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Chapter Five CHAPTER FIVE The Ectocarpus Genome and Brown Algal Genomics The Ectocarpus Genome Consortium J. Mark Cock*,y,1, Lieven Sterckz,x, Sophia Ahmed*,y, Andrew E. Allen{, Grigoris Amoutziasz,x,2, Veronique Anthouardk, François Artiguenavek, Alok Arun*,y, Jean-Marc Auryk, Jonathan H. Badger{, Bank Beszteri#,3, Kenny Billiauz,x, Eric Bonnetz,x,4, John H. Bothwell**,yy,zz, Chris Bowlerxx,{{, Catherine Boyen*,y, Colin Brownleezz, Carl J. Carranokk, Bénédicte Charrier*,y, Ga Youn Cho*,y, Susana M. Coelho*,y, Jonas Collén*,y, Gildas Le Corguillé##, Erwan Corre##, Laurence Dartevelle*,y, Corinne Da Silvak, Ludovic Delage*,y, Nicolas Delaroque***, Simon M. Dittami*,y, Sylvie Doulbeauyyy, Marek Eliaszzz, Garry Farnhamzz, Claire M.M. Gachonxxx, Olivier Godfroy*,y, Bernhard Gschloessl*,y, Svenja Heesch*,y, Kamel Jabbarik, Claire Jubink, Hiroshi Kawai{{{, Kei Kimurakkk, Bernard Kloareg*,y, Frithjof C. Kupper€ xxx,5, Daniel Lang###, Aude Le Bail*,y, Rémy Luthringer*,y, Catherine Leblanc*,y, Patrice Lerouge****, Martin Lohryyyy, Pascal J. Lopezxx,6, Nicolas Macaisne*,y, Cindy Martensz,x, Florian Maumusxx, Gurvan Michel*,y, Diego Miranda-Saavedrazzzz, Julia Moralesxxxx,{{{{, Hervé Moreaukkkk, Taizo Motomurakkk, Chikako Nagasatokkk, Carolyn A. Napoli####, David R. Nelson*****, Pi Nyvall-Collén*,y, Akira F. Peters*,y,7, Cyril Pommieryyyyy, Philippe Potin*,y, Julie Poulaink, Hadi Quesnevilleyyyyy, Betsy Readzzzzz, Stefan A. Rensing###, Andrés Ritter*,y,xxxxx, Sylvie Rousvoal*,y, Manoj Samanta{{{{{, Gaelle Samsonk, Declan C. Schroederzz, Delphine Scornet*,y, Béatrice Ségurensk, Martina Strittmatterxxx, Thierry Tonon*,y, James W. Tregearyyy, Klaus Valentin#, Peter Von Dassowkkkkk, Takahiro Yamagishi{{{, Pierre Rouzéz,x, Yves Van de Peerz,x, Patrick Winckerk *UPMC Université Paris 6, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France Ó Advances in Botanical Research, Volume 64 2012 Elsevier Ltd. 141j ISSN 0065-2296, All rights reserved. http://dx.doi.org/10.1016/B978-0-12-391499-6.00005-0 142 J. Mark Cock et al. y CNRS, UMR 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France z Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium x Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium { J. Craig Venter Institute, San Diego, California 92121, USA k CEA, DSV, Institut de Génomique, Génoscope, 2 rue Gaston Crémieux, CP5706, 91057 Evry, France #Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany **School of Biological Sciences, Queen’s University Belfast, Belfast BT9 7BL, United Kingdom yy Queen’s University Marine Laboratory, Portaferry, Co. Down BT22 1PF, United Kingdom zz Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth PL1 2PB, United Kingdom xx Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique UMR8197, Ecole Normale Supérieure, 75005 Paris, France {{ Stazione Zoologica, Villa Comunale, I 80121 Naples, Italy kk San Diego State University, San Diego, California 92182-1030, USA ##Computer and Genomics Resource Centre, FR 2424, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France ***Fraunhofer Institute for Cell Therapy and Immunology IZI, Perlickstrasse 1, 04103 Leipzig, Germany yyy IRD, IRD/CIRAD Palm Developmental Biology Group, UMR 1097 DIAPC, 34394 Montpellier, France zzz Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic xxx Scottish Association for Marine Science, Culture Collection for Algae and Protozoa, Scottish Marine Institute, Oban PA37 1QA, United Kingdom {{{ Kobe University Research Center for Inland Seas, 1-1, Rokkodai, Nadaku, Kobe 657-8501, Japan kkk Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran 051-0003, Hokkaido, Japan ###Faculty of Biology, University of Freiburg, Hauptstr. 1, 79104 Freiburg, Germany ****Laboratoire Glyco-MEV EA 4358, IFRMP 23, Université de Rouen, 76821 Mont-Saint-Aignan, France yyyy Institut fur€ Allgemeine Botanik, Johannes Gutenberg-Universit€at Mainz, 55099 Mainz, Germany zzzz World Premier International (WPI) Immunology Frontier Research Center (IFReC), Osaka University, 3-1 Yamadaoka, Suita, 565-0871 Osaka, Japan xxxx UPMC Université Paris 6, UMR 7150 Mer & Santé, Equipe Traduction Cycle Cellulaire et Développement, Station Biologique de Roscoff, 29680 Roscoff, France {{{{ CNRS, UMR 7150 Mer & Santé, Station Biologique de Roscoff, 29680 Roscoff, France kkkk Laboratoire ARAGO, BP44, 66651 Banyuls-sur-mer, France ####Bio5 Institute and Department of Plant Sciences, University of Arizona, Tucson, Arizona 85719, USA *****Department of Molecular Sciences, University of Tennessee Health Science Center, Suite G01, Memphis, Tennessee 38163, USA yyyyy Unité de Recherches en Génomique-Info (UR INRA 1164), INRA, Centre de recherche de Versailles, bat.18, RD10, Route de Saint Cyr, 78026 Versailles Cedex, France zzzzz Biological Sciences, California State University, San Marcos, California 92096-0001, USA xxxxx Departamento de Ecología, Center for Advanced Studies in Ecology & Biodiversity, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Santiago, Chile {{{{{ Systemix Institute, Redmond, Washington 98053, USA kkkkk CNRS, UMR 7144, Evolution du Plancton et PaleOceans, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France 1Corresponding author: Email: [email protected] 2Department of Biochemistry and Biotechnology, University of Thessaly, Larisa, 41221, Greece. 3Present addresses: Department of Microbiology, Oregon State University, Corvallis, Oregon 97331, USA. 4Present addresses: Institut Curie, 26 rue d'Ulm, Paris, F-75248 France; INSERM, U900, Paris, F-75248 France; and Mines ParisTech, Fontainebleau, F-77300 France. 5Present addresses: Oceanlab, University of Aberdeen, Main Street, Newburgh AB41 6 AA, Scotland, UK. 6Present addresses: CNRS UMR 7208 BOREA, Muséum National d’Histoire Naturelle, 75005, Paris. 7Present addresses: Bezhin Rosko, 40 Rue des pêcheurs, 29250 Santec, France. Contents 1. Introduction 143 1.1. The Brown Algae 143 1.2. Ectocarpus, a Model Organism For The Brown Algae 144 1.3. The Ectocarpus Genome Project 146 The Ectocarpus Genome and Brown Algal Genomics 143 2. Structure of the Ectocarpus Genome 146 2.1. Large-scale Structure 146 2.2. Gene Structure and Gene Organization 147 2.3. Non-coding RNAs 149 2.4. Repeated Sequences 150 2.5. An Integrated Viral Genome 156 3. Evolutionary History of the Ectocarpus Genome 158 3.1. Evolution of Genome Gene Content 158 3.2. Endosymbiosis and Organellar Genomes 159 4. Insights into Brown Algal Metabolism 161 4.1. Photosynthesis and Photosynthetic Pigments 161 4.2. Carbon Metabolism 163 4.3. Nitrogen Metabolism 164 4.4. Halogen Metabolism 164 4.5. Uptake and Storage of Iron 165 4.6. Lipid Metabolism 166 4.7. Secondary Metabolism 167 5. Cellular Processes 168 5.1. Receptors, Ion Channels and Signal Transduction Pathways 168 5.2. Cell Cycle, Endoreduplication and Meiosis 171 5.3. Cytoskeleton, Flagella and Vesicle Trafficking 172 6. Future Directions 174 Acknowledgements 176 References 176 Abstract Brown algae are important organisms both because of their key ecological roles in coastal ecosystems and because of the remarkable biological features that they have acquired during their unusual evolutionary history. The recent sequencing of the complete genome of the filamentous brown alga Ectocarpus has provided unprece- dented access to the molecular processes that underlie brown algal biology. Analysis of the genome sequence, which exhibits several unusual structural features, identified genes that are predicted to play key roles in several aspects of brown algal metabolism, in the construction of the multicellular bodyplan and in resistance to biotic and abiotic stresses. Information from the genome sequence is currently being used in combi- nation with other genomic, genetic and biochemical tools to further investigate these and other aspects of brown algal biology at the molecular level. Here, we review some of the major discoveries that emerged from the analysis of the Ectocarpus genome sequence, with a particular focus on the unusual genome structure, inferences about brown algal evolution and novel aspects of brown algal metabolism. 1. INTRODUCTION 1.1. The Brown Algae Brown algae (or Phaeophyceae) are a group of multicellular algae that belong to the stramenopile lineage (also known as heterokonts). They occur 144 J. Mark Cock et al. almost exclusively in marine environments, particularly rocky coastlines in temperate regions of the globe. Brown algae are often the main primary producers of such ecosystems and therefore play an important ecological role, creating habitats for a broad range of other marine organisms. As a consequence, there has been considerable interest in understanding the biology and ecology of the brown algae. These organisms have also attracted interest for a number of other reasons. The stramenopiles are very distantly related to well-studied groups such as the opisthokonts (animals and fungi) and the green lineage (which includes land plants); the common ancestor of these major lineages dating back to the crown
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