The Integrated Microbial Genomes Database and Comparative Analysis System
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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. -
Senegalemassilia Anaerobia Gen. Nov., Sp. Nov
Standards in Genomic Sciences (2013) 7:343-356 DOI:10.4056/sigs.3246665 Non contiguous-finished genome sequence and description of Senegalemassilia anaerobia gen. nov., sp. nov. Jean-Christophe Lagier1, Khalid Elkarkouri1, Romain Rivet1, Carine Couderc1, Didier Raoult1 and Pierre-Edouard Fournier1* 1 Aix-Marseille Université, URMITE, Faculté de médecine, Marseille, France *Corresponding author: Pierre-Edouard Fournier ([email protected]) Keywords: Senegalemassilia anaerobia, genome Senegalemassilia anaerobia strain JC110T sp.nov. is the type strain of Senegalemassilia anaer- obia gen. nov., sp. nov., the type species of a new genus within the Coriobacteriaceae family, Senegalemassilia gen. nov. This strain, whose genome is described here, was isolated from the fecal flora of a healthy Senegalese patient. S. anaerobia is a Gram-positive anaerobic coccobacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,383,131 bp long genome contains 1,932 protein- coding and 58 RNA genes. Introduction Classification and features Senegalemassilia anaerobia strain JC110T (= CSUR A stool sample was collected from a healthy 16- P147 = DSMZ 25959) is the type strain of S. anaer- year-old male Senegalese volunteer patient living obia gen. nov., sp. nov. This bacterium was isolat- in Dielmo (rural village in the Guinean-Sudanian ed from the feces of a healthy Senegalese patient. zone in Senegal), who was included in a research It is a Gram-positive, anaerobic, indole-negative protocol. Written assent was obtained from this coccobacillus. Classically, the polyphasic taxono- individual. No written consent was needed from his my is used to classify the prokaryotes by associat- guardians for this study because he was older than ing phenotypic and genotypic characteristics [1]. -
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. -
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. -
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. -
Across Bacterial Phyla, Distantly-Related Genomes with Similar Genomic GC Content Have Similar Patterns of Amino Acid Usage
University of South Carolina Scholar Commons Faculty Publications Biological Sciences, Department of 3-10-2011 Across Bacterial Phyla, Distantly-Related Genomes with Similar Genomic GC Content Have Similar Patterns of Amino Acid Usage John Lightfield Noah R. Fram Bert Ely University of South Carolina - Columbia, [email protected] Follow this and additional works at: https://scholarcommons.sc.edu/biol_facpub Part of the Biology Commons Publication Info Published in PLoS ONE, Volume 6, Issue 3, 2011, pages e17677-. © 2011 Lightfield et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. This Article is brought to you by the Biological Sciences, Department of at Scholar Commons. It has been accepted for inclusion in Faculty Publications by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. Across Bacterial Phyla, Distantly-Related Genomes with Similar Genomic GC Content Have Similar Patterns of Amino Acid Usage John Lightfield¤a, Noah R. Fram¤b, Bert Ely* Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America Abstract The GC content of bacterial genomes ranges from 16% to 75% and wide ranges of genomic GC content are observed within many bacterial phyla, including both Gram negative and Gram positive phyla. Thus, divergent genomic GC content has evolved repeatedly in widely separated bacterial taxa. Since genomic GC content influences codon usage, we examined codon usage patterns and predicted protein amino acid content as a function of genomic GC content within eight different phyla or classes of bacteria. -
Various Complexes of the Oral Microbial Flora in Periodontal Disease
ISSN: 2394-8418 DOI: https://doi.org/10.17352/jdps CLINICAL GROUP Received: 01 April, 2021 Short Communication Accepted: 08 April, 2021 Published: 10 April, 2021 *Corresponding author: Dr. Sukhvinder Singh Oberoi, Various complexes of the oral BDS, MDS, Associate Professor, Public Health Den- tistry, ESIC Dental College and Hospital, Rohini, Guru microbial fl ora in periodontal Gobind Singh Indraprastha University, India, E-mail: disease Keywords: Periodontal diseases; Red complex; Orange complex Sukhvinder Singh Oberoi1*, Shabina Sachdeva2 and https://www.peertechzpublications.com Shibani Grover3 1Associate Professor, Public Health Dentistry, ESIC Dental College and Hospital, Rohini, Guru Gobind Singh Indraprastha University, India 2Professor, Prosthodontics, Faculty of Dentistry, Jamia Milia Islamia, India 3Dean and Director Professor, Conservative Dentistry and Endodontics, ESIC Dental College and Hospital, Rohini, Guru Gobind Singh Indraprastha University, India Abstract Periodontal diseases, is the infection of the periodontal tissues which eventually can lead to loss of teeth, is a form of aberrant infl ammation resulting from a complex biofi lm of friendly commensal and periodontopathic bacteria and their products, triggering the human infl ammatory response. The cluster analysis has shown that 6 closely associated bacterial complexes are associated with it which are designated with different color codes. The early colonizers are “Blue complex” consisting of Actinomyces species, “Yellow complex” comprising of various Streptococci, “Green complex” comprising Eiknella corrodens and Capnocytophaga species, and “Purple complex” comprising Veillonella parvula and Actinomyces odontolyticus. The late colonizers are “Orange complex” comprising Prevotella, Fusobacterium, Campylobacter and other bacteria and the “Red complex” chiefl y consisting of Porphyromonas gingivalis, Tannerella forsythia, and Treponema Denticola. Periodontal disease is the commonest oral disease affecting are facultative, spirochetes and motile rods. -
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. -
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. -
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. -
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. -
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.