DOCSLIB.ORG

Coevolution of Plastid Genomes and Transcript Processing Pathways in Photosynthetic Alveolates

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Coevolution of plastid genomes and transcript processing pathways in photosynthetic alveolates !"#$%&'()*+&,*(-+&&*../(0"1,23(4+..*,* Initial submission dated 31/05/2014 Corrected submission dated 08/08/2014 This dissertation is submitted for the degree of Doctor of Philosophy Declaration This dissertation is the result of my own work and includes nothing which is the outcome of work done in collaboration except where specifically indicated in the text. None of the material in this dissertation has been previously submitted for any other academic qualification. Some of the material within this dissertation has previously been published, in the following papers: Barbrook AC, Dorrell RG, Burrows J, Plenderleith LJ, Nisbet RER, Howe CJ. 2012. Polyuridylylation and processing of transcripts from multiple gene minicircles in chloroplasts of the dinoflagellate Amphidinium carterae. Plant Molecular Biology 79, 347-357. Dorrell RG, Howe CJ. 2012. What makes a chloroplast? Reconstructing the establishment of photosynthetic symbioses. Journal of Cell Science 125, 1865-1875. Dorrell RG, Howe CJ. 2012. Functional remodeling of RNA processing in replacement chloroplasts by pathways retained from their predecessors. Proceedings of the National Academy of Sciences USA. 109: 18879-18884 Dorrell RG, Butterfield ER, Nisbet RER, Howe CJ. 2013. Evolution: unveiling early alveolates. Current Biology 23, 1093-1096. Dorrell RG, Drew J, Nisbet RE, Howe CJ. 2014. Evolution of chloroplast transcript processing in Plasmodium and its chromerid algal relatives. PLoS Genetics 10, e1004008. Richardson E*, Dorrell RG* (joint first authors), Howe CJ. 2014. Genome-wide transcript profiling reveals the coevolution of chloroplast gene sequences and transcript processing pathways in the fucoxanthin dinoflagellate Karlodinium veneficum. Molecular Biology and Evolution, in press. All of the material from these publications that is included in this thesis was my own work, and was written by me. This dissertation is 51903 words length, excluding preface, abstract, figure legends, bibliography and appendices. !" " Thanks Thank you to Chris, for being such a generous and patient supervisor, and to members of the Howe Group for providing a warm and intellectually supportive research environment over the last four years. Particular thanks are due to Ellen Nisbet, for providing critical feedback on a great deal of the material in this thesis; to David Lea-Smith, Joanna McKenzie, Adrian Barbrook, and Davy Kurniawan, for training me in experimental techniques used in my PhD; and to Erin Butterfield, for reminding me to view everything with perspective. Thanks also to Martin Embley and to Ross Waller for a most enlightening viva examination, which I feel has made a very positive impact on this thesis. Thank you to the BBSRC for providing financial support for my work, and the British Phycological Society, British Society for Protist Biology, International Society of !"#$%&$#'#(%&$&)*+,-*.%,(/&*0#''1(1)*0+23"%-(1*4#"*1,+3'%,(*21*$#*+$$1,-*&#21*51"6* intellectually stimulating conferences. Thank you to my students- each and every one- for having provided me with a great deal to think about, challenging me on the assumptions that I make, and reminding me on a weekly basis of why I got into this job in the first place. Particular thanks to Beth Richardson, George Hinksman, and James Drew, who worked so hard and (I think) grew so much as research students under my supervision. Thank you to my parents, Mary and Peter Dorrell, for teaching me early on and continuing to teach me today to be inquisitive, limit myself only in the capacity of my imagination, and strive to be the kind of person that I want to see in the world. Finally, thank you to Anil: my love; the most beautiful person I know inside and out; for keeping me in one piece over the months spent writing this. OK, '1$/&*(#7 !!" " Abstract Following their endosymbiotic uptake, plastids undergo profound changes to genome content and to their associated biochemistry. I have investigated how evolutionary transitions in plastid genomes may impact on biochemical pathways associated with plastid gene expression, focusing on the highly unusual plastids found in one group of eukaryotes, the alveolates. The principal photosynthetic alveolate lineage is the dinoflagellate algae. Most dinoflagellate species harbour unusual plastids derived from red algae. The genome of this plastid has been fragmented into small, plasmid-!"#$%$!$&$'()%($*&$+%,&"'"-"*-!$)./% 0*1')-*"2()%34%(5")%6$'3&$%*$-$"7$%1%89%23!:;<=%(1"!%1'+>%"'%)3&$%)2$-"$)>%?'+$*63%$@($')"7$% sequence editing. Some dinoflagellates have replaced their original plastids with others, in a 2*3-$))%($*&$+%,)$*"1!%$'+3):&A"3)")./%05$%&1B3*%'3'-photosynthetic alveolates are the apicomplexans, which include the malaria parasite Plasmodium. Apicomplexans are descended from free-living algae and possess a vestigial plastid, which originated through the same endosymbiosis as the ancestral red dinoflagellate plastid. This plastid has lost all genes involved in photosynthesis and does not possess a poly(U) tail addition pathway. I have investigated the consequences of the fragmentation of the red algal dinoflagellate plastid genome on plastid transcription. I have characterised non-coding transcripts in plastids of the dinoflagellate Amphidinium carterae, including the first evidence for antisense transcripts in an algal plastid. Antisense transcripts in dinoflagellate plastids do not receive poly(U) tails, suggesting that poly(U) tail addition may play a role in strand discrimination during transcript processing. I have additionally characterised transcript processing in dinoflagellate plastids that were acquired through serial endosymbiosis. I have shown that poly(U) tail addition and editing occur in the haptophyte-derived serial endosymbionts of the fucoxanthin-containing dinoflagellates Karenia mikimotoi and Karlodinium veneficum. This is the first evidence that plastids acquired through serial endosymbiosis may be supported by pathways retained from previous symbioses. Transcript editing constrains the phenotypic consequences of divergent mutations in fucoxanthin plastid genomes, whereas poly(U) tail addition plays a central role in recognising and processing translationally functional fucoxanthin plastid mRNAs. I have additionally shown that certain genes within fucoxanthin plastids are located on minicircles. This demonstrates convergent evolution in the organisation of the fucoxanthin and red algal dinoflagellate plastid genomes since their endosymbiotic acquisition. Finally, I have investigated transcript processing in the algae Chromera velia and Vitrella brassicaformis. These species are closely related to apicomplexans but are still !!!" " photosynthetic and apply poly(U) tails to plastid transcripts, as with dinoflagellates. I have shown that poly(U) tails in these species are preferentially associated with translationally functional mRNAs of photosynthesis genes. This is the first plastid transcript processing pathway documented to target a specific functional gene category. Poly(U) tail addition may direct transcript cleavage and allow photosynthesis gene transcripts to accumulate to high levels. The loss of this pathway from ancestors of apicomplexans may have contributed to their transition from photosynthesis to parasitism. !"# # Contents Chapter One: Thesis Introduction...................................................................................1-24 -The origins of photosynthesis in the eukaryotes.....................................................................1 -Taxonomic distribution of plastid lineages..............................................................................3 -Identifying model systems for studying plastid evolution........................................................5 -Evolutionary diversity of the alveolates...................................................................................5 -Alveolates possess highly unusual plastids............................................................................8 -Thesis aims...........................................................................................................................10 -Theme 1: Genome reduction in plastid evolution..................................................................10 -Theme 2: Post-endosymbiotic changes to plastid genome organisation..............................14 -!"#$#%&'%(#)*+,%#-./01$2*/0*0%+-.%3"#%40"/55*-6%2+67%$/.#,...........................................15 -Transcript processing in plastids...........................................................................................18 -Outline of thesis chapters......................................................................................................21 Chapter Two: Materials and Methods............................................................................25-38 Chapter Three: Processing of core-containing and antisense transcripts generated from plastid minicircles in the peridinin dinoflagellate Amphidinium carterae........39-70 -Rolling circle transcription occurs in A. carterae plastids......................................................42 -Multi-copy transcripts can receive poly(U) tails.....................................................................45 -Multi-8/51%3)+-08)*530%8+-%5/00#00%$+39)#%:;%#-.0<..............................................................46 -Short core-containing transcripts are present in dinoflagellate plastid transcript
Recommended publications

  • Molecular Data and the Evolutionary History of Dinoflagellates by Juan Fernando Saldarriaga Echavarria Diplom, Ruprecht-Karls-Un

    Molecular data and the evolutionary history of dinoflagellates by Juan Fernando Saldarriaga Echavarria Diplom, Ruprecht-Karls-Universitat Heidelberg, 1993 A THESIS SUBMITTED IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE STUDIES Department of Botany We accept this thesis as conforming to the required standard THE UNIVERSITY OF BRITISH COLUMBIA November 2003 © Juan Fernando Saldarriaga Echavarria, 2003 ABSTRACT New sequences of ribosomal and protein genes were combined with available morphological and paleontological data to produce a phylogenetic framework for dinoflagellates. The evolutionary history of some of the major morphological features of the group was then investigated in the light of that framework. Phylogenetic trees of dinoflagellates based on the small subunit ribosomal RNA gene (SSU) are generally poorly resolved but include many well- supported clades, and while combined analyses of SSU and LSU (large subunit ribosomal RNA) improve the support for several nodes, they are still generally unsatisfactory. Protein-gene based trees lack the degree of species representation necessary for meaningful in-group phylogenetic analyses, but do provide important insights to the phylogenetic position of dinoflagellates as a whole and on the identity of their close relatives. Molecular data agree with paleontology in suggesting an early evolutionary radiation of the group, but whereas paleontological data include only taxa with fossilizable cysts, the new data examined here establish that this radiation event included all dinokaryotic lineages, including athecate forms. Plastids were lost and replaced many times in dinoflagellates, a situation entirely unique for this group. Histones could well have been lost earlier in the lineage than previously assumed.
  • Patrons De Biodiversité À L'échelle Globale Chez Les Dinoflagellés

    Patrons De Biodiversité À L'échelle Globale Chez Les Dinoflagellés

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emerciements* ! Remerciements* A!l'issue!de!ce!travail!de!recherche!et!de!sa!rédaction,!j’ai!la!preuve!que!la!thèse!est!loin!d'être!un!travail! solitaire.! En! effet,! je! n'aurais! jamais! pu! réaliser! ce! travail! doctoral! sans! le! soutien! d'un! grand! nombre! de! personnes!dont!l’amitié,!la!générosité,!la!bonne!humeur%et%l'intérêt%manifestés%à%l'égard%de%ma%recherche%m'ont% permis!de!progresser!dans!cette!phase!délicate!de!«!l'apprentiGchercheur!».!
  • TEXT-BOOKS of ANIMAL BIOLOGY a General Zoology of The

    TEXT-BOOKS of ANIMAL BIOLOGY a General Zoology of The

    TEXT-BOOKS OF ANIMAL BIOLOGY * Edited by JULIAN S. HUXLEY, F.R.S. A General Zoology of the Invertebrates by G. S. Carter Vertebrate Zoology by G. R. de Beer Comparative Physiology by L. T. Hogben Animal Ecology by Challes Elton Life in Inland Waters by Kathleen Carpenter The Development of Sex in Vertebrates by F. W. Rogers Brambell * Edited by H. MUNRO Fox, F.R.S. Animal Evolution / by G. S. Carter Zoogeography of the Land and Inland Waters by L. F. de Beaufort Parasitism and Symbiosis by M. Caullery PARASITISM AND ~SYMBIOSIS BY MAURICE CAULLERY Translated by Averil M. Lysaght, M.Sc., Ph.D. SIDGWICK AND JACKSON LIMITED LONDON First Published 1952 !.lADE AND PRINTED IN GREAT BRITAIN BY WILLIAM CLOWES AND SONS, LlMITED, LONDON AND BECCLES CONTENTS LIST OF ILLUSTRATIONS vii PREFACE TO THE ENGLISH EDITION xi CHAPTER I Commensalism Introduction-commensalism in marine animals-fishes and sea anemones-associations on coral reefs-widespread nature of these relationships-hermit crabs and their associates CHAPTER II Commensalism in Terrestrial Animals Commensals of ants and termites-morphological modifications in symphiles-ants.and slavery-myrmecophilous plants . 16 CHAPTER III From Commensalism to Inquilinism and Parasitism Inquilinism-epizoites-intermittent parasites-general nature of modifications produced by parasitism 30 CHAPTER IV Adaptations to Parasitism in Annelids and Molluscs Polychates-molluscs; lamellibranchs; gastropods 40 CHAPTER V Adaptation to Parasitism in the Crustacea Isopoda-families of Epicarida-Rhizocephala-Ascothoracica
  • COEVOLUTIONARY RELATIONSHIPS in a NEW TRIPARTITE MARINE SYMBIOSIS Phylogenetic Affinities of the Symbiotic Protist Nephromyces

    COEVOLUTIONARY RELATIONSHIPS in a NEW TRIPARTITE MARINE SYMBIOSIS Phylogenetic Affinities of the Symbiotic Protist Nephromyces

    COEVOLUTIONARY RELATIONSHIPS IN A NEW TRIPARTITE MARINE SYMBIOSIS Phylogenetic affinities of the symbiotic protist Nephromyces Mary Beth Saffo Marine Biological Laboratory, Woods Hole & Museum of Comparative Zoology, Harvard University Abstract 2. Phenotypic features suggestive of general protistan affinities All molgulid ascidian tunicates (Urochordata, phylum Chordata) : •tubular mitochondrial cristae (fig. 5,8) contain, in the lumen of the peculiar, ductless “renal sac,” an equally •thraustochytrid-like sporangia (fig. 4); other developmental stages bear vague peculiar symbiotic protist, Nephromyces. From the first description of resemblances to various other protistan taxa. Nephromyces in the 1870’s, the phylogenetic affinities, even existence, of this taxon has been a matter of debate. Though classified by Alfred Giard in 1888 as a chytridiomycete, Nephromyces has 3. Ssu rDNA sequences indicate that Nephromyces is an apicomplexan clade (preliminary phylogenetic analysis: a sample resisted definitive identification with any particular fungal or protistan Maximum likelihood trees shown) taxa. While its chitinous walls and hyphal-like cells support the notion of fungal affinities for Nephromyces, many other features , including the divergent phylogenetic implications of its morphologically eclectic life cycle , do not. Sequencing of ssu rDNA, indicates, however, that Nephromyces is an apicomplexan; these molecular data are supported by apicomplexan-like characters in the morphology Nephromyces’ host-transfer and infective stages. Other morphological and biochemical features of Nephromyces , some of Phylogenetic analyses, still in progress, consistently indicate thatNephromyces is a distinct them unusual among apicomplexa, or even protists generally, clade within the Apicomplexa. Although the challenge us to consider the significance of certain phenotypic relationship of Nephromyces to other apicomplexan characters as diagnostic tools in inferring deep phylogenies.
  • Checklist of Mediterranean Free-Living Dinoflagellates Institutional Rate: € 938,-/Approx

    Checklist of Mediterranean Free-Living Dinoflagellates Institutional Rate: € 938,-/Approx

    Botanica Marina Vol. 46,2003, pp. 215-242 © 2003 by Walter de Gruyter • Berlin ■ New York Subscriptions Botanica Marina is published bimonthly. Annual subscription rate (Volume 46,2003) Checklist of Mediterranean Free-living Dinoflagellates Institutional rate: € 938,-/approx. SFr1 50 1 in the US and Canada US $ 938,-. Individual rate: € 118,-/approx. SFr 189,-; in the US and Canada US $ 118,-. Personal rates apply only when copies are sent to F. Gómez a private address and payment is made by a personal check or credit card. Personal subscriptions must not be donated to a library. Single issues: € 178,-/approx. SFr 285,-. All prices exclude postage. Department of Aquatic Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan, [email protected] Orders Institutional subscription orders should be addressed to the publishers orto your usual subscription agent. Individual subscrip­ tion orders must be sent directly to one of the addresses indicated below. The Americas: An annotated checklist of the free-living dinoflagellates (Dinophyceae) of the Mediterranean Sea, based on Walter de Gruyter, Inc., 200 Saw Mill River Road, Hawthorne, N.Y. 10532, USA, Tel. 914-747-0110, Fax 914-747-1326, literature records, is given. The distribution of 673 species in 9 Mediterranean sub-basins is reported. The e-mail: [email protected]. number of taxa among the sub-basins was as follows: Ligurian (496 species), Balear-Provençal (360), Adri­ Australia and New Zealand: atic (322), Tyrrhenian (284), Ionian (283), Levantine (268), Aegean (182), Alborán (179) and Algerian Seas D. A. Information Services, 648 Whitehorse Road, P.O.
  • Real-Time Dynamics of Plasmodium NDC80 Reveals Unusual Modes of Chromosome Segregation During Parasite Proliferation Mohammad Zeeshan1,*, Rajan Pandey1,*, David J

    Real-Time Dynamics of Plasmodium NDC80 Reveals Unusual Modes of Chromosome Segregation During Parasite Proliferation Mohammad Zeeshan1,*, Rajan Pandey1,*, David J

    © 2020. Published by The Company of Biologists Ltd | Journal of Cell Science (2021) 134, jcs245753. doi:10.1242/jcs.245753 RESEARCH ARTICLE SPECIAL ISSUE: CELL BIOLOGY OF HOST–PATHOGEN INTERACTIONS Real-time dynamics of Plasmodium NDC80 reveals unusual modes of chromosome segregation during parasite proliferation Mohammad Zeeshan1,*, Rajan Pandey1,*, David J. P. Ferguson2,3, Eelco C. Tromer4, Robert Markus1, Steven Abel5, Declan Brady1, Emilie Daniel1, Rebecca Limenitakis6, Andrew R. Bottrill7, Karine G. Le Roch5, Anthony A. Holder8, Ross F. Waller4, David S. Guttery9 and Rita Tewari1,‡ ABSTRACT eukaryotic organisms to proliferate, propagate and survive. During Eukaryotic cell proliferation requires chromosome replication and these processes, microtubular spindles form to facilitate an equal precise segregation to ensure daughter cells have identical genomic segregation of duplicated chromosomes to the spindle poles. copies. Species of the genus Plasmodium, the causative agents of Chromosome attachment to spindle microtubules (MTs) is malaria, display remarkable aspects of nuclear division throughout their mediated by kinetochores, which are large multiprotein complexes life cycle to meet some peculiar and unique challenges to DNA assembled on centromeres located at the constriction point of sister replication and chromosome segregation. The parasite undergoes chromatids (Cheeseman, 2014; McKinley and Cheeseman, 2016; atypical endomitosis and endoreduplication with an intact nuclear Musacchio and Desai, 2017; Vader and Musacchio, 2017). Each membrane and intranuclear mitotic spindle. To understand these diverse sister chromatid has its own kinetochore, oriented to facilitate modes of Plasmodium cell division, we have studied the behaviour movement to opposite poles of the spindle apparatus. During and composition of the outer kinetochore NDC80 complex, a key part of anaphase, the spindle elongates and the sister chromatids separate, the mitotic apparatus that attaches the centromere of chromosomes to resulting in segregation of the two genomes during telophase.
  • Protist Phylogeny and the High-Level Classification of Protozoa

    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).
  • Plenary Lecture & Symposium

    Plenary Lecture & Symposium

    PLENARY LECTURE & SYMPOSIUM SYMPOSIuM From genomics to flagellar and ciliary struc - MONDAY 29 JulY tures and cytoskeleton dynamics (by FEPS) PlENARY lECTuRE (ISoP Honorary Member lECTuRE) Chairs (by ISoP) Cristina Miceli , University of Camerino, Camerino, Italy Helena Soares , University of Lisbon and Gulbenkian Foun - Introduction - John Dolan , CNRS-Sorbonne University, Ville - dation, Lisbon, Portugal franche-sur-Mer, France. Jack Sunter - Oxford Brookes University, Oxford, UK- Genome Tom Fenchel University of Copenhagen, Copenhagen, Den - wide tagging in trypanosomes uncovers flagellum asymmetries mark Dorota Wloga - Nencki Institute of Experimental Biology, War - ISoP Honorary Member saw, Poland - Deciphering the molecular mechanisms that coor - dinate ciliary outer doublet complexes – search for “missing Size, Shape and Function among Protozoa links” Helena Soares - University of Lisbon and Polytechnic Institute of Lisbon, Lisbon, Portugal - From centrosomal microtubule an - SYMPOSIuM on ciliate biology and taxonomy in memory choring and organization to basal body positioning: TBCCD1 an of Denis lynn (by FEPS/ISoP) elusive protein Chairs Pierangelo luporini , University of Camerino, Camerino, Italy Roberto Docampo , University of Georgia, Athens, Georgia TuESDAY 30 JulY Alan Warren - Natural History Museum, London, UK. The bio - logy and systematics of peritrich ciliates: old concepts and new PlENARY lECTuRE (PAST-PRESIDENT LECTURE, by ISoP) findings Rebecca Zufall - University of Houston, Houston, USA. Amitosis Introduction - Avelina Espinosa , Roger Williams University, and the Evolution of Asexuality in Tetrahymena Ciliates Bristol, USA Sabine Agatha - University of Salzburg, Salzburg, Austria. The biology and systematics of oligotrichean ciliates: new findings David Bass and old concepts Natural History Museum London, London & Cefas, Weymouth, laura utz - School of Sciences, PUCRS, Porto Alegre, Brazil.
  • Supplementary Materials - Methods

    Supplementary Materials - Methods

    Supplementary Materials - Methods Bacterial Phylogeny Using the predicted phylogenetic positions from the Microbial Gene Atlas (MiGA), all complete genomes for the classes betaproteobacteria, alphaproteobacteria, and Bacteroides available on NCBI were collected. The GToTree pipeline was run on each of these datasets, including the Nephromyces endosymbiont, using the relevant ​ ​ HMM set of single copy gene targets (57–62). This included 138 gene targets and 722 genomes in alphaproteobacteria, 203 gene targets and 471 genomes in betaproteobacteria, and 90 gene targets and 388 genomes in Bacteroidetes. In betaproteobacteria, 5 genomes were removed for having either too few hits to the single copy gene targets, or multiple hits. The final trees were created with FastTree v2 (63), and formatted in FigTree (S Figure 2,3). Amplicon Methods Detailed Fifty Molgula manhattensis tunicates were collected from a single floating dock ​ ​ located in Greenwich Bay, RI (41.653N, -71.452W), and 29 Molgula occidentalis were ​ ​ collected from Alligator Harbor, FL (29.899N, -84.381W) by Gulf Specimens Marine Laboratories, Inc. (https://gulfspecimen.org/). All 79 samples were collected in August ​ ​ of 2016 and prepared for a single Illumina MiSeq flow cell (hereafter referred to as Run One). An additional 25 Molgula occidentalis were collected by Gulf Specimens Marine ​ ​ Laboratories, Inc. in March of 2018 from the same location and prepared for a second MiSeq flow cell (hereafter referred to as Run Two). Tunicates were dissected to remove renal sacs and Nephromyces cells contained within were collected by a micropipette and ​ ​ placed in 1.5 ml eppendorf tubes. Dissecting tools were sterilized in a 10% bleach solution for 15 min and then rinsed between tunicates.
  • Phylogenomics Identifies a New Major Subgroup of Apicomplexans

    Phylogenomics Identifies a New Major Subgroup of Apicomplexans

    GBE Phylogenomics Identifies a New Major Subgroup of Apicomplexans, Marosporida class nov., with Extreme Apicoplast Genome Reduction Varsha Mathur1,*, Waldan K. Kwong1, Filip Husnik 2, Nicholas A.T. Irwin 1, Arni Kristmundsson3, Camino Gestal4, Mark Freeman5, and Patrick J. Keeling1 Downloaded from https://academic.oup.com/gbe/article/13/2/evaa244/5988525 by guest on 16 March 2021 1Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada 2Okinawa Institute of Science and Technology, Okinawa, Japan 3Fish Disease Laboratory, Institute for Experimental Pathology, University of Iceland, Reykjavık, Iceland 4Institute of Marine Research (IIM-CSIC), Vigo, Spain 5Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis, West Indies *Corresponding author: E-mail: [email protected]. Accepted: 17 November 2020 Abstract The phylum Apicomplexa consists largely of obligate animal parasites that include the causative agents of human diseases such as malaria. Apicomplexans have also emerged as models to study the evolution of nonphotosynthetic plastids, as they contain a relict chloroplast known as the apicoplast. The apicoplast offers important clues into how apicomplexan parasites evolved from free-living ancestors and can provide insights into reductive organelle evolution. Here, we sequenced the transcriptomes and apicoplast genomes of three deep-branching apicomplexans, Margolisiella islandica, Aggregata octopiana,andMerocystis kathae. Phylogenomic analyses show that these taxa, together with Rhytidocystis, form a new lineage of apicomplexans that is sister to the Coccidia and Hematozoa (the lineages including most medically significant taxa). Members of this clade retain plastid genomes and the canonical apicomplexan plastid metabolism. However, the apicoplast genomes of Margolisiella and Rhytidocystis are the most reduced of any apicoplast, are extremely GC-poor, and have even lost genes for the canonical plastidial RNA polymerase.
  • VII EUROPEAN CONGRESS of PROTISTOLOGY in Partnership with the INTERNATIONAL SOCIETY of PROTISTOLOGISTS (VII ECOP - ISOP Joint Meeting)

    VII EUROPEAN CONGRESS of PROTISTOLOGY in Partnership with the INTERNATIONAL SOCIETY of PROTISTOLOGISTS (VII ECOP - ISOP Joint Meeting)

    See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/283484592 FINAL PROGRAMME AND ABSTRACTS BOOK - VII EUROPEAN CONGRESS OF PROTISTOLOGY in partnership with THE INTERNATIONAL SOCIETY OF PROTISTOLOGISTS (VII ECOP - ISOP Joint Meeting) Conference Paper · September 2015 CITATIONS READS 0 620 1 author: Aurelio Serrano Institute of Plant Biochemistry and Photosynthesis, Joint Center CSIC-Univ. of Seville, Spain 157 PUBLICATIONS 1,824 CITATIONS SEE PROFILE Some of the authors of this publication are also working on these related projects: Use Tetrahymena as a model stress study View project Characterization of true-branching cyanobacteria from geothermal sites and hot springs of Costa Rica View project All content following this page was uploaded by Aurelio Serrano on 04 November 2015. The user has requested enhancement of the downloaded file. VII ECOP - ISOP Joint Meeting / 1 Content VII ECOP - ISOP Joint Meeting ORGANIZING COMMITTEES / 3 WELCOME ADDRESS / 4 CONGRESS USEFUL / 5 INFORMATION SOCIAL PROGRAMME / 12 CITY OF SEVILLE / 14 PROGRAMME OVERVIEW / 18 CONGRESS PROGRAMME / 19 Opening Ceremony / 19 Plenary Lectures / 19 Symposia and Workshops / 20 Special Sessions - Oral Presentations / 35 by PhD Students and Young Postdocts General Oral Sessions / 37 Poster Sessions / 42 ABSTRACTS / 57 Plenary Lectures / 57 Oral Presentations / 66 Posters / 231 AUTHOR INDEX / 423 ACKNOWLEDGMENTS-CREDITS / 429 President of the Organizing Committee Secretary of the Organizing Committee Dr. Aurelio Serrano
  • Scrippsiella Trochoidea (F.Stein) A.R.Loebl

    Scrippsiella Trochoidea (F.Stein) A.R.Loebl

    MOLECULAR DIVERSITY AND PHYLOGENY OF THE CALCAREOUS DINOPHYTES (THORACOSPHAERACEAE, PERIDINIALES) Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften (Dr. rer. nat.) der Fakultät für Biologie der Ludwig-Maximilians-Universität München zur Begutachtung vorgelegt von Sylvia Söhner München, im Februar 2013 Erster Gutachter: PD Dr. Marc Gottschling Zweiter Gutachter: Prof. Dr. Susanne Renner Tag der mündlichen Prüfung: 06. Juni 2013 “IF THERE IS LIFE ON MARS, IT MAY BE DISAPPOINTINGLY ORDINARY COMPARED TO SOME BIZARRE EARTHLINGS.” Geoff McFadden 1999, NATURE 1 !"#$%&'(&)'*!%*!+! +"!,-"!'-.&/%)$"-"!0'* 111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111 2& ")3*'4$%/5%6%*!+1111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111 7! 8,#$0)"!0'*+&9&6"*,+)-08!+ 111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111 :! 5%*%-"$&0*!-'/,)!0'* 11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111 ;! "#$!%"&'(!)*+&,!-!"#$!'./+,#(0$1$!2! './+,#(0$1$!-!3+*,#+4+).014!1/'!3+4$0&41*!041%%.5.01".+/! 67! './+,#(0$1$!-!/&"*.".+/!1/'!4.5$%"(4$! 68! ./!5+0&%!-!"#$!"#+*10+%,#1$*10$1$! 69! "#+*10+%,#1$*10$1$!-!5+%%.4!1/'!$:"1/"!'.;$*%."(! 6<! 3+4$0&41*!,#(4+)$/(!-!0#144$/)$!1/'!0#1/0$! 6=! 1.3%!+5!"#$!"#$%.%! 62! /0+),++0'* 1111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111<=!