DOCSLIB.ORG

Genome Evolution of Symbiodiniaceae

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Genome Evolution of Symbiodiniaceae Genome evolution of Symbiodiniaceae Raúl Augusto González Pech MSc in Evolution, Ecology and Systematics BSc in Biology A thesis submitted for the degree of Doctor of Philosophy at The University of Queensland in 2020 Institute for Molecular Bioscience Abstract Symbiotic interactions between dinoflagellates (Symbiodiniaceae) and corals give rise to the ecological complexity and biodiversity of reef ecosystems. Comparative genomic studies can aid in tracing the evolutionary history of these dinoflagellates, and thus elucidate the evolutionary forces that drove their diversification and adaptation as predominantly symbiotic lineages. However, genome data from these ecologically important organisms remain scarce, largely due to their immense sizes and idiosyncratic genome features. The incorporation of genome-scale data from diverse lineages in a comprehensive comparative analysis is essential to better understand the molecular and evolutionary mechanisms that underpin the diversification of Symbiodiniaceae. In this thesis, I first review and discuss the state-of-the-art of Symbiodiniaceae genomics in depth, highlighting the genetic and ecological diversity of these dinoflagellates. In addition, I present a theoretical framework, based on our current knowledge of intracellular bacterial symbionts and parasites, to approach the study of genome evolution in Symbiodiniaceae along the broad spectrum of symbiotic associations they can establish. I also summarise and explain how common methods in comparative genomics can be implemented to improve our understanding of Symbiodiniaceae evolution. Using available genome and transcriptome data in a comparative analysis (Chapter 3), I identified gene functions that distinguish Symbiodiniaceae from other dinoflagellates in Order Suessiales, as well as functions specific to the major lineages within the family. These results show that gene functions shared by all lineages in Symbiodiniaceae are relevant to adaptation to the environment, as well as to the establishment and maintenance of symbiosis. I also determined functions specific to each lineage and highlight their potential use in future research to understand niche specialisation. The basal genus Symbiodinium consists of both free-living and symbiotic forms, and most dinoflagellates external to Symbiodiniaceae are free-living. Genome data from Symbiodinium therefore represent a key analysis platform to assess genome features related to the evolutionary transition from a free-living to a symbiotic lifestyle. Next, I generated and compared high-quality de novo genome assemblies from two Symbiodinium isolates (Chapter 4): the symbiotic Symbiodinium tridacnidorum CCMP2592 and the free-living Symbiodinium natans CCMP2548; these assemblies were generated using both short- and long-read sequence data. My results reveal extensive genome-sequence divergence between these two genomes, and suggest that increased structural rearrangements in the genome of S. tridacnidorum, characterised as distinct types of gene duplication and transposable elements, contribute to the extensive genome divergence between these two species. The distinguishing genome features between these two isolates potentially associate with their evolution towards the distinct ii lifestyles. The results also agree with the notion that the symbiotic lifestyle is a derived trait in Symbiodinium, and that the free-living lifestyle is ancestral. To further assess the divergence within this genus and within family Symbiodiniaceae, I generated de novo genome assemblies from additional five Symbiodinium isolates, encompassing diverse ecological niches. In a comprehensive analysis (Chapter 5) that incorporated all other available genome data of Suessiales (a total of 15 dinoflagellate genomes, nine of which are from Symbiodinium), I assessed, for the first time, genome-sequence divergence within Order Suessiales, within Family Symbiodiniaceae, within Genus Symbiodinium, and among isolates of individual species (i.e. Symbiodinium microadriaticum and Symbiodinium tridacnidorum). Whole-genome comparisons reveal extensive sequence divergence, with no sequence regions common to all 15. Based on similarity of k-mers from whole-genome sequences, the distances among Symbiodinium isolates are similar to those between isolates of distinct genera. Gene functions related to symbiosis and stress response exhibit similar abundance in all analysed genomes. These results suggest that structural rearrangements contribute to genome sequence divergence in Symbiodiniaceae even within a same species, but the gene functions have remained largely conserved in Suessiales. This thesis work is the most comprehensive assessment to date of genome evolution of Symbiodiniaceae, and of the basal genus Symbiodinium. The thesis includes, for the first time, comparisons at the intra-generic and intra-specific levels using extensive whole-genome sequence data. Through this thesis research, seven de novo genome assemblies from diverse Symbiodinium isolates, as well as their corresponding transcriptomes and predicted protein-coding genes, were generated. Customised and novel bioinformatic methods were implemented to accommodate the complexity and idiosyncrasy of dinoflagellate genomes. Knowledge generated from this body of research provide novel insights into genome evolution of Symbiodiniaceae linked to their transition to symbiosis, and the molecular mechanisms that underpin the diversification of the family. The data and analytic workflows from this research can be readily applied in comparative genomic studies of other dinoflagellates and microbial eukaryotes. iii Declaration by author This thesis is composed of my original work, and contains no material previously published or written by another person except where due reference has been made in the text. I have clearly stated the contribution by others to jointly authored works that I have included in my thesis. I have clearly stated the contribution of others to my thesis as a whole, including statistical assistance, survey design, data analysis, significant technical procedures, professional editorial advice, financial support and any other original research work used or reported in my thesis. The content of my thesis is the result of work I have carried out since the commencement of my higher degree by research candidature and does not include a substantial part of work that has been submitted to qualify for the award of any other degree or diploma in any university or other tertiary institution. I have clearly stated which parts of my thesis, if any, have been submitted to qualify for another award. I acknowledge that an electronic copy of my thesis must be lodged with the University Library and, subject to the policy and procedures of The University of Queensland, the thesis be made available for research and study in accordance with the Copyright Act 1968 unless a period of embargo has been approved by the Dean of the Graduate School. I acknowledge that copyright of all material contained in my thesis resides with the copyright holder(s) of that material. Where appropriate I have obtained copyright permission from the copyright holder to reproduce material in this thesis and have sought permission from co-authors for any jointly authored works included in the thesis. iv Publications included in this thesis González-Pech RA, Ragan MA & Chan CX. (2017). Signatures of adaptation and symbiosis in genomes and transcriptomes of Symbiodinium. Scientific Reports 7(1), 15021. DOI: 10.1038/s41598- 017-15029-w González-Pech RA, Bhattacharya D, Ragan MA & Chan CX. (2019). Genome evolution of coral reef symbionts as intracellular residents. Trends in Ecology and Evolution 34(9), 799-806. DOI: 10.1016/j.tree.2019.04.010 González-Pech RA, Stephens TG, Chen Y, Mohamed AR, Cheng Y, Burt DW, Bhattacharya D, Ragan MA & Chan CX. (2019). Structural rearrangements drive extensive genome divergence between symbiotic and free-living Symbiodinium. bioRxiv, 783902. DOI: 10.1101/783902 González-Pech RA, Chen Y, Stephens TG, Shah S, Mohamed AR, Lagorce R, Bhattacharya D, Ragan MA & Chan CX. (2019). Genomes of Symbiodiniaceae reveal extensive sequence divergence but conserved functions at family and genus levels. bioRxiv, 800482. DOI: 10.1101/800482 v Submitted manuscripts included in this thesis No manuscripts submitted for publication. Other publications during candidature Peer-reviewed papers and pre-prints: González-Pech RA, Vargas S, Francis WR & Wörheide G. (2017). Transcriptomic resilience of the Montipora digitata holobiont to low pH. Frontiers in Marine Science 4, 403. DOI: 10.3389/fmars.2017.00403 Voigt O, Erpenbeck D, González-Pech RA, Al-Aidaroos AM, Berumen ML & Wörheide G. (2017). Calcinea of the Red Sea: providing a DNA barcode inventory with description of four new species. Marine Biodiversity, 1-26. DOI: 10.1007/s12526-017-0671-x Liu H, Stephens TG, González-Pech RA, Beltran VH, Lapeyre B, Bongaerts P, Cooke I, Aranda M, Bourne DG, Forêt S, Miller DJ, van Oppen MJH, Voolstra CR, Ragan MA & Chan CX. (2018). Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis. Communications Biology 1, 95. DOI: 10.1038/s42003-018-0098-3 González-Pech RA, Stephens TG & Chan CX. (2018). Commonly misunderstood parameters of NCBI BLAST and important considerations for users. Bioinformatics 35(15), 2697-2698. DOI: 10.1093/bioinformatics/bty1018 Stephens TG, González-Pech RA, Cheng Y, Mohamed AR, Bhattacharya D, Ragan MA & Chan CX. (2019).
Load more

Recommended publications
  • Molecular Data and the Evolutionary History of Dinoflagellates by Juan Fernando Saldarriaga Echavarria Diplom, Ruprecht-Karls-Un
    Molecular data and the evolutionary history of dinoflagellates by Juan Fernando Saldarriaga Echavarria Diplom, Ruprecht-Karls-Universitat Heidelberg, 1993 A THESIS SUBMITTED IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE STUDIES Department of Botany We accept this thesis as conforming to the required standard THE UNIVERSITY OF BRITISH COLUMBIA November 2003 © Juan Fernando Saldarriaga Echavarria, 2003 ABSTRACT New sequences of ribosomal and protein genes were combined with available morphological and paleontological data to produce a phylogenetic framework for dinoflagellates. The evolutionary history of some of the major morphological features of the group was then investigated in the light of that framework. Phylogenetic trees of dinoflagellates based on the small subunit ribosomal RNA gene (SSU) are generally poorly resolved but include many well- supported clades, and while combined analyses of SSU and LSU (large subunit ribosomal RNA) improve the support for several nodes, they are still generally unsatisfactory. Protein-gene based trees lack the degree of species representation necessary for meaningful in-group phylogenetic analyses, but do provide important insights to the phylogenetic position of dinoflagellates as a whole and on the identity of their close relatives. Molecular data agree with paleontology in suggesting an early evolutionary radiation of the group, but whereas paleontological data include only taxa with fossilizable cysts, the new data examined here establish that this radiation event included all dinokaryotic lineages, including athecate forms. Plastids were lost and replaced many times in dinoflagellates, a situation entirely unique for this group. Histones could well have been lost earlier in the lineage than previously assumed.
    [Show full text]
  • Microsatellite Loci for Symbiodinium Goreaui and Other Clade C Symbiodinium
    Conservation Genet Resour DOI 10.1007/s12686-013-0023-5 MICROSATELLITE LETTERS Microsatellite loci for Symbiodinium goreaui and other Clade C Symbiodinium Drew C. Wham • Margaux Carmichael • Todd C. LaJeunesse Received: 27 June 2013 / Accepted: 12 August 2013 Ó Springer Science+Business Media Dordrecht 2013 Abstract The genus Symbiodinium comprises a diverse of ‘‘Clades’’, with the most ecologically dominant and group of dinoflagellates known for their obligate relation- diverse being Clade C (LaJeunesse et al. 2004). While the ship with reef–building corals. Members of the sub-genus group includes phylogenetic types that display narrow and ‘clade C’ are abundant, geographically wide-spread, as broad thermal tolerances, members of clade C are often the well as genetically and ecologically diverse. Coral colonies most severely impacted during bleaching events. For this harboring clade C are often the most exposed to physical reason, their symbiosis biology, dispersal capabilities and stressors. The genotypic diversity, dispersal and genetic genetic identities are of increasing importance to conser- connectivity exhibited by these Symbiodinium are the vation efforts as climates change globally, further affecting subjects of an increasing number of population genetic reef coral communities. studies utilizing microsatellites. Here we describe 18 new Coral endosymbionts are increasingly being studied with microsatellite loci and test their utility across four common multi-locus techniques because this approach offers genetic clade C types. We obtained multi-locus genotypes with resolution to the level of the individual. High-resolution individual level resolution in each of these types. Our markers, however, are not yet available for most Symbiodi- results indicate that multi-locus genotypes can be obtained nium spp.
    [Show full text]
  • (Symbiodinium) in Scleractinian Corals from Tropical Reefs in Southern Hainan
    Journal of Systematics and Evolution 49 (6): 598–605 (2011) doi: 10.1111/j.1759-6831.2011.00161.x Research Article Low genetic diversity of symbiotic dinoflagellates (Symbiodinium) in scleractinian corals from tropical reefs in southern Hainan Island, China 1,2Guo-Wei ZHOU 1,2Hui HUANG∗ 1(Key Laboratory of Marine Bio-resources Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China) 2(Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China) Abstract Endosymbiotic dinoflagellates in the genus Symbiodinium are among the most abundant and important group of photosynthetic protists found in coral reef ecosystems. In order to further characterize this diversity and compare with other regions of the Pacific, samples from 44 species of scleractinian corals representing 20 genera and 9 families, were collected from tropical reefs in southern Hainan Island, China. Denaturing gradient gel electrophoresis fingerprinting of the ribosomal internal transcribed spacer 2 identified 11 genetically distinct Symbiodinium types that have been reported previously. The majority of reef-building coral species (88.6%) harbored only one subcladal type of symbiont, dominated by host-generalist C1 and C3, and was influenced little by the host’s apparent mode of symbiont acquisition. Some species harbored more than one clade of Symbiodinium (clades C, D) concurrently. Although geographically isolated from the rest of the Pacific, the symbiont diversity in southern Hainan Island was relatively low and similar to both the Great Barrier Reef and Hawaii symbiont assemblages (dominated by clade C Symbiodinium). These results indicate that a specialist symbiont is not a prerequisite for existence in remote and isolated areas, but additional work in other geographic regions is necessary to test this idea.
    [Show full text]
  • Microbial Invasion of the Caribbean by an Indo-Pacific Coral Zooxanthella
    Microbial invasion of the Caribbean by an Indo-Pacific coral zooxanthella D. Tye Pettaya,b,1, Drew C. Whama, Robin T. Smithc,d, Roberto Iglesias-Prietoc, and Todd C. LaJeunessea,e,1 aDepartment of Biology, The Pennsylvania State University, University Park, PA 16802; bCollege of Earth, Ocean, and Environment, University of Delaware, Lewes, DE 19958; cUnidad Académica de Sistemas Arrecifales (Puerto Morelos), Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, CP 77500 Cancún, Mexico; dScience Under Sail Institute for Exploration, Sarasota, FL 34230; and ePenn State Institutes of Energy and the Environment, University Park, PA 16802 Edited by Nancy A. Moran, University of Texas at Austin, Austin, TX, and approved April 28, 2015 (received for review February 11, 2015) Human-induced environmental changes have ushered in the rapid coral communities distributed across broad geographic areas decline of coral reef ecosystems, particularly by disrupting the over the decadal ecological timescales that are necessary to keep symbioses between reef-building corals and their photosymbionts. pace with the current rate of warming. However, escalating stressful conditions enable some symbionts Research on the diversity and ecology of coral symbionts to thrive as opportunists. We present evidence that a stress-tolerant suggests that episodes of stressful warming may facilitate the “zooxanthella” from the Indo-Pacific Ocean, Symbiodinium trenchii, spread of ecologically rare or opportunistic species (13). The has rapidly spread to coral communities across the Greater Carib- severe mass bleaching and mortality of eastern Caribbean corals bean. In marked contrast to populations from the Indo-Pacific, in 2005 corresponded with an increased prevalence and abun- Atlantic populations of S.
    [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]
  • PROTISTS Shore and the Waves Are Large, Often the Largest of a Storm Event, and with a Long Period
    (seas), and these waves can mobilize boulders. During this phase of the storm the rapid changes in current direction caused by these large, short-period waves generate high accelerative forces, and it is these forces that ultimately can move even large boulders. Traditionally, most rocky-intertidal ecological stud- ies have been conducted on rocky platforms where the substrate is composed of stable basement rock. Projec- tiles tend to be uncommon in these types of habitats, and damage from projectiles is usually light. Perhaps for this reason the role of projectiles in intertidal ecology has received little attention. Boulder-fi eld intertidal zones are as common as, if not more common than, rock plat- forms. In boulder fi elds, projectiles are abundant, and the evidence of damage due to projectiles is obvious. Here projectiles may be one of the most important defi ning physical forces in the habitat. SEE ALSO THE FOLLOWING ARTICLES Geology, Coastal / Habitat Alteration / Hydrodynamic Forces / Wave Exposure FURTHER READING Carstens. T. 1968. Wave forces on boundaries and submerged bodies. Sarsia FIGURE 6 The intertidal zone on the north side of Cape Blanco, 34: 37–60. Oregon. The large, smooth boulders are made of serpentine, while Dayton, P. K. 1971. Competition, disturbance, and community organi- the surrounding rock from which the intertidal platform is formed zation: the provision and subsequent utilization of space in a rocky is sandstone. The smooth boulders are from a source outside the intertidal community. Ecological Monographs 45: 137–159. intertidal zone and were carried into the intertidal zone by waves. Levin, S. A., and R.
    [Show full text]
  • 0Ca27eedadadd00c93df6016e4
    Long-Range Dispersal and High-Latitude Environments Influence the Population Structure of a “Stress-Tolerant” Dinoflagellate Endosymbiont D. Tye Pettay1,2*, Todd C. LaJeunesse1 1 Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America, 2 College of Earth, Ocean, and Environment, University of Delaware, Lewes, Delaware, United States of America Abstract The migration and dispersal of stress-tolerant symbiotic dinoflagellates (genus Symbiodinium) may influence the response of symbiotic reef-building corals to a warming climate. We analyzed the genetic structure of the stress- tolerant endosymbiont, Symbiodinium glynni nomen nudum (ITS2 - D1), obtained from Pocillopora colonies that dominate eastern Pacific coral communities. Eleven microsatellite loci identified genotypically diverse populations with minimal genetic subdivision throughout the Eastern Tropical Pacific, encompassing 1000’s of square kilometers from mainland Mexico to the Galapagos Islands. The lack of population differentiation over these distances corresponds with extensive regional host connectivity and indicates that Pocillopora larvae, which maternally inherit their symbionts, aid in the dispersal of this symbiont. In contrast to its host, however, subtropical populations of S. glynni in the Gulf of California (Sea of Cortez) were strongly differentiated from populations in tropical eastern Pacific. Selection pressures related to large seasonal fluctuations in temperature and irradiance likely explain this abrupt genetic
    [Show full text]
  • Bleaching' Event
    Downloaded from rspb.royalsocietypublishing.org on 26 October 2009 Outbreak and persistence of opportunistic symbiotic dinoflagellates during the 2005 Caribbean mass coral 'bleaching' event Todd C. LaJeunesse, Robin T. Smith, Jennifer Finney and Hazel Oxenford Proc. R. Soc. B 2009 276, 4139-4148 first published online 9 September 2009 doi: 10.1098/rspb.2009.1405 Supplementary data "Data Supplement" http://rspb.royalsocietypublishing.org/content/suppl/2009/09/09/rspb.2009.1405.DC1.h tml References This article cites 46 articles, 11 of which can be accessed free http://rspb.royalsocietypublishing.org/content/276/1676/4139.full.html#ref-list-1 Subject collections Articles on similar topics can be found in the following collections ecology (956 articles) environmental science (231 articles) Receive free email alerts when new articles cite this article - sign up in the box at the top Email alerting service right-hand corner of the article or click here To subscribe to Proc. R. Soc. B go to: http://rspb.royalsocietypublishing.org/subscriptions This journal is © 2009 The Royal Society Downloaded from rspb.royalsocietypublishing.org on 26 October 2009 Proc. R. Soc. B (2009) 276, 4139–4148 doi:10.1098/rspb.2009.1405 Published online 9 September 2009 Outbreak and persistence of opportunistic symbiotic dinoflagellates during the 2005 Caribbean mass coral ‘bleaching’ event Todd C. LaJeunesse1,*, Robin T. Smith2, Jennifer Finney3 and Hazel Oxenford3 1Department of Biology, Pennsylvania State University, University Park, PA 16802, USA 2Department of Biology, Florida International University, Miami, FL 33199, USA 3Center for Resource Management and Environmental Studies, University of the West Indies, Cave Hill Campus, Barbados Reef corals are sentinels for the adverse effects of rapid global warming on the planet’s ecosystems.
    [Show full text]
  • The Windblown: Possible Explanations for Dinophyte DNA
    bioRxiv preprint doi: https://doi.org/10.1101/2020.08.07.242388; this version posted August 10, 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. The windblown: possible explanations for dinophyte DNA in forest soils Marc Gottschlinga, Lucas Czechb,c, Frédéric Mahéd,e, Sina Adlf, Micah Dunthorng,h,* a Department Biologie, Systematische Botanik und Mykologie, GeoBio-Center, Ludwig- Maximilians-Universität München, D-80638 Munich, Germany b Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, D- 69118 Heidelberg, Germany c Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA d CIRAD, UMR BGPI, F-34398, Montpellier, France e BGPI, Université de Montpellier, CIRAD, IRD, Montpellier SupAgro, Montpellier, France f Department of Soil Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, S7N 5A8, SK, Canada g Eukaryotic Microbiology, Faculty of Biology, Universität Duisburg-Essen, D-45141 Essen, Germany h Centre for Water and Environmental Research (ZWU), Universität Duisburg-Essen, D- 45141 Essen, Germany Running title: Dinophytes in soils Correspondence M. Dunthorn, Eukaryotic Microbiology, Faculty of Biology, Universität Duisburg-Essen, Universitätsstrasse 5, D-45141 Essen, Germany Telephone number: +49-(0)-201-183-2453; email: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.08.07.242388; this version posted August 10, 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.
    [Show full text]
  • Scrippsiella Trochoidea (F.Stein) A.R.Loebl
    MOLECULAR DIVERSITY AND PHYLOGENY OF THE CALCAREOUS DINOPHYTES (THORACOSPHAERACEAE, PERIDINIALES) Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften (Dr. rer. nat.) der Fakultät für Biologie der Ludwig-Maximilians-Universität München zur Begutachtung vorgelegt von Sylvia Söhner München, im Februar 2013 Erster Gutachter: PD Dr. Marc Gottschling Zweiter Gutachter: Prof. Dr. Susanne Renner Tag der mündlichen Prüfung: 06. Juni 2013 “IF THERE IS LIFE ON MARS, IT MAY BE DISAPPOINTINGLY ORDINARY COMPARED TO SOME BIZARRE EARTHLINGS.” Geoff McFadden 1999, NATURE 1 !"#$%&'(&)'*!%*!+! +"!,-"!'-.&/%)$"-"!0'* 111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111 2& ")3*'4$%/5%6%*!+1111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111 7! 8,#$0)"!0'*+&9&6"*,+)-08!+ 111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111 :! 5%*%-"$&0*!-'/,)!0'* 11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111 ;! "#$!%"&'(!)*+&,!-!"#$!'./+,#(0$1$!2! './+,#(0$1$!-!3+*,#+4+).014!1/'!3+4$0&41*!041%%.5.01".+/! 67! './+,#(0$1$!-!/&"*.".+/!1/'!4.5$%"(4$! 68! ./!5+0&%!-!"#$!"#+*10+%,#1$*10$1$! 69! "#+*10+%,#1$*10$1$!-!5+%%.4!1/'!$:"1/"!'.;$*%."(! 6<! 3+4$0&41*!,#(4+)$/(!-!0#144$/)$!1/'!0#1/0$! 6=! 1.3%!+5!"#$!"#$%.%! 62! /0+),++0'* 1111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111<=!
    [Show full text]
  • Sequencing and Comparative Analysis of <I>De Novo</I> Genome
    University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Dissertations and Theses in Biological Sciences Biological Sciences, School of 7-2016 Sequencing and Comparative Analysis of de novo Genome Assemblies of Streptomyces aureofaciens ATCC 10762 Julien S. Gradnigo University of Nebraska - Lincoln, [email protected] Follow this and additional works at: http://digitalcommons.unl.edu/bioscidiss Part of the Bacteriology Commons, Bioinformatics Commons, and the Genomics Commons Gradnigo, Julien S., "Sequencing and Comparative Analysis of de novo Genome Assemblies of Streptomyces aureofaciens ATCC 10762" (2016). Dissertations and Theses in Biological Sciences. 88. http://digitalcommons.unl.edu/bioscidiss/88 This Article is brought to you for free and open access by the Biological Sciences, School of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Dissertations and Theses in Biological Sciences by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. SEQUENCING AND COMPARATIVE ANALYSIS OF DE NOVO GENOME ASSEMBLIES OF STREPTOMYCES AUREOFACIENS ATCC 10762 by Julien S. Gradnigo A THESIS Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Master of Science Major: Biological Sciences Under the Supervision of Professor Etsuko Moriyama Lincoln, Nebraska July, 2016 SEQUENCING AND COMPARATIVE ANALYSIS OF DE NOVO GENOME ASSEMBLIES OF STREPTOMYCES AUREOFACIENS ATCC 10762 Julien S. Gradnigo, M.S. University of Nebraska, 2016 Advisor: Etsuko Moriyama Streptomyces aureofaciens is a Gram-positive Actinomycete used for commercial antibiotic production. Although it has been the subject of many biochemical studies, no public genome resource was available prior to this project.
    [Show full text]
  • Morphology, Molecular Phylogeny, and Pigment Characterization of a Novel Phenotype of the Dinoflagellate Genuspelagodinium from Korean Waters
    Research Article Algae 2015, 30(3): 183-195 http://dx.doi.org/10.4490/algae.2015.30.3.183 Open Access Morphology, molecular phylogeny, and pigment characterization of a novel phenotype of the dinoflagellate genus Pelagodinium from Korean waters Éric Potvin1,*, Hae Jin Jeong2, Nam Seon Kang2, Jae Hoon Noh3 and Eun Jin Yang1 1Division of Polar Ocean Environment, Korea Polar Research Institute, Incheon 406-840, Korea 2School of Earth and Environmental Sciences, College of Natural Sciences, Seoul National University, Seoul 151-747, Korea 3Marine Resources Research Department, KIOST, Ansan 425-600, Korea The dinoflagellate genusPelagodinium is genetically classified in distinct sub-clades and subgroups. However, it is dif- ficult to determine whether this genetic diversity represents intra- or interspecific divergence within the genus since only the morphology of the type strain of the genus Pelagodinium, Pelagodinium bei, is available. An isolate associated with the genus Pelagodinium from Shiwha Bay, Korea, was recently cultured. This isolate formed a subgroup with 3 to 4 strains from the Atlantic Ocean, Mediterranean Sea, and Indian Ocean. This subgroup was distinct from the subgroup contain- ing P. bei. The morphology of the isolate was analyzed using optical and scanning electron microscopy and was almost identical to that of P. bei except that this isolate had two series of amphiesmal vesicles (AVs) in the cingulum, unlike P. bei that has one series. When the pigment compositions of the isolate and P. bei were analyzed using high-performance liquid chromatography, these two strains had peridinin as a major accessory pigment and their pigment compositions were almost identical.
    [Show full text]