DOCSLIB.ORG

RNA Based Research - Development, Application and Analysis Within the MIMAS Project

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
RNA Based Research - Development, Application and Analysis Within the MIMAS Project RNA based research - development, application and analysis within the MIMAS project by Dipl. Biol. Anna Klindworth A thesis submitted in partial fulfilment of requirements for the degree of DOCTOR OF PHILOSOPHY in Biology Approved Thesis Committee: Prof. Dr. Frank Oliver Glöckner (chair) Max Planck Institute for Marine Microbiology, Bremen, Germany Jacobs University, Bremen, Germany Prof. Dr. Matthias Ullrich Jacobs University, Bremen, Germany Prof. Dr. Jack Gilbert University of Chicago, USA Argonne National Laboratory Date of Defense: October, 08th 2012 School of Engineering and Science Statement of Sources DECLARATION I declare that this thesis is my own work and has not been submitted in any form for another degree or diploma at any university or other institution of tertiary education. Information derived from published or unpublished scientifc work has been cited in the text and listed in the references. Signature Date I Thesis abstract Every prokaryotic cell contains different sorts of ribonucleic acid (RNA) molecules, which are mainly dedicated to processing and regulating gene expression. The wide palette of functions is reflected by distinct RNA types, and each of them is represented by a complex and comprehensive research field. In particular, different culture-independent applications have attracted attention recently because the majority of microbes still resists cultivation until today. For example, the standard approach for microbial diversity studies is based on the comparative analysis of the evolutionarily conserved 16S ribosomal RNA gene (16S rDNA), and messenger RNA (mRNA) based metatranscriptomics allows culture independent gene expression analysis without prior knowledge of the present microbes or transcripts. 16S rDNA biodiversity studies, metatranscriptomics and other ‘omic’ applications play a central role within the MIMAS project, which aims at characterizing a bacterioplankton community at the long-term ecological research site Helgoland Roads. However, culture- independent applications have their limitations, and a careful design of experimental procedures is crucial to assure that these limitations do not overtly bias the results. Therefore, this thesis outlines the development and application of an improved pipeline for the analysis of metatranscriptomic data and the evaluation of PCR primers used to amplify 16S rRNA. In particular, the outcome of the latter serves as a guideline for enhanced research to find the most suitable primer pair for 16S rDNA biodiversity analysis in any habitat using any currently available sequencing technology. The methods developed were used in a multi ‘omic’ study to characterize the phylogenetic and functional potential of the microbial community. The results identified the key players of an observed bacterioplankton bloom at Helgoland Roads and provided the first insights into taxonomically distinct nutrient strategies. They indicated that Flavobacteria, Gammaproteobacteria and Alphaproteobacteria are specialized for successive degradation of different algal primary products. This provided a series of ecological niches, allowing certain community members to grow. The results helped to uncover the secret of how members of the bacterioplankton can evade extinction despite the limited resources in the habitat. The work accomplished allows future follow-up studies and furnishes scientific society with guidelines to perform accurate diversity studies. Moreover the outcome serves as basis for future ecosystem monitoring. II III Table of contents Statement of Sources ................................................................................................................... I Thesis abstract ........................................................................................................................... II Table of contents ....................................................................................................................... II List of abbreviations ................................................................................................................. VI List of figures ........................................................................................................................... IX List of tables .......................................................................................................................... XIII 1. Chapter .............................................................................................................................. 1 Introduction 1.1. The multiple facets of the RNA ...................................................................................... 1 1.2. 16S rDNA based research ............................................................................................... 4 1.2.1. 16S rDNA as a marker gene ........................................................................................ 4 1.2.2. Sequencing of the 16S rDNA gene .............................................................................. 6 1.2.3. Limitations of PCR based 16S rDNA analysis ............................................................ 8 1.3. mRNA based gene expression analysis in prokaryotes ................................................... 9 1.3.1. Metatranscriptomics in prokaryotes ............................................................................ 9 1.3.2. Limitations of metatranscriptomics ........................................................................... 11 II 1.4. DNA Sequencing technologies ..................................................................................... 13 1.4.1. Next generation sequencing technologies ................................................................. 13 1.5. The MIMAS project ...................................................................................................... 18 1.5.1. Aims of the MIMAS project (the big picture) ........................................................... 18 1.5.2. Project partner and contributions .................................................................................. 18 1.6. Helgoland Roads: one sampling site of choice within the MIMAS project.................. 20 1.7. Rhodopirellula baltica SH1T: one model organism within the MIMAS project .......... 21 1.8. Research aims and thesis structure ................................................................................ 22 1.9. Evaluation of 16S rDNA primer and primer pairs ........................................................ 22 1.10. NGS based 16S rDNA analysis – proof of concept ...................................................... 22 1.11. Functional analysis the of bacterial community at Helgoland Roads in the North Sea 23 1.12. Impact from pure culture studies ................................................................................... 23 1.13. Publication overview ..................................................................................................... 25 2. Chapter ......................................................................................................................... 28 Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next generation sequencing based diversity studies 2.1. Abstract ......................................................................................................................... 28 2.2. Introduction ................................................................................................................... 29 2.3. Material and Methods.................................................................................................... 30 2.4. Results and Diskussion.................................................................................................. 35 2.5. Conclusion ..................................................................................................................... 47 III 3. Chapter ............................................................................................................................ 50 Substrate-controlled succession of marine bacterioplankton populations induced by phytoplankton bloom 3.1. Abstract ......................................................................................................................... 50 3.2. Manuscript ..................................................................................................................... 51 4. Chapter ............................................................................................................................ 60 Comparative metatranscriptome analysis of a diatome-induced bacterioplankton North Sea bloom 4.1. Abstract ......................................................................................................................... 60 4.2. Introduction ................................................................................................................... 60 4.3. Materials and Methods .................................................................................................. 62 4.4. Results and Discussion .................................................................................................. 67 4.5. Conclusion ..................................................................................................................... 76 5. Chapter ......................................................................................................................... 80 Expression of sulfatases in Rhodopirellula baltica and the diversity of sulfatases
Load more

Recommended publications
  • Comparative Genomic Analysis of Three Pseudomonas
    microorganisms Article Comparative Genomic Analysis of Three Pseudomonas Species Isolated from the Eastern Oyster (Crassostrea virginica) Tissues, Mantle Fluid, and the Overlying Estuarine Water Column Ashish Pathak 1, Paul Stothard 2 and Ashvini Chauhan 1,* 1 Environmental Biotechnology Laboratory, School of the Environment, 1515 S. Martin Luther King Jr. Blvd., Suite 305B, FSH Science Research Center, Florida A&M University, Tallahassee, FL 32307, USA; [email protected] 2 Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G2P5, Canada; [email protected] * Correspondence: [email protected]; Tel.: +1-850-412-5119; Fax: +1-850-561-2248 Abstract: The eastern oysters serve as important keystone species in the United States, especially in the Gulf of Mexico estuarine waters, and at the same time, provide unparalleled economic, ecological, environmental, and cultural services. One ecosystem service that has garnered recent attention is the ability of oysters to sequester impurities and nutrients, such as nitrogen (N), from the estuarine water that feeds them, via their exceptional filtration mechanism coupled with microbially-mediated denitrification processes. It is the oyster-associated microbiomes that essentially provide these myriads of ecological functions, yet not much is known on these microbiota at the genomic scale, especially from warm temperate and tropical water habitats. Among the suite of bacterial genera that appear to interplay with the oyster host species, pseudomonads deserve further assessment because Citation: Pathak, A.; Stothard, P.; of their immense metabolic and ecological potential. To obtain a comprehensive understanding on Chauhan, A. Comparative Genomic this aspect, we previously reported on the isolation and preliminary genomic characterization of Analysis of Three Pseudomonas Species three Pseudomonas species isolated from minced oyster tissue (P.
    [Show full text]
  • Three New Genome Assemblies Support a Rapid Radiation in Musa Acuminata (Wild Banana)
    GBE Three New Genome Assemblies Support a Rapid Radiation in Musa acuminata (Wild Banana) Mathieu Rouard1,*, Gaetan Droc2,3, Guillaume Martin2,3,JulieSardos1, Yann Hueber1, Valentin Guignon1, Alberto Cenci1,Bjo¨rnGeigle4,MarkS.Hibbins5,6, Nabila Yahiaoui2,3, Franc-Christophe Baurens2,3, Vincent Berry7,MatthewW.Hahn5,6, Angelique D’Hont2,3,andNicolasRoux1 1Bioversity International, Parc Scientifique Agropolis II, Montpellier, France 2CIRAD, UMR AGAP, Montpellier, France 3AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, France 4Computomics GmbH, Tuebingen, Germany 5Department of Biology, Indiana University 6Department of Computer Science, Indiana University 7LIRMM, Universite de Montpellier, CNRS, Montpellier, France *Corresponding author: E-mail: [email protected]. Accepted: October 10, 2018 Data deposition: Raw sequence reads for de novo assemblies were deposited in the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) (BioProject: PRJNA437930 and SRA: SRP140622). Genome Assemblies and gene annotation data are available on the Banana Genome Hub (Droc G, Lariviere D, Guignon V, Yahiaoui N, This D, Garsmeur O, Dereeper A, Hamelin C, Argout X, Dufayard J-F, Lengelle J, Baurens F–C, Cenci A, Pitollat B, D’Hont A, Ruiz M, Rouard M, Bocs S. The Banana Genome Hub. Database (2013) doi:10.1093/ database/bat035) (http://banana-genome-hub.southgreen.fr/species-list). Cluster and gene tree results are available on a dedicated database (http://panmusa.greenphyl.org) hosted on the South Green Bioinformatics Platform (Guignon et al. 2016). Additional data sets are made available on Dataverse: https://doi.org/10.7910/DVN/IFI1QU. Abstract Edible bananas result from interspecific hybridization between Musa acuminata and Musa balbisiana,aswellasamongsubspeciesin M.
    [Show full text]
  • UNIVERSITY of CALIFORNIA, SAN DIEGO the Comparative Genomics
    UNIVERSITY OF CALIFORNIA, SAN DIEGO The Comparative Genomics of Salinispora and the Distribution and Abundance of Secondary Metabolite Genes in Marine Plankton A Dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Marine Biology by Kevin Matthew Penn Committee in charge: Paul R. Jensen, Chair Eric Allen Lin Chao Bradley Moore Brian Palenik Forest Rohwer 2012 UMI Number: 3499839 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent on the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. UMI 3499839 Copyright 2012 by ProQuest LLC. All rights reserved. This edition of the work is protected against unauthorized copying under Title 17, United States Code. ProQuest LLC. 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, MI 48106 - 1346 Copyright Kevin Matthew Penn, 2012 All rights reserved The Dissertation of Kevin Matthew Penn is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Chair University of California, San Diego 2012 iii DEDICATION I dedicate this dissertation to my Mom Gail Penn and my Father Lawrence Penn they deserve more credit then any person could imagine. They have supported me through the good times and the bad times. They have never given up on me and they are always excited to know that I am doing well. They just want the best for me.
    [Show full text]
  • Compact Graphical Representation of Phylogenetic Data and Metadata with Graphlan
    Compact graphical representation of phylogenetic data and metadata with GraPhlAn The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Asnicar, Francesco, George Weingart, Timothy L. Tickle, Curtis Huttenhower, and Nicola Segata. 2015. “Compact graphical representation of phylogenetic data and metadata with GraPhlAn.” PeerJ 3 (1): e1029. doi:10.7717/peerj.1029. http://dx.doi.org/10.7717/ peerj.1029. Published Version doi:10.7717/peerj.1029 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:17820708 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Compact graphical representation of phylogenetic data and metadata with GraPhlAn Francesco Asnicar1, George Weingart2, Timothy L. Tickle3, Curtis Huttenhower2,3 and Nicola Segata1 1 Centre for Integrative Biology (CIBIO), University of Trento, Italy 2 Biostatistics Department, Harvard School of Public Health, USA 3 Broad Institute of MIT and Harvard, USA ABSTRACT The increased availability of genomic and metagenomic data poses challenges at multiple analysis levels, including visualization of very large-scale microbial and microbial community data paired with rich metadata. We developed GraPhlAn (Graphical Phylogenetic Analysis), a computational tool that produces high-quality, compact visualizations of microbial genomes and metagenomes. This includes phylogenies spanning up to thousands of taxa, annotated with metadata ranging from microbial community abundances to microbial physiology or host and environmental phenotypes. GraPhlAn has been developed as an open-source command-driven tool in order to be easily integrated into complex, publication- quality bioinformatics pipelines.
    [Show full text]
  • Comparative and Genetic Analysis of the Four Sequenced Paenibacillus
    Eastman et al. BMC Genomics 2014, 15:851 http://www.biomedcentral.com/1471-2164/15/851 RESEARCH ARTICLE Open Access Comparative and genetic analysis of the four sequenced Paenibacillus polymyxa genomes reveals a diverse metabolism and conservation of genes relevant to plant-growth promotion and competitiveness Alexander W Eastman1,2, David E Heinrichs2 and Ze-Chun Yuan1,2* Abstract Background: Members of the genus Paenibacillus are important plant growth-promoting rhizobacteria that can serve as bio-reactors. Paenibacillus polymyxa promotes the growth of a variety of economically important crops. Our lab recently completed the genome sequence of Paenibacillus polymyxa CR1. As of January 2014, four P. polymyxa genomes have been completely sequenced but no comparative genomic analyses have been reported. Results: Here we report the comparative and genetic analyses of four sequenced P. polymyxa genomes, which revealed a significantly conserved core genome. Complex metabolic pathways and regulatory networks were highly conserved and allow P. polymyxa to rapidly respond to dynamic environmental cues. Genes responsible for phytohormone synthesis, phosphate solubilization, iron acquisition, transcriptional regulation, σ-factors, stress responses, transporters and biomass degradation were well conserved, indicating an intimate association with plant hosts and the rhizosphere niche. In addition, genes responsible for antimicrobial resistance and non-ribosomal peptide/polyketide synthesis are present in both the core and accessory genome of each strain. Comparative analyses also reveal variations in the accessory genome, including large plasmids present in strains M1 and SC2. Furthermore, a considerable number of strain-specific genes and genomic islands are irregularly distributed throughout each genome. Although a variety of plant-growth promoting traits are encoded by all strains, only P.
    [Show full text]
  • Downloaded from a Variety of Sources (For Details, See Table S1) and Between Metazoa and Dictyostelium
    UC Riverside UC Riverside Previously Published Works Title This Déjà vu feeling--analysis of multidomain protein evolution in eukaryotic genomes. Permalink https://escholarship.org/uc/item/5398f2x3 Journal PLoS computational biology, 8(11) ISSN 1553-734X Authors Zmasek, Christian M Godzik, Adam Publication Date 2012 DOI 10.1371/journal.pcbi.1002701 Peer reviewed eScholarship.org Powered by the California Digital Library University of California This De´ja` Vu Feeling—Analysis of Multidomain Protein Evolution in Eukaryotic Genomes Christian M. Zmasek*, Adam Godzik* Program in Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America Abstract Evolutionary innovation in eukaryotes and especially animals is at least partially driven by genome rearrangements and the resulting emergence of proteins with new domain combinations, and thus potentially novel functionality. Given the random nature of such rearrangements, one could expect that proteins with particularly useful multidomain combinations may have been rediscovered multiple times by parallel evolution. However, existing reports suggest a minimal role of this phenomenon in the overall evolution of eukaryotic proteomes. We assembled a collection of 172 complete eukaryotic genomes that is not only the largest, but also the most phylogenetically complete set of genomes analyzed so far. By employing a maximum parsimony approach to compare repertoires of Pfam domains and their combinations, we show that independent evolution of domain combinations is significantly more prevalent than previously thought. Our results indicate that about 25% of all currently observed domain combinations have evolved multiple times. Interestingly, this percentage is even higher for sets of domain combinations in individual species, with, for instance, 70% of the domain combinations found in the human genome having evolved independently at least once in other species.
    [Show full text]
  • Analysis of Class C G-Protein Coupled Receptors Using Supervised
    Analysis of class C G-Protein Coupled Receptors using supervised classification methods Caroline Leonore König Supervised by: Dr. René Alquézar Mancho and Dr. Alfredo Vellido Alcacena Computer Science Department Universitat Politècnica de Catalunya A thesis submitted for the degree of Ph.D. in Artificial Intelligence Acknowledgments I would like to thank my advisors Dr. Alfredo Vellido and Dr. René Alquézar from the SOCO research group of the UPC, for giving me the opportunity to develop my Ph.D. thesis as part of the KAPPA-AIM1 project and work on the investigation of G protein-coupled receptors with Artificial Intelligence methods. Both of them helped me with questions and provided me useful feedback, as well as valuable advice and input at every stage of this thesis, spending a long time during the preparation of this work. As well, I would like to thank to Dr. Jesús Giraldo from the ’Institut de Neurociencies’ of the ’Universitat Autònoma de Barcelona’ (UAB) for the large collaboration in this PhD research providing so many biological insight to the study. 1KAPPA-AIM: Knowledge Acquisition in Pharmacoproteomics using Advanced Artificial Intel- ligence Methods i Abstract G protein-coupled receptors (GPCRs) are cell membrane proteins with a key role in regulating the function of cells. This is the result of their ability to transmit extracellular signals, which makes them relevant for pharmacology and has led, over the last decade, to active research in the field of proteomics. The current thesis specifically targets class C of GPCRs, which are relevant in therapies for various central nervous system disorders, such as Alzheimer’s disease, anxiety, Parkinson’s disease and schizophrenia.
    [Show full text]
  • Comparative Analysis of Plant Genomes Through Data Integration
    Comparative Analysis of Plant Genomes through Data Integration Michiel Van Bel Promoter: Prof. Dr. Yves Van de Peer Co-Promoter: Prof. Dr. Klaas Vandepoele Ghent University Faculty of Sciences Department of Plant Biotechnology and Bioinformatics VIB Department of Plant Systems Biology Bioinformatics and Systems Biology Dissertation submitted in fulfillment of the requirements for the degree of Doctor (PhD) in Sciences, Bioinformatics). Academic year: 2012-2013 Examination Committee Prof. Dr. Geert De Jaeger (chair) Faculty of Sciences, Department of Plant Biotechnology and Bioinformatics, Ghent University Prof. Dr. Yves Van de Peer (promoter) Faculty of Sciences, Department of Plant Biotechnology and Bioinformatics, Ghent University Prof. Dr. Klaas Vandepoele (co-promoter) Faculty of Sciences, Department of Plant Biotechnology and Bioinformatics, Ghent University Prof. Dr. Jan Fostier Faculty of Engineering, Department of Information Technology, Ghent University Prof. Dr. Peter Dawyndt Faculty of Science, Department of Applied Mathematics and Computer Science, Ghent University Dr. Steven Robbens Bayer Cropscience, Belgium Dr. Matthieu Conte Syngenta Seeds, France II Acknowledgements While the cover of this book carries my name, this thesis did not come to fruition by my hand only. These past years have been a great experience, for which I would like to express my gratitude to several people. First of all, I would like to thank Thomas Abeel, for getting me in touch with Yves’ research group, and encouraging me to start a PhD in bioinformatics. Without a chance encounter with him, I never would have dreamed obtaining a PhD would be possible. Secondly, I would like to thank my promoter and co-promoter, Yves Van de Peer and Klaas Vande- poele.
    [Show full text]
  • Combining Morphological and Metabarcoding Approaches Reveals the Freshwater Eukaryotic Phytoplankton Community
    Prime Archives in Environmental Research Book Chapter Combining Morphological and Metabarcoding Approaches Reveals the Freshwater Eukaryotic Phytoplankton Community Shouliang Huo1, Xiaochuang Li1*, Beidou Xi1, Hanxiao Zhang1,2, Chunzi Ma1 and Zhuoshi He1 1State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, PR China 2College of Water Sciences, Beijing Normal University, PR China *Corresponding Author: Xiaochuang Li, State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China Published December 10, 2020 This Book Chapter is a republication of an article published by Xiaochuang Li, et al. at Environmental Sciences Europe in March 2020. (Huo, S., Li, X., Xi, B. et al. Combining morphological and metabarcoding approaches reveals the freshwater eukaryotic phytoplankton community. Environ Sci Eur 32, 37 (2020). https://doi.org/10.1186/s12302-020-00321-w) How to cite this book chapter: Shouliang Huo, Xiaochuang Li, Beidou Xi, Hanxiao Zhang, Chunzi Ma, Zhuoshi He. Combining Morphological and Metabarcoding Approaches Reveals the Freshwater Eukaryotic Phytoplankton Community. In: Anna Strunecka, editor. Prime Archives in Environmental Research. Hyderabad, India: Vide Leaf. 2020. 1 www.videleaf.com Prime Archives in Environmental Research © The Author(s) 2020. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License(http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Acknowledgements and Funding: This work was supported by the National Key Research and Development program of China [No. 2017YFA0605003] and the National Natural Science Foundation of China [No.
    [Show full text]
  • Structural Genomics Analysis of Uncharacterized Protein Families Overrepresented in Human Gut Bacteria Identifies a Novel Glycoside Hydrolase
    UC Riverside UC Riverside Previously Published Works Title Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase. Permalink https://escholarship.org/uc/item/20c4w1fz Journal BMC bioinformatics, 15(1) ISSN 1471-2105 Authors Sheydina, Anna Eberhardt, Ruth Y Rigden, Daniel J et al. Publication Date 2014-04-17 DOI 10.1186/1471-2105-15-112 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Sheydina et al. BMC Bioinformatics 2014, 15:112 http://www.biomedcentral.com/1471-2105/15/112 RESEARCH ARTICLE Open Access Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase Anna Sheydina1,2, Ruth Y Eberhardt3,4, Daniel J Rigden5, Yuanyuan Chang1,2, Zhanwen Li2, Christian C Zmasek2, Herbert L Axelrod1,6 and Adam Godzik1,2,7* Abstract Background: Bacteroides spp. form a significant part of our gut microbiome and are well known for optimized metabolism of diverse polysaccharides. Initial analysis of the archetypal Bacteroides thetaiotaomicron genome identified 172 glycosyl hydrolases and a large number of uncharacterized proteins associated with polysaccharide metabolism. Results: BT_1012 from Bacteroides thetaiotaomicron VPI-5482 is a protein of unknown function and a member of a large protein family consisting entirely of uncharacterized proteins. Initial sequence analysis predicted that this protein has two domains, one on the N- and one on the C-terminal. A PSI-BLAST search found over 150 full length and over 90 half size homologs consisting only of the N-terminal domain. The experimentally determined three-dimensional structure of the BT_1012 protein confirms its two-domain architecture and structural analysis of both domains suggests their specific functions.
    [Show full text]
  • Evolutionary Mechanisms of Long-Term Genome Diversification Associated with Niche Partitioning in Marine Picocyanobacteria
    fmicb-11-567431 September 11, 2020 Time: 18:26 # 1 ORIGINAL RESEARCH published: 15 September 2020 doi: 10.3389/fmicb.2020.567431 Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria Edited by: Hugo Doré1, Gregory K. Farrant1, Ulysse Guyet1, Julie Haguait2, Florian Humily1, Osvaldo Ulloa, Morgane Ratin1, Frances D. Pitt3, Martin Ostrowski3†, Christophe Six1, University of Concepción, Chile Loraine Brillet-Guéguen4,5, Mark Hoebeke4, Antoine Bisch4, Gildas Le Corguillé4, 4 6 6 7 8,9 Reviewed by: Erwan Corre , Karine Labadie , Jean-Marc Aury , Patrick Wincker , Dong Han Choi , Eric Daniel Becraft, Jae Hoon Noh8,10, Damien Eveillard2,11, David J. Scanlan3, Frédéric Partensky1 and University of North Alabama, Laurence Garczarek1,11* United States 1 Adam Martiny, Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique 2 University of California, Irvine, de Roscoff (SBR), Roscoff, France, LS2N, UMR CNRS 6004, IMT Atlantique, ECN, Université de Nantes, Nantes, France, 3 4 United States School of Life Sciences, University of Warwick, Coventry, United Kingdom, CNRS, FR 2424, ABiMS Platform, Station Biologique de Roscoff (SBR), Roscoff, France, 5 Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine *Correspondence: Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France, 6 Genoscope, Institut de Biologie François-Jacob, Laurence Garczarek Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay,
    [Show full text]
  • Automatic Customization and Visualization Of
    bioRxiv preprint doi: https://doi.org/10.1101/106138; this version posted September 28, 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 Iroki: automatic customization and 2 visualization of phylogenetic trees 1 2 2 3 Ryan M. Moore , Amelia O. Harrison , Sean M. McAllister , Shawn W. 1 1 4 Polson , and K. Eric Wommack 1 5 Center for Bioinformatics and Computational Biology, University of Delaware, Newark, 6 DE, USA 2 7 School of Marine Science and Policy, University of Delaware, Newark, DE, USA 8 Corresponding author: 1 9 K. Eric Wommack 10 Email address: [email protected] 11 ABSTRACT 12 Phylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary 13 history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to 14 generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history 15 of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that 16 can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can 17 be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time- 18 consuming and error prone, and programs designed to assist in batch tree customization often require 19 programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface 20 for tree visualization, addresses these issues by providing automatic customization of large trees based 21 on metadata contained in tab-separated text files.
    [Show full text]