Comparative Genomics of Endosymbiotically-Derived Organelles in Cryptophyte Algae
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Sex Is a Ubiquitous, Ancient, and Inherent Attribute of Eukaryotic Life
PAPER Sex is a ubiquitous, ancient, and inherent attribute of COLLOQUIUM eukaryotic life Dave Speijera,1, Julius Lukešb,c, and Marek Eliášd,1 aDepartment of Medical Biochemistry, Academic Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands; bInstitute of Parasitology, Biology Centre, Czech Academy of Sciences, and Faculty of Sciences, University of South Bohemia, 370 05 Ceské Budejovice, Czech Republic; cCanadian Institute for Advanced Research, Toronto, ON, Canada M5G 1Z8; and dDepartment of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic Edited by John C. Avise, University of California, Irvine, CA, and approved April 8, 2015 (received for review February 14, 2015) Sexual reproduction and clonality in eukaryotes are mostly Sex in Eukaryotic Microorganisms: More Voyeurs Needed seen as exclusive, the latter being rather exceptional. This view Whereas absence of sex is considered as something scandalous for might be biased by focusing almost exclusively on metazoans. a zoologist, scientists studying protists, which represent the ma- We analyze and discuss reproduction in the context of extant jority of extant eukaryotic diversity (2), are much more ready to eukaryotic diversity, paying special attention to protists. We accept that a particular eukaryotic group has not shown any evi- present results of phylogenetically extended searches for ho- dence of sexual processes. Although sex is very well documented mologs of two proteins functioning in cell and nuclear fusion, in many protist groups, and members of some taxa, such as ciliates respectively (HAP2 and GEX1), providing indirect evidence for (Alveolata), diatoms (Stramenopiles), or green algae (Chlor- these processes in several eukaryotic lineages where sex has oplastida), even serve as models to study various aspects of sex- – not been observed yet. -
A Resurgence in Field Research Is Essential to Better Understand
Received Date : 15-Mar-2013 Revised Date : 21-Oct-2013 Accepted Date : 29-Oct-2013 Article type : Symposium Article Heger et al. --- Importance of Field Protistology A Resurgence in Field Research is Essential to Better Understand the Diversity, Ecology, and Evolution of Microbial Eukaryotes Thierry J. Hegera, Virginia P. Edgcombb, Eunsoo Kimc, Julius Lukešd, Brian S. Leandera & Naoji Yubukia a The Departments of Botany and Zoology, Beaty Biodiversity Research Centre and Museum, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada b Woods Hole Oceanographic Institution, Geology and Geophysics Department, Woods Hole, Article MA 02543, USA c Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA d Institute of Parasitology, Biology Centre, Czech Academy of Sciences, and Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic Correspondence T. J. Heger and N. Yubuki, The Departments of Botany and Zoology, Beaty Biodiversity Research Centre and Museum, University of British Columbia, 6270 University Blvd., Vancouver, British Columbia, V6T 1Z4, Canada Telephone number: +1 604 822 4892; FAX number: +1 604 822 6089; emails: [email protected] and [email protected] ABSTRACT The discovery and characterization of protist communities from diverse environments are crucial for understanding the overall evolutionary history of life on earth. However, major questions about the diversity, ecology, and evolutionary history of protists remain unanswered, -
Table of Contents
PLASTID-TARGETED PROTEINS ARE ABSENT FROM THE PROTEOMES OF ACHLYA HYPOGYNA AND THRAUSTOTHECA CLAVATA (OOMYCOTA, STRAMENOPILA): IMPLICATIONS FOR THE ORIGIN OF CHROMALVEOLATE PLASTIDS AND THE ‘GREEN GENE’ HYPOTHESIS Lindsay Rukenbrod A Thesis Submitted to the University of North Carolina Wilmington in Partial Fulfillment of the Requirements for the Degree of Master of Science Center for Marine Science University of North Carolina Wilmington 2012 Approved by Advisory Committee D. Wilson Freshwater Jeremy Morgan Allison Taylor J. Craig Bailey Chair Accepted by Dean, Graduate School This thesis has been prepared in the style and format consistent with the Journal of Eukaryotic Microbiology. ii TABLE OF CONTENTS ABSTRACT .....................................................................................................................iv ACKNOWLEDGMENTS ..................................................................................................vi DEDICATION ................................................................................................................. vii LIST OF TABLES .......................................................................................................... viii LIST OF FIGURES ..........................................................................................................ix CHAPTER 1: Implications for the origin of chromalveolate plastids ............................... X INTRODUCTION .................................................................................................. 1 METHODS........................................................................................................... -
Diversity and Evolution of Protist Mitochondria: Introns, Gene Content and Genome Architecture
Diversity and Evolution of Protist Mitochondria: Introns, Gene Content and Genome Architecture 著者 西村 祐貴 内容記述 この博士論文は内容の要約のみの公開(または一部 非公開)になっています year 2016 その他のタイトル プロティストミトコンドリアの多様性と進化:イン トロン、遺伝子組成、ゲノム構造 学位授与大学 筑波大学 (University of Tsukuba) 学位授与年度 2015 報告番号 12102甲第7737号 URL http://hdl.handle.net/2241/00144261 Diversity and Evolution of Protist Mitochondria: Introns, Gene Content and Genome Architecture A Dissertation Submitted to the Graduate School of Life and Environmental Sciences, the University of Tsukuba in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Science (Doctral Program in Biologial Sciences) Yuki NISHIMURA Table of Contents Abstract ........................................................................................................................... 1 Genes encoded in mitochondrial genomes of eukaryotes ..................................................... 3 Terminology .......................................................................................................................... 4 Chapter 1. General introduction ................................................................................ 5 The origin and evolution of mitochondria ............................................................................ 5 Mobile introns in mitochondrial genome .............................................................................. 6 The organisms which are lacking in mitochondrial genome data ........................................ 8 Chapter 2. Lateral transfers of mobile introns -
PDF Proof: Mol. Biol. Evol. 14 15 16 17 18 19 20 21 22 23 24 25 26 27 FIG
Page 1 of 61 Molecular Biology and Evolution 1 2 3 Submission intended as an Article for the section Resources of MBE 4 5 6 PhyloToL: A taxon/gene rich phylogenomic pipeline to explore genome evolution of 7 8 diverse eukaryotes 9 10 11 Cerón-Romero M. A a,b, Maurer-Alcalá, X. X. a,b,d, Grattepanche, J-D. a, e, Yan, Y. a, Fonseca, M. 12 c a,b. 13 M. , Katz, L. PDFA Proof: Mol. Biol. Evol. 14 15 16 a Department of Biological Sciences, Smith College, Northampton, Massachusetts, USA. 17 b Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, 18 19 Amherst, Massachusetts, USA. 20 c 21 CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of 22 Porto, Porto, Portugal. 23 24 d Current address: Institute of Cell Biology, University of Bern, Bern, Switzerland. 25 e Current address: Biology Department, Temple University, Philadelphia, Pennsylvania, USA. 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 ScholarOne, 375 Greenbrier Drive, Charlottesville, VA, 22901 Support: (434) 964-4100 Molecular Biology and Evolution Page 2 of 61 1 2 3 ABSTRACT 4 5 Estimating multiple sequence alignments (MSAs) and inferring phylogenies are essential for 6 many aspects of comparative biology. Yet, many bioinformatics tools for such analyses have 7 8 focused on specific clades, with greatest attention paid to plants, animals and fungi. The rapid 9 10 increase of high-throughput sequencing (HTS) data from diverse lineages now provides 11 opportunities to estimate evolutionary relationships and gene family evolution across the 12 13 eukaryotic treePDF of life. -
Introns, Gene Content and Genome Architecture
Diversity and Evolution of Protist Mitochondria: Introns, Gene Content and Genome Architecture A Dissertation Submitted to the Graduate School of Life and Environmental Sciences, the University of Tsukuba in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Science (Doctral Program in Biologial Sciences) Yuki NISHIMURA Table of Contents Abstract ........................................................................................................................... 1 Genes encoded in mitochondrial genomes of eukaryotes ..................................................... 3 Terminology .......................................................................................................................... 4 Chapter 1. General introduction ................................................................................ 5 The origin and evolution of mitochondria ............................................................................ 5 Mobile introns in mitochondrial genome .............................................................................. 6 The organisms which are lacking in mitochondrial genome data ........................................ 8 Chapter 2. Lateral transfers of mobile introns among distantly related mitochondrial genomes ................................................................................................ 11 Summary ................................................................................................................................ 11 2-1. Leucocryptos -
Bangor University DOCTOR of PHILOSOPHY
Bangor University DOCTOR OF PHILOSOPHY Studies on micro algal fine-structure, taxonomy and systematics : cryptophyceae and bacillariophyceae. Novarino, Gianfranco Award date: 1990 Link to publication General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Download date: 02. Oct. 2021 Studies on microalgal fine-structure, taxonomy, and systematics: Cryptopbyceae and Bacillariopbyceae In Two Volumes Volume I (Text) ,, ý,ý *-ýýI Twl by Gianfranco Novarino, Dottore in Scienze Biologiche (Rom) A Thesis submitted to the University of Wales in candidature for the degree of Philosophiae Doctor University of Wales (Bangor) School of Ocean Sciences Marine Science Laboratories Menai Bridge, Isle of Anglesey, United Kingdom December 1990 Lýýic. JýýVt. BEST COPY AVAILABLE Acknowledge mehts Dr I. A. N. Lucas, who supervised this work, kindly provided his helpful guidance, sharing his knowledge and expertise with patience and concern, critically reading the manuscripts of papers on the Cryptophyceae, and supplying many starter cultures of the strains studied here. -
Nanoplankton Protists from the Western Mediterranean Sea. II. Cryptomonads (Cryptophyceae = Cryptomonadea)*
sm69n1047 4/3/05 20:30 Página 47 SCI. MAR., 69 (1): 47-74 SCIENTIA MARINA 2005 Nanoplankton protists from the western Mediterranean Sea. II. Cryptomonads (Cryptophyceae = Cryptomonadea)* GIANFRANCO NOVARINO Department of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, U.K. E-mail: [email protected] SUMMARY: This paper is an electron microscopical account of cryptomonad flagellates (Cryptophyceae = Cryptomon- adea) in the plankton of the western Mediterranean Sea. Bottle samples collected during the spring-summer of 1998 in the Sea of Alboran and Barcelona coastal waters contained a total of eleven photosynthetic species: Chroomonas (sensu aucto- rum) sp., Cryptochloris sp., 3 species of Hemiselmis, 3 species of Plagioselmis including Plagioselmis nordica stat. nov/sp. nov., Rhinomonas reticulata (Lucas) Novarino, Teleaulax acuta (Butcher) Hill, and Teleaulax amphioxeia (Conrad) Hill. Identification was based largely on cell surface features, as revealed by scanning electron microscopy (SEM). Cells were either dispersed in the water-column or associated with suspended particulate matter (SPM). Plagioselmis prolonga was the most common species both in the water-column and in association with SPM, suggesting that it might be a key primary pro- ducer of carbon. Taxonomic keys are given based on SEM. Key words: Cryptomonadea, cryptomonads, Cryptophyceae, flagellates, nanoplankton, taxonomy, ultrastructure. RESUMEN: PROTISTAS NANOPLANCTÓNICOS DEL MAR MEDITERRANEO NOROCCIDENTAL II. CRYPTOMONADALES (CRYPTOPHY- CEAE = CRYPTOMONADEA). – Este estudio describe a los flagelados cryptomonadales (Cryptophyceae = Cryptomonadea) planctónicos del Mar Mediterraneo Noroccidental mediante microscopia electrónica. La muestras recogidas en botellas durante la primavera-verano de 1998 en el Mar de Alboran y en aguas costeras de Barcelona, contenian un total de 11 espe- cies fotosintéticas: Chroomonas (sensu auctorum) sp., Cryptochloris sp., 3 especies de Hemiselmis, 3 especies de Plagio- selmis incluyendo Plagioselmis nordica stat. -
Nuclear Genome Sequence of the Plastid-Lacking
Cenci et al. BMC Biology (2018) 16:137 https://doi.org/10.1186/s12915-018-0593-5 RESEARCH ARTICLE Open Access Nuclear genome sequence of the plastid- lacking cryptomonad Goniomonas avonlea provides insights into the evolution of secondary plastids Ugo Cenci1,2†, Shannon J. Sibbald1,2†, Bruce A. Curtis1,2, Ryoma Kamikawa3, Laura Eme1,2,11, Daniel Moog1,2,12, Bernard Henrissat4,5,6, Eric Maréchal7, Malika Chabi8, Christophe Djemiel8, Andrew J. Roger1,2,9, Eunsoo Kim10 and John M. Archibald1,2,9* Abstract Background: The evolution of photosynthesis has been a major driver in eukaryotic diversification. Eukaryotes have acquired plastids (chloroplasts) either directly via the engulfment and integration of a photosynthetic cyanobacterium (primary endosymbiosis) or indirectly by engulfing a photosynthetic eukaryote (secondary or tertiary endosymbiosis). The timing and frequency of secondary endosymbiosis during eukaryotic evolution is currently unclear but may be resolved in part by studying cryptomonads, a group of single-celled eukaryotes comprised of both photosynthetic and non-photosynthetic species. While cryptomonads such as Guillardia theta harbor a red algal-derived plastid of secondary endosymbiotic origin, members of the sister group Goniomonadea lack plastids. Here, we present the genome of Goniomonas avonlea—the first for any goniomonad—to address whether Goniomonadea are ancestrally non-photosynthetic or whether they lost a plastid secondarily. Results: We sequenced the nuclear and mitochondrial genomes of Goniomonas avonlea and carried out a comparative analysis of Go. avonlea, Gu. theta, and other cryptomonads. The Go. avonlea genome assembly is ~ 92 Mbp in size, with 33,470 predicted protein-coding genes. Interestingly, some metabolic pathways (e.g., fatty acid biosynthesis) predicted to occur in the plastid and periplastidal compartment of Gu. -
EEF2 Analysis Challenges the Monophyly of Archaeplastida and Chromalveolata
EEF2 Analysis Challenges the Monophyly of Archaeplastida and Chromalveolata Eunsoo Kim¤*, Linda E. Graham Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, United States of America Abstract Background: Classification of eukaryotes provides a fundamental phylogenetic framework for ecological, medical, and industrial research. In recent years eukaryotes have been classified into six major supergroups: Amoebozoa, Archaeplastida, Chromalveolata, Excavata, Opisthokonta, and Rhizaria. According to this supergroup classification, Archaeplastida and Chromalveolata each arose from a single plastid-generating endosymbiotic event involving a cyanobacterium (Archaeplastida) or red alga (Chromalveolata). Although the plastids within members of the Archaeplastida and Chromalveolata share some features, no nucleocytoplasmic synapomorphies supporting these supergroups are currently known. Methodology/Principal Findings: This study was designed to test the validity of the Archaeplastida and Chromalveolata through the analysis of nucleus-encoded eukaryotic translation elongation factor 2 (EEF2) and cytosolic heat-shock protein of 70 kDa (HSP70) sequences generated from the glaucophyte Cyanophora paradoxa, the cryptophytes Goniomonas truncata and Guillardia theta, the katablepharid Leucocryptos marina, the rhizarian Thaumatomonas sp. and the green alga Mesostigma viride. The HSP70 phylogeny was largely unresolved except for certain well-established groups. In contrast, EEF2 phylogeny recovered many well-established eukaryotic groups -
Freshwater Algae in Britain and Ireland - Bibliography
Freshwater algae in Britain and Ireland - Bibliography Floras, monographs, articles with records and environmental information, together with papers dealing with taxonomic/nomenclatural changes since 2003 (previous update of ‘Coded List’) as well as those helpful for identification purposes. Theses are listed only where available online and include unpublished information. Useful websites are listed at the end of the bibliography. Further links to relevant information (catalogues, websites, photocatalogues) can be found on the site managed by the British Phycological Society (http://www.brphycsoc.org/links.lasso). Abbas A, Godward MBE (1964) Cytology in relation to taxonomy in Chaetophorales. Journal of the Linnean Society, Botany 58: 499–597. Abbott J, Emsley F, Hick T, Stubbins J, Turner WB, West W (1886) Contributions to a fauna and flora of West Yorkshire: algae (exclusive of Diatomaceae). Transactions of the Leeds Naturalists' Club and Scientific Association 1: 69–78, pl.1. Acton E (1909) Coccomyxa subellipsoidea, a new member of the Palmellaceae. Annals of Botany 23: 537–573. Acton E (1916a) On the structure and origin of Cladophora-balls. New Phytologist 15: 1–10. Acton E (1916b) On a new penetrating alga. New Phytologist 15: 97–102. Acton E (1916c) Studies on the nuclear division in desmids. 1. Hyalotheca dissiliens (Smith) Bréb. Annals of Botany 30: 379–382. Adams J (1908) A synopsis of Irish algae, freshwater and marine. Proceedings of the Royal Irish Academy 27B: 11–60. Ahmadjian V (1967) A guide to the algae occurring as lichen symbionts: isolation, culture, cultural physiology and identification. Phycologia 6: 127–166 Allanson BR (1973) The fine structure of the periphyton of Chara sp. -
Nusuttodinium Aeruginosum/Acidotum As a Case Study
Acquisition of Photoautotrophy in Kleptoplastic Dinoflagellates – Nusuttodinium aeruginosum/acidotum as a case study I n a u g u r a l – D i s s e r t a t i o n zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Universität zu Köln vorgelegt von Sebastian Wittek aus Krefeld 2018 Berichterstatter: Prof. Dr. Michael Melkonian Prof. Dr. Hartmut Arndt Prof. Dr. John M. Archibald Tag der mündlichen Prüfung: 16.01.2017 Kurzzusammenfassung in deutscher Sprache ------------------------------------------------------------------------------------------------------------------------------ Kurzzusammenfassung in deutscher Sprache Die Integrierung stabiler Plastiden durch Endosymbiosen führte zu einer enormen Vielfalt an photosynthetischen eukaryotischen Organismen auf der Erde. Allerdings sind die Schritte während der Etablierung stabiler Endosymbiosen nur schlecht verstanden. Um Licht auf diesen frühen Schritt der Evolution zu werfen, wurden viele Studien an Organismen mit vorübergehenden Plastiden durchgeführt. Ursprünglich heterotroph, sind diese Organismen in der Lage, Photoautotrophie durch die Aufnahme photosynthetischer Beute zu erwerben. Anstatt verdaut zu werden, behält die Beute ihre Fähigkeit zur Photosynthese bei und versorgt den Wirt mit Photosyntheseprodukten. Der Beuteorganismus kann entweder zu einem Endosymbiont oder sogar zu einem Plastid reduziert werden. Im letzteren Fall werden die Plastiden der photosynthetischen Beute gestohlen und daher ‚Kleptoplastiden‘ genannt. Kleptoplastiden sind innerhalb der Eukaryoten weit verbreitet und kommen in vielzelligen, wie auch in einzelligen Organismen vor. Eine der bekanntesten Gruppen, welche Kleptoplastiden beherbergt, sind die Dinoflagellaten. Diese Studie fokussiert auf Süßwasserisolate der Kleptoplastiden beherbergenden Gattung Nusuttodinium mit einem besonderen Fokus auf die Art N. aeruginosum/acidotum, welche ihre Kleptoplastiden von der blau-grünen cryptophytischen Gattung Chroomonas erlangt. Es wurden von N. aeruginosum/acidotum, sowie einer weiteren Art, N.