Estimating the Timing of Early Eukaryotic Diversification With
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Protozoologica Special Issue: Protists in Soil Processes
Acta Protozool. (2012) 51: 201–208 http://www.eko.uj.edu.pl/ap ActA doi:10.4467/16890027AP.12.016.0762 Protozoologica Special issue: Protists in Soil Processes Review paper Ecology of Soil Eumycetozoans Steven L. STEPHENSON1 and Alan FEEST2 1Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA; 2Institute of Advanced Studies, University of Bristol and Ecosulis ltd., Newton St Loe, Bath, United Kingdom Abstract. Eumycetozoans, commonly referred to as slime moulds, are common to abundant organisms in soils. Three groups of slime moulds (myxogastrids, dictyostelids and protostelids) are recognized, and the first two of these are among the most important bacterivores in the soil microhabitat. The purpose of this paper is first to provide a brief description of all three groups and then to review what is known about their distribution and ecology in soils. Key words: Amoebae, bacterivores, dictyostelids, myxogastrids, protostelids. INTRODUCTION that they are amoebozoans and not fungi (Bapteste et al. 2002, Yoon et al. 2008, Baudalf 2008). Three groups of slime moulds (myxogastrids, dic- One of the idiosyncratic branches of the eukary- tyostelids and protostelids) are recognized (Olive 1970, otic tree of life consists of an assemblage of amoe- 1975). Members of the three groups exhibit consider- boid protists referred to as the supergroup Amoebozoa able diversity in the type of aerial spore-bearing struc- (Fiore-Donno et al. 2010). The most diverse members tures produced, which can range from exceedingly of the Amoebozoa are the eumycetozoans, common- small examples (most protostelids) with only a single ly referred to as slime moulds. Since their discovery, spore to the very largest examples (certain myxogas- slime moulds have been variously classified as plants, trids) that contain many millions of spores. -
Comparative Genomics of the Social Amoebae Dictyostelium Discoideum
Sucgang et al. Genome Biology 2011, 12:R20 http://genomebiology.com/2011/12/2/R20 RESEARCH Open Access Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum Richard Sucgang1†, Alan Kuo2†, Xiangjun Tian3†, William Salerno1†, Anup Parikh4, Christa L Feasley5, Eileen Dalin2, Hank Tu2, Eryong Huang4, Kerrie Barry2, Erika Lindquist2, Harris Shapiro2, David Bruce2, Jeremy Schmutz2, Asaf Salamov2, Petra Fey6, Pascale Gaudet6, Christophe Anjard7, M Madan Babu8, Siddhartha Basu6, Yulia Bushmanova6, Hanke van der Wel5, Mariko Katoh-Kurasawa4, Christopher Dinh1, Pedro M Coutinho9, Tamao Saito10, Marek Elias11, Pauline Schaap12, Robert R Kay8, Bernard Henrissat9, Ludwig Eichinger13, Francisco Rivero14, Nicholas H Putnam3, Christopher M West5, William F Loomis7, Rex L Chisholm6, Gad Shaulsky3,4, Joan E Strassmann3, David C Queller3, Adam Kuspa1,3,4* and Igor V Grigoriev2 Abstract Background: The social amoebae (Dictyostelia) are a diverse group of Amoebozoa that achieve multicellularity by aggregation and undergo morphogenesis into fruiting bodies with terminally differentiated spores and stalk cells. There are four groups of dictyostelids, with the most derived being a group that contains the model species Dictyostelium discoideum. Results: We have produced a draft genome sequence of another group dictyostelid, Dictyostelium purpureum, and compare it to the D. discoideum genome. The assembly (8.41 × coverage) comprises 799 scaffolds totaling 33.0 Mb, comparable to the D. discoideum genome size. Sequence comparisons suggest that these two dictyostelids shared a common ancestor approximately 400 million years ago. In spite of this divergence, most orthologs reside in small clusters of conserved synteny. Comparative analyses revealed a core set of orthologous genes that illuminate dictyostelid physiology, as well as differences in gene family content. -
Aquatic Microbial Ecology 62:139–152 (2011)
The following supplement accompanies the article Airborne microeukaryote colonists in experimental water containers: diversity, succession, life histories and established food webs Savvas Genitsaris1, Maria Moustaka-Gouni1,*, Konstantinos A. Kormas2 1Department of Botany, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece 2Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46 Nea Ionia, Magnisia, Greece *Corresponding author. Email: [email protected] Aquatic Microbial Ecology 62:139–152 (2011) Supplement. Additional data Fig. S1. Clone library coverage based on Good’s C estimator of the eukaryotic 18S rDNA clone libraries from the water containers. The ratio observed phylotypes: predicted phylotypes (SChao1) was 0.7 in autumn, 0.87 in winter and 0.47 in spring. 2 Fig. S2. Phylogenetic tree of relationships of 18S rDNA (ca. 1600 bp) of the representative unique (grouped on ≥98% similarity) eukaryotic clones (in bold) found in the tap water containers, based on the neighbour-joining method as determined by distance Jukes–Cantor analysis. One thousand bootstrap analyses (distance) were conducted. GenBank numbers are shown in parentheses. Scale bar represents 2% estimated. 3 Table S1. Daily meteorological data in the city of Thessaloniki during the sampling periods of the study Air temperature (oC) Rainfall Sunshine RH Wind speed (mm) (min) (%) (m s-1) min max mean min max mean min max mean min max mean min max mean Autumn 2007 7.1 17.1 11.9 0 18.3 1.9 0 494.5 203.4 33.2 90.5 70.7 0.9 5.5 2.0 Winter 2007–8 –0.7 13.5 7.6 0 17.8 0.7 0 555.7 277.6 24.5 88.7 63.4 0.8 7.7 2.1 Spring 2008 8.5 16.9 13.0 0 34.7 1.9 0 663.7 363.7 36.8 91.0 66.8 1.2 3.6 1.8 Table S2. -
Multigene Eukaryote Phylogeny Reveals the Likely Protozoan Ancestors of Opis- Thokonts (Animals, Fungi, Choanozoans) and Amoebozoa
Accepted Manuscript Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opis- thokonts (animals, fungi, choanozoans) and Amoebozoa Thomas Cavalier-Smith, Ema E. Chao, Elizabeth A. Snell, Cédric Berney, Anna Maria Fiore-Donno, Rhodri Lewis PII: S1055-7903(14)00279-6 DOI: http://dx.doi.org/10.1016/j.ympev.2014.08.012 Reference: YMPEV 4996 To appear in: Molecular Phylogenetics and Evolution Received Date: 24 January 2014 Revised Date: 2 August 2014 Accepted Date: 11 August 2014 Please cite this article as: Cavalier-Smith, T., Chao, E.E., Snell, E.A., Berney, C., Fiore-Donno, A.M., Lewis, R., Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts (animals, fungi, choanozoans) and Amoebozoa, Molecular Phylogenetics and Evolution (2014), doi: http://dx.doi.org/10.1016/ j.ympev.2014.08.012 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. 1 1 Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts 2 (animals, fungi, choanozoans) and Amoebozoa 3 4 Thomas Cavalier-Smith1, Ema E. Chao1, Elizabeth A. Snell1, Cédric Berney1,2, Anna Maria 5 Fiore-Donno1,3, and Rhodri Lewis1 6 7 1Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK. -
Evidence for Glycolytic Reactions in the Mitochondrion?
Broad Distribution of TPI-GAPDH Fusion Proteins among Eukaryotes: Evidence for Glycolytic Reactions in the Mitochondrion? Takuro Nakayama1, Ken-ichiro Ishida2, John M. Archibald1* 1 Department of Biochemistry & Molecular Biology, Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Dalhousie University, Halifax, Nova Scotia, Canada, 2 Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan Abstract Glycolysis is a central metabolic pathway in eukaryotic and prokaryotic cells. In eukaryotes, the textbook view is that glycolysis occurs in the cytosol. However, fusion proteins comprised of two glycolytic enzymes, triosephosphate isomerase (TPI) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), were found in members of the stramenopiles (diatoms and oomycetes) and shown to possess amino-terminal mitochondrial targeting signals. Here we show that mitochondrial TPI- GAPDH fusion protein genes are widely spread across the known diversity of stramenopiles, including non-photosynthetic species (Bicosoeca sp. and Blastocystis hominis). We also show that TPI-GAPDH fusion genes exist in three cercozoan taxa (Paulinella chromatophora, Thaumatomastix sp. and Mataza hastifera) and an apusozoan protist, Thecamonas trahens. Interestingly, subcellular localization predictions for other glycolytic enzymes in stramenopiles and a cercozoan show that a significant fraction of the glycolytic enzymes in these species have mitochondrial-targeted isoforms. These results suggest that part -
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 ...................................................... -
GIULIA MAGRI RIBEIRO Sequenciamento E
GIULIA MAGRI RIBEIRO Sequenciamento e anota¸c˜ao do transcriptoma da ameba tecada Arcella intermedia: Descri¸c˜ao de vias e descobertas de genes. Transcriptome sequencing and annotation of the testate amoeba Arcella intermedia: Pathway description and gene discovery. S˜aoPaulo 2018 GIULIA MAGRI RIBEIRO Sequenciamento e anota¸c˜ao do transcriptoma da ameba tecada Arcella intermedia: Descri¸c˜ao de vias e descobertas de genes. Transcriptome sequencing and annotation of the testate amoeba Arcella intermedia: Pathway description and gene discovery. Disserta¸c˜aoapresentada ao Instituto de Biociˆencias da Universidade de S˜ao Paulo para obten¸c˜aodo t´ıtulo de Mestre em Zoologia pelo Programa de P´os-gradua¸c˜ao em Zoologia. Vers˜ao corrigida contendo as altera¸c˜oes solicitadas pela comiss˜aojulgadora em 30 de Outubro de 2018. A vers˜aooriginal encontra-se no Instituto de Biociˆencias da USP e na Biblioteca Digital de Teses e Disserta¸c˜oes da USP. Supervisor: Prof. Dr. Daniel J.G. Lahr S˜aoPaulo 2018 Ficha catalográfica elaborada pelo Serviço de Biblioteca do Instituto de Biociências da USP, com os dados fornecidos pelo autor no formulário: http://www.ib.usp.br/biblioteca/ficha-catalografica/ficha.php Ribeiro, Giulia Magri Sequenciamento e anotação do transcriptoma da ameba tecada Arcella intermedia: Descrição de vias e descobertas de genes. / Giulia Magri Ribeiro; orientador Daniel José Galafasse Lahr. -- São Paulo, 2018. 118 f. Dissertação (Mestrado) - Instituto de Biociências da Universidade de São Paulo, Departamento de Zoologia. 1. Teca ameba. 2. Transcriptoma. 3. Transferências laterais de genes. 4. Metabolismo anaeróbio. I. Lahr, Daniel José Galafasse, orient. -
Protozoologica
Acta Protozool. (2014) 53: 207–213 http://www.eko.uj.edu.pl/ap ACTA doi:10.4467/16890027AP.14.017.1598 PROTOZOOLOGICA Broad Taxon Sampling of Ciliates Using Mitochondrial Small Subunit Ribosomal DNA Micah DUNTHORN1, Meaghan HALL2, Wilhelm FOISSNER3, Thorsten STOECK1 and Laura A. KATZ2,4 1Department of Ecology, University of Kaiserslautern, 67663 Kaiserslautern, Germany; 2Department of Biological Sciences, Smith College, Northampton, MA 01063, USA; 3FB Organismische Biologie, Universität Salzburg, A-5020 Salzburg, Austria; 4Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA 01003, USA Abstract. Mitochondrial SSU-rDNA has been used recently to infer phylogenetic relationships among a few ciliates. Here, this locus is compared with nuclear SSU-rDNA for uncovering the deepest nodes in the ciliate tree of life using broad taxon sampling. Nuclear and mitochondrial SSU-rDNA reveal the same relationships for nodes well-supported in previously-published nuclear SSU-rDNA studies, al- though support for many nodes in the mitochondrial SSU-rDNA tree are low. Mitochondrial SSU-rDNA infers a monophyletic Colpodea with high node support only from Bayesian inference, and in the concatenated tree (nuclear plus mitochondrial SSU-rDNA) monophyly of the Colpodea is supported with moderate to high node support from maximum likelihood and Bayesian inference. In the monophyletic Phyllopharyngea, the Suctoria is inferred to be sister to the Cyrtophora in the mitochondrial, nuclear, and concatenated SSU-rDNA trees with moderate to high node support from maximum likelihood and Bayesian inference. Together these data point to the power of adding mitochondrial SSU-rDNA as a standard locus for ciliate molecular phylogenetic inferences. -
Novel Lineages of Oxymonad Flagellates from the Termite Porotermes Adamsoni (Stolotermitidae): the Genera Oxynympha and Termitim
Protist, Vol. 170, 125683, December 2019 http://www.elsevier.de/protis Published online date 21 October 2019 ORIGINAL PAPER Novel Lineages of Oxymonad Flagellates from the Termite Porotermes adamsoni (Stolotermitidae): the Genera Oxynympha and Termitimonas a,1 b a c b,1 Renate Radek , Katja Meuser , Samet Altinay , Nathan Lo , and Andreas Brune a Evolutionary Biology, Institute for Biology/Zoology, Freie Universität Berlin, 14195 Berlin, Germany b Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany c School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia Submitted January 21, 2019; Accepted October 9, 2019 Monitoring Editor: Alastair Simpson The symbiotic gut flagellates of lower termites form host-specific consortia composed of Parabasalia and Oxymonadida. The analysis of their coevolution with termites is hampered by a lack of informa- tion, particularly on the flagellates colonizing the basal host lineages. To date, there are no reports on the presence of oxymonads in termites of the family Stolotermitidae. We discovered three novel, deep-branching lineages of oxymonads in a member of this family, the damp-wood termite Porotermes adamsoni. One tiny species (6–10 m), Termitimonas travisi, morphologically resembles members of the genus Monocercomonoides, but its SSU rRNA genes are highly dissimilar to recently published sequences of Polymastigidae from cockroaches and vertebrates. A second small species (9–13 m), Oxynympha loricata, has a slight phylogenetic affinity to members of the Saccinobaculidae, which are found exclusively in wood-feeding cockroaches of the genus Cryptocercus, the closest relatives of termites, but shows a combination of morphological features that is unprecedented in any oxymonad family. -
Molecular Identification and Evolution of Protozoa Belonging to the Parabasalia Group and the Genus Blastocystis
UNIVERSITAR DEGLI STUDI DI SASSARI SCUOLA DI DOTTORATO IN SCIENZE BIOMOLECOLARI E BIOTECNOLOGICHE (Intenational PhD School in Biomolecular and Biotechnological Sciences) Indirizzo: Microbiologia molecolare e clinica Molecular identification and evolution of protozoa belonging to the Parabasalia group and the genus Blastocystis Direttore della scuola: Prof. Masala Bruno Relatore: Prof. Pier Luigi Fiori Correlatore: Dott. Eric Viscogliosi Tesi di Dottorato : Dionigia Meloni XXIV CICLO Nome e cognome: Dionigia Meloni Titolo della tesi : Molecular identification and evolution of protozoa belonging to the Parabasalia group and the genus Blastocystis Tesi di dottorato in scienze Biomolecolari e biotecnologiche. Indirizzo: Microbiologia molecolare e clinica Universit degli studi di Sassari UNIVERSITAR DEGLI STUDI DI SASSARI SCUOLA DI DOTTORATO IN SCIENZE BIOMOLECOLARI E BIOTECNOLOGICHE (Intenational PhD School in Biomolecular and Biotechnological Sciences) Indirizzo: Microbiologia molecolare e clinica Molecular identification and evolution of protozoa belonging to the Parabasalia group and the genus Blastocystis Direttore della scuola: Prof. Masala Bruno Relatore: Prof. Pier Luigi Fiori Correlatore: Dott. Eric Viscogliosi Tesi di Dottorato : Dionigia Meloni XXIV CICLO Nome e cognome: Dionigia Meloni Titolo della tesi : Molecular identification and evolution of protozoa belonging to the Parabasalia group and the genus Blastocystis Tesi di dottorato in scienze Biomolecolari e biotecnologiche. Indirizzo: Microbiologia molecolare e clinica Universit degli studi di Sassari Abstract My thesis was conducted on the study of two groups of protozoa: the Parabasalia and Blastocystis . The first part of my work was focused on the identification, pathogenicity, and phylogeny of parabasalids. We showed that Pentatrichomonas hominis is a possible zoonotic species with a significant potential of transmission by the waterborne route and could be the aetiological agent of gastrointestinal troubles in children.