Chlorophyta, Ulvophyceae
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Lateral Gene Transfer of Anion-Conducting Channelrhodopsins Between Green Algae and Giant Viruses
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.15.042127; this version posted April 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 5 Lateral gene transfer of anion-conducting channelrhodopsins between green algae and giant viruses Andrey Rozenberg 1,5, Johannes Oppermann 2,5, Jonas Wietek 2,3, Rodrigo Gaston Fernandez Lahore 2, Ruth-Anne Sandaa 4, Gunnar Bratbak 4, Peter Hegemann 2,6, and Oded 10 Béjà 1,6 1Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel. 2Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, Berlin 10115, Germany. 3Present address: Department of Neurobiology, Weizmann 15 Institute of Science, Rehovot 7610001, Israel. 4Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway. 5These authors contributed equally: Andrey Rozenberg, Johannes Oppermann. 6These authors jointly supervised this work: Peter Hegemann, Oded Béjà. e-mail: [email protected] ; [email protected] 20 ABSTRACT Channelrhodopsins (ChRs) are algal light-gated ion channels widely used as optogenetic tools for manipulating neuronal activity 1,2. Four ChR families are currently known. Green algal 3–5 and cryptophyte 6 cation-conducting ChRs (CCRs), cryptophyte anion-conducting ChRs (ACRs) 7, and the MerMAID ChRs 8. Here we 25 report the discovery of a new family of phylogenetically distinct ChRs encoded by marine giant viruses and acquired from their unicellular green algal prasinophyte hosts. -
Neoproterozoic Origin and Multiple Transitions to Macroscopic Growth in Green Seaweeds
bioRxiv preprint doi: https://doi.org/10.1101/668475; this version posted June 12, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds Andrea Del Cortonaa,b,c,d,1, Christopher J. Jacksone, François Bucchinib,c, Michiel Van Belb,c, Sofie D’hondta, Pavel Škaloudf, Charles F. Delwicheg, Andrew H. Knollh, John A. Raveni,j,k, Heroen Verbruggene, Klaas Vandepoeleb,c,d,1,2, Olivier De Clercka,1,2 Frederik Leliaerta,l,1,2 aDepartment of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium bDepartment of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Zwijnaarde, Belgium cVIB Center for Plant Systems Biology, Technologiepark 71, 9052 Zwijnaarde, Belgium dBioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052 Zwijnaarde, Belgium eSchool of Biosciences, University of Melbourne, Melbourne, Victoria, Australia fDepartment of Botany, Faculty of Science, Charles University, Benátská 2, CZ-12800 Prague 2, Czech Republic gDepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA hDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138, USA. iDivision of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee, DD2 5DA, UK jSchool of Biological Sciences, University of Western Australia (M048), 35 Stirling Highway, WA 6009, Australia kClimate Change Cluster, University of Technology, Ultimo, NSW 2006, Australia lMeise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium 1To whom correspondence may be addressed. Email [email protected], [email protected], [email protected] or [email protected]. -
Microvegetation on the Top of Mt. Roraima, Venezuela
Fottea 11(1): 171–186, 2011 171 Microvegetation on the top of Mt. Roraima, Venezuela Jan KA š T O V S K Ý 1*, Karolina Fu č í k o v á 2, Tomáš HAUER 1,3 & Markéta Bo h u n i c k á 1 1Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice 37005, Czech Republic; *e–mail: [email protected] 2University of Connecticut, Department of Ecology and Evolutionary Biology, 75 North Eagleville Road, Storrs, CT 06269–3043, U.S.A. 3Institute of Botany of the Academy of Sciences, Czech Republic, Dukelská 135, Třeboň 37982, Czech Republic. Abstract: Venezuelan Table Mountains (tepuis) are among world’s most unique ecological systems and have been shown to have high incidence of endemics. The top of Roraima, the highest Venezuelan tepui, represents an isolated enclave of species without any contact with the surrounding landscape. Daily precipitation enables algae and cyanobacteria to cover the otherwise bare substrate surfaces on the summit in form of a black biofilm. In the present study, 139 samples collected over 4 years from various biotopes (vertical and horizontal moist rock walls, small rock pools, peat bogs, and small streams and waterfalls) were collected and examined for algal diversity and species composition. A very diverse algal flora was recognized in the habitats of the top of Mt. Roraima; 96 Bacillariophyceae, 44 Cyanobacteria including two species new to science, 37 Desmidiales, 5 Zygnematales, 6 Chlorophyta, 1 Klebsormidiales, 1 Rhodophyta, 1 Dinophyta, and 1 Euglenophyta were identified. Crucial part of the total biomass consisted of Cyanobacteria; other significantly represented groups were Zygnematales and Desmidiales. -
Chloroplast Phylogenomic Analysis of Chlorophyte Green Algae Identifies a Novel Lineage Sister to the Sphaeropleales (Chlorophyceae) Claude Lemieux*, Antony T
Lemieux et al. BMC Evolutionary Biology (2015) 15:264 DOI 10.1186/s12862-015-0544-5 RESEARCHARTICLE Open Access Chloroplast phylogenomic analysis of chlorophyte green algae identifies a novel lineage sister to the Sphaeropleales (Chlorophyceae) Claude Lemieux*, Antony T. Vincent, Aurélie Labarre, Christian Otis and Monique Turmel Abstract Background: The class Chlorophyceae (Chlorophyta) includes morphologically and ecologically diverse green algae. Most of the documented species belong to the clade formed by the Chlamydomonadales (also called Volvocales) and Sphaeropleales. Although studies based on the nuclear 18S rRNA gene or a few combined genes have shed light on the diversity and phylogenetic structure of the Chlamydomonadales, the positions of many of the monophyletic groups identified remain uncertain. Here, we used a chloroplast phylogenomic approach to delineate the relationships among these lineages. Results: To generate the analyzed amino acid and nucleotide data sets, we sequenced the chloroplast DNAs (cpDNAs) of 24 chlorophycean taxa; these included representatives from 16 of the 21 primary clades previously recognized in the Chlamydomonadales, two taxa from a coccoid lineage (Jenufa) that was suspected to be sister to the Golenkiniaceae, and two sphaeroplealeans. Using Bayesian and/or maximum likelihood inference methods, we analyzed an amino acid data set that was assembled from 69 cpDNA-encoded proteins of 73 core chlorophyte (including 33 chlorophyceans), as well as two nucleotide data sets that were generated from the 69 genes coding for these proteins and 29 RNA-coding genes. The protein and gene phylogenies were congruent and robustly resolved the branching order of most of the investigated lineages. Within the Chlamydomonadales, 22 taxa formed an assemblage of five major clades/lineages. -
Algologielgologie 2021 ● 42 ● 2 DIRECTEUR DE LA PUBLICATION / PUBLICATION DIRECTOR : Bruno DAVID Président Du Muséum National D’Histoire Naturelle
cryptogamie AAlgologielgologie 2021 ● 42 ● 2 DIRECTEUR DE LA PUBLICATION / PUBLICATION DIRECTOR : Bruno DAVID Président du Muséum national d’Histoire naturelle RÉDACTRICE EN CHEF / EDITOR-IN-CHIEF : Line LE GALL Muséum national d’Histoire naturelle ASSISTANTE DE RÉDACTION / ASSISTANT EDITOR : Marianne SALAÜN ([email protected]) MISE EN PAGE / PAGE LAYOUT : Marianne SALAÜN RÉDACTEURS ASSOCIÉS / ASSOCIATE EDITORS Ecoevolutionary dynamics of algae in a changing world Stacy KRUEGER-HADFIELD Department of Biology, University of Alabama, 1300 University Blvd, Birmingham, AL 35294 (United States) Jana KULICHOVA Department of Botany, Charles University, Prague (Czech Republic) Cecilia TOTTI Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona (Italy) Phylogenetic systematics, species delimitation & genetics of speciation Sylvain FAUGERON UMI3614 Evolutionary Biology and Ecology of Algae, Departamento de Ecología, Facultad de Ciencias Biologicas, Pontifi cia Universidad Catolica de Chile, Av. Bernardo O’Higgins 340, Santiago (Chile) Marie-Laure GUILLEMIN Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia (Chile) Diana SARNO Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli (Italy) Comparative evolutionary genomics of algae Nicolas BLOUIN Department of Molecular Biology, University of Wyoming, Dept. 3944, 1000 E University Ave, Laramie, WY 82071 (United States) Heroen VERBRUGGEN School of -
An Unrecognized Ancient Lineage of Green Plants Persists in Deep Marine Waters
FAU Institutional Repository http://purl.fcla.edu/fau/fauir This paper was submitted by the faculty of FAU’s Harbor Branch Oceanographic Institute. Notice: ©2010 Phycological Society of America. This manuscript is an author version with the final publication available at http://www.wiley.com/WileyCDA/ and may be cited as: Zechman, F. W., Verbruggen, H., Leliaert, F., Ashworth, M., Buchheim, M. A., Fawley, M. W., Spalding, H., Pueschel, C. M., Buchheim, J. A., Verghese, B., & Hanisak, M. D. (2010). An unrecognized ancient lineage of green plants persists in deep marine waters. Journal of Phycology, 46(6), 1288‐1295. (Suppl. material). doi:10.1111/j.1529‐8817.2010.00900.x J. Phycol. 46, 1288–1295 (2010) Ó 2010 Phycological Society of America DOI: 10.1111/j.1529-8817.2010.00900.x AN UNRECOGNIZED ANCIENT LINEAGE OF GREEN PLANTS PERSISTS IN DEEP MARINE WATERS1 Frederick W. Zechman2,3 Department of Biology, California State University Fresno, 2555 East San Ramon Ave, Fresno, California 93740, USA Heroen Verbruggen,3 Frederik Leliaert Phycology Research Group, Ghent University, Krijgslaan 281 S8, 9000 Ghent, Belgium Matt Ashworth University Station MS A6700, 311 Biological Laboratories, University of Texas at Austin, Austin, Texas 78712, USA Mark A. Buchheim Department of Biological Science, University of Tulsa, Tulsa, Oklahoma 74104, USA Marvin W. Fawley School of Mathematical and Natural Sciences, University of Arkansas at Monticello, Monticello, Arkansas 71656, USA Department of Biological Sciences, North Dakota State University, Fargo, North Dakota 58105, USA Heather Spalding Botany Department, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA Curt M. Pueschel Department of Biological Sciences, State University of New York at Binghamton, Binghamton, New York 13901, USA Julie A. -
7 Systematics of the Green Algae
7989_C007.fm Page 123 Monday, June 25, 2007 8:57 PM Systematics of the green 7 algae: conflict of classic and modern approaches Thomas Pröschold and Frederik Leliaert CONTENTS Introduction ....................................................................................................................................124 How are green algae classified? ........................................................................................125 The morphological concept ...............................................................................................125 The ultrastructural concept ................................................................................................125 The molecular concept (phylogenetic concept).................................................................131 Classic versus modern approaches: problems with identification of species and genera.....................................................................................................................134 Taxonomic revision of genera and species using polyphasic approaches....................................139 Polyphasic approaches used for characterization of the genera Oogamochlamys and Lobochlamys....................................................................................140 Delimiting phylogenetic species by a multi-gene approach in Micromonas and Halimeda .....................................................................................................................143 Conclusions ....................................................................................................................................144 -
Stream Periphyton Monitoring Manual Stream Periphyton Monitoring Manual
Stream Periphyton Monitoring Manual Stream Periphyton Monitoring Manual Prepared for The New Zealand Ministry for the Environment by Barry J. F. Biggs Cathy Kilroy NIWA, Christchurch Published by: NIWA, P.O. Box 8602, Christchurch, New Zealand (Phone: 03 348 8987 Fax: 03 348 5548) for the New Zealand Ministry for the Environment ISBN 0-478-09099-4 Stream Periphyton Monitoring Manual Biggs, B.J.F. Kilroy, C. © The Crown (acting through the Minister for the Environment), 2000. Copyright exists in this work in accordance with the Copyright Act 1994. However, the Crown authorises and grants a licence for the copying, adaptation and issuing of this work for any non-profit purpose. All applications for reproduction of this work for any other purpose should be made to the Ministry for the Environment. Stream Periphyton Monitoring Manual Contents Summary of figures ....................................................................................................................................vi Summary of tables ................................................................................................................................... viii Acknowledgements ..................................................................................................................................... x 1 Introduction ...................................................................................................................................... 1 1.1 Background ........................................................................................................................... -
Codiolophyceae, a New Class of Chlorophyta
Helgoliinder wiss. Meeresunters. 25, 1-13 (1973) Codiolophyceae, a new class of Chlorophyta P. KORNMANN BioIogische AnstaIt Helgoland (Meeresstation); Helgoland, FederalRepublic of Germany KURZFASSUNG: Codiolophyceaen, eine neue Griinalgen-Klasse. ROUND (1971) gliedert die Chlorophyta in die Klassen der Zygnemaphyceae, Oedogoniophyceae, Bryopsldophyceae und Chlorophyceae. Ihnen fiige ich als weitere Klasse die Codiolophyceae zu. Sie vereinigt Formen mit heteromorphem Generationswechsei; ihr Sporophyt ist das einzellige Codiolum-Stadium. Zu der neuen Klasse gehSren die Uiotrichales, Monostromatales, Codiolales und Acro- siphoniales. Die Morphoiogie der Gametophyten zeigt eigene kennzeichnende Merkmale; sie trennen diese Ordnungen untereinander ebenso wie yon alien anderen Griinalgengruppen. Ge- melnsames Merkmal ist nicht nut das Vorhandensein des einzelligen Sporophyten, sondern auch dessen vSllig iiberelnstimmende Entwicklung. Bisher waren die Vertreter der obigen Ord- nungen in den verschiedensten Gruppen des Systems untergebracht, wo fie als FremdkSrper empfunden werden miissen. In der Zusammenfassung zu einer Klasse stelten sie dagegen eine wohlbegriindete systematische Einheit dar. INTRODUCTION Just at the time when the article of ROUND (197t) on "The Taxonomy of the Chlorophyta. II" was published, I presented details of my previously suggested (KoI~N- MANN 1970) concept of the new class of Codiolophyceae in Hamburg. As taxonomic problems and literature have been extensively discussed by ROUND, I am restricting this contribution to my own observations from culture work and consider it as an addition to ROUND'S paper. Some years ago, I referred to the importance of the Codiolum sporophyte as a fundamental character for the classification of some groups of green algae (KORNMANN 1963, 1965a). At that time, I also tried to find morphological similarities in the gametophytic phase, supporting the union of Ulotrichaceae, Monostromataceae and Codiolaceae in the order of the Ulotrichales. -
Toward a Monograph of Non-Marine Ulvophyceae Using an Integrative Approach (Molecular Phylogeny and Systematics of Terrestrial Ulvophyceae II.)
Phytotaxa 324 (1): 001–041 ISSN 1179-3155 (print edition) http://www.mapress.com/j/pt/ PHYTOTAXA Copyright © 2017 Magnolia Press Article ISSN 1179-3163 (online edition) https://doi.org/10.11646/phytotaxa.324.1.1 Toward a monograph of non-marine Ulvophyceae using an integrative approach (Molecular phylogeny and systematics of terrestrial Ulvophyceae II.) TATYANA DARIENKO1 & THOMAS PRÖSCHOLD2 1 University of Göttingen, Experimental Phycology and Culture Collection of Algae, Nikolausberger Weg 18, D-37073 Göttingen, Ger- many, and Kholodny Institute of Botany, National Academy of Science, Tereschenkivska Str. 2, Kyiv 01601, Ukraine 2 University of Innsbruck, Research Institute for Limnology, Mondseestr. 9, A-5310 Mondsee, Austria Corresponding author: Thomas Pröschold, E-mail: [email protected] Abstract Phylogenetic analyses of SSU rDNA sequences have shown that coccoid and filamentous green algae are distributed among all classes of the Chlorophyta. One of these classes, the Ulvophyceae, mostly contains marine seaweeds and microalgae. However, new studies have shown that there are filamentous and sarcinoid freshwater and terrestrial spe- cies (including symbionts in lichens) among the Ulvophyceae, but very little is known about these species. Ultrastruc- tural studies of some of them have confirmed that the flagellar apparatus of zoospores (counterclockwise basal body orientation) is typical for the Ulvophyceae. In addition to ultrastructural features, the presence of a “Codiolum”-stage is characteristic of some members of this algal class. We studied more than 50 strains of freshwater and terrestrial ulvophycean microalgae obtained from the different public culture collection and our own isolates using an integra- tive approach. Three independent lineages of the Ulvophyceae containing terrestrial species were revealed by these methods. -
Green Algae and the Origin of Land Plants1
American Journal of Botany 91(10): 1535±1556. 2004. GREEN ALGAE AND THE ORIGIN OF LAND PLANTS1 LOUISE A. LEWIS2,4 AND RICHARD M. MCCOURT3,4 2Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269 USA; and 3Department of Botany, Academy of Natural Sciences, 1900 Benjamin Franklin Parkway, Philadelphia, Pennsylvania 19103 USA Over the past two decades, molecular phylogenetic data have allowed evaluations of hypotheses on the evolution of green algae based on vegetative morphological and ultrastructural characters. Higher taxa are now generally recognized on the basis of ultrastruc- tural characters. Molecular analyses have mostly employed primarily nuclear small subunit rDNA (18S) and plastid rbcL data, as well as data on intron gain, complete genome sequencing, and mitochondrial sequences. Molecular-based revisions of classi®cation at nearly all levels have occurred, from dismemberment of long-established genera and families into multiple classes, to the circumscription of two major lineages within the green algae. One lineage, the chlorophyte algae or Chlorophyta sensu stricto, comprises most of what are commonly called green algae and includes most members of the grade of putatively ancestral scaly ¯agellates in Prasinophyceae plus members of Ulvophyceae, Trebouxiophyceae, and Chlorophyceae. The other lineage (charophyte algae and embryophyte land plants), comprises at least ®ve monophyletic groups of green algae, plus embryophytes. A recent multigene analysis corroborates a close relationship between Mesostigma (formerly in the Prasinophyceae) and the charophyte algae, although sequence data of the Mesostigma mitochondrial genome analysis places the genus as sister to charophyte and chlorophyte algae. These studies also support Charales as sister to land plants. -
Systematics of Coccal Green Algae of the Classes Chlorophyceae and Trebouxiophyceae
School of Doctoral Studies in Biological Sciences University of South Bohemia in České Budějovice Faculty of Science SYSTEMATICS OF COCCAL GREEN ALGAE OF THE CLASSES CHLOROPHYCEAE AND TREBOUXIOPHYCEAE Ph.D. Thesis Mgr. Lenka Štenclová Supervisor: Doc. RNDr. Jan Kaštovský, Ph.D. University of South Bohemia in České Budějovice České Budějovice 2020 This thesis should be cited as: Štenclová L., 2020: Systematics of coccal green algae of the classes Chlorophyceae and Trebouxiophyceae. Ph.D. Thesis Series, No. 20. University of South Bohemia, Faculty of Science, School of Doctoral Studies in Biological Sciences, České Budějovice, Czech Republic, 239 pp. Annotation Aim of the review part is to summarize a current situation in the systematics of the green coccal algae, which were traditionally assembled in only one order: Chlorococcales. Their distribution into the lower taxonomical unites (suborders, families, subfamilies, genera) was based on the classic morphological criteria as shape of the cell and characteristics of the colony. Introduction of molecular methods caused radical changes in our insight to the system of green (not only coccal) algae and green coccal algae were redistributed in two of newly described classes: Chlorophyceae a Trebouxiophyceae. Representatives of individual morphologically delimited families, subfamilies and even genera and species were commonly split in several lineages, often in both of mentioned classes. For the practical part, was chosen two problematical groups of green coccal algae: family Oocystaceae and family Scenedesmaceae - specifically its subfamily Crucigenioideae, which were revised using polyphasic approach. Based on the molecular phylogeny, relevance of some old traditional morphological traits was reevaluated and replaced by newly defined significant characteristics.