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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. -
その4. 大型植物化石 半田久美子・植村和彦 Part 4.Plant Macrofossils
そ の4. 大 型 植 物 化 石 半田久美子・植村和彦 Part 4. Plant Macrofossils Kumiko Hand a and Kazuhiko Uemura 化石リスト(List of Fossils): 162 p ~207 p 化石産地図(Map of Fossil Localities): 208 p ~218 p 化石産出地点番号索引(lndex of Fossil Localities): 219 p ~223 p 文献(Literatures): 224 p ~225 p 化石リスト 化石産出地点番号索引 産出化石 番号 Caldesia tertiaria 273 産出化石 番号 Catlicarpa sp. 256 Abies firma 236,245.254,263,266,272,273,274 Camellia protojaponica 99 Abies homolepis 245,262 Camellia sasanqua 273 Abies sp. 254,256,261,264 Carex rhynchophysa 244 Abies veitchii 263,272 Carex sp. 196,254,255,256 Acanthopanax sp. 266 Carpinus grandis 228 Acer diabolicum 272 Carpinus heigunensis 229 Acer ezoanum 273 Carpinus japonica 227 Acer miyabei 274 Carpinus miocenica 81,88,117,126,131,157 Acer mono 256 Carpinus sp. 26,34,39,52,115.143,179,209,217,218.219, Acer nordenskioeldi 54.211.212.215.216.254 220,221,222,223,237,256 Acer pictum 26,42 Carpinus subcordata 196,228 Acer prototrifidium 211,212,215,216 Carpinus subyedoensis 229 Acer rotundatum 229 Carya miocathayensis 72 Acer rubrum var. pyc 89 Caryophyllaceae gen. indet. 255 Acer rufinerve 254 Castanea crenata 54 Acer sp. 29,34,60,72,81,88,93,126,131,137,138,145, Castanea Kubinyi 28.30.34.38.50 172,177,179,180,181,185,188,194,228,229, Castanea miocrenata 65.81,93,122,138 243,256,272 Castanea miomollissima 56,59,65.74,79,81.87.90,93,95,104,107,118, Acer subpictum 54,75,76,86,93,115,132 124,126,131,132,157.159.162,164 Acer trilobatum 53 Castanea sp. -
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. -
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). -
HARDY FERN FOUNDATION QUARTERLY the HARDY FERN FOUNDATION QUARTERLY Volume 15 • No
THE HARDY FERN FOUNDATION P.O. Box 166 Medina, WA 98039-0166 Web site: www.hardyfems.org The Hardy Fern Foundation was founded in 1989 to establish a comprehen¬ sive collection of the world’s hardy ferns for display, testing, evaluation, public education and introduction to the gardening and horticultural community. Many rare and unusual species, hybrids and varieties are being propagated from spores and tested in selected environments for their different degrees of hardiness and ornamental garden value. The primary fern display and test garden is located at, and in conjunction with, The Rhododendron Species Botanical Garden at the Weyerhaeuser Corpo¬ rate Headquarters, in Federal Way, Washington. Satellite fern gardens are at the Stephen Austin Arboretum, Nacogdoches, Texas, Birmingham Botanical Gardens, Birmingham, Alabama, California State University at Sacramento, Sacramento, California, Coastal Maine Botanical Garden, Boothbay, Maine, Dallas Arboretum, Dallas, Texas, Denver Botanic Gardens. Denver, Colorado, Georgeson Botanical Garden, University of Alaska, Fairbanks, Alaska, Harry P. Leu Garden, Orlando, Florida, Inniswood Metro Gardens, Columbus, Ohio, Lewis Ginter Botanical Garden, Richmond, Virginia, New York Botanical Garden, Bronx, New York, and Strybing Arboretum, San Francisco, California. The fern display gardens are at Bainbridge Island Library, Bainbridge Island, WA, Lakewold, Tacoma, Washington, Les Jardins de Metis, Quebec, Canada, University of Northern Colorado, Greeley, Colorado, and Whitehall Historic Home and Garden, Louisville, KY. Hardy Fern Foundation members participate in a spore exchange, receive a quarterly newsletter and have first access to ferns as they are ready for distribution. Cover Design by Willanna Bradner HARDY FERN FOUNDATION QUARTERLY THE HARDY FERN FOUNDATION QUARTERLY Volume 15 • No. -
Field Instructions for The
FIELD INSTRUCTIONS FOR THE INVENTORY OF THE PACIFIC ISLANDS 2013 Hawaii Edition Forest Inventory and Analysis Program Pacific Northwest Research Station USDA Forest Service THIS MANUAL IS BASED ON: FOREST INVENTORY AND ANALYSIS NATIONAL CORE FIELD GUIDE FIELD DATA COLLECTION PROCEDURES FOR PHASE 2 PLOTS VERSION 5.1 TABLE OF CONTENTS 1 INTRODUCTION ........................................................................................................................................................................ 1 1.1 PURPOSES OF THIS MANUAL ................................................................................................................................................... 1 1.2 ORGANIZATION OF THIS MANUAL .......................................................................................................................................... 1 1.2.1 UNITS OF MEASURE ................................................................................................................................................................. 2 1.2.2 GENERAL DESCRIPTION ............................................................................................................................................................ 2 1.2.3 PLOT SETUP .............................................................................................................................................................................. 3 1.2.4 PLOT INTEGRITY ...................................................................................................................................................................... -
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. -
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. -
Keanekaragaman Flora Di Pulau Samosir, Sumatera Utara
Berk. Penel. Hayati Edisi Khusus: 3A (7–16), 2009 KEANEKARAGAMAN FLORA DI PULAU SAMOSIR, SUMATERA UTARA Sri Hartini Pusat Konservasi Tumbuhan-Kebun Raya Bogor, LIPI Jl. Ir. H. Juanda 13 P.O. BOX 309 Bogor 16003 ABSTRACT Samosir Island is located in Toba Lake, North Sumatra. Although this island is looked barren, but some potential plants which are not used by people yet found there. Data of flora diversity in Samosir Island is still limited. The aims of this research was to inventory plant diversity in this Island. The method used in the research was explorative. The result showed that there were approximately 232 number of plants in the place. They consist of trees, shrubs, water plants, ferns, and orchids. Some of them are potential plants. Key words: Inventory, flora, Samosir Island PENGANTAR Penelitian ini bertujuan mendata jenis-jenis tumbuhan di Pulau Samosir beserta potensinya. Data ini diharapkan Pulau Samosir adalah sebuah pulau vulkanik di tengah dapat dijadikan data yang bermanfaat. Danau Toba di Provinsi Sumatra Utara. Sebuah pulau dalam pulau dengan ketinggian 1.000 m di atas permukaan laut BAHAN DAN CARA KERJA menjadikan pulau ini menjadi sebuah pulau yang menarik. Pulau Samosir terletak di Kabupaten Samosir dan memiliki Penelitian flora di kawasan Pulau Samosir difokuskan 9 kecamatan. di 4 Kecamatan yaitu Kecamatan Simanindo, Kecamatan Pulau Samosir terletak di tengah Danau Toba. Danau Ronggur Nihuta, Kecamatan Sianjur Mula Mula, serta Toba adalah sebuah danau vulkanik dengan ukuran panjang di Kecamatan Harian. Penelitian dilakukan pada bulan 100 km dan lebar 30 km. Di pulau Samosir sendiri terdapat Agustus 2008. Metode yang digunakan dalam penelitian dua buah danau kecil sebagai daerah wisata yaitu Danau ini adalah metode eksploratif. -
Origin Inspection Programs (Food and Agricultural Code, Section 6404)
CALIFORNIA DEPARTMENT OF FOOD AND AGRICULTURE 110.1 PLANT QUARANTINE MANUAL 5 -01-12 Origin Inspection Programs (Food and Agricultural Code, Section 6404) FLORIDA No Approved Nurseries 110.2 CALIFORNIA DEPARTMENT OF FOOD AND AGRICULTURE 10-07-03 PLANT QUARANTINE MANUAL CUT FLOWERS INSPECTED AT ORIGIN MAY BE RELEASED The release of plant material without inspection is limited to the following types when from an approved nursery. This approval does not preclude inspection and sampling and/or testing at the discretion of the destination California Agricultural Commissioner, and rejection is required as a consequence of inspection and/or test(s). (Section 6404, Food and Agricultural Code). Hawaii Approved Nurseries, Certificate Number, and Commodities Asia Pacific Flowers, Inc., Hilo, Hawaii (HIOI-HO104) Dendrobium spp. (orchids and leis), Oncidium spp. (orchids). Big Island Floral, Pahoa, Hawaii (HIOI-O0026) No Longer A Participant. Floral Resources, Inc., Hilo, Hawaii (HIOI-H0043) Anthurium spp., Cordyline terminalis (red & green varigated ti). Goble’s Flower Farm, Kula, Hawaii (HIOI-M0076) No Longer A Participant. Gordon’s Nursery, Haleiwa, Hawaii (HIOI-00171) Dendrobium spp. (orchids), Oncidium spp. (orchids), Rumohra (Polystichum) adiantiformis (leather leaf fern from California). Green Point Nurseries, Inc., Hilo, Hawaii (HIOI-HOOO7) Anthurim spp., Cordyline terminalis (green, red, varigated ti). Green Valley Tropical, Punaluu, Hawaii (HIOI-O0136) Alpinia purpurata (red, pink ginger), Etlingera elatior (torch ginger), Zingiber spectabile (shampoo ginger), Costas pulverulentus, C. stenophyllus,Calathea crotalifera, Strelitzia reginae, Heliconia caribaea, H. bihai, H. stricta, H. orthotricha, H. bourgeana, H. indica, H. psittacorum, H. aurentiaca, H. latispatha, H. rostrata, H. pendula, H. chartacea, H. collinsiana, Anthurium andraeanum , Dendrobium spp. -
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. -
A Roadmap for Fern Genome Sequencing
A Roadmap for Fern Genome Sequencing Authors: Li-Yaung Kuo, and Fay-Wei Li Source: American Fern Journal, 109(3) : 212-223 Published By: The American Fern Society URL: https://doi.org/10.1640/0002-8444-109.3.212 BioOne Complete (complete.BioOne.org) is a full-text database of 200 subscribed and open-access titles in the biological, ecological, and environmental sciences published by nonprofit societies, associations, museums, institutions, and presses. Your use of this PDF, the BioOne Complete website, and all posted and associated content indicates your acceptance of BioOne’s Terms of Use, available at www.bioone.org/terms-of-use. Usage of BioOne Complete content is strictly limited to personal, educational, and non-commercial use. Commercial inquiries or rights and permissions requests should be directed to the individual publisher as copyright holder. BioOne sees sustainable scholarly publishing as an inherently collaborative enterprise connecting authors, nonprofit publishers, academic institutions, research libraries, and research funders in the common goal of maximizing access to critical research. Downloaded From: https://bioone.org/journals/American-Fern-Journal on 15 Oct 2019 Terms of Use: https://bioone.org/terms-of-use Access provided by Cornell University American Fern Journal 109(3):212–223 (2019) Published on 16 September 2019 A Roadmap for Fern Genome Sequencing LI-YAUNG KUO AND FAY-WEI LI* Boyce Thompson Institute, Ithaca, New York 14853, USA and Plant Biology Section, Cornell University, New York 14853, USA ABSTRACT.—The large genomes of ferns have long deterred genome sequencing efforts. To date, only two heterosporous ferns with remarkably small genomes, Azolla filiculoides and Salvinia cucullata, have been sequenced.