Stages of Perkinsus Karlssoni (Apicomplexa: Argopecten Irradians
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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. -
Phylogenetic Relationships of the Genus Frenkelia
International Journal for Parasitology 29 (1999) 957±972 Phylogenetic relationships of the genus Frenkelia: a review of its history and new knowledge gained from comparison of large subunit ribosomal ribonucleic acid gene sequencesp N.B. Mugridge a, D.A. Morrison a, A.M. Johnson a, K. Luton a, 1, J.P. Dubey b, J. Voty pka c, A.M. Tenter d, * aMolecular Parasitology Unit, University of Technology, Sydney NSW, Australia bUS Department of Agriculture, ARS, LPSI, PBEL, Beltsville MD, USA cDepartment of Parasitology, Charles University, Prague, Czech Republic dInstitut fuÈr Parasitologie, TieraÈrztliche Hochschule Hannover, BuÈnteweg 17, D-30559 Hannover, Germany Received 3 April 1999; accepted 3 May 1999 Abstract The dierent genera currently classi®ed into the family Sarcocystidae include parasites which are of signi®cant medical, veterinary and economic importance. The genus Sarcocystis is the largest within the family Sarcocystidae and consists of species which infect a broad range of animals including mammals, birds and reptiles. Frenkelia, another genus within this family, consists of parasites that use rodents as intermediate hosts and birds of prey as de®nitive hosts. Both genera follow an almost identical pattern of life cycle, and their life cycle stages are morphologically very similar. How- ever, the relationship between the two genera remains unresolved because previous analyses of phenotypic characters and of small subunit ribosomal ribonucleic acid gene sequences have questioned the validity of the genus Frenkelia or the monophyly of the genus Sarcocystis if Frenkelia was recognised as a valid genus. We therefore subjected the large subunit ribosomal ribonucleic acid gene sequences of representative taxa in these genera to phylogenetic analyses to ascertain a de®nitive relationship between the two genera. -
De Novo Transcriptome Assembly of Perkinsus Olseni Trophozoite Stimulated in Vitro with Manila Clam (Ruditapes Philippinarum) Plasma
Journal of Invertebrate Pathology 135 (2016) 22–33 Contents lists available at ScienceDirect Journal of Invertebrate Pathology journal homepage: www.elsevier.com/locate/jip De novo transcriptome assembly of Perkinsus olseni trophozoite stimulated in vitro with Manila clam (Ruditapes philippinarum) plasma Abul Farah Md. Hasanuzzaman a,b, Diego Robledo c, Antonio Gómez-Tato d, Jose A. Alvarez-Dios e, ⇑ Peter W. Harrison f, Asunción Cao g, Sergio Fernández-Boo g, Antonio Villalba g, Belén G. Pardo a, , Paulino Martínez a a Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain b Fisheries and Marine Resource Technology Discipline, Khulna University, Khulna 9208, Bangladesh c Departamento de Xenética, Facultade de Bioloxía, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain d Departamento de Xeometría e Topoloxía, Facultade de Matemáticas, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain e Departamento de Matemática Aplicada, Facultade de Matemáticas, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain f Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom g Centro de Investigacións Mariñas (CIMA), Consellería do Medio Rural e do Mar, Xunta de Galicia, 36620 Vilanova de Arousa, Spain article info abstract Article history: The protistan parasite Perkinsus olseni is a deadly causative agent of perkinsosis, a molluscan disease Received 16 September 2015 affecting Manila clam (Ruditapes philippinarum), having a significant impact on world mollusc production. Revised 18 January 2016 Deciphering the underlying molecular mechanisms in R. philippinarum-P. olseni interaction is crucial for Accepted 24 January 2016 controlling this parasitosis. The present study investigated the transcriptional expression in the parasite Available online 25 January 2016 trophozoite using RNA-seq. -
The Planktonic Protist Interactome: Where Do We Stand After a Century of Research?
bioRxiv preprint doi: https://doi.org/10.1101/587352; this version posted May 2, 2019. 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. Bjorbækmo et al., 23.03.2019 – preprint copy - BioRxiv The planktonic protist interactome: where do we stand after a century of research? Marit F. Markussen Bjorbækmo1*, Andreas Evenstad1* and Line Lieblein Røsæg1*, Anders K. Krabberød1**, and Ramiro Logares2,1** 1 University of Oslo, Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), Blindernv. 31, N- 0316 Oslo, Norway 2 Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37-49, ES-08003, Barcelona, Catalonia, Spain * The three authors contributed equally ** Corresponding authors: Ramiro Logares: Institute of Marine Sciences (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Catalonia, Spain. Phone: 34-93-2309500; Fax: 34-93-2309555. [email protected] Anders K. Krabberød: University of Oslo, Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), Blindernv. 31, N-0316 Oslo, Norway. Phone +47 22845986, Fax: +47 22854726. [email protected] Abstract Microbial interactions are crucial for Earth ecosystem function, yet our knowledge about them is limited and has so far mainly existed as scattered records. Here, we have surveyed the literature involving planktonic protist interactions and gathered the information in a manually curated Protist Interaction DAtabase (PIDA). In total, we have registered ~2,500 ecological interactions from ~500 publications, spanning the last 150 years. -
University of Oklahoma
UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By JOSHUA THOMAS COOPER Norman, Oklahoma 2017 MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION APPROVED FOR THE DEPARTMENT OF MICROBIOLOGY AND PLANT BIOLOGY BY ______________________________ Dr. Boris Wawrik, Chair ______________________________ Dr. J. Phil Gibson ______________________________ Dr. Anne K. Dunn ______________________________ Dr. John Paul Masly ______________________________ Dr. K. David Hambright ii © Copyright by JOSHUA THOMAS COOPER 2017 All Rights Reserved. iii Acknowledgments I would like to thank my two advisors Dr. Boris Wawrik and Dr. J. Phil Gibson for helping me become a better scientist and better educator. I would also like to thank my committee members Dr. Anne K. Dunn, Dr. K. David Hambright, and Dr. J.P. Masly for providing valuable inputs that lead me to carefully consider my research questions. I would also like to thank Dr. J.P. Masly for the opportunity to coauthor a book chapter on the speciation of diatoms. It is still such a privilege that you believed in me and my crazy diatom ideas to form a concise chapter in addition to learn your style of writing has been a benefit to my professional development. I’m also thankful for my first undergraduate research mentor, Dr. Miriam Steinitz-Kannan, now retired from Northern Kentucky University, who was the first to show the amazing wonders of pond scum. Who knew that studying diatoms and algae as an undergraduate would lead me all the way to a Ph.D. -
Symbiodinium Genomes Reveal Adaptive Evolution of Functions Related to Symbiosis
bioRxiv preprint doi: https://doi.org/10.1101/198762; this version posted October 5, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Article 2 Symbiodinium genomes reveal adaptive evolution of 3 functions related to symbiosis 4 Huanle Liu1, Timothy G. Stephens1, Raúl A. González-Pech1, Victor H. Beltran2, Bruno 5 Lapeyre3,4, Pim Bongaerts5, Ira Cooke3, David G. Bourne2,6, Sylvain Forêt7,*, David J. 6 Miller3, Madeleine J. H. van Oppen2,8, Christian R. Voolstra9, Mark A. Ragan1 and Cheong 7 Xin Chan1,10,† 8 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, 9 Australia 10 2Australian Institute of Marine Science, Townsville, QLD 4810, Australia 11 3ARC Centre of Excellence for Coral Reef Studies and Department of Molecular and Cell 12 Biology, James Cook University, Townsville, QLD 4811, Australia 13 4Laboratoire d’excellence CORAIL, Centre de Recherches Insulaires et Observatoire de 14 l’Environnement, Moorea 98729, French Polynesia 15 5Global Change Institute, The University of Queensland, Brisbane, QLD 4072, Australia 16 6College of Science and Engineering, James Cook University, Townsville, QLD 4811, 17 Australia 18 7Research School of Biology, Australian National University, Canberra, ACT 2601, Australia 19 8School of BioSciences, The University of Melbourne, VIC 3010, Australia 1 bioRxiv preprint doi: https://doi.org/10.1101/198762; this version posted October 5, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. -
A Parasite of Marine Rotifers: a New Lineage of Dinokaryotic Dinoflagellates (Dinophyceae)
Hindawi Publishing Corporation Journal of Marine Biology Volume 2015, Article ID 614609, 5 pages http://dx.doi.org/10.1155/2015/614609 Research Article A Parasite of Marine Rotifers: A New Lineage of Dinokaryotic Dinoflagellates (Dinophyceae) Fernando Gómez1 and Alf Skovgaard2 1 Laboratory of Plankton Systems, Oceanographic Institute, University of Sao˜ Paulo, Prac¸a do Oceanografico´ 191, Cidade Universitaria,´ 05508-900 Butanta,˜ SP, Brazil 2Department of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 7, 1870 Frederiksberg C, Denmark Correspondence should be addressed to Fernando Gomez;´ [email protected] Received 11 July 2015; Accepted 27 August 2015 Academic Editor: Gerardo R. Vasta Copyright © 2015 F. Gomez´ and A. Skovgaard. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Dinoflagellate infections have been reported for different protistan and animal hosts. We report, for the first time, the association between a dinoflagellate parasite and a rotifer host, tentatively Synchaeta sp. (Rotifera), collected from the port of Valencia, NW Mediterranean Sea. The rotifer contained a sporangium with 100–200 thecate dinospores that develop synchronically through palintomic sporogenesis. This undescribed dinoflagellate forms a new and divergent fast-evolved lineage that branches amongthe dinokaryotic dinoflagellates. 1. Introduction form independent lineages with no evident relation to other dinoflagellates [12]. In this study, we describe a new lineage of The alveolates (or Alveolata) are a major lineage of protists an undescribed parasitic dinoflagellate that largely diverged divided into three main phyla: ciliates, apicomplexans, and from other known dinoflagellates. -
Structure of Protistan Parasites Found in Bivalve Molluscs
W&M ScholarWorks VIMS Books and Book Chapters Virginia Institute of Marine Science 1988 Structure of Protistan Parasites Found in Bivalve Molluscs Frank O. Perkins Follow this and additional works at: https://scholarworks.wm.edu/vimsbooks Part of the Marine Biology Commons, and the Parasitology Commons American Fisheries Society Special Publication 18:93- 111 , 1988 CC> Copyrighl by !he American Fisheries Sociely 1988 PARASITE MORPHOLOGY, STRATEGY, AND EVOLUTION Structure of Protistan Parasites Found in Bivalve Molluscs 1 FRANK 0. PERKINS Virginia In stitute of Marine Science. School of Marine Science, College of William and Mary Gloucester Point, Virginia 23062, USA Abstral'I.-The literature on the structure of protists parasitizing bivalve molluscs is reviewed, and previously unpubli shed observations of species of class Perkinsea, phylum Haplosporidia, and class Paramyxea are presented. Descriptions are given of the flagellar apparatus of Perkin.His marinus zoospores, the ultrastructure of Perkinsus sp. from the Baltic macoma Maconw balthica, and the development of haplosporosome-like bodies in Haplosporidium nelsoni. The possible origin of stem cells of Marreilia sydneyi from the inner two sporoplasms is discussed. New research efforts are suggested which could help elucidate the phylogenetic interrelationships and taxonomic positions of the various taxa and help in efforts to better understand life cycles of selected species. Studies of the structure of protistan parasites terization of the parasite species, to elucidation of found in bivalve moll uscs have been fruitful to the many parasite life cycles, and to knowledge of morphologist interested in comparative morphol- parasite metabolism. The latter, especially, is ogy, evolu tion, and taxonomy. -
Drawing the Tree of Eukaryotic Life Based on the Analysis of 2,269 Comment Manually Annotated Myosins from 328 Species Florian Odronitz and Martin Kollmar
Open Access Research2007OdronitzVolume 8, and Issue Kollmar 9, Article R196 Drawing the tree of eukaryotic life based on the analysis of 2,269 comment manually annotated myosins from 328 species Florian Odronitz and Martin Kollmar Address: Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg, 37077 Goettingen, Germany. Correspondence: Martin Kollmar. Email: [email protected] reviews Published: 18 September 2007 Received: 6 March 2007 Revised: 17 September 2007 Genome Biology 2007, 8:R196 (doi:10.1186/gb-2007-8-9-r196) Accepted: 18 September 2007 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2007/8/9/R196 © 2007 Odronitz and Kollmar; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which reports permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The<p>Thesome eukaryotic accepted tree of relationshipstreeeukaryotic of life life of was major reconstr taxa anducted resolving based on disputed the analysis and preliminary of 2,269 myosin classifications.</p> motor domains from 328 organisms, confirming Abstract deposited research Background: The evolutionary history of organisms is expressed in phylogenetic trees. The most widely used phylogenetic trees describing the evolution of all organisms have been constructed based on single-gene phylogenies that, however, often produce conflicting results. Incongruence between phylogenetic trees can result from the violation of the orthology assumption and stochastic and systematic errors. Results: Here, we have reconstructed the tree of eukaryotic life based on the analysis of 2,269 myosin motor domains from 328 organisms. -
The Mitochondrial Genome and Transcriptome of the Basal
View metadata, citation and similar papers at core.ac.uk brought to you by CORE GBEprovided by PubMed Central The Mitochondrial Genome and Transcriptome of the Basal Dinoflagellate Hematodinium sp.: Character Evolution within the Highly Derived Mitochondrial Genomes of Dinoflagellates C. J. Jackson, S. G. Gornik, and R. F. Waller* School of Botany, University of Melbourne, Australia *Corresponding author: E-mail: [email protected]. Accepted: 12 November 2011 Abstract The sister phyla dinoflagellates and apicomplexans inherited a drastically reduced mitochondrial genome (mitochondrial DNA, mtDNA) containing only three protein-coding (cob, cox1, and cox3) genes and two ribosomal RNA (rRNA) genes. In apicomplexans, single copies of these genes are encoded on the smallest known mtDNA chromosome (6 kb). In dinoflagellates, however, the genome has undergone further substantial modifications, including massive genome amplification and recombination resulting in multiple copies of each gene and gene fragments linked in numerous combinations. Furthermore, protein-encoding genes have lost standard stop codons, trans-splicing of messenger RNAs (mRNAs) is required to generate complete cox3 transcripts, and extensive RNA editing recodes most genes. From taxa investigated to date, it is unclear when many of these unusual dinoflagellate mtDNA characters evolved. To address this question, we investigated the mitochondrial genome and transcriptome character states of the deep branching dinoflagellate Hematodinium sp. Genomic data show that like later-branching dinoflagellates Hematodinium sp. also contains an inflated, heavily recombined genome of multicopy genes and gene fragments. Although stop codons are also lacking for cox1 and cob, cox3 still encodes a conventional stop codon. Extensive editing of mRNAs also occurs in Hematodinium sp. -
Symbiodinium Genomes Reveal Adaptive Evolution of Functions Related to Coral-Dinoflagellate Symbiosis
Corrected: Publisher correction ARTICLE DOI: 10.1038/s42003-018-0098-3 OPEN Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis Huanle Liu1, Timothy G. Stephens1, Raúl A. González-Pech1, Victor H. Beltran2, Bruno Lapeyre3,4,12, Pim Bongaerts5,6, Ira Cooke4, Manuel Aranda7, David G. Bourne2,8, Sylvain Forêt3,9, David J. Miller3,4, Madeleine J.H. van Oppen2,10, Christian R. Voolstra7, Mark A. Ragan1 & Cheong Xin Chan1,11 1234567890():,; Symbiosis between dinoflagellates of the genus Symbiodinium and reef-building corals forms the trophic foundation of the world’s coral reef ecosystems. Here we present the first draft genome of Symbiodinium goreaui (Clade C, type C1: 1.03 Gbp), one of the most ubiquitous endosymbionts associated with corals, and an improved draft genome of Symbiodinium kawagutii (Clade F, strain CS-156: 1.05 Gbp) to further elucidate genomic signatures of this symbiosis. Comparative analysis of four available Symbiodinium genomes against other dinoflagellate genomes led to the identification of 2460 nuclear gene families (containing 5% of Symbiodinium genes) that show evidence of positive selection, including genes involved in photosynthesis, transmembrane ion transport, synthesis and modification of amino acids and glycoproteins, and stress response. Further, we identify extensive sets of genes for meiosis and response to light stress. These draft genomes provide a foundational resource for advancing our understanding of Symbiodinium biology and the coral-algal symbiosis. 1 Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia. 2 Australian Institute of Marine Science, Townsville, QLD 4810, Australia. 3 ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia. -
Effects of Triclosan on Growth, Viability and Fatty Acid Synthesis of the Oyster Protozoan Parasite Perkinsus Marinus
DISEASES OF AQUATIC ORGANISMS Vol. 67: 217–224, 2005 Published November 28 Dis Aquat Org Effects of triclosan on growth, viability and fatty acid synthesis of the oyster protozoan parasite Perkinsus marinus Eric D. Lund1, Philippe Soudant2, Fu-Lin E. Chu1,*, Ellen Harvey1, Stephanie Bolton3, Adolph Flowers4 1Virginia Institute of Marine Science, College of William and Mary, Gloucester Point, Virginia 23062, USA 2Université de Bretagne Occidentale, Institut Universitaire Européen de la Mer LEMAR–Laboratoire des Sciences de l’Environnement Marin (UMR 6539), Technopole Brest Iroise, Place Nicolas Copernic, 29280 Plouzané, France 3Wake Forest University, 1834 Wake Forest Road, Winston-Salem, North Carolina 27106, USA 4Morehouse College, 830 Westview Drive SW, Atlanta, Georgia 30314, USA ABSTRACT: Perkinsus marinus, a protozoan parasite of the Eastern oyster Crassostrea virginica, has severely impacted oyster populations from the Mid-Atlantic region to the Gulf of Mexico coast of North America for more than 30 yr. Although a chemotherapeutic treatment to reduce or eliminate P. marinus from infected oysters would be useful for research and hatchery operations, an effective and practical drug treatment does not currently exist. In this study, the antimicrobial drug triclosan 5-chloro-2-(2,4 dichlorophenoxy) phenol, a specific inhibitor of Fab1 (enoyl-acyl-carrier-protein reductase), an enzyme in the Type II class of fatty acid synthetases, was tested for its effects on via- bility, proliferation and fatty acid synthesis of in vitro-cultured P. marinus meronts. Treatment of P. marinus meront cell cultures with concentrations of ≥2 µM triclosan at 28°C (a temperature favorable for parasite proliferation) for up to 6 d stopped proliferation of the parasite.