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Transcriptional Landscapes of Lipid Producing Microalgae Benoît M
Transcriptional landscapes of lipid producing microalgae Benoît M. Carrères 2019 Transcriptional landscapes of lipid producing microalgae Benoî[email protected]:~$ ▮ Transcriptional landscapes of lipid producing microalgae Benoît Manuel Carrères Thesis committee Promotors Prof. Dr Vitor A. P. Martins dos Santos Professor of Systems and Synthetic Biology Wageningen University & Research Prof. Dr René H. Wij$els Professor of Bioprocess Engineering Wageningen University & Research Co-promotors Dr Peter J. Schaa% Associate professor* Systems and Synthetic Biology Wageningen University & Research Dr Dirk E. Martens Associate professor* Bioprocess Engineering Wageningen University & Research ,ther mem-ers Prof. Dr Alison Smith* University of Cam-ridge Prof. Dr. Dic+ de Ridder* Wageningen University & Research Dr Aalt D.). van Di#+* Wageningen University & Research Dr Ga-ino Sanche/(Pere/* Genetwister* Wageningen This research 0as cond1cted under the auspices of the .rad1ate School V2A. 3Advanced studies in Food Technology* Agro-iotechnology* Nutrition and Health Sciences). Transcriptional landscapes of lipid producing microalgae Benoît Manuel Carrères Thesis su-mitted in ful8lment of the re9uirements for the degree of doctor at Wageningen University -y the authority of the Rector Magnificus, Prof. Dr A.P.). Mol* in the presence of the Thesis' ommittee a%%ointed by the Academic Board to be defended in pu-lic on Wednesday 2; Novem-er 2;<= at 1.>; p.m in the Aula. Benoît Manuel Carrères 5ranscriptional landsca%es of lipid producing -
Uncovering Unique Green Algae and Cyanobacteria Isolated from Biocrusts in Highly Saline Potash Tailing Pile Habitats, Using an Integrative Approach
microorganisms Article Uncovering Unique Green Algae and Cyanobacteria Isolated from Biocrusts in Highly Saline Potash Tailing Pile Habitats, Using an Integrative Approach Veronika Sommer 1,2, Tatiana Mikhailyuk 3, Karin Glaser 1 and Ulf Karsten 1,* 1 Institute for Biological Sciences, Applied Ecology and Phycology, University of Rostock, 18059 Rostock, Germany; [email protected] (V.S.); [email protected] (K.G.) 2 upi UmweltProjekt Ingenieursgesellschaft mbH, 39576 Stendal, Germany 3 National Academy of Sciences of Ukraine, M.G. Kholodny Institute of Botany, 01601 Kyiv, Ukraine; [email protected] * Correspondence: [email protected] Received: 4 September 2020; Accepted: 22 October 2020; Published: 27 October 2020 Abstract: Potash tailing piles caused by fertilizer production shape their surroundings because of the associated salt impact. A previous study in these environments addressed the functional community “biocrust” comprising various micro- and macro-organisms inhabiting the soil surface. In that previous study, biocrust microalgae and cyanobacteria were isolated and morphologically identified amongst an ecological discussion. However, morphological species identification maybe is difficult because of phenotypic plasticity, which might lead to misidentifications. The present study revisited the earlier species list using an integrative approach, including molecular methods. Seventy-six strains were sequenced using the markers small subunit (SSU) rRNA gene and internal transcribed spacer (ITS). Phylogenetic analyses confirmed some morphologically identified species. However, several other strains could only be identified at the genus level. This indicates a high proportion of possibly unknown taxa, underlined by the low congruence of the previous morphological identifications to our results. In general, the integrative approach resulted in more precise species identifications and should be considered as an extension of the previous morphological species list. -
Neoproterozoic Origin and Multiple Transitions to Macroscopic Growth in Green Seaweeds
bioRxiv preprint doi: https://doi.org/10.1101/668475; this version posted June 12, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds Andrea Del Cortonaa,b,c,d,1, Christopher J. Jacksone, François Bucchinib,c, Michiel Van Belb,c, Sofie D’hondta, Pavel Škaloudf, Charles F. Delwicheg, Andrew H. Knollh, John A. Raveni,j,k, Heroen Verbruggene, Klaas Vandepoeleb,c,d,1,2, Olivier De Clercka,1,2 Frederik Leliaerta,l,1,2 aDepartment of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium bDepartment of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Zwijnaarde, Belgium cVIB Center for Plant Systems Biology, Technologiepark 71, 9052 Zwijnaarde, Belgium dBioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052 Zwijnaarde, Belgium eSchool of Biosciences, University of Melbourne, Melbourne, Victoria, Australia fDepartment of Botany, Faculty of Science, Charles University, Benátská 2, CZ-12800 Prague 2, Czech Republic gDepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA hDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138, USA. iDivision of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee, DD2 5DA, UK jSchool of Biological Sciences, University of Western Australia (M048), 35 Stirling Highway, WA 6009, Australia kClimate Change Cluster, University of Technology, Ultimo, NSW 2006, Australia lMeise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium 1To whom correspondence may be addressed. Email [email protected], [email protected], [email protected] or [email protected]. -
The Draft Genome of Hariotina Reticulata (Sphaeropleales
Protist, Vol. 170, 125684, December 2019 http://www.elsevier.de/protis Published online date 19 October 2019 ORIGINAL PAPER Protist Genome Reports The Draft Genome of Hariotina reticulata (Sphaeropleales, Chlorophyta) Provides Insight into the Evolution of Scenedesmaceae a,b,2 c,d,2 b e f Yan Xu , Linzhou Li , Hongping Liang , Barbara Melkonian , Maike Lorenz , f g a,g e,1 a,g,1 Thomas Friedl , Morten Petersen , Huan Liu , Michael Melkonian , and Sibo Wang a BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China b BGI Education Center, University of Chinese Academy of Sciences, Beijing, China c China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China d Department of Biotechnology and Biomedicine, Technical University of Denmark, Copenhagen, Denmark e University of Duisburg-Essen, Campus Essen, Faculty of Biology, Universitätsstr. 5, 45141 Essen, Germany f Department ‘Experimentelle Phykologie und Sammlung von Algenkulturen’ (EPSAG), University of Göttingen, Nikolausberger Weg 18, 37073 Göttingen, Germany g Department of Biology, University of Copenhagen, Copenhagen, Denmark Submitted October 9, 2019; Accepted October 13, 2019 Hariotina reticulata P. A. Dangeard 1889 (Sphaeropleales, Chlorophyta) is a common member of the summer phytoplankton of meso- to highly eutrophic water bodies with a worldwide distribution. Here, we report the draft whole-genome shotgun sequencing of H. reticulata strain SAG 8.81. The final assembly comprises 107,596,510 bp with over 15,219 scaffolds (>100 bp). This whole-genome project is publicly available in the CNSA (https://db.cngb.org/cnsa/) of CNGBdb under the accession number CNP0000705. © 2019 Elsevier GmbH. All rights reserved. Key words: Scenedesmaceae; genome; algae; comparative genomics. -
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. -
Structural Variation and Evolution of Chloroplast Trnas in Green Algae
Structural variation and evolution of chloroplast tRNAs in green algae Fangbing Qi, Yajing Zhao, Ningbo Zhao, Kai Wang, Zhonghu Li and Yingjuan Wang State Key Laboratory of Biotechnology of Shannxi Province, Key Laboratory of Resource Biology and Biotech- nology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China ABSTRACT As one of the important groups of the core Chlorophyta (Green algae), Chlorophyceae plays an important role in the evolution of plants. As a carrier of amino acids, tRNA plays an indispensable role in life activities. However, the structural variation of chloroplast tRNA and its evolutionary characteristics in Chlorophyta species have not been well studied. In this study, we analyzed the chloroplast genome tRNAs of 14 species in five categories in the green algae. We found that the number of chloroplasts tRNAs of Chlorophyceae is maintained between 28–32, and the length of the gene sequence ranges from 71 nt to 91 nt. There are 23–27 anticodon types of tRNAs, and some tRNAs have missing anticodons that are compensated for by other types of anticodons of that tRNA. In addition, three tRNAs were found to contain introns in the anti-codon loop of the tRNA, but the analysis scored poorly and it is presumed that these introns are not functional. After multiple sequence alignment, the 9-loop is the most conserved structural unit in the tRNA secondary structure, containing mostly U-U-C-x-A-x-U conserved sequences. The number of transitions in tRNA is higher than the number of transversions. In the replication loss analysis, it was found that green algal chloroplast tRNAs may have undergone substantial gene loss during the course of evolution. -
Sphaeropleales) from Periyar River, Kerala
International Journal of Botany Studies ISSN: 2455-541X; Impact Factor: RJIF 5.12 Received: 14-11-2020; Accepted: 29-11-2020: Published: 13-12-2020 www.botanyjournals.com Volume 5; Issue 6; 2020; Page No. 482-488 A systematic account of scenedesmaceae (sphaeropleales) from Periyar River, Kerala Jayalakshmi PS*, Jose John Centre for Post Graduate Studies and Advanced Research, Department of Botany, Sacred Heart College, Thevara, Kochi, Kerala, India Abstract The present study deals with the systematic account of 28 taxa of family Scenedesmaceae, order Sphaeropleales, (formerly belonging to the order Chlorococcales), collected from Periyar River in Kerala. They include the genera, namely, Acutodesmus (1), Desmodesmus (7), Scenedesmus (7), Tetradesmus (4), Westella (1), Coelastrum (5) Hariotina (1), Asterarcys (1) and Dimorphococcus (1). Out of these, three taxa are new to Kerala and most of them are new records from Periyar River. Keywords: Chlorococcales, chlorophyceae, freshwater algae, biodiversity, new report to Kerala 1. Introduction samples were deposited in the Phycology Division, The Chlorococcales comprises of an interesting group of Department of Botany, Sacred Heart College, Thevara, green algae represented by non-motile unicellular or Kochi, Kerala. colonial forms. Most of the members are aquatic and microscopic in nature but some may be macroscopic forms. 3. Results and Discussion Among planktonic Chlorococcales, Scenedesmaceae is one A total of twenty-eight taxa have been collected during the of most diversified and ubiquitous families in freshwater study period. They belong to the genera Acutodesmus (1), ecosystems. On the basis of morphology, Komárek & Fott Desmodesmus (7), Scenedesmus (7), Tetradesmus (4), included Scenedesmaceae in the order Chlorococcales Westella (1), Coelastrum (5) Hariotina (1), Asterarcys (1) (Chlorophyceae), while the family was transferred to the and Dimorphococcus (1). -
A Model Suite of Green Algae Within the Scenedesmaceae for Investigating Contrasting Desiccation Tolerance and Morphology Zoe G
© 2018. Published by The Company of Biologists Ltd | Journal of Cell Science (2018) 131, jcs212233. doi:10.1242/jcs.212233 RESEARCH ARTICLE A model suite of green algae within the Scenedesmaceae for investigating contrasting desiccation tolerance and morphology Zoe G. Cardon1,*, Elena L. Peredo1, Alice C. Dohnalkova2, Hannah L. Gershone3 and Magdalena Bezanilla4,5,‡ ABSTRACT desert-dwelling and aquatic representatives. These related species Microscopic green algae inhabiting desert microbiotic crusts are harbor rich, natural variation that has developed in the presence of remarkably diverse phylogenetically, and many desert lineages have selective pressures within aquatic and desert environments. independently evolved from aquatic ancestors. Here we worked with Lewis and Flechtner (2004) described three independently five desert and aquatic species within the family Scenedesmaceae to evolved lineages of desert-dwelling green algae that fell within Scenedesmus: S. rotundus S. deserticola examine mechanisms that underlie desiccation tolerance and release the genus , and S. bajacalifornicus of unicellular versus multicellular progeny. Live cell staining and time- , that were isolated from the Sevilleta desert, lapse confocal imaging coupled with transmission electron microscopy San Nicolas Island (off the coast of California) and Baja California, established that the desert and aquatic species all divide by multiple respectively. These organisms are particularly intriguing because (rather than binary) fission, although progeny were unicellular in three aquatic relatives within the Scenedesmaceae have been studied for species and multicellular ( joined in a sheet-like coenobium) in two. decades by a number of researchers, who focused on genetic and During division, Golgi complexes were localized near nuclei, and all physiological controls over cell division by multiple fission (e.g. -
A Phylogenetic Study on Scenedesmaceae with The
Fottea, Olomouc, 13(2): 149–164, 2013 149 In memorium to the phycologists Antal Schmidt, Hungary and Theodor Holtmann, Germany. A phylogenetic study on Scenedesmaceae with the description of a new species of Pectinodesmus and the new genera Verrucodesmus and Chodatodesmus (Chlorophyta, Chlorophyceae) Eberhard HEGEWALD1*, Christina BOCK2 & Lothar KRIENITZ3 1 D–52382 Niederzier, Grüner Weg 20, Germany; *Corresponding author e–mail: [email protected] 2 University Duisburg–Essen, Department General Botany, Universitätsstr. 5, D–45141 Essen, Germany 3 Leibniz–Institute of Freshwater Ecology and Inland Fisheries, D–16775 Stechlin–Neuglobsow, Germany Abstract: A comparative study of the phylogeny of Scenedesmaceae based on rRNA gene sequences (ITS1/5.8S/ITS2), cell morphology and cell wall ultrastructure resulted in the acceptance of the genus Acutodesmus and the description of the new genera Verrucodesmus and Chodatodesmus. A new species Pectinodesmus holtmannii and 11 new combinations were erected: Chodatodesmus mucronulatus, Verrucodesmus verrucosus, V. parvus, Pectinodesmus pectinatus f. tortuosus, Acutodesmus bajacalifornicus, A. bernardii, A. deserticola, A. dissociatus, A. distendus, A. nygaardii, A. obliquus var. dactylococcoides. It was shown that the new genera Verrucodesmus and two of the Chodatodesmus strains have enlarged ITS2 helices (helix I in Verrucodesmus and helix III in Chodatodesmus). The occurrence of zoospores of Scenedesmaceae in nature was discussed. Key words: Acutodesmus, Chlorophyta, Chodatodesmus, 5.8S, ITS1, ITS2, Pectinodesmus, Scenedesmaceae, Taxonomy, Verrucodesmus, zoospores INTRODUCTION et al. 2003). Subgenera of Scenedesmus were first erected The genus Scenedesmus was interpreted in a broad by CHODAT (1926) (see also KIRIAKOV 1976; HEGEWALD sense that included many species with very different 1978). Based upon electron microscopy, the mainly morphological characters (e.g. -
Provides an Insight Into Genome Evolution And
www.nature.com/scientificreports OPEN Raphidocelis subcapitata (=Pseudokirchneriella subcapitata) provides an insight into genome Received: 18 November 2017 Accepted: 8 May 2018 evolution and environmental Published: xx xx xxxx adaptations in the Sphaeropleales Shigekatsu Suzuki, Haruyo Yamaguchi , Nobuyoshi Nakajima & Masanobu Kawachi The Sphaeropleales are a dominant group of green algae, which contain species important to freshwater ecosystems and those that have potential applied usages. In particular, Raphidocelis subcapitata is widely used worldwide for bioassays in toxicological risk assessments. However, there are few comparative genome analyses of the Sphaeropleales. To reveal genome evolution in the Sphaeropleales based on well-resolved phylogenetic relationships, nuclear, mitochondrial, and plastid genomes were sequenced in this study. The plastid genome provides insights into the phylogenetic relationships of R. subcapitata, which is located in the most basal lineage of the four species in the family Selenastraceae. The mitochondrial genome shows dynamic evolutionary histories with intron expansion in the Selenastraceae. The 51.2 Mbp nuclear genome of R. subcapitata, encoding 13,383 protein-coding genes, is more compact than the genome of its closely related oil- rich species, Monoraphidium neglectum (Selenastraceae), Tetradesmus obliquus (Scenedesmaceae), and Chromochloris zofngiensis (Chromochloridaceae); however, the four species share most of their genes. The Sphaeropleales possess a large number of genes for glycerolipid metabolism and sugar assimilation, which suggests that this order is capable of both heterotrophic and mixotrophic lifestyles in nature. Comparison of transporter genes suggests that the Sphaeropleales can adapt to diferent natural environmental conditions, such as salinity and low metal concentrations. Chlorophyceae are genetically, morphologically, and ecologically diverse class of green algae1. -
Chlorophyta, Chlorophyceae): Life Cycle and Taxonomy
Fottea 12(1): 75–81, 2012 75 Ettliella tetraspora (Chlorophyta, Chlorophyceae): life cycle and taxonomy František HINDÁK & Alica HINDÁKOVÁ Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, SK–84523 Bratislava, Slovakia; e–mail: [email protected]; [email protected] Abstract: The morphology and mode of reproduction in Ettiella tetraspora HINDÁK 1988, a green coenobial alga described from the Czech Republic and Finland, were studied from the plankton of the water reservoir Förmitzspeicher in NE Bavaria, Germany. The morphology of cells and coenobia of the species in this population was in agreement with published data for the species, but its reproduction was not of the Oocystis – type as it has been declared in the relevant literature. The protoplast of mother cells does not divide simultaneously into 4 autospores as in many coccal green algae, but always in two autospores. The first division of the mother cell is perpendicular to the longitudinal axis of the cell and two walled daughter cells arise. Subsequently, the newly formed daughter cells divide again, but this time perpendicular to the new formed cell cross wall. Ultimately, in a new coenobium all four daughter cells are arranged in parallel. Daughter cells remain inside a slightly enlarged mother cell wall (well visible only near the cross wall) and are released by its gelatinisation. Such subsequent production of four autospores from the mother cell represents a special type of multiplication in the green coccal algae known also in some other species [e.g. Tetrastrum komarekii HINDÁK 1977, Willea irregularis (WILLE ) SC H MIDLE 1900, Makinoella tosaensis OKADA 1949]. -
Dynamic Evolution of Mitochondrial Genomes in Trebouxiophyceae
www.nature.com/scientificreports OPEN Dynamic evolution of mitochondrial genomes in Trebouxiophyceae, including the frst completely Received: 27 September 2018 Accepted: 22 May 2019 assembled mtDNA from a lichen- Published: xx xx xxxx symbiont microalga (Trebouxia sp. TR9) Fernando Martínez-Alberola1, Eva Barreno 1, Leonardo M. Casano 2, Francisco Gasulla2, Arántzazu Molins1 & Eva M. del Campo 2 Trebouxiophyceae (Chlorophyta) is a species-rich class of green algae with a remarkable morphological and ecological diversity. Currently, there are a few completely sequenced mitochondrial genomes (mtDNA) from diverse Trebouxiophyceae but none from lichen symbionts. Here, we report the mitochondrial genome sequence of Trebouxia sp. TR9 as the frst complete mtDNA sequence available for a lichen-symbiont microalga. A comparative study of the mitochondrial genome of Trebouxia sp. TR9 with other chlorophytes showed important organizational changes, even between closely related taxa. The most remarkable change is the enlargement of the genome in certain Trebouxiophyceae, which is principally due to larger intergenic spacers and seems to be related to a high number of large tandem repeats. Another noticeable change is the presence of a relatively large number of group II introns interrupting a variety of tRNA genes in a single group of Trebouxiophyceae, which includes Trebouxiales and Prasiolales. In addition, a fairly well-resolved phylogeny of Trebouxiophyceae, along with other Chlorophyta lineages, was obtained based on a set of seven well-conserved mitochondrial genes. Te use of organelle genomic information has become a common practice for comparative studies and phy- logenetic analyses of entire genomes (phylogenomics). Te sequencing of organelle genomes provides valuable information about the evolution of both the organelles and the organisms that carry them.