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METABOLIC EVOLUTION in GALDIERIA SULPHURARIA By
METABOLIC EVOLUTION IN GALDIERIA SULPHURARIA By CHAD M. TERNES Bachelor of Science in Botany Oklahoma State University Stillwater, Oklahoma 2009 Submitted to the Faculty of the Graduate College of the Oklahoma State University in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY May, 2015 METABOLIC EVOLUTION IN GALDIERIA SUPHURARIA Dissertation Approved: Dr. Gerald Schoenknecht Dissertation Adviser Dr. David Meinke Dr. Andrew Doust Dr. Patricia Canaan ii Name: CHAD M. TERNES Date of Degree: MAY, 2015 Title of Study: METABOLIC EVOLUTION IN GALDIERIA SULPHURARIA Major Field: PLANT SCIENCE Abstract: The thermoacidophilic, unicellular, red alga Galdieria sulphuraria possesses characteristics, including salt and heavy metal tolerance, unsurpassed by any other alga. Like most plastid bearing eukaryotes, G. sulphuraria can grow photoautotrophically. Additionally, it can also grow solely as a heterotroph, which results in the cessation of photosynthetic pigment biosynthesis. The ability to grow heterotrophically is likely correlated with G. sulphuraria ’s broad capacity for carbon metabolism, which rivals that of fungi. Annotation of the metabolic pathways encoded by the genome of G. sulphuraria revealed several pathways that are uncharacteristic for plants and algae, even red algae. Phylogenetic analyses of the enzymes underlying the metabolic pathways suggest multiple instances of horizontal gene transfer, in addition to endosymbiotic gene transfer and conservation through ancestry. Although some metabolic pathways as a whole appear to be retained through ancestry, genes encoding individual enzymes within a pathway were substituted by genes that were acquired horizontally from other domains of life. Thus, metabolic pathways in G. sulphuraria appear to be composed of a ‘metabolic patchwork’, underscored by a mosaic of genes resulting from multiple evolutionary processes. -
A Morphological and Phylogenetic Study of the Genus Chondria (Rhodomelaceae, Rhodophyta)
Title A morphological and phylogenetic study of the genus Chondria (Rhodomelaceae, Rhodophyta) Author(s) Sutti, Suttikarn Citation 北海道大学. 博士(理学) 甲第13264号 Issue Date 2018-06-29 DOI 10.14943/doctoral.k13264 Doc URL http://hdl.handle.net/2115/71176 Type theses (doctoral) File Information Suttikarn_Sutti.pdf Instructions for use Hokkaido University Collection of Scholarly and Academic Papers : HUSCAP A morphological and phylogenetic study of the genus Chondria (Rhodomelaceae, Rhodophyta) 【紅藻ヤナギノリ属(フジマツモ科)の形態学的および系統学的研究】 Suttikarn Sutti Department of Natural History Sciences, Graduate School of Science Hokkaido University June 2018 1 CONTENTS Abstract…………………………………………………………………………………….2 Acknowledgement………………………………………………………………………….5 General Introduction………………………………………………………………………..7 Chapter 1. Morphology and molecular phylogeny of the genus Chondria based on Japanese specimens……………………………………………………………………….14 Introduction Materials and Methods Results and Discussions Chapter 2. Neochondria gen. nov., a segregate of Chondria including N. ammophila sp. nov. and N. nidifica comb. nov………………………………………………………...39 Introduction Materials and Methods Results Discussions Conclusion Chapter 3. Yanagi nori—the Japanese Chondria dasyphylla including a new species and a probable new record of Chondria from Japan………………………………………51 Introduction Materials and Methods Results Discussions Conclusion References………………………………………………………………………………...66 Tables and Figures 2 ABSTRACT The red algal tribe Chondrieae F. Schmitz & Falkenberg (Rhodomelaceae, Rhodophyta) currently -
Biodata of Juan M. Lopez-Bautista, Author of “Red Algal Genomics: a Synopsis”
Biodata of Juan M. Lopez-Bautista, author of “Red Algal Genomics: A Synopsis” Dr. Juan M. Lopez-Bautista is currently an Associate Professor in the Department of Biological Sciences of The University of Alabama, Tuscaloosa, AL, USA, and algal curator for The University of Alabama Herbarium (UNA). He received his PhD from Louisiana State University, Baton Rouge, in 2000 (under the advisory of Dr. Russell L. Chapman). He spent 3 years as a postdoctoral researcher at The University of Louisiana at Lafayette with Dr. Suzanne Fredericq. Dr. Lopez- Bautista’s research interests include algal biodiversity, molecular systematics and evolution of red seaweeds and tropical subaerial algae. E-mail: [email protected] 227 J. Seckbach and D.J. Chapman (eds.), Red Algae in the Genomic Age, Cellular Origin, Life in Extreme Habitats and Astrobiology 13, 227–240 DOI 10.1007/978-90-481-3795-4_12, © Springer Science+Business Media B.V. 2010 RED ALGAL GENOMICS: A SYNOPSIS JUAN M. LOPEZ-BAUTISTA Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, 35487, USA 1. Introduction The red algae (or Rhodophyta) are an ancient and diversified group of photo- autotrophic organisms. A 1,200-million-year-old fossil has been assigned to Bangiomorpha pubescens, a Bangia-like fossil suggesting sexual differentiation (Butterfield, 2000). Most rhodophytes inhabit marine environments (98%), but many well-known taxa are from freshwater habitats and acidic hot springs. Red algae have also been reported from tropical rainforests as members of the suba- erial community (Gurgel and Lopez-Bautista, 2007). Their sizes range from uni- cellular microscopic forms to macroalgal species that are several feet in length. -
Proposal for Practical Multi-Kingdom Classification of Eukaryotes Based on Monophyly 2 and Comparable Divergence Time Criteria
bioRxiv preprint doi: https://doi.org/10.1101/240929; this version posted December 29, 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 4.0 International license. 1 Proposal for practical multi-kingdom classification of eukaryotes based on monophyly 2 and comparable divergence time criteria 3 Leho Tedersoo 4 Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia 5 Contact: email: [email protected], tel: +372 56654986, twitter: @tedersoo 6 7 Key words: Taxonomy, Eukaryotes, subdomain, phylum, phylogenetic classification, 8 monophyletic groups, divergence time 9 Summary 10 Much of the ecological, taxonomic and biodiversity research relies on understanding of 11 phylogenetic relationships among organisms. There are multiple available classification 12 systems that all suffer from differences in naming, incompleteness, presence of multiple non- 13 monophyletic entities and poor correspondence of divergence times. These issues render 14 taxonomic comparisons across the main groups of eukaryotes and all life in general difficult 15 at best. By using the monophyly criterion, roughly comparable time of divergence and 16 information from multiple phylogenetic reconstructions, I propose an alternative 17 classification system for the domain Eukarya to improve hierarchical taxonomical 18 comparability for animals, plants, fungi and multiple protist groups. Following this rationale, 19 I propose 32 kingdoms of eukaryotes that are treated in 10 subdomains. These kingdoms are 20 further separated into 43, 115, 140 and 353 taxa at the level of subkingdom, phylum, 21 subphylum and class, respectively (http://dx.doi.org/10.15156/BIO/587483). -
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, -
Impact of Sulfur Starvation in Autotrophic and Heterotrophic
Impact of Sulfur Starvation in Autotrophic and Heterotrophic Cultures of the Extremophilic Microalga Galdieria phlegrea (Cyanidiophyceae) 1, 1 1 2 1 Regular Paper Simona Carfagna *, Claudia Bottone , Pia Rosa Cataletto , Milena Petriccione , Gabriele Pinto , Giovanna Salbitani1, Vincenza Vona1, Antonino Pollio1 and Claudia Ciniglia3 1Department of Biology, University of Naples Federico II, Via Foria 223, I-80139 Naples, Italy 2Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Unita` di ricerca per la Frutticoltura, Via Torrino 2, I-81100 Caserta, Italy cDepartment of Biological and Pharmaceutical Science and Technology, Second University of Naples, Via Vivaldi 43, I-81100 Caserta, Italy *Corresponding author: E-mail, [email protected]; Fax, +39-081-2538523. (Received October 02, 2015; Accepted June 3, 2016) Downloaded from https://academic.oup.com/pcp/article/57/9/1890/2223225 by guest on 24 September 2021 In plants and algae, sulfate assimilation and cysteine synthe- Cyanidiophyceae, one of the most ancient groups of algae, sis are regulated by sulfur (S) accessibility from the environ- which diverged from the base of Rhodophyta approximately ment. This study reports the effects of S deprivation in 1.3 billion years (Mu¨ller et al. 2001, Yoon et al. 2006). Three autotrophic and heterotrophic cultures of Galdieria phlegrea genera, Cyanidium, Cyanidioschyzon and Galdieria, are recog- (Cyanidiophyceae), a unicellular red alga isolated in the nized in the class Cyanidiophyceae, and presently five Galdieria Solfatara crater located in Campi Flegrei (Naples, Italy), species, G. sulphuraria, G. daedala, G. partita, G. maxima and where H2S is the prevalent form of gaseous S in the fumarolic G. phlegrea, have been described based on morphological char- fluids and S is widespread in the soils near the fumaroles. -
Organellar Genome Evolution in Red Algal Parasites: Differences in Adelpho- and Alloparasites
University of Rhode Island DigitalCommons@URI Open Access Dissertations 2017 Organellar Genome Evolution in Red Algal Parasites: Differences in Adelpho- and Alloparasites Eric Salomaki University of Rhode Island, [email protected] Follow this and additional works at: https://digitalcommons.uri.edu/oa_diss Recommended Citation Salomaki, Eric, "Organellar Genome Evolution in Red Algal Parasites: Differences in Adelpho- and Alloparasites" (2017). Open Access Dissertations. Paper 614. https://digitalcommons.uri.edu/oa_diss/614 This Dissertation is brought to you for free and open access by DigitalCommons@URI. It has been accepted for inclusion in Open Access Dissertations by an authorized administrator of DigitalCommons@URI. For more information, please contact [email protected]. ORGANELLAR GENOME EVOLUTION IN RED ALGAL PARASITES: DIFFERENCES IN ADELPHO- AND ALLOPARASITES BY ERIC SALOMAKI A DISSERTATION SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN BIOLOGICAL SCIENCES UNIVERSITY OF RHODE ISLAND 2017 DOCTOR OF PHILOSOPHY DISSERTATION OF ERIC SALOMAKI APPROVED: Dissertation Committee: Major Professor Christopher E. Lane Jason Kolbe Tatiana Rynearson Nasser H. Zawia DEAN OF THE GRADUATE SCHOOL UNIVERSITY OF RHODE ISLAND 2017 ABSTRACT Parasitism is a common life strategy throughout the eukaryotic tree of life. Many devastating human pathogens, including the causative agents of malaria and toxoplasmosis, have evolved from a photosynthetic ancestor. However, how an organism transitions from a photosynthetic to a parasitic life history strategy remains mostly unknown. Parasites have independently evolved dozens of times throughout the Florideophyceae (Rhodophyta), and often infect close relatives. This framework enables direct comparisons between autotrophs and parasites to investigate the early stages of parasite evolution. -
Parallel Evolution of Highly Conserved Plastid Genome Architecture in Red Seaweeds and Seed Plants
Lee et al. BMC Biology (2016) 14:75 DOI 10.1186/s12915-016-0299-5 RESEARCH ARTICLE Open Access Parallel evolution of highly conserved plastid genome architecture in red seaweeds and seed plants JunMo Lee1, Chung Hyun Cho1, Seung In Park1, Ji Won Choi1, Hyun Suk Song1, John A. West2, Debashish Bhattacharya3† and Hwan Su Yoon1*† Abstract Background: The red algae (Rhodophyta) diverged from the green algae and plants (Viridiplantae) over one billion years ago within the kingdom Archaeplastida. These photosynthetic lineages provide an ideal model to study plastid genome reduction in deep time. To this end, we assembled a large dataset of the plastid genomes that were available, including 48 from the red algae (17 complete and three partial genomes produced for this analysis) to elucidate the evolutionary history of these organelles. Results: We found extreme conservation of plastid genome architecture in the major lineages of the multicellular Florideophyceae red algae. Only three minor structural types were detected in this group, which are explained by recombination events of the duplicated rDNA operons. A similar high level of structural conservation (although with different gene content) was found in seed plants. Three major plastid genome architectures were identified in representatives of 46 orders of angiosperms and three orders of gymnosperms. Conclusions: Our results provide a comprehensive account of plastid gene loss and rearrangement events involving genome architecture within Archaeplastida and lead to one over-arching conclusion: from an ancestral pool of highly rearranged plastid genomes in red and green algae, the aquatic (Florideophyceae) and terrestrial (seed plants) multicellular lineages display high conservation in plastid genome architecture. -
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.