and other parts of the world. -
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, -
<I>Sirolpidium Bryopsidis</I>, a Parasite of Green Algae, Is Probably
VOLUME 7 JUNE 2021 Fungal Systematics and Evolution PAGES 223–231 doi.org/10.3114/fuse.2021.07.11 Sirolpidium bryopsidis, a parasite of green algae, is probably conspecific with Pontisma lagenidioides, a parasite of red algae A.T. Buaya1, B. Scholz2, M. Thines1,3,4* 1Senckenberg Biodiversity and Climate Research Center, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany 2BioPol ehf, Marine Biotechnology, Einbúastig 2, 545 Skagaströnd, Iceland 3Goethe-University Frankfurt am Main, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue Str. 13, D-60438 Frankfurt am Main, Germany 4LOEWE Centre for Translational Biodiversity Genomics, Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany *Corresponding author: [email protected] Key words: Abstract: The genus Sirolpidium (Sirolpidiaceae) of the Oomycota includes several species of holocarpic obligate aquatic chlorophyte algae parasites. These organisms are widely occurring in marine and freshwater habitats, mostly infecting filamentous green early-diverging algae. Presently, all species are only known from their morphology and descriptive life cycle traits. None of the seven new taxa species classified in Sirolpidium, including the type species, S. bryopsidis, has been rediscovered and studied for their Oomycota molecular phylogeny, so far. Originally, the genus was established to accommodate all parasites of filamentous marine Petersenia green algae. In the past few decades, however, Sirolpidium has undergone multiple taxonomic revisions and several species phylogeny parasitic in other host groups were added to the genus. While the phylogeny of the marine rhodophyte- and phaeophyte- Pontismataceae infecting genera Pontisma and Eurychasma, respectively, has only been resolved recently, the taxonomic placement Sirolpidiaceae of the chlorophyte-infecting genus Sirolpidium remained unresolved. -
Controlled Sampling of Ribosomally Active Protistan Diversity in Sediment-Surface Layers Identifies Putative Players in the Marine Carbon Sink
The ISME Journal (2020) 14:984–998 https://doi.org/10.1038/s41396-019-0581-y ARTICLE Controlled sampling of ribosomally active protistan diversity in sediment-surface layers identifies putative players in the marine carbon sink 1,2 1 1 3 3 Raquel Rodríguez-Martínez ● Guy Leonard ● David S. Milner ● Sebastian Sudek ● Mike Conway ● 1 1 4,5 6 7 Karen Moore ● Theresa Hudson ● Frédéric Mahé ● Patrick J. Keeling ● Alyson E. Santoro ● 3,8 1,9 Alexandra Z. Worden ● Thomas A. Richards Received: 6 October 2019 / Revised: 4 December 2019 / Accepted: 17 December 2019 / Published online: 9 January 2020 © The Author(s) 2020. This article is published with open access Abstract Marine sediments are one of the largest carbon reservoir on Earth, yet the microbial communities, especially the eukaryotes, that drive these ecosystems are poorly characterised. Here, we report implementation of a sampling system that enables injection of reagents into sediments at depth, allowing for preservation of RNA in situ. Using the RNA templates recovered, we investigate the ‘ribosomally active’ eukaryotic diversity present in sediments close to the water/sediment interface. We 1234567890();,: 1234567890();,: demonstrate that in situ preservation leads to recovery of a significantly altered community profile. Using SSU rRNA amplicon sequencing, we investigated the community structure in these environments, demonstrating a wide diversity and high relative abundance of stramenopiles and alveolates, specifically: Bacillariophyta (diatoms), labyrinthulomycetes and ciliates. The identification of abundant diatom rRNA molecules is consistent with microscopy-based studies, but demonstrates that these algae can also be exported to the sediment as active cells as opposed to dead forms. -
The Classification of Lower Organisms
The Classification of Lower Organisms Ernst Hkinrich Haickei, in 1874 From Rolschc (1906). By permission of Macrae Smith Company. C f3 The Classification of LOWER ORGANISMS By HERBERT FAULKNER COPELAND \ PACIFIC ^.,^,kfi^..^ BOOKS PALO ALTO, CALIFORNIA Copyright 1956 by Herbert F. Copeland Library of Congress Catalog Card Number 56-7944 Published by PACIFIC BOOKS Palo Alto, California Printed and bound in the United States of America CONTENTS Chapter Page I. Introduction 1 II. An Essay on Nomenclature 6 III. Kingdom Mychota 12 Phylum Archezoa 17 Class 1. Schizophyta 18 Order 1. Schizosporea 18 Order 2. Actinomycetalea 24 Order 3. Caulobacterialea 25 Class 2. Myxoschizomycetes 27 Order 1. Myxobactralea 27 Order 2. Spirochaetalea 28 Class 3. Archiplastidea 29 Order 1. Rhodobacteria 31 Order 2. Sphaerotilalea 33 Order 3. Coccogonea 33 Order 4. Gloiophycea 33 IV. Kingdom Protoctista 37 V. Phylum Rhodophyta 40 Class 1. Bangialea 41 Order Bangiacea 41 Class 2. Heterocarpea 44 Order 1. Cryptospermea 47 Order 2. Sphaerococcoidea 47 Order 3. Gelidialea 49 Order 4. Furccllariea 50 Order 5. Coeloblastea 51 Order 6. Floridea 51 VI. Phylum Phaeophyta 53 Class 1. Heterokonta 55 Order 1. Ochromonadalea 57 Order 2. Silicoflagellata 61 Order 3. Vaucheriacea 63 Order 4. Choanoflagellata 67 Order 5. Hyphochytrialea 69 Class 2. Bacillariacea 69 Order 1. Disciformia 73 Order 2. Diatomea 74 Class 3. Oomycetes 76 Order 1. Saprolegnina 77 Order 2. Peronosporina 80 Order 3. Lagenidialea 81 Class 4. Melanophycea 82 Order 1 . Phaeozoosporea 86 Order 2. Sphacelarialea 86 Order 3. Dictyotea 86 Order 4. Sporochnoidea 87 V ly Chapter Page Orders. Cutlerialea 88 Order 6. -
CATALOG of SPECIES
ARSARSARSARSARSARS ARSARS CollectionCollectionef ofof EntomopathogenicEntomopathogenic FungalFungal CulturesCultures CATALOG of SPECIES FULLY INDEXED [INCLUDES 9773 ISOLAtes] USDA-ARS Biological Integrated Pest Management Research Robert W. Holley Center for Agriculture and Health 538 Tower Road Ithaca, New York 14853-2901 28 July 2011 Search the ARSEF catalog online at http://www.ars.usda.gov/Main/docs.htm?docid=12125 ARSEF Collection Staff Richard A. Humber, Curator phone: [+1] 607-255-1276 fax: [+1] 607-255-1132 email: [email protected] Karen S. Hansen phone: [+1] 607-255-1274 fax: [+1] 607-255-1132 email: [email protected] Micheal M. Wheeler phone: [+1] 607-255-1274 fax: [+1] 607-255-1132 email: [email protected] USDA-ARS Biological IPM Research Unit Robert W. Holley Center for Agriculture & Health 538 Tower Road Ithaca, New York 14853-2901, USA IMPORTANT NOTE Recent phylogenetically based reclassifications of fungal pathogens of invertebrates Richard A. Humber Insect Mycologist and Curator, ARSEF UPDATED July 2011 Some seemingly dramatic and comparatively recent changes in the classification of a number of fungi may continue to cause confusion or a degree of discomfort to many of the clients of the cultures and informational resources provided by the ARSEF culture collection. This short treatment is an attempt to summarize some of these changes, the reasons for them, and to provide the essential references to the literature in which the changes are proposed. As the Curator of the ARSEF collection I wish to assure you that these changes are appropriate, progressive, and necessary to modernize and to stabilize the systematics of the fungal pathogens affecting insects and other invertebrates, and I urge you to adopt them into your own thinking, teaching, and publications. -
Seven Gene Phylogeny of Heterokonts
ARTICLE IN PRESS Protist, Vol. 160, 191—204, May 2009 http://www.elsevier.de/protis Published online date 9 February 2009 ORIGINAL PAPER Seven Gene Phylogeny of Heterokonts Ingvild Riisberga,d,1, Russell J.S. Orrb,d,1, Ragnhild Klugeb,c,2, Kamran Shalchian-Tabrizid, Holly A. Bowerse, Vishwanath Patilb,c, Bente Edvardsena,d, and Kjetill S. Jakobsenb,d,3 aMarine Biology, Department of Biology, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway bCentre for Ecological and Evolutionary Synthesis (CEES),Department of Biology, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway cDepartment of Plant and Environmental Sciences, P.O. Box 5003, The Norwegian University of Life Sciences, N-1432, A˚ s, Norway dMicrobial Evolution Research Group (MERG), Department of Biology, University of Oslo, P.O. Box 1066, Blindern, NO-0316, Oslo, Norway eCenter of Marine Biotechnology, 701 East Pratt Street, Baltimore, MD 21202, USA Submitted May 23, 2008; Accepted November 15, 2008 Monitoring Editor: Mitchell L. Sogin Nucleotide ssu and lsu rDNA sequences of all major lineages of autotrophic (Ochrophyta) and heterotrophic (Bigyra and Pseudofungi) heterokonts were combined with amino acid sequences from four protein-coding genes (actin, b-tubulin, cox1 and hsp90) in a multigene approach for resolving the relationship between heterokont lineages. Applying these multigene data in Bayesian and maximum likelihood analyses improved the heterokont tree compared to previous rDNA analyses by placing all plastid-lacking heterotrophic heterokonts sister to Ochrophyta with robust support, and divided the heterotrophic heterokonts into the previously recognized phyla, Bigyra and Pseudofungi. Our trees identified the heterotrophic heterokonts Bicosoecida, Blastocystis and Labyrinthulida (Bigyra) as the earliest diverging lineages. -
Clade (Kingdom Fungi, Phylum Chytridiomycota)
TAXONOMIC STATUS OF GENERA IN THE “NOWAKOWSKIELLA” CLADE (KINGDOM FUNGI, PHYLUM CHYTRIDIOMYCOTA): PHYLOGENETIC ANALYSIS OF MOLECULAR CHARACTERS WITH A REVIEW OF DESCRIBED SPECIES by SHARON ELIZABETH MOZLEY (Under the Direction of David Porter) ABSTRACT Chytrid fungi represent the earliest group of fungi to have emerged within the Kingdom Fungi. Unfortunately despite the importance of chytrids to understanding fungal evolution, the systematics of the group is in disarray and in desperate need of revision. Funding by the NSF PEET program has provided an opportunity to revise the systematics of chytrid fungi with an initial focus on four specific clades in the order Chytridiales. The “Nowakowskiella” clade was chosen as a test group for comparing molecular methods of phylogenetic reconstruction with the more traditional morphological and developmental character system used for classification in determining generic limits for chytrid genera. Portions of the 18S and 28S nrDNA genes were sequenced for isolates identified to genus level based on morphology to seven genera in the “Nowakowskiella” clade: Allochytridium, Catenochytridium, Cladochytrium, Endochytrium, Nephrochytrium, Nowakowskiella, and Septochytrium. Bayesian, parsimony, and maximum likelihood methods of phylogenetic inference were used to produce trees based on one (18S or 28S alone) and two-gene datasets in order to see if there would be a difference depending on which optimality criterion was used and the number of genes included. In addition to the molecular analysis, taxonomic summaries of all seven genera covering all validly published species with a listing of synonyms and questionable species is provided to give a better idea of what has been described and the morphological and developmental characters used to circumscribe each genus.