DOCSLIB.ORG

Comparative Phylogenomic Analysis Reveals Evolutionary Genomic

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Comparative Phylogenomic Analysis Reveals Evolutionary Genomic bioRxiv preprint doi: https://doi.org/10.1101/2021.06.02.446850; this version posted June 5, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Comparative phylogenomic analysis reveals evolutionary genomic 2 changes and novel toxin families in endophytic Liberibacter 3 pathogens 4 5 Yongjun Tan1, Cindy Wang1, Theresa Schneider1, Huan Li1, Robson Francisco de Souza2, 6 Xueming Tang3, Tzung-Fu Hsieh4,5, Xu Wang6,7,8, Xu Li4,5, and Dapeng Zhang1,9,* 7 8 1Department of Biology, College of Arts & Sciences, Saint Louis University, St. Louis, MO 63103 9 2Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, 10 São Paulo 05508-900, Brazil 11 3School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China 12 4Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695 13 5Plants for Human Health Institute, North Carolina State University, Kannapolis, NC 28081 14 6Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 15 36849 16 7Alabama Agricultural Experiment Station, Auburn University, Auburn, AL 36849 17 8HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 18 9Bioinformatics and Computational Biology Program, College of Arts & Sciences, Saint Louis 19 University, St. Louis, MO 63103 20 21 Correspondence and requests for materials should be addressed to D.Z. (email: 22 [email protected]) 23 24 Running title: Comparative Phylogenomics of Liberibacter Pathogens 25 Keywords: Liberibacter pathogens, huanglongbing, zebra chip, toxins, prophages, 26 pathogenesis, evolution, comparative genomics 27 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.06.02.446850; this version posted June 5, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. 28 Abstract 29 Liberibacter pathogens are the causative agents of several severe crop diseases worldwide, 30 including citrus Huanglongbing and potato Zebra Chip. These bacteria are endophytic and non- 31 culturable, which makes experimental approaches challenging and highlights the need for 32 bioinformatic analysis in advancing our understanding about Liberibacter pathogenesis. Here, 33 we performed an in-depth comparative phylogenomic analysis of the Liberibacter pathogens 34 and their free-living, nonpathogenic, ancestral species, aiming to identify the major genomic 35 changes and determinants associated with their evolutionary transitions in living habitats and 36 pathogenicity. We found that prophage loci represent the most variable regions among 37 Liberibacter genomes. Using gene neighborhood analysis and phylogenetic classification, we 38 systematically recovered, annotated, and classified all prophage loci into four types, including 39 one previously unrecognized group. We showed that these prophages originated through 40 independent gene transfers at different evolutionary stages of Liberibacter and only the SC-type 41 prophage was associated with the emergence of the pathogens. Using ortholog clustering, we 42 vigorously identified two additional sets of genomic genes, which were either lost or gained in 43 the ancestor of the pathogens. Consistent with the habitat change, the lost genes were 44 enriched for biosynthesis of cellular building blocks. Importantly, among the gained genes, we 45 uncovered several previously unrecognized toxins, including a novel class of polymorphic toxins, 46 a YdjM phospholipase toxin, and a secreted EEP protein. Our results substantially extend the 47 knowledge on the evolutionary events and potential determinants leading to the emergence of 48 endophytic, pathogenic Liberibacter species and will facilitate the design of functional 49 experiments and the development of new detection and blockage methods of these pathogens. 50 51 Importance 52 Liberibacter pathogens are associated with several severe crop diseases, including citrus 53 Huanglongbing, the most destructive disease to the citrus industry. Currently, no effective cure 54 or treatments are available, and no resistant citrus variety has been found. The fact that these 55 obligate endophytic pathogens are not culturable has made it extremely challenging to 2 bioRxiv preprint doi: https://doi.org/10.1101/2021.06.02.446850; this version posted June 5, 2021. 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. 56 experimentally uncover from the whole genome the genes/proteins important to Liberibacter 57 pathogenesis. Further, earlier bioinformatics studies failed to identify the key genomic 58 determinants, such as toxins and effector proteins, that underlie the pathogenicity of the 59 bacteria. In this study, an in-depth comparative genomic analysis of Liberibacter pathogens 60 together with their ancestral non-pathogenic species identified the prophage loci and several 61 novel toxins that are evolutionarily associated with the emergence of the pathogens. These 62 results shed new lights on the disease mechanism of Liberibacter pathogens and will facilitate 63 the development of new detection and blockage methods targeting the toxins. 64 65 66 3 bioRxiv preprint doi: https://doi.org/10.1101/2021.06.02.446850; this version posted June 5, 2021. 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. 67 Introduction 68 Candidatus Liberibacter, a genus of Gram-negative bacteria in the order of Rhizobiales, 69 has recently received increasing attention due to the fact that several of its species are 70 associated with severe diseases on multiple crop plants, such as citrus, potato, and tomato. 71 These include three species, Candidatus Liberibacter asiaticus found in Asia and North America, 72 Candidatus Liberibacter africanus found in Africa 1, and Candidatus Liberibacter americanus 73 found in Brazil 2, that cause the citrus Huanglongbing (HLB) disease, and Candidatus 74 Liberibacter solanacearum, that causes similar diseases in tomato and potato, referred to as 75 Psyllid yellows and Zebra Chip (ZC), respectively 3,4. The HLB disease, also known as citrus 76 greening, is the most destructive, worldwide disease of citrus 5. It is characterized by yellowing 77 of citrus tree leaves, premature defoliation, decay of feeder rootlets and lateral roots, production 78 of small bitter fruit, and eventually death of the citrus tree 6. Thus, HLB has led to a substantial 79 loss of citrus production and severe damage to the economy and job market 7. Unfortunately, 80 there is currently no effective cure or treatments available, and no resistant citrus variety has 81 been found so far. In a similar vein, ZC is a new disease of potato that was first identified in 82 Mexico in 1994 8 and has quickly spread to many countries in recent years. It negatively affects 83 growth, yield, propagation potential, and qualities of tubers and thus impacts international trade 84 and the economy significantly 9. 85 Given the severity and rapid spread of these diseases in commercial crops, extensive 86 research efforts have been made to better understand the basic biology of these pathogens and 87 the pathogenesis mechanisms of the diseases, especially on HLB. However, the progress has 88 been slow due to two main obstacles. First, the Liberibacter pathogens of these diseases are 89 endophytic bacteria, whose transmissions are naturally vectored by several psyllids, such as 90 Asian citrus psyllid (Diaphorina citri) 10, African citrus psyllid (Trioza erytreae) 11, and Bactericera 91 cockerelli 9. Therefore, they are not culturable which makes it difficult for wet-lab researchers to 92 conduct functional studies. Second, secretion of toxins or effectors represents one of the most 93 important mechanisms of bacterial pathogenesis and virulence. These toxins either manipulate 94 host/vector immunity and physiology or damage the host cells 12. However, such molecules 95 involved in the HLB disease have remained elusive for years. Previous research has focused 96 primarily on secreted proteins in HLB-associated pathogens which carry T2SS specific signal 97 peptides 13. Thus far, the only proteins claimed to be the potential toxins behind the HLB 98 disease have been the short proteins carrying these signal peptides 14-17. However, these 99 proteins are mainly present in one strain of the C.L. asiaticus species, and not found in other 4 bioRxiv preprint doi: https://doi.org/10.1101/2021.06.02.446850; this version posted June 5, 2021. 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. 100 C.L. asiaticus strains and other Liberibacter pathogens associated with HLB (C.L. americanus 101 and C.L. africanus)14,16-21, suggesting that other types of toxins
Load more

Recommended publications
  • Archaea, Bacteria and Termite, Nitrogen Fixation and Sustainable Plants Production
    Sun W et al . (2021) Notulae Botanicae Horti Agrobotanici Cluj-Napoca Volume 49, Issue 2, Article number 12172 Notulae Botanicae Horti AcademicPres DOI:10.15835/nbha49212172 Agrobotanici Cluj-Napoca Re view Article Archaea, bacteria and termite, nitrogen fixation and sustainable plants production Wenli SUN 1a , Mohamad H. SHAHRAJABIAN 1a , Qi CHENG 1,2 * 1Chinese Academy of Agricultural Sciences, Biotechnology Research Institute, Beijing 100081, China; [email protected] ; [email protected] 2Hebei Agricultural University, College of Life Sciences, Baoding, Hebei, 071000, China; Global Alliance of HeBAU-CLS&HeQiS for BioAl-Manufacturing, Baoding, Hebei 071000, China; [email protected] (*corresponding author) a,b These authors contributed equally to the work Abstract Certain bacteria and archaea are responsible for biological nitrogen fixation. Metabolic pathways usually are common between archaea and bacteria. Diazotrophs are categorized into two main groups namely: root- nodule bacteria and plant growth-promoting rhizobacteria. Diazotrophs include free living bacteria, such as Azospirillum , Cupriavidus , and some sulfate reducing bacteria, and symbiotic diazotrophs such Rhizobium and Frankia . Three types of nitrogenase are iron and molybdenum (Fe/Mo), iron and vanadium (Fe/V) or iron only (Fe). The Mo-nitrogenase have a higher specific activity which is expressed better when Molybdenum is available. The best hosts for Rhizobium legumiosarum are Pisum , Vicia , Lathyrus and Lens ; Trifolium for Rhizobium trifolii ; Phaseolus vulgaris , Prunus angustifolia for Rhizobium phaseoli ; Medicago, Melilotus and Trigonella for Rhizobium meliloti ; Lupinus and Ornithopus for Lupini, and Glycine max for Rhizobium japonicum . Termites have significant key role in soil ecology, transporting and mixing soil. Termite gut microbes supply the enzymes required to degrade plant polymers, synthesize amino acids, recycle nitrogenous waste and fix atmospheric nitrogen.
    [Show full text]
  • Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
    Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341
    [Show full text]
  • Understanding the Composition and Role of the Prokaryotic Diversity in the Potato Rhizosphere for Crop Improvement in the Andes
    Understanding the composition and role of the prokaryotic diversity in the potato rhizosphere for crop improvement in the Andes Jonas Ghyselinck Dissertation submitted in fulfilment of the requirements for the degree of Doctor (Ph.D.) in Sciences, Biotechnology Promotor - Prof. Dr. Paul De Vos Co-promotor - Dr. Kim Heylen Ghyselinck Jonas – Understanding the composition and role of the prokaryotic diversity in the potato rhizosphere for crop improvement in the Andes Copyright ©2013 Ghyselinck Jonas ISBN-number: 978-94-6197-119-7 No part of this thesis protected by its copyright notice may be reproduced or utilized in any form, or by any means, electronic or mechanical, including photocopying, recording or by any information storage or retrieval system without written permission of the author and promotors. Printed by University Press | www.universitypress.be Ph.D. thesis, Faculty of Sciences, Ghent University, Ghent, Belgium. This Ph.D. work was financially supported by European Community's Seventh Framework Programme FP7/2007-2013 under grant agreement N° 227522 Publicly defended in Ghent, Belgium, May 28th 2013 EXAMINATION COMMITTEE Prof. Dr. Savvas Savvides (chairman) Faculty of Sciences Ghent University, Belgium Prof. Dr. Paul De Vos (promotor) Faculty of Sciences Ghent University, Belgium Dr. Kim Heylen (co-promotor) Faculty of Sciences Ghent University, Belgium Prof. Dr. Anne Willems Faculty of Sciences Ghent University, Belgium Prof. Dr. Peter Dawyndt Faculty of Sciences Ghent University, Belgium Prof. Dr. Stéphane Declerck Faculty of Biological, Agricultural and Environmental Engineering Université catholique de Louvain, Louvain-la-Neuve, Belgium Dr. Angela Sessitsch Department of Health and Environment, Bioresources Unit AIT Austrian Institute of Technology GmbH, Tulln, Austria Dr.
    [Show full text]
  • Characterization of Sheath Rot Pathogens from Major Rice-Growing
    Promotor: Prof. Dr. Ir. Monica Höfte Laboratory of Phytopathology Department of Crop Protection Faculty of Bioscience Engineering Ghent University Co-Promoter: Dr. Ir. Obedi I. Nyamangyoku Department of Crop Science School of agriculture, Rural Development and Agricultural Economics College of Agriculture, Animal Science and Veterinary Medicine University of Rwanda, RWANDA Dean : Prof. Dr. Ir. Marc Van Meirvenne Rector : Prof. Dr. Anne De Paepe ii Ir. Vincent de Paul Bigirimana Characterization of sheath rot pathogens from major rice- growing areas in Rwanda Thesis submitted in fulfilment of the requirements for the degree of Doctor (PhD) in Applied Biological Sciences iii Dutch translation of the title: Karakterisatie van pathogenen die “sheath rot” veroorzaken in de belangrijkste rijstgebieden in Rwanda Cover illustration: Some sheath rot disease features: - Left upper side: microscopic picture of the reverse side of Fusarium andiyazi isolate RFNG10 on PDA medium; - Left lower side: microscopic picture of the front side of Fusarium andiyazi isolate RFNG10 isolate on PDA medium; - Center: illustration of rice sheath rot symptoms on a rice plant; - Right side: illustration of a phylogenetic tree of Pseudomonas isolates associated with rice sheath rot symptoms in Rwanda and the Philippines. This work was financially supported by a PhD grant from the Belgian Technical Cooperation (BTC) (reference number: 10RWA/0018). Additional funding was provided by the Ghent University. Cite as: BIGIRIMANA V.P. 2016. Characterisation of sheath rot pathogens from major rice-growing areas in Rwanda. PhD thesis, Ghent University, Belgium. ISBN Number: 978-90-5989-904-9 The author and the Promoters give the authorization to consult and to copy parts of this work for personal use only.
    [Show full text]
  • Saline and Arid Soils: Impact on Bacteria, Plants, and Their Interaction
    biology Review Saline and Arid Soils: Impact on Bacteria, Plants, and Their Interaction Elisa Gamalero 1, Elisa Bona 2,* , Valeria Todeschini 2 and Guido Lingua 1 1 Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Viale T. Michel 11, 15121 Alessandria, Italy; [email protected] (E.G.); [email protected] (G.L.) 2 Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Piazza San Eusebio 5, 13100 Vercelli, Italy; [email protected] * Correspondence: [email protected] Received: 14 April 2020; Accepted: 29 May 2020; Published: 2 June 2020 Abstract: Salinity and drought are the most important abiotic stresses hampering crop growth and yield. It has been estimated that arid areas cover between 41% and 45% of the total Earth area worldwide. At the same time, the world’s population is going to soon reach 9 billion and the survival of this huge amount of people is dependent on agricultural products. Plants growing in saline/arid soil shows low germination rate, short roots, reduced shoot biomass, and serious impairment of photosynthetic efficiency, thus leading to a substantial loss of crop productivity, resulting in significant economic damage. However, plants should not be considered as single entities, but as a superorganism, or a holobiont, resulting from the intimate interactions occurring between the plant and the associated microbiota. Consequently, it is very complex to define how the plant responds to stress on the basis of the interaction with its associated plant growth-promoting bacteria (PGPB). This review provides an overview of the physiological mechanisms involved in plant survival in arid and saline soils and aims at describing the interactions occurring between plants and its bacteriome in such perturbed environments.
    [Show full text]
  • Control of Phytopathogenic Microorganisms with Pseudomonas Sp. and Substances and Compositions Derived Therefrom
    (19) TZZ Z_Z_T (11) EP 2 820 140 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: A01N 63/02 (2006.01) A01N 37/06 (2006.01) 10.01.2018 Bulletin 2018/02 A01N 37/36 (2006.01) A01N 43/08 (2006.01) C12P 1/04 (2006.01) (21) Application number: 13754767.5 (86) International application number: (22) Date of filing: 27.02.2013 PCT/US2013/028112 (87) International publication number: WO 2013/130680 (06.09.2013 Gazette 2013/36) (54) CONTROL OF PHYTOPATHOGENIC MICROORGANISMS WITH PSEUDOMONAS SP. AND SUBSTANCES AND COMPOSITIONS DERIVED THEREFROM BEKÄMPFUNG VON PHYTOPATHOGENEN MIKROORGANISMEN MIT PSEUDOMONAS SP. SOWIE DARAUS HERGESTELLTE SUBSTANZEN UND ZUSAMMENSETZUNGEN RÉGULATION DE MICRO-ORGANISMES PHYTOPATHOGÈNES PAR PSEUDOMONAS SP. ET DES SUBSTANCES ET DES COMPOSITIONS OBTENUES À PARTIR DE CELLE-CI (84) Designated Contracting States: • O. COUILLEROT ET AL: "Pseudomonas AL AT BE BG CH CY CZ DE DK EE ES FI FR GB fluorescens and closely-related fluorescent GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO pseudomonads as biocontrol agents of PL PT RO RS SE SI SK SM TR soil-borne phytopathogens", LETTERS IN APPLIED MICROBIOLOGY, vol. 48, no. 5, 1 May (30) Priority: 28.02.2012 US 201261604507 P 2009 (2009-05-01), pages 505-512, XP55202836, 30.07.2012 US 201261670624 P ISSN: 0266-8254, DOI: 10.1111/j.1472-765X.2009.02566.x (43) Date of publication of application: • GUANPENG GAO ET AL: "Effect of Biocontrol 07.01.2015 Bulletin 2015/02 Agent Pseudomonas fluorescens 2P24 on Soil Fungal Community in Cucumber Rhizosphere (73) Proprietor: Marrone Bio Innovations, Inc.
    [Show full text]
  • Table S8. Species Identified by Random Forests Analysis of Shotgun Sequencing Data That Exhibit Significant Differences In
    Table S8. Species identified by random forests analysis of shotgun sequencing data that exhibit significant differences in their representation in the fecal microbiomes between each two groups of mice. (a) Species discriminating fecal microbiota of the Soil and Control mice. Mean importance of species identified by random forest are shown in the 5th column. Random forests assigns an importance score to each species by estimating the increase in error caused by removing that species from the set of predictors. In our analysis, we considered a species to be “highly predictive” if its importance score was at least 0.001. T-test was performed for the relative abundances of each species between the two groups of mice. P-values were at least 0.05 to be considered statistically significant. Microbiological Taxonomy Random Forests Mean of relative abundance P-Value Species Microbiological Function (T-Test) Classification Bacterial Order Importance Score Soil Control Rhodococcus sp. 2G Engineered strain Bacteria Corynebacteriales 0.002 5.73791E-05 1.9325E-05 9.3737E-06 Herminiimonas arsenitoxidans Engineered strain Bacteria Burkholderiales 0.002 0.005112829 7.1580E-05 1.3995E-05 Aspergillus ibericus Engineered strain Fungi 0.002 0.001061181 9.2368E-05 7.3057E-05 Dichomitus squalens Engineered strain Fungi 0.002 0.018887472 8.0887E-05 4.1254E-05 Acinetobacter sp. TTH0-4 Engineered strain Bacteria Pseudomonadales 0.001333333 0.025523638 2.2311E-05 8.2612E-06 Rhizobium tropici Engineered strain Bacteria Rhizobiales 0.001333333 0.02079554 7.0081E-05 4.2000E-05 Methylocystis bryophila Engineered strain Bacteria Rhizobiales 0.001333333 0.006513543 3.5401E-05 2.2044E-05 Alteromonas naphthalenivorans Engineered strain Bacteria Alteromonadales 0.001 0.000660472 2.0747E-05 4.6463E-05 Saccharomyces cerevisiae Engineered strain Fungi 0.001 0.002980726 3.9901E-05 7.3043E-05 Bacillus phage Belinda Antibiotic Phage 0.002 0.016409765 6.8789E-07 6.0681E-08 Streptomyces sp.
    [Show full text]
  • Redalyc.Análisis De Pseudomonas Fitopatógenas Usando Métodos
    Revista Mexicana de Fitopatología ISSN: 0185-3309 [email protected] Sociedad Mexicana de Fitopatología, A.C. México Slabbinck, Bram; De Baets, Bernard; Dawyndt, Peter; Vos, Paul De Análisis de Pseudomonas Fitopatógenas Usando Métodos Inteligentes de Aprendizaje: Un Enfoque General Sobre Taxonomía y Análisis de Ácidos Grasos Dentro del Género Pseudomonas Revista Mexicana de Fitopatología, vol. 28, núm. 1, 2010, pp. 1-16 Sociedad Mexicana de Fitopatología, A.C. Texcoco, México Disponible en: http://www.redalyc.org/articulo.oa?id=61214206001 Cómo citar el artículo Número completo Sistema de Información Científica Más información del artículo Red de Revistas Científicas de América Latina, el Caribe, España y Portugal Página de la revista en redalyc.org Proyecto académico sin fines de lucro, desarrollado bajo la iniciativa de acceso abierto REVISTA MEXICANA DE FITOPATOLOGÍA/1 Análisis de Pseudomonas Fitopatógenas Usando Métodos Inteligentes de Aprendizaje: Un Enfoque General Sobre Taxonomía y Análisis de Ácidos Grasos Dentro del Género Pseudomonas Analysis of Plant-Pathogenic Pseudomonas Species Using Intelligent Learning Methods: A General Focus on Taxonomy and Fatty Acid Analysis Within the Genus Pseudomonas Bram Slabbinck, Bernard De Baets, Research Group Knowledge-based Systems, Department of Applied Mathematics, Biometrics and Process Control, Ghent University, Coupure links 653, 9000 Ghent, Belgium, Peter Dawyndt, Department of Applied Mathematics and Computer Science, Ghent University, Krijgslaan 281 S9, 9000 Ghent, Belgium y Paul De Vos, Research Group Knowledge-based Systems, Department of Applied Mathematics, Biometrics and Process Control, Ghent University, Coupure links 653, 9000 Ghent, Belgium. (Recibido: Septiembre 20, 2009 Aceptado Enero 12, 2010) Slabbinck, B., De Baets, B., Dawyndt, P., y De Vos, P.
    [Show full text]
  • Phylogenomic Analyses of the Genus Pseudomonas Lead to the Rearrangement of Several Species and the Definition of New Genera
    biology Article Phylogenomic Analyses of the Genus Pseudomonas Lead to the Rearrangement of Several Species and the Definition of New Genera Zaki Saati-Santamaría 1,2,* , Ezequiel Peral-Aranega 1,2 , Encarna Velázquez 1,2,3, Raúl Rivas 1,2,3 and Paula García-Fraile 1,2,3 1 Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; [email protected] (E.P.-A.); [email protected] (E.V.); [email protected] (R.R.); [email protected] (P.G.-F.) 2 Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain 3 Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain * Correspondence: [email protected] Simple Summary: Pseudomonas represents a very important bacterial genus that inhabits many environments and plays either prejudicial or beneficial roles for higher hosts. However, there are many Pseudomonas species which are too divergent to the rest of the genus. This may interfere in the correct development of biological and ecological studies in which Pseudomonas are involved. Thus, we aimed to study the correct taxonomic placement of Pseudomonas species. Based on the study of their genomes and some evolutionary-based methodologies, we suggest the description of three new genera (Denitrificimonas, Parapseudomonas and Neopseudomonas) and many reclassifications of species Citation: Saati-Santamaría, Z.; previously included in Pseudomonas. Peral-Aranega, E.; Velázquez, E.; Rivas, R.; García-Fraile, P. Abstract: Pseudomonas is a large and diverse genus broadly distributed in nature. Its species play Phylogenomic Analyses of the Genus relevant roles in the biology of earth and living beings. Because of its ubiquity, the number of new Pseudomonas Lead to the species is continuously increasing although its taxonomic organization remains quite difficult to Rearrangement of Several Species and unravel.
    [Show full text]
  • Names of Plant Pathogenic Bacteria, 1864-2003
    Names of Plant Pathogenic Bacteria, 1864–2004 J.M. Young, Landcare Research, Private Bag 92170, Auckland, New Zealand: [email protected] (Convener) C.T. Bull, US Department of Agriculture, 1636 E Alisal Street, Salinas, CA 93905, USA: [email protected] S.H. De Boer, Centre for Animal and Plant Health, 93 Mount Edward Road, Charlottetown, PE C1A 5T1, Canada: [email protected] G. Firrao, Dipartimento di Biologia Applicata alla Difesa delle Piante, Universita, via Scienze 208, 33100 Udine, Italy: [email protected] G.E. Saddler, Scottish Agricultural Science Agency, 82 Craigs Road, Edinburgh EH12 8NJ, Scotland: [email protected] D.E. Stead, Central Science Laboratory, Ministry of Agriculture, Fisheries and Food, Sand Hutton, York, YO4 1LN, United Kingdom: [email protected] Y. Takikawa Plant Pathology Laboratory, Shizuoka University, 836 Ohya, Shizuoka 422, Japan: [email protected] This list contains the names of all plant pathogenic bacteria that have been effectively and validly published in terms of the International Code of Nomenclature of Prokaryotes (‘the Code’ – hitherto the International Code of Nomenclature of Bacteria) (Lapage et al. 1992) and the Standards for Naming Pathovars (Dye et al. 1980), and their revision (Young et al. 1991a). Included are species names from the Approved Lists of Bacterial Names (Skerman et al. 1980), pathovar names listed by Dye et al. (1980), and names of pathogens reported since 1980. In recent years, the taxonomy of plant pathogenic bacteria has been extensively revised. For several taxa, especially the Enterobacteriaceae, Pseudomonas syringae van Hall 1902 and Xanthomonas campestris (Pammel 1895) Dowson 1939, these revisions are incomplete.
    [Show full text]
  • Comprehensive List of Names of Plant Pathogenic Bacteria, 1980-2007
    001_JPP_Letter_551 16-11-2010 14:12 Pagina 551 Journal of Plant Pathology (2010), 92 (3), 551-592 Edizioni ETS Pisa, 2010 551 LETTER TO THE EDITOR COMPREHENSIVE LIST OF NAMES OF PLANT PATHOGENIC BACTERIA, 1980-2007 C.T. Bull1, S.H. De Boer2, T.P. Denny3, G. Firrao4, M. Fischer-Le Saux5, G.S. Saddler6, M. Scortichini7, D.E. Stead8 and Y. Takikawa9 1United States Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905, USA 2Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PE C1A 5T1, Canada 3University of Georgia, Plant Pathology Department, Plant Science Building, Athens, GA 30602-7274, USA 4Dipartimento di Biologia Applicata alla Difesa delle Piante, Università degli Studi, Via Scienze 208, 33100 Udine, Italy 5UMR de Pathologie Végétale, INRA, BP 60057, 49071 Beaucouzé Cedex, France 6Science and Advice for Scottish Agriculture, Roddinglaw Road, Edinburgh EH12 9FJ, UK 7CRA. Centro di Ricerca per la Frutticoltura, Via di Fioranello 52, 00134 Roma, Italy 8Food and Environment Research Agency, Department for Environment, Food and Rural Affairs, Sand Hutton, York, YO41 1LZ, UK 9Faculty of Agriculture, Shizuoka University, 836 Ohya, Shizuoka 422-8529, Japan SUMMARY INTRODUCTION The names of all plant pathogenic bacteria which The nomenclature of bacterial plant pathogens, like have been effectively and validly published in terms of that of many other life forms, is constantly changing in the International Code of Nomenclature of Bacteria and response to new insights and our understanding of rela- the Standards for Naming Pathovars are listed to pro- tionships among bacteria. For example, the taxonomy vide an authoritative register of names for use by au- of the family Enterobacteriaceae has been extensively re- thors, journal editors and others who require access to vised since the publication of the previous comprehen- currently correct nomenclature.
    [Show full text]
  • Low Bacterial Community Diversity in Two Introduced Aphid Pests Revealed with 16S Rrna Amplicon Sequencing
    Low bacterial community diversity in two introduced aphid pests revealed with 16S rRNA amplicon sequencing Francisca Zepeda-Paulo1, Sebastían Ortiz-Martínez1, Andrea X. Silva2 and Blas Lavandero1 1 Laboratorio de Control Biológico/Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile 2 AUSTRAL-omics Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile ABSTRACT Bacterial endosymbionts that produce important phenotypic effects on their hosts are common among plant sap-sucking insects. Aphids have become a model system of insect-symbiont interactions. However, endosymbiont research has focused on a few aphid species, making it necessary to make greater efforts to other aphid species through different regions, in order to have a better understanding of the role of endosymbionts in aphids as a group. Aphid endosymbionts have frequently been studied by PCR-based techniques, using species-specific primers, nevertheless this approach may omit other non-target bacteria cohabiting a particular host species. Advances in high-throughput sequencing technologies are complementing our knowledge of microbial communities by allowing us the study of whole microbiome of different organisms. We used a 16S rRNA amplicon sequencing approach to study the microbiome of aphids in order to describe the bacterial community diversity in introduced populations of the cereal aphids, Sitobion avenae and Rhopalosiphum padi in Chile (South America). An absence of secondary endosymbionts and two common secondary endosymbionts of aphids were found in the aphids R. padi and S. avenae, respectively. Of those endosymbionts, Regiella insecticola was the dominant secondary endosymbiont among the aphid samples. In addition, the presence of a previously unidentified bacterial species closely related to a phytopathogenic Pseudomonad species was detected.
    [Show full text]