DOCSLIB.ORG

Phylogenomics Provides New Insights Into Gains and Losses of Selenoproteins Among Archaeplastida

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Phylogenomics Provides New Insights Into Gains and Losses of Selenoproteins Among Archaeplastida bioRxiv preprint doi: https://doi.org/10.1101/674895; this version posted July 1, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 Phylogenomics provides new insights into gains and 2 losses of selenoproteins among Archaeplastida 3 Hongping Liang1,2,3#, Tong Wei2,3,4#, Yan Xu1,2,3#, Linzhou Li2,3,6, Sunil Kumar Sahu2,3,4, Hongli 4 Wang1,2,3, Haoyuan Li1,2, Xian Fu2,3, Gengyun Zhang2,4, Michael Melkonian7, Xin Liu2,3,4, Sibo 5 Wang2,4,5*,Huan Liu2,4,5* 6 1 BGI Education Center, University of Chinese Academy of Sciences, Beijing, China. 7 2 BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China. 8 3 China National Gene Bank, Institute of New Agricultural Resources, BGI-Shenzhen, Jinsha Road, 9 Shenzhen 518120, China. 10 4 State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China. 11 5 Department of Biology, University of Copenhagen, Copenhagen, Denmark. 12 6 School of Biology and Biological Engineering, South China University of Technology, 510006, China. 13 7 Botanical Institute, Cologne Biocenter, University of Cologne, Cologne D-50674, Germany. 14 #these authors contributed equally to this work 15 * Correspondence: *[email protected] 16 Abstract: Selenoproteins that contain selenocysteine (Sec) are found in all kingdoms of life. 17 Although they constitute a small proportion of the proteome, selenoproteins play essential roles in 18 many organisms. In photosynthetic eukaryotes, selenoproteins have been found in algae but are 19 missing in land plants (embryophytes). In this study, we explored the evolutionary dynamics of Sec 20 incorporation by conveying a genomic search for the Sec machinery and selenoproteins across 21 Archaeplastida. We identified a complete Sec machinery and variable sizes of selenoproteomes in 22 the main algal lineages. However, the entire Sec machinery was missing in the BV clade 23 (Bangiophyceae-Florideophyceae) of Rhodoplantae (red algae) and only partial machinery was 24 found in three species of Archaeplastida, indicating parallel loss of Sec incorporation in different 25 groups of algae. Further analysis of genome and transcriptome data suggests that all major lineages 26 of streptophyte algae display a complete Sec machinery, although the number of selenoproteins is 27 low in this group, especially in subaerial taxa. We conclude that selenoproteins tend to be lost in 28 Archaeplastida upon adaptation to a subaerial or acidic environment. The high number of redox- 29 active selenoproteins found in some bloom-forming marine microalgae may be related to defense 30 against viral infections. Some of the selenoproteins in these organisms may have been gained by 31 horizontal gene transfer from bacteria. 32 Keywords: Evolution; Horizontal gene transfer; Phylogenomics; Selenoproteins; Selenocysteine; Sec 33 machinery; 34 35 1. Introduction 36 Selenium (Se) is an essential trace element for human health and its deficiency leads to various 37 diseases, such as Keshan and Kashin-Beck diseases, and affects the immune system and promotes 38 cancer development [1,2]. An essential Se metabolism is present in many organisms, including 39 bacteria, archaea, and eukaryotes [1,3,4]. However, higher concentrations of Se are toxic by 40 functioning as a pro-oxidant, which affects the intracellular glutathione (GSH) pool leading to an 41 enhanced level of ROS accumulation [5,6]. Se is essential for growth and development of numerous 42 algal species but not for terrestrial plants (embryophytes), although it accumulates in certain plant 43 species and can serve as dietary sources for Se uptake [3,7-9]. 44 Se is incorporated into nascent polypeptides in the form of selenocysteine (Sec), the 21st amino 45 acid [10]. Se incorporation requires a specialized machinery and Sec insertion sequence (SECIS) 46 elements present in selenoprotein mRNAs [11,12]. In eukaryotes, it consists of Sec synthesis and Sec 47 incorporation. Sec synthesis starts with tRNASec, aminoacylated with serine, which is phosphorylated bioRxiv preprint doi: https://doi.org/10.1101/674895; this version posted July 1, 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. 48 by O-phosphoseryl-transfer tRNASec kinase (PSTK) and then catalyzed by Sec synthase (SecS) to 49 produce selenocysteinyl-tRNASec from selenophosphate [10-13]. The Sec donor, selenophosphate, is 50 generated from selenide by selenophosphate synthetase 2 (SPS2), which is often a selenoprotein itself 51 [14,15]. During Sec incorporation, SECIS-binding protein 2 (SBP2) recognizes the SECIS elements in 52 the 3’-untranslated region (3’-UTR) and recruits the Sec-specific elongation factor (eEFSec) that 53 delivers selenocysteinyl-tRNASec to the ribosome at the in-frame Sec-coding UGA stop codon (Figure 54 2a). Bacteria possess a similar machinery including selB (Sec-specific elongation factor), selC (tRNASec) 55 and selD (selenophosphate synthase), except that Sec synthesis is catalyzed by a single bacterial Sec 56 synthase, SelA [10]. 57 Although selenoproteins constitute only a small fraction of the proteome in any living organism, 58 they play important roles in redox regulation, antioxidation, and thyroid hormone activation in 59 animals including humans [16]. Sec incorporation has been well documented in animals, bacteria, 60 and archaea, while the largest selenoproteome was reported in algae. In the pelagophyte alga 61 Aureococcus anophagefferens, 59 selenoproteins were identified in its genome, compared with 25 62 selenoproteins in humans [17,18]. The green alga Chlamydomonas reinhardtii has at least ten 63 selenoproteins, whereas the picoplanktonic, marine green alga Ostreococcus lucimarinus harbors 20 64 selenoprotein genes in its genome [3,19]. Considering that Se is essential for growth in at least 33 algal 65 species that belong to six phyla, Sec incorporation is thought to be universal in diverse algal lineages 66 [20]. In a previous study, no selenoproteins were found in any land plants [7], suggesting a complete 67 loss of Sec incorporation after streptophyte terrestrialization. Exploring the Sec machinery across the 68 Archaeplastida, especially in algae, would provide insight into its evolutionary dynamics in this 69 important lineage of photosynthetic eukaryotes. Here in this study, we searched 38 plant genomes, 70 including 33 algal species that represent the major algal lineages, for the Sec machinery and 71 selenoproteins. 72 2. Results 73 bioRxiv preprint doi: https://doi.org/10.1101/674895; this version posted July 1, 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. 74 2.1. Sec machinery in algae 75 To cover the plant tree of life, we selected 33 genomes of algal species and 5 embryophyte species 76 with a focus on Archaeplastida, the major group of photosynthetic eukaryotes with primary plastids. 77 The 33 algal species include one glaucophyte, six rhodophytes, 16 chlorophytes, and seven 78 streptophyte algae. Another three species, the pelagophyte A. anophagefferens, the diatom Thalassiosira 79 pseudonana, and the coccolithophorid Emiliania huxleyi, were also included to represent other distinct 80 algal lineages (Supplementary Table S1A). 81 The Sec machinery was searched in 38 genome assemblies using Selenoprofiles [21] (See 82 Methods). As shown in Figure 1, embryophytes lack the entire Sec machinery as previously reported 83 [7]. Interestingly, the Sec machinery is not intact in all tested algal species. Among 33 algae, three 84 Rhodoplantae lack the entire Sec machinery as in embryophytes. The chlorophyte Monoraphidium 85 neglectum, and the rhodophyte Cyanidioschyzon merolae lack PSTK, and the glaucophyte Cyanophora 86 paradoxa SBP2. According to the species tree, it seems that the Sec machinery was lost completely in 87 one rhodophyte clade that includes Porphyra umbilicalis, Pyropia yezoensis, and Chondrus crispus and 88 partially in a few other algal species (Figure 1). 89 90 91 Figure 1. The number and distribution of selenoproteins, and enzymes involved in the Sec 92 machinery. The phylogenetic tree was retrieved from the NCBI taxonomy database and the 1 KP 93 Project (http://www.onekp.com). Presence (green symbols) or absence (empty symbols) of the 94 enzymes involved in the Sec machinery (circles) and tRNASec (triangles) across sequenced 95 embryophyte, streptophyte algae, chlorophyte, Rhodoplantae, Glaucoplantae and protist 96 genomes are shown in the left panel. The distribution and number of selenoproteins are plotted 97 in the yellow column in the second panel, and the predicted SECIS elements are represented by 98 the blue bars. Distribution and number of selenoprotein homologues (Cys) are plotted in an 99 orange column on the right panel. Prasinophyte algae (Mamiellophyceae) are highlighted in red. 100 2.2. Sec incorporation in the major algal lineages 101 In addition, we also identified the complete Sec machinery in some Rhodoplantae (Figure 1). 102 The Rhodoplantae are often classified at the subphylum level into two clades,
Load more

Recommended publications
  • General Botany Lab Review Fungi, Algae, Bryophytes, Ferns & Fern Allies
    General Botany Lab Review Fungi, Algae, Bryophytes, Ferns & Fern Allies You have looked at a lot of stuff – both live and via prepared slides. You’ve also labeled at least one Life Cycle Diagram for each of the groups. Know what your benchmarks are for a general life cycle diagram and be able to label them. I will not ask you to identify anything to species or genus; be able to identify things to “group” (i.e., ascomycete, bryophyta, etc.) Be able to identify growth form (e.g., unicell, filamentous, etc.). Recognize the differences between sexual and asexual reroductive structures. All questions will be multiple choice. Material looked at: UNIT 1: FUNGI EXERCISE 1: CHYTRIDS/ CHYTRIDOMYCOTA: Allmyces arbusculus – life and prepared slides EXERCISE 2: ZYGOMYCETES/ ZYGOMYCOTA: Rhizopus stolonifer – live and prepared slides EXERCISE 2: MYCORRHIZA and the GLOMEROMYCETES/ GLOMEROMYCOTA – prepared slides only EXERCISE 3: ASCOMYCETES/ ASCOMYCOTA Aspergillus sp., Penicillium sp., Saccharomyces cerevisiae, Peziza sp., Sordaria fimicola, and Morchella sp. – a mixture of live and prepared materials EXERCISE 4: BASIDIOMYCETES/BASIDIOMYCETES Agaricus, Coprinus, Cronartium (a rust), Ustilago (a smut) – slides, fresh, and dried EXERCISE 5: SLIME MOLDS – live and prepared Physarum EXERCISE 6: LICHENS – live and prepared slides be able to identify the various growth forms UNIT 2: ALGAE EXERCISE 1: CYANOBACTERIA Anabaena sp., Nostoc, and Oscillaroria – live and prepared material EXERCISE 2: SUPERGROUP EXCAVATA (Phylum Euglenophyta) – live and prepared material
    [Show full text]
  • The Analysis of Pinus Pinaster Snrks Reveals Clues of the Evolution of This Family and a New Set of Abiotic Stress Resistance Biomarkers
    agronomy Article The Analysis of Pinus pinaster SnRKs Reveals Clues of the Evolution of This Family and a New Set of Abiotic Stress Resistance Biomarkers Francisco Javier Colina * , María Carbó , Ana Álvarez , Luis Valledor * and María Jesús Cañal Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology (IUBA), University of Oviedo, 33006 Oviedo, Spain; [email protected] (M.C.); [email protected] (A.Á.); [email protected] (M.J.C.) * Correspondence: [email protected] (F.J.C.); [email protected] (L.V.) Received: 15 January 2020; Accepted: 17 February 2020; Published: 19 February 2020 Abstract: Climate change is increasing the intensity and incidence of environmental stressors, reducing the biomass yields of forestry species as Pinus pinaster. Selection of new stress-tolerant varieties is thus required. Many genes related to plant stress signaling pathways have proven useful for this purpose with sucrose non-fermenting related kinases (SnRK), conserved across plant evolution and connected to different phosphorylation cascades within ABA- and Ca2+-mediated signaling pathways, as a good example. The modulation of SnRKs and/or the selection of specific SnRK alleles have proven successful strategies to increase plant stress resistance. Despite this, SnRKs have been barely studied in gymnosperms. In this work P. pinaster SnRK sequences (PpiSnRK) were identified through a homology- and domain-based sequence analysis using Arabidopsis SnRK sequences as query. Moreover, PpiSnRKs links to the gymnosperm stress response were modeled out of the known interactions of PpiSnRKs orthologs from other species with different signaling complexity. This approach successfully identified the pine SnRK family and predicted their central role into the gymnosperm stress response, linking them to ABA, Ca2+, sugar/energy and possibly ethylene signaling.
    [Show full text]
  • Distribution of the Water-Soluble Astaxanthin Binding Carotenoprotein (Astap) in Scenedesmaceae
    marine drugs Article Distribution of the Water-Soluble Astaxanthin Binding Carotenoprotein (AstaP) in Scenedesmaceae Hiroki Toyoshima 1, Ami Miyata 1, Risako Yoshida 1, Taichiro Ishige 2, Shinichi Takaichi 3 and Shinji Kawasaki 1,3,* 1 Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan; [email protected] (H.T.); [email protected] (A.M.); [email protected] (R.Y.) 2 NODAI Genome Research Centre, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan; [email protected] 3 Department of Molecular Microbiology, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan; [email protected] * Correspondence: [email protected]; Tel.: +81-3-5477-2764 Abstract: Photooxidative stress-inducible water-soluble astaxanthin-binding proteins, designated as AstaP,were identified in two Scenedesmaceae strains, Coelastrella astaxanthina Ki-4 and Scenedesmus obtusus Oki-4N; both strains were isolated under high light conditions. These AstaPs are classified as a novel family of carotenoprotein and are useful for providing valuable astaxanthin in water-soluble form; however, the distribution of AstaP orthologs in other microalgae remains unknown. Here, we exam- ined the distribution of AstaP orthologs in the family Scenedesmaceae with two model microalgae, Chlamydomonas reinhardtii and Chlorella variabilis. The expression of AstaP orthologs under photooxida- Citation: Toyoshima, H.; Miyata, A.; tive stress conditions was detected in cell extracts of Scenedesmaceae strains, but not in model algal Yoshida, R.; Ishige, T.; Takaichi, S.; strains. Aqueous orange proteins produced by Scenedesmaceae strains were shown to bind astaxanthin.
    [Show full text]
  • CH28 PROTISTS.Pptx
    9/29/14 Biosc 41 Announcements 9/29 Review: History of Life v Quick review followed by lecture quiz (history & v How long ago is Earth thought to have formed? phylogeny) v What is thought to have been the first genetic material? v Lecture: Protists v Are we tetrapods? v Lab: Protozoa (animal-like protists) v Most atmospheric oxygen comes from photosynthesis v Lab exam 1 is Wed! (does not cover today’s lab) § Since many of the first organisms were photosynthetic (i.e. cyanobacteria), a LOT of excess oxygen accumulated (O2 revolution) § Some organisms adapted to use it (aerobic respiration) Review: History of Life Review: Phylogeny v Which organelles are thought to have originated as v Homology is similarity due to shared ancestry endosymbionts? v Analogy is similarity due to convergent evolution v During what event did fossils resembling modern taxa suddenly appear en masse? v A valid clade is monophyletic, meaning it consists of the ancestor taxon and all its descendants v How many mass extinctions seem to have occurred during v A paraphyletic grouping consists of an ancestral species and Earth’s history? Describe one? some, but not all, of the descendants v When is adaptive radiation likely to occur? v A polyphyletic grouping includes distantly related species but does not include their most recent common ancestor v Maximum parsimony assumes the tree requiring the fewest evolutionary events is most likely Quiz 3 (History and Phylogeny) BIOSC 041 1. How long ago is Earth thought to have formed? 2. Why might many organisms have evolved to use aerobic respiration? PROTISTS! Reference: Chapter 28 3.
    [Show full text]
  • The Origin of Alternation of Generations in Land Plants
    Theoriginof alternation of generations inlandplants: afocuson matrotrophy andhexose transport Linda K.E.Graham and LeeW .Wilcox Department of Botany,University of Wisconsin, 430Lincoln Drive, Madison,WI 53706, USA (lkgraham@facsta¡.wisc .edu ) Alifehistory involving alternation of two developmentally associated, multicellular generations (sporophyteand gametophyte) is anautapomorphy of embryophytes (bryophytes + vascularplants) . Microfossil dataindicate that Mid ^Late Ordovicianland plants possessed such alifecycle, and that the originof alternationof generationspreceded this date.Molecular phylogenetic data unambiguously relate charophyceangreen algae to the ancestryof monophyletic embryophytes, and identify bryophytes as early-divergentland plants. Comparison of reproduction in charophyceans and bryophytes suggests that the followingstages occurredduring evolutionary origin of embryophytic alternation of generations: (i) originof oogamy;(ii) retention ofeggsand zygotes on the parentalthallus; (iii) originof matrotrophy (regulatedtransfer ofnutritional and morphogenetic solutes fromparental cells tothe nextgeneration); (iv)origin of a multicellularsporophyte generation ;and(v) origin of non-£ agellate, walled spores. Oogamy,egg/zygoteretention andmatrotrophy characterize at least some moderncharophyceans, and arepostulated to represent pre-adaptativefeatures inherited byembryophytes from ancestral charophyceans.Matrotrophy is hypothesizedto have preceded originof the multicellularsporophytes of plants,and to represent acritical innovation.Molecular
    [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]
  • 23.3 Groups of Protists
    Chapter 23 | Protists 639 cysts that are a protective, resting stage. Depending on habitat of the species, the cysts may be particularly resistant to temperature extremes, desiccation, or low pH. This strategy allows certain protists to “wait out” stressors until their environment becomes more favorable for survival or until they are carried (such as by wind, water, or transport on a larger organism) to a different environment, because cysts exhibit virtually no cellular metabolism. Protist life cycles range from simple to extremely elaborate. Certain parasitic protists have complicated life cycles and must infect different host species at different developmental stages to complete their life cycle. Some protists are unicellular in the haploid form and multicellular in the diploid form, a strategy employed by animals. Other protists have multicellular stages in both haploid and diploid forms, a strategy called alternation of generations, analogous to that used by plants. Habitats Nearly all protists exist in some type of aquatic environment, including freshwater and marine environments, damp soil, and even snow. Several protist species are parasites that infect animals or plants. A few protist species live on dead organisms or their wastes, and contribute to their decay. 23.3 | Groups of Protists By the end of this section, you will be able to do the following: • Describe representative protist organisms from each of the six presently recognized supergroups of eukaryotes • Identify the evolutionary relationships of plants, animals, and fungi within the six presently recognized supergroups of eukaryotes • Identify defining features of protists in each of the six supergroups of eukaryotes. In the span of several decades, the Kingdom Protista has been disassembled because sequence analyses have revealed new genetic (and therefore evolutionary) relationships among these eukaryotes.
    [Show full text]
  • Abstract Use of the Green Microalga Monoraphidium Sp. Dek19 to Remediate Wastewater
    ABSTRACT USE OF THE GREEN MICROALGA MONORAPHIDIUM SP. DEK19 TO REMEDIATE WASTEWATER: SALINITY STRESS AND SCALING TO MESOCOSM CULTURES Anthony Robert Kephart, M.S. Department of Biological Sciences Northern Illinois University, 2016 Gabriel Holbrook, Director The purpose of this thesis was to investigate the growth of the green microalga Monoraphidium sp. Dek19 in the context of phycoremediation under conditions representative of wastewater media of a Midwest wastewater treatment facility. Microalgae were grown in effluent collected from four different wastewater streams at the DeKalb Sanitary District (DSD), DeKalb, Illinois, USA in volumes from 1 L to 380 L. It was determined through preliminary modeling of public data that Monoraphidium sp. Dek19 will likely outcompete local heterospecifics in final effluent wastewaters at the DSD 51.8% of the year. It was also determined that neither nitrogen nor phosphorus should become a limiting nutrient throughout the year. Study of the response of Monoraphidium sp. Dek19 to salinity stress was also completed. Salt stress caused a significant increase in lipid accumulation in salt stressed cultures compared to control cultures (37.0-50.5% increase) with a reduction in biomass productivity. Increases in photosynthetic pigments per cell were seen under salt stress, though the ratio of chlorophyll a and b remained constant. Finally, nitrate uptake was not greatly affected by salinity stress except when biomass accumulation became a corollary for uptake (nitrogen saturation). Luxury uptake of phosphate was significantly affected by wastewater salinity (p<0.001). High sodium potentially interrupts phosphate stress response proteins, slowing internalization of phosphate. Phosphate removal was still possible as some protein binding proteins appear to operate independent of sodium.
    [Show full text]
  • Brown Algae and 4) the Oomycetes (Water Molds)
    Protista Classification Excavata The kingdom Protista (in the five kingdom system) contains mostly unicellular eukaryotes. This taxonomic grouping is polyphyletic and based only Alveolates on cellular structure and life styles not on any molecular evidence. Using molecular biology and detailed comparison of cell structure, scientists are now beginning to see evolutionary SAR Stramenopila history in the protists. The ongoing changes in the protest phylogeny are rapidly changing with each new piece of evidence. The following classification suggests 4 “supergroups” within the Rhizaria original Protista kingdom and the taxonomy is still being worked out. This lab is looking at one current hypothesis shown on the right. Some of the organisms are grouped together because Archaeplastida of very strong support and others are controversial. It is important to focus on the characteristics of each clade which explains why they are grouped together. This lab will only look at the groups that Amoebozoans were once included in the Protista kingdom and the other groups (higher plants, fungi, and animals) will be Unikonta examined in future labs. Opisthokonts Protista Classification Excavata Starting with the four “Supergroups”, we will divide the rest into different levels called clades. A Clade is defined as a group of Alveolates biological taxa (as species) that includes all descendants of one common ancestor. Too simplify this process, we have included a cladogram we will be using throughout the SAR Stramenopila course. We will divide or expand parts of the cladogram to emphasize evolutionary relationships. For the protists, we will divide Rhizaria the supergroups into smaller clades assigning them artificial numbers (clade1, clade2, clade3) to establish a grouping at a specific level.
    [Show full text]
  • The Draft Genome of the Small, Spineless Green Alga
    Protist, Vol. 170, 125697, December 2019 http://www.elsevier.de/protis Published online date 25 October 2019 ORIGINAL PAPER Protist Genome Reports The Draft Genome of the Small, Spineless Green Alga Desmodesmus costato-granulatus (Sphaeropleales, Chlorophyta) a,b,2 a,c,2 d,e f g Sibo Wang , Linzhou Li , Yan Xu , Barbara Melkonian , Maike Lorenz , g b a,e f,1 Thomas Friedl , Morten Petersen , Sunil Kumar Sahu , Michael Melkonian , and a,b,1 Huan Liu a BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China b Department of Biology, University of Copenhagen, Copenhagen, Denmark c Department of Biotechnology and Biomedicine, Technical University of Denmark, Copenhagen, Denmark d BGI Education Center, University of Chinese Academy of Sciences, Beijing, China e State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China f University of Duisburg-Essen, Campus Essen, Faculty of Biology, Universitätsstr. 2, 45141 Essen, Germany g Department ‘Experimentelle Phykologie und Sammlung von Algenkulturen’, University of Göttingen, Nikolausberger Weg 18, 37073 Göttingen, Germany Submitted October 9, 2019; Accepted October 21, 2019 Desmodesmus costato-granulatus (Skuja) Hegewald 2000 (Sphaeropleales, Chlorophyta) is a small, spineless green alga that is abundant in the freshwater phytoplankton of oligo- to eutrophic waters worldwide. It has a high lipid content and is considered for sustainable production of diverse compounds, including biofuels. Here, we report the draft whole-genome shotgun sequencing of D. costato-granulatus strain SAG 18.81. The final assembly comprises 48,879,637 bp with over 4,141 scaffolds. This whole-genome project is publicly available in the CNSA (https://db.cngb.org/cnsa/) of CNGBdb under the accession number CNP0000701.
    [Show full text]
  • TRADITIONAL GENERIC CONCEPTS VERSUS 18S Rrna GENE PHYLOGENY in the GREEN ALGAL FAMILY SELENASTRACEAE (CHLOROPHYCEAE, CHLOROPHYTA) 1
    J. Phycol. 37, 852–865 (2001) TRADITIONAL GENERIC CONCEPTS VERSUS 18S rRNA GENE PHYLOGENY IN THE GREEN ALGAL FAMILY SELENASTRACEAE (CHLOROPHYCEAE, CHLOROPHYTA) 1 Lothar Krienitz2 Institut für Gewässerökologie und Binnenfischerei, D-16775 Stechlin, Neuglobsow, Germany Iana Ustinova Institut für Botanik und Pharmazeutische Biologie der Universität, Staudtstrasse 5, D-91058 Erlangen, Germany Thomas Friedl Albrecht-von-Haller-Institut für Pflanzenwissenschaften, Abteilung Experimentelle Phykologie und Sammlung von Algenkulturen, Universität Göttingen, Untere Karspüle 2, D-37037 Göttingen, Germany and Volker A. R. Huss Institut für Botanik und Pharmazeutische Biologie der Universität, Staudtstrasse 5, D-91058 Erlangen, Germany Coccoid green algae of the Selenastraceae were in- few diacritic characteristics and that contain only a vestigated by means of light microscopy, TEM, and small number of species) and to reestablish “large” 18S rRNA analyses to evaluate the generic concept in genera of Selenastraceae such as Ankistrodesmus. this family. Phylogenetic trees inferred from the 18S Key index words: 18S rRNA, Ankistrodesmus, Chloro- rRNA gene sequences showed that the studied spe- phyta, Kirchneriella, Monoraphidium, molecular system- cies of autosporic Selenastraceae formed a well- atics, morphology, Podohedriella, pyrenoid, Quadrigula, resolved monophyletic clade within the DO group of Selenastraceae Chlorophyceae. Several morphological characteris- tics that are traditionally used as generic features Abbreviations: LM, light microscopy
    [Show full text]
  • Evolution of the Life Cycle in Land Plants
    Journal of Systematics and Evolution 50 (3): 171–194 (2012) doi: 10.1111/j.1759-6831.2012.00188.x Review Evolution of the life cycle in land plants ∗ 1Yin-Long QIU 1Alexander B. TAYLOR 2Hilary A. McMANUS 1(Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA) 2(Department of Biological Sciences, Le Moyne College, Syracuse, NY 13214, USA) Abstract All sexually reproducing eukaryotes have a life cycle consisting of a haploid and a diploid phase, marked by meiosis and syngamy (fertilization). Each phase is adapted to certain environmental conditions. In land plants, the recently reconstructed phylogeny indicates that the life cycle has evolved from a condition with a dominant free-living haploid gametophyte to one with a dominant free-living diploid sporophyte. The latter condition allows plants to produce more genotypic diversity by harnessing the diversity-generating power of meiosis and fertilization, and is selectively favored as more solar energy is fixed and fed into the biosystem on earth and the environment becomes more heterogeneous entropically. Liverworts occupy an important position for understanding the origin of the diploid generation in the life cycle of land plants. Hornworts and lycophytes represent critical extant transitional groups in the change from the gametophyte to the sporophyte as the independent free-living generation. Seed plants, with the most elaborate sporophyte and the most reduced gametophyte (except the megagametophyte in many gymnosperms), have the best developed sexual reproduction system that can be matched only by mammals among eukaryotes: an ancient and stable sex determination mechanism (heterospory) that enhances outcrossing, a highly bimodal and skewed distribution of sperm and egg numbers, a male-driven mutation system, female specialization in mutation selection and nourishment of the offspring, and well developed internal fertilization.
    [Show full text]