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The Genomes of Polyextremophilic Cyanidiales Contain 1% 2 Horizontally Transferred Genes with Diverse Adaptive Functions 3 4 Alessandro W
bioRxiv preprint doi: https://doi.org/10.1101/526111; this version posted January 23, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 The genomes of polyextremophilic Cyanidiales contain 1% 2 horizontally transferred genes with diverse adaptive functions 3 4 Alessandro W. Rossoni1#, Dana C. Price2, Mark Seger3, Dagmar Lyska1, Peter Lammers3, 5 Debashish Bhattacharya4 & Andreas P.M. Weber1* 6 7 1Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich 8 Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany 9 2Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA 10 3Arizona Center for Algae Technology and Innovation, Arizona State University, Mesa, AZ 11 85212, USA 12 4Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 13 08901, USA 14 15 *Corresponding author: Prof. Dr. Andreas P.M. Weber, 16 e-mail: [email protected] 17 bioRxiv preprint doi: https://doi.org/10.1101/526111; this version posted January 23, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. 18 Abstract 19 The role and extent of horizontal gene transfer (HGT) in eukaryotes are hotly disputed topics 20 that impact our understanding regarding the origin of metabolic processes and the role of 21 organelles in cellular evolution. -
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. -
The Genome of Prasinoderma Coloniale Unveils the Existence of a Third Phylum Within Green Plants
SUPPLEMENTARY INFORMATIONARTICLES https://doi.org/10.1038/s41559-020-1221-7 In the format provided by the authors and unedited. The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants Linzhou Li1,2,13, Sibo Wang1,3,13, Hongli Wang1,4, Sunil Kumar Sahu 1, Birger Marin 5, Haoyuan Li1, Yan Xu1,4, Hongping Liang1,4, Zhen Li 6, Shifeng Cheng1, Tanja Reder5, Zehra Çebi5, Sebastian Wittek5, Morten Petersen3, Barbara Melkonian5,7, Hongli Du8, Huanming Yang1, Jian Wang1, Gane Ka-Shu Wong 1,9, Xun Xu 1,10, Xin Liu 1, Yves Van de Peer 6,11,12 ✉ , Michael Melkonian5,7 ✉ and Huan Liu 1,3 ✉ 1State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China. 2Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark. 3Department of Biology, University of Copenhagen, Copenhagen, Denmark. 4BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China. 5Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, Cologne, Germany. 6Department of Plant Biotechnology and Bioinformatics (Ghent University) and Center for Plant Systems Biology, Ghent, Belgium. 7Central Collection of Algal Cultures, Faculty of Biology, University of Duisburg-Essen, Essen, Germany. 8School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China. 9Department of Biological Sciences and Department of Medicine, University of Alberta, Edmonton, Alberta, Canada. 10Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China. 11College of Horticulture, Nanjing Agricultural University, Nanjing, China. 12Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa. -
Phylogenomics Provides Robust Support for a Two-Domains Tree of Life
ARTICLES https://doi.org/10.1038/s41559-019-1040-x Phylogenomics provides robust support for a two-domains tree of life Tom A. Williams! !1*, Cymon J. Cox! !2, Peter G. Foster3, Gergely J. Szöllősi4,5,6 and T. Martin Embley7* Hypotheses about the origin of eukaryotic cells are classically framed within the context of a universal ‘tree of life’ based on conserved core genes. Vigorous ongoing debate about eukaryote origins is based on assertions that the topology of the tree of life depends on the taxa included and the choice and quality of genomic data analysed. Here we have reanalysed the evidence underpinning those claims and apply more data to the question by using supertree and coalescent methods to interrogate >3,000 gene families in archaea and eukaryotes. We find that eukaryotes consistently originate from within the archaea in a two-domains tree when due consideration is given to the fit between model and data. Our analyses support a close relation- ship between eukaryotes and Asgard archaea and identify the Heimdallarchaeota as the current best candidate for the closest archaeal relatives of the eukaryotic nuclear lineage. urrent hypotheses about eukaryotic origins generally pro- Indeed, it has previously been suggested that it is the 3D tree, rather pose at least two partners in that process: a bacterial endo- than the 2D tree, that is an artefact of long-branch attraction5,9–11, symbiont that became the mitochondrion and a host cell for both because analyses under better-fitting models have recovered C 1–4 that endosymbiosis . The identity of the host has been informed a 2D tree but also because the 3D topology is one in which the two by analyses of conserved genes for the transcription and transla- longest branches in the tree of life—the stems leading to bacteria and tion machinery that are considered essential for cellular life5. -
Toxicity, Physiological, and Ultrastructural Effects of Arsenic
International Journal of Environmental Research and Public Health Article Toxicity, Physiological, and Ultrastructural Effects of Arsenic and Cadmium on the Extremophilic Microalga Chlamydomonas acidophila Silvia Díaz 1, Patricia De Francisco 1,2, Sanna Olsson 3 , Ángeles Aguilera 2,*, Elena González-Toril 2 and Ana Martín-González 1 1 Department of Genetics, Physiology and Microbiology, Faculty of Biology, Universidad Complutense de Madrid (UCM), C/José Antonio Novais, 12, 28040 Madrid, Spain; [email protected] (S.D.); [email protected] (P.d.F.); [email protected] (A.M.-G.) 2 Astrobiology Center (INTA-CSIC), Carretera de Ajalvir km 4, Torrejón de Ardoz, 28850 Madrid, Spain; [email protected] 3 Department of Forest Ecology and Genetics, INIA Forest Research Center (INIA-CIFOR), Carretera de A Coruña km 7.5, 28040 Madrid, Spain; sanna.olsson@helsinki.fi * Correspondence: [email protected]; Tel.: +34-91-520-6434 Received: 17 December 2019; Accepted: 24 February 2020; Published: 3 March 2020 Abstract: The cytotoxicity of cadmium (Cd), arsenate (As(V)), and arsenite (As(III)) on a strain of Chlamydomonas acidophila, isolated from the Rio Tinto, an acidic environment containing high metal(l)oid concentrations, was analyzed. We used a broad array of methods to produce complementary information: cell viability and reactive oxygen species (ROS) generation measures, ultrastructural observations, transmission electron microscopy energy dispersive x-ray microanalysis (TEM–XEDS), and gene expression. This acidophilic microorganism was affected differently by the tested metal/metalloid: It showed high resistance to arsenic while Cd was the most toxic heavy metal, showing an LC50 = 1.94 µM. -
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. -
The Effects of Contemporary Selection and Dispersal Limitation on the Community Assembly of Acidophilic Microalgae1
J. Phycol. 54, 720–733 (2018) © 2018 Phycological Society of America DOI: 10.1111/jpy.12771 THE EFFECTS OF CONTEMPORARY SELECTION AND DISPERSAL LIMITATION ON THE COMMUNITY ASSEMBLY OF ACIDOPHILIC MICROALGAE1 Chia-Jung Hsieh3 Department of Life Science, Tunghai University, Taichung 40704, Taiwan Shing Hei Zhan3 Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada Chen-Pan Liao3 Department of Life Science, Tunghai University, Taichung 40704, Taiwan Sen-Lin Tang Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan Liang-Chi Wang Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan Tsuyoshi Watanabe Tohoku National Fisheries Research Institute, Fisheries Research Agency, Miyagi 985-0001, Japan Paul John L. Geraldino Department of Biology, University of San Carlos, Cebu 6000, Philippines and Shao-Lun Liu 2 Department of Life Science, Tunghai University, Taichung 40704, Taiwan Extremophilic microalgae are primary producers partitioning revealed that dispersal limitation has a in acidic habitats, such as volcanic sites and acid greater influence on the community assembly of mine drainages, and play a central role in microalgae than contemporary selection. Consistent biogeochemical cycles. Yet, basic knowledge about with this finding, community similarity among the their species composition and community assembly sampled sites decayed more quickly over is lacking. Here, we begin to fill this knowledge gap geographical distance than differences in by performing the first large-scale survey of environmental factors. Our work paves the way for microalgal diversity in acidic geothermal sites across future studies to understand the ecology and the West Pacific Island Chain. We collected 72 biogeography of microalgae in extreme habitats. -
Riotinto: Un Universo De Mundos Microbianos
Ecosistemas 14 (2): 52-65. Mayo 2005. http://www.revistaecosistemas.net/articulo.asp?Id=110 Riotinto: un universo de mundos microbianos A. I. López-Archilla Departamento de Ecología. Facultad de Ciencias. Universidad Autónoma de Madrid. 28049 Cantoblanco, Madrid. España El río Tinto es un ambiente extremo caracterizado por un pH muy bajo y altas concentraciones de metales en disolución. Las extremas condiciones del río son en gran medida producidas y mantenidas por el componente biológico del ecosistema, principalmente por organismos procarióticos quimiolitótrofos. Las algas eucarióticas son los otros productores primarios del sistema mientras que hongos y bacterias heterotróficas juegan el papel de consumidores y descomponedores. Otros consumidores son protistas heterotróficos y, en ocasiones, rotíferos. El río en sí tiene una amplia variedad de ambientes en donde se desarrollan distintas comunidades (bentónicas en zonas aerobias, neustónicas en la superficie de aguas semiquietas, planctónicas en la columna de agua óxica y anóxica), además, las zonas adyacentes al río como los montones de mineral, las galerías mineras o el acuífero son ambientes distintos y aún inexplorados. A pesar de las condiciones extremas de este ecosistema, el río Tinto posee una gran diversidad de comunidades microbianas, cuyas interacciones son de gran interés para la ecología microbiana. The Tinto River is an extreme environment characterized by a very low pH and high concentration of heavy metals in solution. The extreme features of the river are produced and sustained by the biological components of the ecosystem, mainly by chemolithoautotrophic prokaryotic organisms. Eukaryotic algae are another primary producers in the system, while fungi and heterotrophic bacteria play the role of consumers and decomposers. -
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.