Classification, Naming and Evolutionary History of Glycosyltransferases from Sequenced Green and Red Algal Genomes
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University of Copenhagen
Classification, Naming and Evolutionary History of Glycosyltransferases from Sequenced Green and Red Algal Genomes Ulvskov, Peter; Paiva, Dionisio Soares; Domozych, David; Harholt, Jesper Published in: P L o S One DOI: 10.1371/journal.pone.0076511 Publication date: 2013 Document version Publisher's PDF, also known as Version of record Citation for published version (APA): Ulvskov, P., Paiva, D. S., Domozych, D., & Harholt, J. (2013). Classification, Naming and Evolutionary History of Glycosyltransferases from Sequenced Green and Red Algal Genomes. P L o S One, 8(10), [e76511.]. https://doi.org/10.1371/journal.pone.0076511 Download date: 02. okt.. 2021 Classification, Naming and Evolutionary History of Glycosyltransferases from Sequenced Green and Red Algal Genomes Peter Ulvskov1, Dionisio Soares Paiva1¤, David Domozych2, Jesper Harholt1* 1 Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark, 2 Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York, United States of America Abstract The Archaeplastida consists of three lineages, Rhodophyta, Virideplantae and Glaucophyta. The extracellular matrix of most members of the Rhodophyta and Viridiplantae consists of carbohydrate-based or a highly glycosylated protein-based cell wall while the Glaucophyte covering is poorly resolved. In order to elucidate possible evolutionary links between the three advanced lineages in Archaeplastida, a genomic analysis was initiated. Fully sequenced genomes from -
Exhaustive Reanalysis of Barcode Sequences from Public
Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution: a case study of the Sea Lettuce. Antoine Fort1, Marcus McHale1, Kevin Cascella2, Philippe Potin2, Marie-Mathilde Perrineau3, Philip Kerrison3, Elisabete da Costa4, Ricardo Calado4, Maria Domingues5, Isabel Costa Azevedo6, Isabel Sousa-Pinto6, Claire Gachon3, Adrie van der Werf7, Willem de Visser7, Johanna Beniers7, Henrice Jansen7, Michael Guiry1, and Ronan Sulpice1 1NUI Galway 2Station Biologique de Roscoff 3Scottish Association for Marine Science 4University of Aveiro 5Universidade de Aveiro 6University of Porto Interdisciplinary Centre of Marine and Environmental Research 7Wageningen University & Research November 24, 2020 Abstract Sea Lettuce (Ulva spp.; Ulvophyceae, Ulvales, Ulvaceae) is an important ecological and economical entity, with a worldwide distribution and is a well-known source of near-shore blooms blighting many coastlines. Species of Ulva are frequently misiden- tified in public repositories, including herbaria and gene banks, making species identification based on traditional barcoding hazardous. We investigated the species distribution of 295 individual distromatic foliose strains from the North East Atlantic by traditional barcoding or next generation sequencing. We found seven distinct species, and compared our results with all worldwide Ulva spp sequences present in the NCBI database for the three barcodes rbcL, tuf A and the ITS1. Our results demonstrate a large degree of species misidentification in the NCBI database. We estimate that 21% of the entries pertaining to foliose species are misannotated. In the extreme case of U. lactuca, 65% of the entries are erroneously labelled specimens of another Ulva species, typically U. fenestrata. In addition, 30% of U. -
UNDERSTANDING the GENOMIC BASIS of STRESS ADAPTATION in PICOCHLORUM GREEN ALGAE by FATIMA FOFLONKER a Dissertation Submitted To
UNDERSTANDING THE GENOMIC BASIS OF STRESS ADAPTATION IN PICOCHLORUM GREEN ALGAE By FATIMA FOFLONKER A dissertation submitted to the School of Graduate Studies Rutgers, The State University of New Jersey In partial fulfillment of the requirements For the degree of Doctor of Philosophy Graduate Program in Microbial Biology Written under the direction of Debashish Bhattacharya And approved by _________________________________________________ _________________________________________________ _________________________________________________ _________________________________________________ New Brunswick, New Jersey January 2018 ABSTRACT OF THE DISSERTATION Understanding the Genomic Basis of Stress Adaptation in Picochlorum Green Algae by FATIMA FOFLONKER Dissertation Director: Debashish Bhattacharya Gaining a better understanding of adaptive evolution has become increasingly important to predict the responses of important primary producers in the environment to climate-change driven environmental fluctuations. In my doctoral research, the genomes from four taxa of a naturally robust green algal lineage, Picochlorum (Chlorophyta, Trebouxiphycae) were sequenced to allow a comparative genomic and transcriptomic analysis. The over-arching goal of this work was to investigate environmental adaptations and the origin of haltolerance. Found in environments ranging from brackish estuaries to hypersaline terrestrial environments, this lineage is tolerant of a wide range of fluctuating salinities, light intensities, temperatures, and has a robust photosystem II. The small, reduced diploid genomes (13.4-15.1Mbp) of Picochlorum, indicative of genome specialization to extreme environments, has resulted in an interesting genomic organization, including the clustering of genes in the same biochemical pathway and coregulated genes. Coregulation of co-localized genes in “gene neighborhoods” is more prominent soon after exposure to salinity shock, suggesting a role in the rapid response to salinity stress in Picochlorum. -
Prevalent Ph Controls the Capacity of Galdieria Maxima to Use Ammonia and Nitrate As a Nitrogen Source
plants Article Prevalent pH Controls the Capacity of Galdieria maxima to Use Ammonia and Nitrate as a Nitrogen Source Manuela Iovinella 1 , Dora Allegra Carbone 2, Diana Cioppa 2, Seth J. Davis 1,3 , Michele Innangi 4 , Sabrina Esposito 4 and Claudia Ciniglia 4,* 1 Department of Biology, University of York, York YO105DD, UK; [email protected] (M.I.); [email protected] (S.J.D.) 2 Department of Biology, University of Naples Federico II, 80126 Naples, Italy; [email protected] (D.A.C.); [email protected] (D.C.) 3 Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng 475004, China 4 Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania “L. Vanvitelli”, 81100 Caserta, Italy; [email protected] (M.I.); [email protected] (S.E.) * Correspondence: [email protected] Received: 7 October 2019; Accepted: 29 January 2020; Published: 11 February 2020 Abstract: Galdieria maxima is a polyextremophilic alga capable of diverse metabolic processes. Ammonia is widely used in culture media typical of laboratory growth. Recent reports that this species can grow on wastes promote the concept that G. maxima might have biotechnological utility. Accordingly, there is a need to know the range of pH levels that can support G. maxima growth in a given nitrogen source. Here, we examined the combined effect of pH and nitrate/ammonium source on the growth and long-term response of the photochemical process to a pH gradient in different G. maxima strains. All were able to use differing nitrogen sources, despite both the growth rate and photochemical activity were significantly affected by the combination with the pH. -
Diversity and Evolution of Algae: Primary Endosymbiosis
CHAPTER TWO Diversity and Evolution of Algae: Primary Endosymbiosis Olivier De Clerck1, Kenny A. Bogaert, Frederik Leliaert Phycology Research Group, Biology Department, Ghent University, Krijgslaan 281 S8, 9000 Ghent, Belgium 1Corresponding author: E-mail: [email protected] Contents 1. Introduction 56 1.1. Early Evolution of Oxygenic Photosynthesis 56 1.2. Origin of Plastids: Primary Endosymbiosis 58 2. Red Algae 61 2.1. Red Algae Defined 61 2.2. Cyanidiophytes 63 2.3. Of Nori and Red Seaweed 64 3. Green Plants (Viridiplantae) 66 3.1. Green Plants Defined 66 3.2. Evolutionary History of Green Plants 67 3.3. Chlorophyta 68 3.4. Streptophyta and the Origin of Land Plants 72 4. Glaucophytes 74 5. Archaeplastida Genome Studies 75 Acknowledgements 76 References 76 Abstract Oxygenic photosynthesis, the chemical process whereby light energy powers the conversion of carbon dioxide into organic compounds and oxygen is released as a waste product, evolved in the anoxygenic ancestors of Cyanobacteria. Although there is still uncertainty about when precisely and how this came about, the gradual oxygenation of the Proterozoic oceans and atmosphere opened the path for aerobic organisms and ultimately eukaryotic cells to evolve. There is a general consensus that photosynthesis was acquired by eukaryotes through endosymbiosis, resulting in the enslavement of a cyanobacterium to become a plastid. Here, we give an update of the current understanding of the primary endosymbiotic event that gave rise to the Archaeplastida. In addition, we provide an overview of the diversity in the Rhodophyta, Glaucophyta and the Viridiplantae (excluding the Embryophyta) and highlight how genomic data are enabling us to understand the relationships and characteristics of algae emerging from this primary endosymbiotic event. -
Cyanidium Chilense (Cyanidiophyceae, Rhodophyta) from Tuff Rocks of the Archeological Site of Cuma, Italy
Phycological Research 2019 doi: 10.1111/pre.12383 ........................................................................................................................................................................................... Cyanidium chilense (Cyanidiophyceae, Rhodophyta) from tuff rocks of the archeological site of Cuma, Italy Claudia Ciniglia ,1* Paola Cennamo,2 Antonino De Natale,3 Mario De Stefano,1 Maria Sirakov,1 Manuela Iovinella,4 Hwan S. Yoon5 and Antonino Pollio3 1Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania “L. Vanvitelli”, Caserta, Italy, 2Department of Biology, Facolta` di Lettere, Universita` degli Studi ‘Suor Orsola Benincasa’, Naples, Italy, 3Department of Biology, University of Naples Federico II, Naples, Italy, 4Department of Biology, University of York, York, UK and 5Department of Biological Sciences, Sungkyunkwan University, Seoul, South Korea ........................................................................................ thermal (35–55C) soils, retrieved from hot springs and fuma- SUMMARY roles, worldwide (Ciniglia et al. 2014; Eren et al. 2018; Iovinella et al. 2018); C. chilense, formerly ‘cave Cyanidium’ Phlegrean Fields is a large volcanic area situated southwest of (Hoffmann 1994), is a neutrophilic (pH around 7.0) and mes- Naples (Italy), including both cave and thermoacidic habitats. ophilic (20–25C) strain isolated by several authors from These extreme environments host the genus Cyanidium; the caves, considered as extreme environments, -
Seaweeds of California Green Algae
PDF version Remove references Seaweeds of California (draft: Sun Nov 24 15:32:39 2019) This page provides current names for California seaweed species, including those whose names have changed since the publication of Marine Algae of California (Abbott & Hollenberg 1976). Both former names (1976) and current names are provided. This list is organized by group (green, brown, red algae); within each group are genera and species in alphabetical order. California seaweeds discovered or described since 1976 are indicated by an asterisk. This is a draft of an on-going project. If you have questions or comments, please contact Kathy Ann Miller, University Herbarium, University of California at Berkeley. [email protected] Green Algae Blidingia minima (Nägeli ex Kützing) Kylin Blidingia minima var. vexata (Setchell & N.L. Gardner) J.N. Norris Former name: Blidingia minima var. subsalsa (Kjellman) R.F. Scagel Current name: Blidingia subsalsa (Kjellman) R.F. Scagel et al. Kornmann, P. & Sahling, P.H. 1978. Die Blidingia-Arten von Helgoland (Ulvales, Chlorophyta). Helgoländer Wissenschaftliche Meeresuntersuchungen 31: 391-413. Scagel, R.F., Gabrielson, P.W., Garbary, D.J., Golden, L., Hawkes, M.W., Lindstrom, S.C., Oliveira, J.C. & Widdowson, T.B. 1989. A synopsis of the benthic marine algae of British Columbia, southeast Alaska, Washington and Oregon. Phycological Contributions, University of British Columbia 3: vi + 532. Bolbocoleon piliferum Pringsheim Bryopsis corticulans Setchell Bryopsis hypnoides Lamouroux Former name: Bryopsis pennatula J. Agardh Current name: Bryopsis pennata var. minor J. Agardh Silva, P.C., Basson, P.W. & Moe, R.L. 1996. Catalogue of the benthic marine algae of the Indian Ocean. -
Ulva L. (Ulvales, Chlorophyta) from Manawatāwhi/ Three Kings Islands, New Zealand: Ulva Piritoka Ngāti Kuri, Heesch & W.A.Nelson, Sp
cryptogamie Algologie 2021 ● 42 ● 9 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, Pontificia 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 BioSciences, -
Chapter 1 Introduction
University of Groningen Photopigments and functional carbohydrates from Cyanidiales Delicia Yunita Rahman, D. IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2018 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Delicia Yunita Rahman, D. (2018). Photopigments and functional carbohydrates from Cyanidiales. University of Groningen. Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license. More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne- amendment. 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. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 30-09-2021 Chapter 1 Introduction Chapter 1 Role of microalgae in the global oxygen and carbon cycles In the beginning there was nothing. -
Molecular Systematics of Red Algae: Building Future Structures on Firm Foundations
Molecular systematics of red algae: building future structures on firm foundations Christine A. Maggs, Heroen Verbruggen and Olivier de Clerck CONTENTS Introduction to the red algae (Rhodophyta)...........................................................................................104 An ancient and diverse group ......................................................................................................104 Unique combination of features..................................................................................................104 Bangiophyceae: relatively shnple morphologies......................................................................104 Diverse, complex Florideophyceae.............................................................................................105 Ordinal classification has firm foundations...............................................................................105 Florideophyceae: the enduring legacy of Schmitz and Kylin.................................... 105 Bangiophyceae: fewer, less robust orders.......................................................................105 Pit-plug ultrastructure: a crucial catalyst.......................................................................106 Molecular tools and their contribution to systematics.........................................................................106 Pioneer papers.................................................................................................................................106 Molecular phylogenetic -
Signatures of Transcription Factor Evolution and the Secondary Gain of Red Algae Complexity
G C A T T A C G G C A T genes Article Signatures of Transcription Factor Evolution and the Secondary Gain of Red Algae Complexity Romy Petroll 1 , Mona Schreiber 1,2 , Hermann Finke 1, J. Mark Cock 3 , Sven B. Gould 1,4 and Stefan A. Rensing 1,5,* 1 Plant Cell Biology, Department of Biology, University of Marburg, 35037 Marburg, Germany; [email protected] (R.P.); [email protected] (M.S.); hermann.fi[email protected] (H.F.); [email protected] (S.B.G.) 2 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany 3 Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, CNRS, UPMC University Paris 06, CS 90074, 29688 Roscoff, France; [email protected] 4 Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany 5 Centre for Biological Signaling Studies (BIOSS), University of Freiburg, 79108 Freiburg, Germany * Correspondence: [email protected] Abstract: Red algae (Rhodophyta) belong to the superphylum Archaeplastida, and are a species-rich group exhibiting diverse morphologies. Theory has it that the unicellular red algal ancestor went through a phase of genome contraction caused by adaptation to extreme environments. More re- cently, the classes Porphyridiophyceae, Bangiophyceae, and Florideophyceae experienced genome expansions, coinciding with an increase in morphological complexity. Transcription-associated proteins (TAPs) regulate transcription, show lineage-specific patterns, and are related to organis- mal complexity. To better understand red algal TAP complexity and evolution, we investigated Citation: Petroll, R.; Schreiber, M.; the TAP family complement of uni- and multi-cellular red algae. -
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Phycology International 2018; volume 1:55 Tolerance and metabolic bacteria5 or plants known for their ability to responses of Cyanidiophytina immobilize heavy metals in the cell wall and Correspondence: Claudia Ciniglia, DIS- compartmentalization in vacuoles. TABIF, “L. Vanvitelli” University of Caserta, (Rhodophyta) towards exposition Interestingly, polyextremophilic algae have Caserta, Italy. to Cl4K2Pd and AuCl4K the intrinsic properties that make them Tel.: +39.0823274582 – Fax: +39.0823274571. capable of selective removal and E-mail: [email protected] 1 1 concentration of metals, thanks to their Maria Sirakov, Elena Toscano, Key words: Metal tolerance; Red algae; Rare Manuela Iovinella,2 Seth J. Davis,2 adaptation to live in geothermal and volcanic Earth elements; Palladium; Gold. 6-8 Milena Petriccione,3 Claudia Ciniglia1 sites. Geothermal fluids leach out of the hot volcanic rocks and are enriched by 1DISTABIF, “L. Vanvitelli” University of Contributions: MS, ET: conduction of experi- enormous amounts of minerals and metals, ments, analysis of results, contribution to draft Caserta, Caserta, Italy; 2Department of including lithium, sulfur, boric acid and writings; MP: experiments on oxidative stress, Biology, University of York, York, UK; precious metals such as gold, platinum, analysis of results; MI, SJD: original concept, 3 Department of Fruit Tree Research palladium and silver.9 provision of resources; CC: original concept, Unit, Council for Agricultural Research Cyanidiophyceae, unicellular red algae, provision of resources, draft editing. and Agricultural Economy Analysis, survive in extreme conditions, very low pH Caserta, Italy Conflict of interest: the authors declare no (0.0-3.0) and high temperatures (37-55°C), potential conflict of interest. and colonize acid and hydrothermal sites, but also rocks and muddy soil around hot Received for publication: 23 December 2017.