DOCSLIB.ORG

The Genome of Prasinoderma Coloniale Unveils the Existence of a Third Phylum Within Green Plants

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
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. 13These authors contributed equally: Linzhou Li, Sibo Wang. ✉e-mail: [email protected]; [email protected]; [email protected] NATURE EcOLOgy & EVOLUTION | www.nature.com/natecolevol Supplementary Figure 1. The chloroplast circos map of Prasinoderma coloniale. Supplementary Figure 2. The mitochondrial circos map of Prasinoderma coloniale. Supplementary Figure 3. The GC depth distribution of Prasinoderma coloniale. Supplementary Figure 4. The concatenated phylogenetic tree of 19 species with 31 single-copy mitochondria gene place Prasinodermophyta (Prasinoderma coloniale) to the sister lineage of other Viridiplantae with high bootstrap support (100.0). Treubia lacunosa 65/- Nardia compressa 100/1 Nothoceros vincentianus 93/1 Phaeoceros sp. 74/- 87/- Takakia lepidozioides 0.05 substitutions/site 100/1 Diphyscium fulvifolium 99/1 Polytrichum juniperinum 78/1 100/1 Physcomitrella patens nuclear rRNA operon Huperzia selago Equisetum arvense 4646 aligned characters 96/1 90/0.99 Angiopteris lygodiifolia 78/1 Arabidopsis thaliana tree topology: ML (IQTree) 87/1 100/1 Pinus taeda Marchantia polymorpha support values: ML/MrBayes 100/1 Nitella hyalina 85/1 Chara braunii 83/1 Chaetosphaeridium globosum 100/1 Entransia_fimbriata Klebsormidium nitens Coleochaete scutata 54/- 100/1 Cosmarium ochthodes 99/1 Penium margaritaceum 78/0.98 86/1 Netrium digitus 91/1 Mesotaenium endlicherianum Streptophyta 76/0.99 Cylindrocystis brebissonii 99/1 Cylindrocystis cushleckae 75/1 Mesotaenium caldariorum 92/1 Mougeotia sp. Mesostigma viride Spirotaenia condensata 89/1 Chlorokybus atmophyticus 69/0.99 100/1 Eudorina sp. 100/1 Yamagishiella unicocca 99/1 Volvox carteri Chlamydomonas reinhardtii 99/1 Spermatozopsis exsultans 100/1 Chromochloris zofingiensis 100/1 Hydrodictyon reticulatum Stigeoclonium helveticum 64/- Oltmannsiellopsis sp. 69/1 100/1 Ulva mutabilis 53/- 80/0.98 Desmochloris halophila Ignatius tetrasporus 58/- 99/1 Tetraselmis cordiformis 99/1 100/1 Tetraselmis striata Scherffelia dubia 100/1 Auxenochlorella protothecoides 100/1 Chlorella varibilis 100/1 Chlorella vulgaris 98/1 100/1 Coccomyxa sp. Botryococcus braunii 58/- 69/- Stichococcus bacillaris 100/1 Koliella longiseta 90/1 Pedinomonas minor 100/1 Marsupiomonas pelliculata 98/1 Chloropicon primus Pycnococcus provasolii 100/1 Nephroselmis pyriformis 100/1 Nephroselmis olivacea 100/1 Monomastix sp. Monomastix opisthostigma 100/1 Dolichomastix tenuilepis 99/1 Crustomastix stigmatica Chlorophyta Mamiella gilva 55/- 100/1 100/1 Bathycoccus prasinos Ostrecoccus tauri 100/1 100/1 Ostreococcus lucimarinus 89/1 Micromonas bravo 100/1 Micromonas commoda Cymbomonas tetramitiformis 59/- Pyramimonas parkeae 100/1 Pyramimonas olivacea 100/1 Pyramimonas tetrarhynchus 98/1 Prasinoderma sp. 100/1 Prasinoderma coloniale 100/1 Prasinoderma singularis Prasinococcus capsulatus Prasinodermophyta 96/1 100/1 Verdigellas peltata Palmophyllum crassum 70/0.94 Glaucocystis nostochinearum Cyanophora paradoxa 100/1 98/- Cyanoptyche gloeocystis Gloeochaete wittrockiana Glaucoplantae 96/1 Rhodogorgon sp. Sporolithon durum Porolithon onkodes 100/1 100/1 73/1 Ahnfeltia plicata Asparagopsis taxiformis Gracilariopsis chorda 96/1 83/- 81/0.99 Chondrus crispus 60/1 58/0.99 Schizymenia dubyi 100/1 Helminthocladia australis Palmaria palmata 99/1 Bangia fuscopurpurea 100/1 Porphyra umbilicalis 98/1 Porphyra purpurea 81/- Pyropia yezoensis 100/1 Rhodochaete parvula 100/1 Madagascaria erythrocladiodes_ 86/0.99 Compsopogon caeruleus 99 Erythrolobus australicus 100/1 Timspurckia oligopyrenoides Rhodoplantae Porphyridium aerugineum 100/1 Bangiopsis sp. 100/1 Rhodosorus marinus CCMP769 Rhodosorus marinus UTEX2760 Rhodella maculata Galdieria sulphuraria Cyanidioschyzon merolae Supplementary Figure 5. The nuclear rRNA operon tree of 109 species with 4,646 aligned characters place Prasinodermophyta (Prasinoderma coloniale) to the sister lineage of other Viridiplantae with high bootstrap support (100.0/1). 100/1 Arabidopsis thaliana Pinus taeda 100/1 Nothoceros vincentianus Phaeoceros sp. Takakia lepidozioides plastid-encoded rRNA operon 78/- Huperzia lucidula 57/- Equisetum diffusum 4172 aligned characters 100/1 Angiopteris fokiensis Polytrichum juniperinum tree topology: ML (IQTree) 100/1 64/1 Diphyscium fulvifolium 57/- Physcomitrella patens support values: ML/MrBayes Nardia compressa 100/1 57/- Treubia lacunosa Streptophyta Marchantia polymorpha 100/1 Nitella hyalina Chara braunii Mesotaenium endlicherianum 100/1 100/1 Cosmarium ochthodes Penium margaritaceum 100/1 72/1 Netrium digitus 100/1 Cylindrocystis cushleckae 81/0.99 Cylindrocystis brebissonii 100/1 60/- 100/1 Mesotaenium caldariorum Mougeotia sp. 98/1 Chaetosphaeridium globosum 100/1 Coleochaete scutata 100/1 Entransia fimbriata 0.05 substitutions/site Klebsormidium nitens 58/- 100/1 Mesostigma viride 100/1 Spirotaenia condensata Chlorokybus atmophyticus 100/1 Cymbomonas tetramitiformis 79/- 89/0.98 Pyramimonas parkeae Pyramimonas olivacea 98/1 Pyramimonas tetrarhynchus grade of 100/1 Nephroselmis pyriformis Nephroselmis olivacea Chlorophyta 100/1 Coccomyxa sp. 99/- Botryococcus braunii -/0.96 (unresolved) 100/1 Auxenochlorella protothecoides 100/1 Chlorella varibilis Chlorella vulgaris 100/1 Stichococcus bacillaris Koliella longiseta 99/1 100/1 Pedinomonas minor Marsupiomonas pelliculata 100/1 Tetraselmis cordiformis 100/1 Tetraselmis striata Scherffelia dubia 73/- Stigeoclonium helveticum 100/1 100/1 Chromochloris zofingiensis 100/1 Hydrodictyon reticulatum Spermatozopsis exsultans 100/1 Eudorina sp. 73/1 100/1 Volvox carteri 50/- Yamagishiella unicocca 94/1 Chlamydomonas reinhardtii 86/0.97 Oltmannsiellopsis sp. 100/1 Ulva mutabilis 62/1 Desmochloris halophila 91/1 Ignatius tetrasporus 96/1 Chloropicon primus Pycnococcus provasolii 100/1 Monomastix sp. Monomastix opisthostigma Crustomastix stigmatica 100/1 100/1 54/1 Dolichomastix tenuilepis 51/- 89/1 Bathycoccus prasinos 100/1 Ostrecoccus tauri 100/1 Ostreococcus lucimarinus Mamiella gilva 100/1 Micromonas bravo 98/0.97 Micromonas commoda 100/1 Prasinoderma sp. 100/1 Prasinoderma coloniale 94/1 Prasinoderma singularis 96/1 Prasinococcus capsulatus Prasinodermophyta 100/1 Verdigellas peltata Palmophyllum crassum Cyanoptyche gloeocystis 98/- Glaucocystis nostochinearum 100/1 Cyanophora paradoxa Gloeochaete wittrockiana Glaucoplantae Asparagopsis taxiformis 96/1 Chondrus crispus Ahnfeltia plicata 97/1 100/1 93/1 Gracilariopsis chorda 99/1 Schizymenia dubyi 100/1 63/0.96 Rhodogorgon sp. Sporolithon durum 68/1 100/1 Porolithon onkodes 97/1 Helminthocladia australis 100/1 Palmaria palmata Bangia fuscopurpurea 100/1 Porphyra umbilicalis 99/1 Porphyra purpurea Pyropia yezoensis 100/1 Rhodochaete pulchella 100/1 Madagascaria erythrocladiodes Compsopogon caeruleus 59/0.99 Erythrolobus australicus 86/0.99 100/1 Timspurckia oligopyrenoides Porphyridium aerugineum Rhodoplantae 58/- Rhodella maculata Bangiopsis sp. 100/1 Rhodosorus marinus CCMP769 100/1 Rhodosorus marinus UTEX2760 Galdieria sulphuraria Cyanidioschyzon merolae Supplementary Figure 6. The plastid-encoded rRNA operon tree of 109 species with 4,172 aligned characters place Prasinodermophyta (Prasinoderma coloniale) to the sister lineage of other Viridiplantae with high bootstrap support (94.0/1). Supplementary Figure 7. The coalescent phylogenetic tree of 23 species with 45 single-copy genes using ASTRAL place Prasinodermophyta (Prasinoderma coloniale) to the sister lineage of other Chlorophyta with high support (85.5). Supplementary Figure 8. The coalescent phylogenetic tree of 28 species with 213 single-copy genes using ASTRAL place Prasinoderma coloniale to the sister lineage of other Chlorophyta with relatively lower support (79.0). In order
Load more

Recommended publications
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • University of Oklahoma
    UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By JOSHUA THOMAS COOPER Norman, Oklahoma 2017 MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION APPROVED FOR THE DEPARTMENT OF MICROBIOLOGY AND PLANT BIOLOGY BY ______________________________ Dr. Boris Wawrik, Chair ______________________________ Dr. J. Phil Gibson ______________________________ Dr. Anne K. Dunn ______________________________ Dr. John Paul Masly ______________________________ Dr. K. David Hambright ii © Copyright by JOSHUA THOMAS COOPER 2017 All Rights Reserved. iii Acknowledgments I would like to thank my two advisors Dr. Boris Wawrik and Dr. J. Phil Gibson for helping me become a better scientist and better educator. I would also like to thank my committee members Dr. Anne K. Dunn, Dr. K. David Hambright, and Dr. J.P. Masly for providing valuable inputs that lead me to carefully consider my research questions. I would also like to thank Dr. J.P. Masly for the opportunity to coauthor a book chapter on the speciation of diatoms. It is still such a privilege that you believed in me and my crazy diatom ideas to form a concise chapter in addition to learn your style of writing has been a benefit to my professional development. I’m also thankful for my first undergraduate research mentor, Dr. Miriam Steinitz-Kannan, now retired from Northern Kentucky University, who was the first to show the amazing wonders of pond scum. Who knew that studying diatoms and algae as an undergraduate would lead me all the way to a Ph.D.
    [Show full text]
  • 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.
    [Show full text]
  • Phylogenetic and Evolutionary Patterns in Microbial Carotenoid Biosynthesis Are Revealed by Comparative Genomics
    Phylogenetic and Evolutionary Patterns in Microbial Carotenoid Biosynthesis Are Revealed by Comparative Genomics Jonathan L. Klassen* Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada Abstract Background: Carotenoids are multifunctional, taxonomically widespread and biotechnologically important pigments. Their biosynthesis serves as a model system for understanding the evolution of secondary metabolism. Microbial carotenoid diversity and evolution has hitherto been analyzed primarily from structural and biosynthetic perspectives, with the few phylogenetic analyses of microbial carotenoid biosynthetic proteins using either used limited datasets or lacking methodological rigor. Given the recent accumulation of microbial genome sequences, a reappraisal of microbial carotenoid biosynthetic diversity and evolution from the perspective of comparative genomics is warranted to validate and complement models of microbial carotenoid diversity and evolution based upon structural and biosynthetic data. Methodology/Principal Findings: Comparative genomics were used to identify and analyze in silico microbial carotenoid biosynthetic pathways. Four major phylogenetic lineages of carotenoid biosynthesis are suggested composed of: (i) Proteobacteria; (ii) Firmicutes; (iii) Chlorobi, Cyanobacteria and photosynthetic eukaryotes; and (iv) Archaea, Bacteroidetes and two separate sub-lineages of Actinobacteria. Using this phylogenetic framework, specific evolutionary mechanisms are proposed for carotenoid desaturase CrtI-family
    [Show full text]
  • Prasinoderma Coloniale Reveals Two Trans-Spliced Group I Introns in the Large Subunit Rrna Gene
    The Mitochondrial Genome of the Prasinophyte Prasinoderma coloniale Reveals Two Trans-Spliced Group I Introns in the Large Subunit rRNA Gene Jean-Franc¸ois Pombert1, Christian Otis2, Monique Turmel2, Claude Lemieux2* 1 Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, Illinois, United States of America, 2 Institut de Biologie Inte´grative et des Syste`mes, De´partement de Biochimie, de Microbiologie et de Bio-informatique, Universite´ Laval, Que´bec, Que´bec, Canada Abstract Organelle genes are often interrupted by group I and or group II introns. Splicing of these mobile genetic occurs at the RNA level via serial transesterification steps catalyzed by the introns’own tertiary structures and, sometimes, with the help of external factors. These catalytic ribozymes can be found in cis or trans configuration, and although trans-arrayed group II introns have been known for decades, trans-spliced group I introns have been reported only recently. In the course of sequencing the complete mitochondrial genome of the prasinophyte picoplanktonic green alga Prasinoderma coloniale CCMP 1220 (Prasinococcales, clade VI), we uncovered two additional cases of trans-spliced group I introns. Here, we describe these introns and compare the 54,546 bp-long mitochondrial genome of Prasinoderma with those of four other prasinophytes (clades II, III and V). This comparison underscores the highly variable mitochondrial genome architecture in these ancient chlorophyte lineages. Both Prasinoderma trans-spliced introns reside within the large subunit rRNA gene (rnl) at positions where cis-spliced relatives, often containing homing endonuclease genes, have been found in other organelles. In contrast, all previously reported trans-spliced group I introns occur in different mitochondrial genes (rns or coxI).
    [Show full text]
  • P^I"~ SUBMITTED to the DEPARTMENT of L \IL.~D EARTH, ATMOSPHERIC and PLANETARY SCIENCES in PARTIAL FULFILLMENT of the REQUIREMENTS for the DEGREE OF
    Molecular studies of the sources and significance of archaeal lipids in the oceans by Sara Ann Lincoln MIA IsJ:S' iNSTITUTE B.S. Geosciences B.S. Geological Oceanography L T University of Rhode Island (2006) P^I"~ SUBMITTED TO THE DEPARTMENT OF L \IL.~d EARTH, ATMOSPHERIC AND PLANETARY SCIENCES IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN GEOCHEMISTRY SEPTEMBER 2013 © Massachusetts Institute of Technology All rights reserved. Author:................. Department of Earth, Atmospheric and Planetary Sciences Certified by:........................... Roger E. Summons Professor of Geobiology Department of Earth, Atmospheric and Planetary Sciences Thesis supervisor ..................#......r....... ........................................................ Edward F. DeLong Morton and Claire Goulder amily P fessor in Environmental Systems Depar e Civil and Environmental Engineering 7) Thesis supervisor Accepted by: ...................................... Robert van der Hilst Schlumberger Professor of Earth Sciences Head, Department of Earth, Atmospheric and Planetary Sciences THIS PAGE INTENTIONALLY LEFT BLANK Molecular studies of the sources and significance of archaeal lipids in the oceans by Sara Ann Lincoln Submitted to the Department of Earth, Atmospheric and Planetary Sciences on July 29, 2013 in partial fulfillment of the requirements for the Degree of Doctor of Philosophy in Geochemistry ABSTRACT Marine archaea are ubiquitous and abundant in the modem oceans and have a geologic record extending >100 million years. However, factors influencing the populations of the major clades - chemolithoautotrophic Marine Group I Thaumarchaeota (MG-I) and heterotrophic Marine Group II Euryarchaeota (MG-II) - and their membrane lipid signatures are not well understood. Here, I paired techniques of organic geochemistry and molecular biology to explore the sources and significance of archaeal tetraether lipids in the marine water column.
    [Show full text]
  • And Thermo-Adaptation in Hyperthermophilic Archaea: Identification of Compatible Solutes, Accumulation Profiles, and Biosynthetic Routes in Archaeoglobus Spp
    Universidade Nova de Lisboa Osmo- andInstituto thermo de Tecnologia-adaptation Química e Biológica in hyperthermophilic Archaea: Subtitle Subtitle Luís Pedro Gafeira Gonçalves Osmo- and thermo-adaptation in hyperthermophilic Archaea: identification of compatible solutes, accumulation profiles, and biosynthetic routes in Archaeoglobus spp. OH OH OH CDP c c c - CMP O O - PPi O3P P CTP O O O OH OH OH OH OH OH O- C C C O P O O P i Dissertation presented to obtain the Ph.D degree in BiochemistryO O- Instituto de Tecnologia Química e Biológica | Universidade Nova de LisboaP OH O O OH OH OH Oeiras, Luís Pedro Gafeira Gonçalves January, 2008 2008 Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica Osmo- and thermo-adaptation in hyperthermophilic Archaea: identification of compatible solutes, accumulation profiles, and biosynthetic routes in Archaeoglobus spp. This dissertation was presented to obtain a Ph. D. degree in Biochemistry at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa. By Luís Pedro Gafeira Gonçalves Supervised by Prof. Dr. Helena Santos Oeiras, January, 2008 Apoio financeiro da Fundação para a Ciência e Tecnologia (POCI 2010 – Formação Avançada para a Ciência – Medida IV.3) e FSE no âmbito do Quadro Comunitário de apoio, Bolsa de Doutoramento com a referência SFRH / BD / 5076 / 2001. ii ACKNOWNLEDGMENTS The work presented in this thesis, would not have been possible without the help, in terms of time and knowledge, of many people, to whom I am extremely grateful. Firstly and mostly, I need to thank my supervisor, Prof. Helena Santos, for her way of thinking science, her knowledge, her rigorous criticism, and her commitment to science.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • The Genome of Prasinoderma Coloniale Unveils the Existence of a Third Phylum Within Green Plants
    Downloaded from orbit.dtu.dk on: Oct 10, 2021 The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants Li, Linzhou; Wang, Sibo; Wang, Hongli; Sahu, Sunil Kumar; Marin, Birger; Li, Haoyuan; Xu, Yan; Liang, Hongping; Li, Zhen; Cheng, Shifeng Total number of authors: 24 Published in: Nature Ecology & Evolution Link to article, DOI: 10.1038/s41559-020-1221-7 Publication date: 2020 Document Version Publisher's PDF, also known as Version of record Link back to DTU Orbit Citation (APA): Li, L., Wang, S., Wang, H., Sahu, S. K., Marin, B., Li, H., Xu, Y., Liang, H., Li, Z., Cheng, S., Reder, T., Çebi, Z., Wittek, S., Petersen, M., Melkonian, B., Du, H., Yang, H., Wang, J., Wong, G. K. S., ... Liu, H. (2020). The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants. Nature Ecology & Evolution, 4, 1220-1231. https://doi.org/10.1038/s41559-020-1221-7 General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal 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.
    [Show full text]