Evidence for Glycolytic Reactions in the Mitochondrion?
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Protist Phylogeny and the High-Level Classification of Protozoa
Europ. J. Protistol. 39, 338–348 (2003) © Urban & Fischer Verlag http://www.urbanfischer.de/journals/ejp Protist phylogeny and the high-level classification of Protozoa Thomas Cavalier-Smith Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK; E-mail: [email protected] Received 1 September 2003; 29 September 2003. Accepted: 29 September 2003 Protist large-scale phylogeny is briefly reviewed and a revised higher classification of the kingdom Pro- tozoa into 11 phyla presented. Complementary gene fusions reveal a fundamental bifurcation among eu- karyotes between two major clades: the ancestrally uniciliate (often unicentriolar) unikonts and the an- cestrally biciliate bikonts, which undergo ciliary transformation by converting a younger anterior cilium into a dissimilar older posterior cilium. Unikonts comprise the ancestrally unikont protozoan phylum Amoebozoa and the opisthokonts (kingdom Animalia, phylum Choanozoa, their sisters or ancestors; and kingdom Fungi). They share a derived triple-gene fusion, absent from bikonts. Bikonts contrastingly share a derived gene fusion between dihydrofolate reductase and thymidylate synthase and include plants and all other protists, comprising the protozoan infrakingdoms Rhizaria [phyla Cercozoa and Re- taria (Radiozoa, Foraminifera)] and Excavata (phyla Loukozoa, Metamonada, Euglenozoa, Percolozoa), plus the kingdom Plantae [Viridaeplantae, Rhodophyta (sisters); Glaucophyta], the chromalveolate clade, and the protozoan phylum Apusozoa (Thecomonadea, Diphylleida). Chromalveolates comprise kingdom Chromista (Cryptista, Heterokonta, Haptophyta) and the protozoan infrakingdom Alveolata [phyla Cilio- phora and Miozoa (= Protalveolata, Dinozoa, Apicomplexa)], which diverged from a common ancestor that enslaved a red alga and evolved novel plastid protein-targeting machinery via the host rough ER and the enslaved algal plasma membrane (periplastid membrane). -
Chromerid Genomes Reveal the Evolutionary Path From
RESEARCH ARTICLE elifesciences.org Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites Yong H Woo1*, Hifzur Ansari1,ThomasDOtto2, Christen M Klinger3†, Martin Kolisko4†, Jan Michalek´ 5,6†, Alka Saxena1†‡, Dhanasekaran Shanmugam7†, Annageldi Tayyrov1†, Alaguraj Veluchamy8†§, Shahjahan Ali9¶,AxelBernal10,JavierdelCampo4, Jaromır´ Cihla´ rˇ5,6, Pavel Flegontov5,11, Sebastian G Gornik12,EvaHajduskovˇ a´ 5, AlesHorˇ ak´ 5,6,JanJanouskovecˇ 4, Nicholas J Katris12,FredDMast13,DiegoMiranda- Saavedra14,15, Tobias Mourier16, Raeece Naeem1,MridulNair1, Aswini K Panigrahi9, Neil D Rawlings17, Eriko Padron-Regalado1, Abhinay Ramaprasad1, Nadira Samad12, AlesTomˇ calaˇ 5,6, Jon Wilkes18,DanielENeafsey19, Christian Doerig20, Chris Bowler8, 4 10 3 21,22 *For correspondence: yong. Patrick J Keeling , David S Roos ,JoelBDacks, Thomas J Templeton , 12,23 5,6,24 5,6,25 1 [email protected] (YHW); arnab. Ross F Waller , Julius Lukesˇ , Miroslav Obornık´ ,ArnabPain* [email protected] (AP) 1Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering † These authors contributed Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia; equally to this work 2Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Present address: ‡Vaccine and Cambridge, United Kingdom; 3Department of Cell Biology, University of Alberta, Infectious Disease Division, Fred Edmonton, Canada; 4Canadian Institute for Advanced Research, Department of Botany, -
Testing the Effect of in Planta RNA Silencing on Plasmodiophorabrassicae Infection
Testing the effect of in planta RNA silencing on Plasmodiophorabrassicae infection A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University S. R. Bulman 2006 ii Contents Abstract. ...................................................................................................., ................ v Acknowledgements .................................................................................................. vii List of Tables ........................................................................................................... viii List of Figures ........................................................................................................... ix CHAPTER 1. Literature Review ................................................................................ 1 Plasmodiophora brassicae ............................................................................................. 1 RNA silencing .................................................................................................................. 5 Plant defence by RNA silencing .................................................................................... 8 RNA silencing versus P. brassicae ............................................................................. 10 Molecular biology of P. brassicae ................................................................................ 10 Choice of cDNA cloning strategy in P. brassicae ...................................................... -
Plasmodiophora Brassicae
Bi et al. Phytopathology Research (2019) 1:12 https://doi.org/10.1186/s42483-019-0018-6 Phytopathology Research RESEARCH Open Access Comparative genomics reveals the unique evolutionary status of Plasmodiophora brassicae and the essential role of GPCR signaling pathways Kai Bi1,2, Tao Chen2, Zhangchao He1,2, Zhixiao Gao1,2, Ying Zhao1,2, Huiquan Liu3, Yanping Fu2, Jiatao Xie1,2, Jiasen Cheng1,2 and Daohong Jiang1,2* Abstract Plasmodiophora brassicae is an important biotrophic eukaryotic plant pathogen and a member of the rhizarian protists. This biotrophic pathogen causes clubroot in cruciferous plants via novel intracellular mechanisms that are markedly different from those of other biotrophic organisms. To date, genomes from six single spore isolates of P. brassicae have been sequenced. An accurate description of the evolutionary status of this biotrophic protist, however, remains lacking. Here, we determined the draft genome of the P. brassicae ZJ-1 strain. A total of 10,951 protein-coding genes were identified from a 24.1 Mb genome sequence. We applied a comparative genomics approach to prove the Rhizaria supergroup is an independent branch in the eukaryotic evolutionary tree. We also found that the GPCR signaling pathway, the versatile signal transduction to multiple intracellular signaling cascades in response to extracellular signals in eukaryotes, is significantly enriched in P. brassicae-expanded and P. brassicae-specific gene sets. Additionally, treatment with a GPCR inhibitor relieved the symptoms of clubroot and significantly suppressed the development of plasmodia. Our findings suggest that GPCR signal transduction pathways play important roles in the growth, development, and pathogenicity of P. brassicae. -
Phylogenomics Supports the Monophyly of the Cercozoa T ⁎ Nicholas A.T
Molecular Phylogenetics and Evolution 130 (2019) 416–423 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev Phylogenomics supports the monophyly of the Cercozoa T ⁎ Nicholas A.T. Irwina, , Denis V. Tikhonenkova,b, Elisabeth Hehenbergera,1, Alexander P. Mylnikovb, Fabien Burkia,2, Patrick J. Keelinga a Department of Botany, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada b Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok 152742, Russia ARTICLE INFO ABSTRACT Keywords: The phylum Cercozoa consists of a diverse assemblage of amoeboid and flagellated protists that forms a major Cercozoa component of the supergroup, Rhizaria. However, despite its size and ubiquity, the phylogeny of the Cercozoa Rhizaria remains unclear as morphological variability between cercozoan species and ambiguity in molecular analyses, Phylogeny including phylogenomic approaches, have produced ambiguous results and raised doubts about the monophyly Phylogenomics of the group. Here we sought to resolve these ambiguities using a 161-gene phylogenetic dataset with data from Single-cell transcriptomics newly available genomes and deeply sequenced transcriptomes, including three new transcriptomes from Aurigamonas solis, Abollifer prolabens, and a novel species, Lapot gusevi n. gen. n. sp. Our phylogenomic analysis strongly supported a monophyletic Cercozoa, and approximately-unbiased tests rejected the paraphyletic topologies observed in previous studies. The transcriptome of L. gusevi represents the first transcriptomic data from the large and recently characterized Aquavolonidae-Treumulida-'Novel Clade 12′ group, and phyloge- nomics supported its position as sister to the cercozoan subphylum, Endomyxa. These results provide insights into the phylogeny of the Cercozoa and the Rhizaria as a whole. -
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1 BROADLY SAMPLED TREE OF EUKARYOTIC LIFE Broadly Sampled Multigene Analyses Yield a Well-resolved Eukaryotic Tree of Life Laura Wegener Parfrey1†, Jessica Grant2†, Yonas I. Tekle2,6, Erica Lasek-Nesselquist3,4, Hilary G. Morrison3, Mitchell L. Sogin3, David J. Patterson5, Laura A. Katz1,2,* 1Program in Organismic and Evolutionary Biology, University of Massachusetts, 611 North Pleasant Street, Amherst, Massachusetts 01003, USA 2Department of Biological Sciences, Smith College, 44 College Lane, Northampton, Massachusetts 01063, USA 3Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, Massachusetts 02543, USA 4Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Providence, Rhode Island 02912, USA 5Biodiversity Informatics Group, Marine Biological Laboratory, 7 MBL Street, Woods Hole, Massachusetts 02543, USA 6Current address: Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut 06520, USA †These authors contributed equally *Corresponding author: L.A.K - [email protected] Phone: 413-585-3825, Fax: 413-585-3786 Keywords: Microbial eukaryotes, supergroups, taxon sampling, Rhizaria, systematic error, Excavata 2 An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations underlying the diversity of microbial and macroscopic (e.g. plants and animals) eukaryotes. Previous work has divided eukaryotic diversity into a small number of high-level ‘supergroups’, many of which receive strong support in phylogenomic analyses. However, the abundance of data in phylogenomic analyses can lead to highly supported but incorrect relationships due to systematic phylogenetic error. Further, the paucity of major eukaryotic lineages (19 or fewer) included in these genomic studies may exaggerate systematic error and reduces power to evaluate hypotheses. -
Ebriid Phylogeny and the Expansion of the Cercozoa
ARTICLE IN PRESS Protist, Vol. 157, 279—290, May 2006 http://www.elsevier.de/protis Published online date 26 May 2006 ORIGINAL PAPER Ebriid Phylogeny and the Expansion of the Cercozoa Mona Hoppenrath1, and Brian S. Leander Canadian Institute for Advanced Research, Program in Evolutionary Biology, Departments of Botany and Zoology, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4 Submitted November 30, 2005; Accepted March 4, 2006 Monitoring Editor: Herve´ Philippe Ebria tripartita is a phagotrophic flagellate present in marine coastal plankton communities worldwide. This is one of two (possibly four) described extant species in the Ebridea, an enigmatic group of eukaryotes with an unclear phylogenetic position. Ebriids have never been cultured, are usually encountered in low abundance and have a peculiar combination of ultrastructural characters including a large nucleus with permanently condensed chromosomes and an internal skeleton composed of siliceous rods. Consequently, the taxonomic history of the group has been tumultuous and has included a variety of affiliations, such as silicoflagellates, dinoflagellates, ‘radiolarians’ and ‘neomonads’. Today, the Ebridea is treated as a eukaryotic taxon incertae sedis because no morphological or molecular features have been recognized that definitively relate ebriids with any other eukaryotic lineage. We conducted phylogenetic analyses of small subunit rDNA sequences from two multi-specimen isolations of Ebria tripartita. The closest relatives to the sequences from Ebria tripartita are environmental sequences from a submarine caldera floor. This newly recognized Ebria clade was most closely related to sequences from described species of Cryothecomonas and Protaspis. These molecular phylogenetic relationships were consistent with current ultrastructural data from all three genera, leading to a robust placement of ebriids within the Cercozoa. -
New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life
bioRxiv preprint doi: https://doi.org/10.1101/403329; this version posted August 30, 2018. 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-NC-ND 4.0 International license. New phylogenomic analysis of the enigmatic phylum Telonemia further resolves the eukaryote tree of life Jürgen F. H. Strassert1, Mahwash Jamy1, Alexander P. Mylnikov2, Denis V. Tikhonenkov2, Fabien Burki1,* 1Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden 2Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Yaroslavl Region, Russia *Corresponding author: E-mail: [email protected] Keywords: TSAR, Telonemia, phylogenomics, eukaryotes, tree of life, protists bioRxiv preprint doi: https://doi.org/10.1101/403329; this version posted August 30, 2018. 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-NC-ND 4.0 International license. Abstract The broad-scale tree of eukaryotes is constantly improving, but the evolutionary origin of several major groups remains unknown. Resolving the phylogenetic position of these ‘orphan’ groups is important, especially those that originated early in evolution, because they represent missing evolutionary links between established groups. Telonemia is one such orphan taxon for which little is known. The group is composed of molecularly diverse biflagellated protists, often prevalent although not abundant in aquatic environments. -
Silicification in the Microalgae
Silicification in the Microalgae Zoe V. Finkel 1 Silicifi cation in the Microalgae the cell wall, or Si may be bound to organic ligands associ- ated with the glycocalyx, or that Si may accumulate in peri- Silicon (Si) is the second most common element in the plasmic spaces associated with the cell wall (Baines et al. Earth’s crust (Williams 1981 ) and has been incorporated in 2012 ). In the case of fi eld populations of marine species from most of the biological kingdoms (Knoll 2003 ). Synechococcus , silicon to phosphorus ratios can approach In this review I focus on what is known about: Si accumula- values found in diatoms, and signifi cant cellular concentra- tion and the formation of siliceous structures in microalgae tions of Si have been confi rmed in some laboratory strains and some related non-photosynthetic groups, molecular and (Baines et al. 2012 ). The hypothesis that Si accumulates genetic mechanisms controlling silicifi cation, and the poten- within the periplasmic space of the outer cell wall is sup- tial costs and benefi ts associated with silicifi cation in the ported by the observation that a silicon layer forms within microalgae. This chapter uses the terminology recommended invaginations of the cell membrane in Bacillus cereus spores by Simpson and Volcani ( 1981 ): Si refers to the element and (Hirota et al. 2010 ). when the form of siliceous compound is unknown, silicic Signifi cant quantities of Si, likely opal, have been detected acid, Si(OH)4 , refers to the dominant unionized form of Si in in freshwater and marine green micro- and macro-algae (Fu aqueous solution at pH 7–8, and amorphous hydrated polym- et al. -
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. -
Protaspis.Pdf
J. Eukaryot. Microbiol., 53(5), 2006 pp. 327–342 r 2006 The Author(s) Journal compilation r 2006 by the International Society of Protistologists DOI: 10.1111/j.1550-7408.2006.00110.x Dinoflagellate, Euglenid, or Cercomonad? The Ultrastructure and Molecular Phylogenetic Position of Protaspis grandis n. sp. MONA HOPPENRATH and BRIAN S. LEANDER Canadian Institute for Advanced Research, Program in Evolutionary Biology, Departments of Botany and Zoology, University of British Columbia, Vancouver, BC, Canada V6T 1Z4 ABSTRACT. Protaspis is an enigmatic genus of marine phagotrophic biflagellates that have been tentatively classified with several different groups of eukaryotes, including dinoflagellates, euglenids, and cercomonads. This uncertainty led us to investigate the phylogenetic position of Protaspis grandis n. sp. with ultrastructural and small subunit (SSU) rDNA sequence data. Our results demonstrated that the cells were dorsoventrally flattened, shaped like elongated ovals with parallel lateral sides, 32.5–55.0 mm long and 20.0–35.0 mm wide. Moreover, two heterodynamic flagella emerged through funnels that were positioned subapically, each within a depression and separated by a distinctive protrusion. A complex multilayered wall surrounded the cell. Like dinoflagellates and euglenids, the nucleus contained permanently condensed chromosomes and a large nucleolus throughout the cell cycle. Pseudopodia containing numerous mitochondria with tubular cristae emerged from a ventral furrow through a longitudinal slit that was positioned posterior to the protrusion and flagellar apparatus. Batteries of extrusomes were present within the cytoplasm and had ejection sites through pores in the cell wall. The SSU rDNA phylogeny demonstrated a very close relationship between the benthic P. grandis n. -
"Plastid Originand Evolution". In: Encyclopedia of Life
CORE Metadata, citation and similar papers at core.ac.uk Provided by University of Queensland eSpace Plastid Origin and Advanced article Evolution Article Contents . Introduction Cheong Xin Chan, Rutgers University, New Brunswick, New Jersey, USA . Primary Plastids and Endosymbiosis . Secondary (and Tertiary) Plastids Debashish Bhattacharya, Rutgers University, New Brunswick, New Jersey, USA . Nonphotosynthetic Plastids . Plastid Theft . Plastid Origin and Eukaryote Evolution . Concluding Remarks Online posting date: 15th November 2011 Plastids (or chloroplasts in plants) are organelles within organisms that emerged ca. 2.8 billion years ago (Olson, which photosynthesis takes place in eukaryotes. The ori- 2006), followed by the evolution of eukaryotic algae ca. 1.5 gin of the widespread plastid traces back to a cyano- billion years ago (Yoon et al., 2004) and finally by the rise of bacterium that was engulfed and retained by a plants ca. 500 million years ago (Taylor, 1988). Photosynthetic reactions occur within the cytosol in heterotrophic protist through a process termed primary prokaryotes. In eukaryotes, however, the reaction takes endosymbiosis. Subsequent (serial) events of endo- place in the organelle, plastid (e.g. chloroplast in plants). symbiosis, involving red and green algae and potentially The plastid also houses many other reactions that are other eukaryotes, yielded the so-called ‘complex’ plastids essential for growth and development in algae and plants; found in photosynthetic taxa such as diatoms, dino- for example, the