Impact of Sulfur Starvation in Autotrophic and Heterotrophic
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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). -
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, -
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. -
Systema Naturae. the Classification of Living Organisms
Systema Naturae. The classification of living organisms. c Alexey B. Shipunov v. 5.601 (June 26, 2007) Preface Most of researches agree that kingdom-level classification of living things needs the special rules and principles. Two approaches are possible: (a) tree- based, Hennigian approach will look for main dichotomies inside so-called “Tree of Life”; and (b) space-based, Linnaean approach will look for the key differences inside “Natural System” multidimensional “cloud”. Despite of clear advantages of tree-like approach (easy to develop rules and algorithms; trees are self-explaining), in many cases the space-based approach is still prefer- able, because it let us to summarize any kinds of taxonomically related da- ta and to compare different classifications quite easily. This approach also lead us to four-kingdom classification, but with different groups: Monera, Protista, Vegetabilia and Animalia, which represent different steps of in- creased complexity of living things, from simple prokaryotic cell to compound Nature Precedings : doi:10.1038/npre.2007.241.2 Posted 16 Aug 2007 eukaryotic cell and further to tissue/organ cell systems. The classification Only recent taxa. Viruses are not included. Abbreviations: incertae sedis (i.s.); pro parte (p.p.); sensu lato (s.l.); sedis mutabilis (sed.m.); sedis possi- bilis (sed.poss.); sensu stricto (s.str.); status mutabilis (stat.m.); quotes for “environmental” groups; asterisk for paraphyletic* taxa. 1 Regnum Monera Superphylum Archebacteria Phylum 1. Archebacteria Classis 1(1). Euryarcheota 1 2(2). Nanoarchaeota 3(3). Crenarchaeota 2 Superphylum Bacteria 3 Phylum 2. Firmicutes 4 Classis 1(4). Thermotogae sed.m. 2(5). -
DNA Contents of Cell Nuclei in Two Cyanidiophyceae: Cyanidioschyzon Merolae and Cyanidium Caldarium Forma A
_??_1995 The Japan Mendel Society Cytologia 60: 183-188, 1995 DNA Contents of Cell Nuclei in Two Cyanidiophyceae: Cyanidioschyzon merolae and Cyanidium caldarium Forma A Kyoko Toda, Hidenori Takahashi, Ryuuichi Itoh and Tsuneyoshi Kuroiwa Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Tokyo 113, Japan Accepted May 18, 1995 DNA contents of cell nuclei in the unicellular red algae Cyanidioschyzon merolae and Cyanidium caldarium Forma A were estimated to be approximately 8 Mbp and 18 Mbp, respectively, using video-intensified microscope photon-counting system (VIMPCS) after stain ing with 4•Œ-6-diamidino-2-phenylindole (DAPI) (Suzuki et al. 1992). In contrast, Malezka (1993) and Takahashi et al. (1993) estimated that cell nuclei in C. merolae contain approxi mately 11.7 Mbp and 12.2 Mbp, respectively, using pulsed-field gel electrophoresis (PFGE). This discrepancy appears to be due to the low AT contents in C. merolae and C. caldarium Forma A (Suzuki et al. 1992) and preferential binding by DAPI to AT-rich DNA (Kapuscinski and Szer 1979). In this study, we again measured DNA contents of cell nuclei in the two algae using VIMPCS after staining with DAPI, Schiff's reagent and propidium iodide (PI). Schiff's reagent binds to purine residues (Lesser 1953) and the stainability of PI is affected by DNA topology (Prosperi et al. 1994). The DNA contents of cell nuclei in C. merolae and C. caldarium Forma A were calculated based on the GC content of these algal DNAs (Suzuki et al. 1992), and on the values obtained by VIMPCS following DAPI, Feulgen and PI staining. -
Biodata of Hwan Su Yoon, Author (With Co-Author Giuseppe C
Biodata of Hwan Su Yoon, author (with co-author Giuseppe C. Zuccarello and Debashish Bhattacharya) of “Evolutionary History and Taxonomy of Red Algae” Dr. Hwan Su Yoon is currently a Senior Research Scientist at the Bigelow Laboratory for Ocean Sciences. He obtained his Ph.D. from Chungnam National University, Korea, in 1999 under the supervision of Prof. Sung Min Boo, and thereafter joined the lab of Debashish Bhattacharya at the University of Iowa. His research interests are in the areas of plastid evolution of chromalveolates, genome evolution of Paulinella, and taxonomy and phylogeny of red algae. E-mail: [email protected] Dr. Giuseppe C. Zuccarello is currently a Senior Lecturer at Victoria University of Wellington. He obtained his Ph.D. from the University of California, Berkeley, in 1993 under the supervision of Prof. John West. His research interests are in the area of algal evolution and speciation. E-mail: [email protected] Hwan Su Yoon Giuseppe C. Zuccarello 25 J. Seckbach and D.J. Chapman (eds.), Red Algae in the Genomic Age, Cellular Origin, Life in Extreme Habitats and Astrobiology 13, 25–42 DOI 10.1007/978-90-481-3795-4_2, © Springer Science+Business Media B.V. 2010 26 Hwan SU YOON ET AL. Dr. Debashish Bhattacharya is currently a Professor at Rutgers University in the Department of Ecology, Evolution and Natural Resources. He obtained his Ph.D. from Simon Fraser University, Burnaby, Canada, in 1989 under the supervision of Prof. Louis Druehl. The Bhattacharya lab has broad interests in algal evolution, endosymbiosis, comparative and functional genomics, and microbial diversity. -
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.