DOCSLIB.ORG

Origins and Evolution of Viruses of Eukaryotes: the Ultimate Modularity Eugene V

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Origins and Evolution of Viruses of Eukaryotes: the Ultimate Modularity Eugene V Origins and evolution of viruses of eukaryotes: The ultimate modularity Eugene V. Koonin, Valerian Dolja, Mart Krupovic To cite this version: Eugene V. Koonin, Valerian Dolja, Mart Krupovic. Origins and evolution of viruses of eukaryotes: The ultimate modularity. Virology, Elsevier, 2015, 479-480, pp.2-25. 10.1016/j.virol.2015.02.039. pasteur-01977389 HAL Id: pasteur-01977389 https://hal-pasteur.archives-ouvertes.fr/pasteur-01977389 Submitted on 10 Jan 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License Virology 479-480 (2015) 2–25 Contents lists available at ScienceDirect Virology journal homepage: www.elsevier.com/locate/yviro Review Origins and evolution of viruses of eukaryotes: The ultimate modularity Eugene V. Koonin a,n, Valerian V. Dolja b, Mart Krupovic c a National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA b Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA c Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Department of Microbiology, Paris 75015, France article info abstract Article history: Viruses and other selfish genetic elements are dominant entities in the biosphere, with respect to both Received 27 January 2015 physical abundance and genetic diversity. Various selfish elements parasitize on all cellular life forms. Returned to author for revisions The relative abundances of different classes of viruses are dramatically different between prokaryotes 19 February 2015 and eukaryotes. In prokaryotes, the great majority of viruses possess double-stranded (ds) DNA Accepted 20 February 2015 genomes, with a substantial minority of single-stranded (ss) DNA viruses and only limited presence of Available online 12 March 2015 RNA viruses. In contrast, in eukaryotes, RNA viruses account for the majority of the virome diversity Keywords: although ssDNA and dsDNA viruses are common as well. Phylogenomic analysis yields tangible clues for Evolution of viruses the origins of major classes of eukaryotic viruses and in particular their likely roots in prokaryotes. Transposable elements Specifically, the ancestral genome of positive-strand RNA viruses of eukaryotes might have been Polintons assembled de novo from genes derived from prokaryotic retroelements and bacteria although a Bacteriophages Recombination primordial origin of this class of viruses cannot be ruled out. Different groups of double-stranded RNA Functional gene modules viruses derive either from dsRNA bacteriophages or from positive-strand RNA viruses. The eukaryotic ssDNA viruses apparently evolved via a fusion of genes from prokaryotic rolling circle-replicating plasmids and positive-strand RNA viruses. Different families of eukaryotic dsDNA viruses appear to have originated from specific groups of bacteriophages on at least two independent occasions. Polintons, the largest known eukaryotic transposons, predicted to also form virus particles, most likely, were the evolutionary intermediates between bacterial tectiviruses and several groups of eukaryotic dsDNA viruses including the proposed order “Megavirales” that unites diverse families of large and giant viruses. Strikingly, evolution of all classes of eukaryotic viruses appears to have involved fusion between structural and replicative gene modules derived from different sources along with additional acquisi- tions of diverse genes. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). Contents Introduction..............................................................................................................3 The contrasting viromes of prokaryotes and eukaryotes. 3 Evolutionary scenarios for the origin of eukaryotes and their impact on the reconstruction of virus evolution . 4 Origins of the major classes of eukaryotic viruses and evolutionary relationships between viruses of prokaryotes and eukaryotes . 5 A general perspective on RNA virus evolution: Out of the primordial RNA world?. 5 Positive-strand RNA viruses: Assembly from diverse prokaryotic progenitors and gene exchanges leading to enormous diversification . 6 dsRNA viruses: Multiple origins from positive-strand RNA viruses . 9 Negative-strand RNA viruses: The emerging positive-strand connection. 10 Synopsis on eukaryotic RNA virome. 10 Retroelements and retroviruses: Viruses as derived forms . 10 n Corresponding author. E-mail addresses: [email protected] (E.V. Koonin), [email protected] (V.V. Dolja), [email protected] (M. Krupovic). http://dx.doi.org/10.1016/j.virol.2015.02.039 0042-6822/Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). E.V. Koonin et al. / Virology 479-480 (2015) 2–25 3 Synopsis on eukaryotic retroelements . 14 Origins of ssDNA viruses of eukaryotes: Multiple crosses between plasmids and RNA viruses . 14 Synopsis on ssDNA virus origins. 17 Origins and primary diversification of eukaryotic dsDNA viruses: The bacteriophage and transposable element connections . 17 Synopsis of dsDNA virus evolution. 20 Conclusions.............................................................................................................20 Acknowledgments. 21 Appendix A. Supporting information . 21 References..............................................................................................................21 Introduction viruses and encompass multiple transitions from capsid-less elements A major discovery of environmental genomics over the last to bona fide viruses and vice versa (Koonin and Dolja, 2013, 2014). decade is that the most common and abundant biological entities Thus, any reconstruction of virus evolution that fails to take into on earth are viruses, in particular bacteriophages (Edwards and account the evolutionary relationships with non-viral selfish elements Rohwer, 2005; Rohwer, 2003; Rohwer and Thurber, 2009; Suttle, is bound to be substantially incomplete. The capsid-less elements as 2005, 2007). In marine, soil and animal-associated environments, well as many viruses differ in their extent of integration with the host virus particles consistently outnumber cells by one to two orders of cells: some insert into the cell genome and are transmitted mainly magnitude. Viruses are major ecological and even geological agents vertically through the host generations, others are largely autonomous, that in large part shape such processes as energy conversion in the and many combine both strategies mixed in different proportions. biosphere and sediment formation in water bodies by killing off Viruses and other selfish elements certainly have not evolved populations of abundant, ecologically important organisms such as from a single common ancestor: indeed, not a single gene is cyanobacteria or eukaryotic algae (Fuhrman, 1999; Rohwer and conserved across the entire “greater virus world” or even in the Thurber, 2009; Suttle, 2007). With the possible exception of some majority of selfish elements (Holmes, 2011; Koonin et al., 2006). highly degraded intracellular parasitic bacteria, viruses and/or other However, these elements form a dense evolutionary network in selfish elements, such as transposons and plasmids, parasitize on all which genomes are linked through different shared genes (Koonin cellular organisms. Complementary to their physical dominance in and Dolja, 2014; Krupovic and Koonin, 2015; Yutin et al., 2013). This the biosphere, viruses collectively appear to encompass the bulk of type of evolutionary relationship results from extensive exchange of the genetic diversity on earth (Hendrix, 2003; Kristensen et al., genes and gene modules, in some cases between widely different 2010, 2013). The ubiquity of viruses in the extant biosphere and the elements, as well as parallel capture of homologous genes from the results of theoretical modeling indicating that emergence of selfish hosts by distinct elements. Viruses with large genomes possess genetic elements is intrinsic to any evolving system of replicators numerous genes that were acquired from the hosts at different together imply that virus-host coevolution had been the mode of stages of evolution; such genes typically are restricted in their the evolution of life ever since its origin (Szathmary and Demeter, spread to a narrow group of viruses. However, a small group of viral 1987; Takeuchi and Hogeweg, 2007, 2012; Takeuchi et al., 2011). hallmark genes that encode key proteins involved in genome All cellular life forms possess genomes consisting of double- replication and virion formation and are shared by overlapping sets stranded (ds) DNA and employ the same, standard scheme for repl- of diverse viruses ensures the connectivity of the evolutionary ication and expression. In contrast, viruses and other selfish network in the virus world (Holmes, 2011; Koonin and Dolja, elements exploit
Load more

Recommended publications
  • Identification of Two Major Virion Protein Genes of White Spot Syndrome Virus of Shrimp
    Virology 266, 227–236 (2000) doi:10.1006/viro.1999.0088, available online at http://www.idealibrary.com on View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Identification of Two Major Virion Protein Genes of White Spot Syndrome Virus of Shrimp Marie¨lle C. W. van Hulten, Marcel Westenberg, Stephen D. Goodall, and Just M. Vlak1 Laboratory of Virology, Wageningen Agricultural University, Binnenhaven 11, 6709 PD Wageningen, The Netherlands Received August 25, 1999; returned to author for revision October 28, 1999; accepted November 8, 1999 White Spot Syndrome Virus (WSSV) is an invertebrate virus, causing considerable mortality in shrimp. Two structural proteins of WSSV were identified. WSSV virions are enveloped nucleocapsids with a bacilliform morphology with an approximate size of 275 ϫ 120 nm, and a tail-like extension at one end. The double-stranded viral DNA has an approximate size 290 kb. WSSV virions, isolated from infected shrimps, contained four major proteins: 28 kDa (VP28), 26 kDa (VP26), 24 kDa (VP24), and 19 kDa (VP19) in size, respectively. VP26 and VP24 were found associated with nucleocapsids; the others were associated with the envelope. N-terminal amino acid sequences of nucleocapsid protein VP26 and the envelope protein VP28 were obtained by protein sequencing and used to identify the respective genes (vp26 and vp28) in the WSSV genome. To confirm that the open reading frames of WSSV vp26 (612) and vp28 (612) are coding for the putative major virion proteins, they were expressed in insect cells using baculovirus vectors and analyzed by Western analysis.
    [Show full text]
  • Development of Biotehcnological Tools for Studying Infectious Pathways of Canine and Human Parvoviruses
    JYVÄSKYLÄ STUDIES IN BIOLOGICAL AND ENVIRONMENTAL SCIENCE 154 Leona Gilbert Development of Biotehcnological Tools for Studying Infectious Pathways of Canine and Human Parvoviruses JYVÄSKYLÄN YLIOPISTO JYVÄSKYLÄ STUDIES IN BIOLOGICAL AND ENVIRONMENTAL SCIENCE 154 Leona Gilbert Development of Biotechnological Tools for Studying Infectious Pathways of Canine and Human Parvoviruses Esitetään Jyväskylän yliopiston matemaattis-luonnontieteellisen tiedekunnan suostumuksella julkisesti tarkastettavaksi yliopiston Ambiotica-rakennuksen salissa (YAA303) kesäkuun 18. päivänä 2005 kello 12. Academic dissertation to be publicly discussed, by permission of the Faculty of Mathematics and Science of the University of Jyväskylä, in the Building Ambiotica, Auditorium YAA303, on June 18th, 2005 at 12 o'clock noon. UNIVERSITY OF JYVÄSKYLÄ JYVÄSKYLÄ 2005 Development of Biotechnological Tools for Studying Infectious Pathways of Canine and Human Parvoviruses JYVÄSKYLÄ STUDIES IN BIOLOGICAL AND ENVIRONMENTAL SCIENCE 154 Leona Gilbert Development of Biotechnological Tools for Studying Infectious Pathways of Canine and Human Parvoviruses UNIVERSITY OF JYVÄSKYLÄ JYVÄSKYLÄ 2005 Editors Jukka Särkkä Department of Biological and Environmental Science, University of Jyväskylä Pekka Olsbo, Irene Ylönen Publishing Unit, University Library of Jyväskylä Cover picture: Molecular models of the fluorescent biotechnological tools for CPV and B19. Picture by Leona Gilbert. ISBN 951-39-2134-4 (nid.) ISSN 1456-9701 Copyright © 2005, by University of Jyväskylä Jyväskylä University Printing House, Jyväskylä 2005 ABSTRACT Gilbert, Leona Development of biotechnological tools for studying infectious pathways of canine and human parvoviruses. Jyväskylä, University of Jyväskylä, 2005, 104 p. (Jyväskylä Studies in Biological and Environmental Science, ISSN 1456-9701; 154) ISBN 951-39-2182-4 Parvoviruses are among the smallest vertebrate DNA viruses known to date. The production of parvovirus-like particles (parvo-VLPs) has been successfully exploited for parvovirus vaccine development.
    [Show full text]
  • Grapevine Virus Diseases: Economic Impact and Current Advances in Viral Prospection and Management1
    1/22 ISSN 0100-2945 http://dx.doi.org/10.1590/0100-29452017411 GRAPEVINE VIRUS DISEASES: ECONOMIC IMPACT AND CURRENT ADVANCES IN VIRAL PROSPECTION AND MANAGEMENT1 MARCOS FERNANDO BASSO2, THOR VINÍCIUS MArtins FAJARDO3, PASQUALE SALDARELLI4 ABSTRACT-Grapevine (Vitis spp.) is a major vegetative propagated fruit crop with high socioeconomic importance worldwide. It is susceptible to several graft-transmitted agents that cause several diseases and substantial crop losses, reducing fruit quality and plant vigor, and shorten the longevity of vines. The vegetative propagation and frequent exchanges of propagative material among countries contribute to spread these pathogens, favoring the emergence of complex diseases. Its perennial life cycle further accelerates the mixing and introduction of several viral agents into a single plant. Currently, approximately 65 viruses belonging to different families have been reported infecting grapevines, but not all cause economically relevant diseases. The grapevine leafroll, rugose wood complex, leaf degeneration and fleck diseases are the four main disorders having worldwide economic importance. In addition, new viral species and strains have been identified and associated with economically important constraints to grape production. In Brazilian vineyards, eighteen viruses, three viroids and two virus-like diseases had already their occurrence reported and were molecularly characterized. Here, we review the current knowledge of these viruses, report advances in their diagnosis and prospection of new species, and give indications about the management of the associated grapevine diseases. Index terms: Vegetative propagation, plant viruses, crop losses, berry quality, next-generation sequencing. VIROSES EM VIDEIRAS: IMPACTO ECONÔMICO E RECENTES AVANÇOS NA PROSPECÇÃO DE VÍRUS E MANEJO DAS DOENÇAS DE ORIGEM VIRAL RESUMO-A videira (Vitis spp.) é propagada vegetativamente e considerada uma das principais culturas frutíferas por sua importância socioeconômica mundial.
    [Show full text]
  • Detection and Complete Genome Characterization of a Begomovirus Infecting Okra (Abelmoschus Esculentus) in Brazil
    Tropical Plant Pathology, vol. 36, 1, 014-020 (2011) Copyright by the Brazilian Phytopathological Society. Printed in Brazil www.sbfito.com.br RESEARCH ARTICLE / ARTIGO Detection and complete genome characterization of a begomovirus infecting okra (Abelmoschus esculentus) in Brazil Silvia de Araujo Aranha1, Leonardo Cunha de Albuquerque1, Leonardo Silva Boiteux2 & Alice Kazuko Inoue-Nagata2 1Departamento de Fitopatologia, Universidade de Brasília, 70910-900, Brasília, DF, Brazil; 2Embrapa Hortaliças, 70359- 970, Brasília, DF, Brazil Author for correspondence: Alice K. Inoue-Nagata, e-mail. [email protected] ABSTRACT A survey of okra begomoviruses was carried out in Central Brazil. Foliar samples were collected in okra production fields and tested by using begomovirus universal primers. Begomovirus infection was confirmed in only one (#5157) out of 196 samples. Total DNA was subjected to PCR amplification and introduced into okra seedlings by a biolistic method; the bombarded DNA sample was infectious to okra plants. The DNA-A and DNA-B of isolate #5157 were cloned and their nucleotide sequences exhibited typical characteristics of New World bipartite begomoviruses. The DNA-A sequence shared 95.6% nucleotide identity with an isolate of Sida micrantha mosaic virus from Brazil and thus identified as its okra strain. The clones derived from #5157 were infectious to okra, Sida santaremnensis and to a group of Solanaceae plants when inoculated by biolistics after circularization of the isolated insert, followed by rolling circle amplification. Key words: Sida micrantha mosaic virus, geminivirus, SimMV. RESUMO Detecção e caracterização do genoma completo de um begomovírus que infecta o quiabeiro (Abelmoschus esculentus) no Brasil Um levantamento de begomovírus de quiabeiro foi realizado no Brasil Central.
    [Show full text]
  • Lack of Viral Mirna Expression in an Experimental Infection
    Núñez-Hernández et al. Veterinary Research (2015) 46:48 DOI 10.1186/s13567-015-0181-4 VETERINARY RESEARCH SHORT REPORT Open Access Evaluation of the capability of the PCV2 genome to encode miRNAs: lack of viral miRNA expression in an experimental infection Fernando Núñez-Hernández1, Lester J Pérez2, Gonzalo Vera3, Sarai Córdoba3, Joaquim Segalés1,4, Armand Sánchez3,5 and José I Núñez1* Abstract Porcine circovirus type 2 (PCV2) is a ssDNA virus causing PCV2-systemic disease (PCV2-SD), one of the most important diseases in swine. MicroRNAs (miRNAs) are a new class of small non-coding RNAs that regulate gene expression post-transcriptionally. Viral miRNAs have recently been described and the number of viral miRNAs has been increasing in the past few years. In this study, small RNA libraries were constructed from two tissues of subclinically PCV2 infected pigs to explore if PCV2 can encode viral miRNAs. The deep sequencing data revealed that PCV2 does not express miRNAs in an in vivo subclinical infection. Introduction, methods, and results family with the highest miRNAs encoding capacity Porcine circovirus type 2-systemic disease (PCV2-SD) is [6,7]. Other viruses belonging to the families Polyoma- a devastating disease that causes important economic viridae, Adenoviridae, Papillomaviridae, Baculoviridae losses [1]. The disease is essentially caused by PCV2, a and Ascoviridae encode miRNAs in low numbers single stranded DNA, non enveloped virus belonging to [8-12]. Recently, a Human Torque Teno virus, a small, the Circoviridae family [2]. The PCV2 genome encodes ssDNA virus from the Anelloviridae family, that en- four ORFs. ORF1 encodes for two proteins (Rep and codes a miRNA involved in interferon modulation has Rep’) which are involved in replication.
    [Show full text]
  • Bemisia Tabaci, Gennadius: Hemiptera Aleyrodidae) Xiomara H
    Journal of General Virology (2005), 86, 1525–1532 DOI 10.1099/vir.0.80665-0 Differential transcriptional activity of plant- pathogenic begomoviruses in their whitefly vector (Bemisia tabaci, Gennadius: Hemiptera Aleyrodidae) Xiomara H. Sinisterra,1 C. L. McKenzie,1 Wayne B. Hunter,1 Charles A. Powell2 and Robert G. Shatters, Jr1 Correspondence 1United States Department of Agriculture, Agricultural Research Service, US Horticultural Robert G. Shatters, Jr Research Laboratory, 2001 South Rock Road, Fort Pierce, FL 34945, USA [email protected] 2Indian River Research and Education Center, IFAS, University of Florida, Fort Pierce, FL 34945, USA Plant-pathogenic begomoviruses have a complex association with their whitefly vector and aspects concerning virus genetic activity (genome replication and gene transcription) within the insect remain highly controversial. Virus transcript abundance was assessed by quantifying selected gene transcripts of Tomato mottle virus (ToMoV, a New World bipartite begomovirus) and Tomato yellow leaf curl virus (TYLCV, an Old World monopartite begomovirus) in whiteflies (Bemisia tabaci biotype B) after feeding on virus-infected tomato plants and after subsequent transfer to cotton, a plant that is immune to the selected begomoviruses. Real-time RT-PCR was performed using specific primers for three ToMoV genes (AV1, BC1 and BV1) and three TYLCV genes (V1, V2 and C3). The ToMoV gene transcripts rapidly became undetectable in whiteflies following transfer from tomato to cotton, probably because degradation was not accompanied by new synthesis. On the other hand, TYLCV transcripts increased after transfer of whiteflies to cotton, indicating active TYLCV transcription. Interestingly, the difference observed Received 5 October 2004 in ToMoV and TYLCV transcripts in the vector parallel observations on the different biological Accepted 4 February 2005 effects of these viruses on whiteflies, i.e.
    [Show full text]
  • Entry of the Membrane-Containing Bacteriophages Into Their Hosts
    Entry of the membrane-containing bacteriophages into their hosts - Institute of Biotechnology and Department of Biosciences Division of General Microbiology Faculty of Biosciences and Viikki Graduate School in Molecular Biosciences University of Helsinki ACADEMIC DISSERTATION To be presented for public examination with the permission of the Faculty of Biosciences, University of Helsinki, in the auditorium 3 of Info center Korona, Viikinkaari 11, Helsinki, on June 18th, at 8 a.m. HELSINKI 2010 Supervisor Professor Dennis H. Bamford Department of Biosciences University of Helsinki, Finland Reviewers Professor Martin Romantschuk Department of Ecological and Environmental Sciences University of Helsinki, Finland Professor Mikael Skurnik Department of Bacteriology and Immunology University of Helsinki, Finland Opponent Dr. Alasdair C. Steven Laboratory of Structural Biology Research National Institute of Arthritis and Musculoskeletal and Skin Diseases National Institutes of Health, USA ISBN 978-952-10-6280-3 (paperback) ISBN 978-952-10-6281-0 (PDF) ISSN 1795-7079 Yliopistopaino, Helsinki University Printing House Helsinki 2010 ORIGINAL PUBLICATIONS This thesis is based on the following publications, which are referred to in the text by their roman numerals: I. 6 - Verkhovskaya R, Bamford DH. 2005. Penetration of enveloped double- stranded RNA bacteriophages phi13 and phi6 into Pseudomonas syringae cells. J Virol. 79(8):5017-26. II. Gaidelyt A*, Cvirkait-Krupovi V*, Daugelaviius R, Bamford JK, Bamford DH. 2006. The entry mechanism of membrane-containing phage Bam35 infecting Bacillus thuringiensis. J Bacteriol. 188(16):5925-34. III. Cvirkait-Krupovi V, Krupovi M, Daugelaviius R, Bamford DH. 2010. Calcium ion-dependent entry of the membrane-containing bacteriophage PM2 into Pseudoalteromonas host.
    [Show full text]
  • Primordial Capsid and Spooled Ssdna Genome Structures Penetrate
    bioRxiv preprint doi: https://doi.org/10.1101/2021.03.14.435335; this version posted March 14, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Primordial capsid and spooled ssDNA genome structures penetrate 2 ancestral events of eukaryotic viruses 3 4 Anna Munke1*#, Kei Kimura2, Yuji Tomaru3, Han Wang1, Kazuhiro Yoshida4, Seiya Mito5, Yuki 5 Hongo6, and Kenta Okamoto1* 6 1. The Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala 7 University, Uppsala, Sweden 8 2. Department of Biological Resource Science, Faculty of Agriculture, Saga University, Saga, Japan 9 3. Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Hatsukaichi, 10 Hiroshima, Japan 11 4. Graduate School of Agriculture, Saga University, Saga, Japan 12 5. Department of Biological Resource Science, Faculty of Agriculture, Saga University, Saga, Japan 13 6. Bioinformatics and Biosciences Division, Fisheries Resources Institute, Japan Fisheries Research 14 and Education Agency, Fukuura, Kanazawa, Yokohama, Kanagawa, Japan 15 16 17 *Corresponding authors 18 Corresponding author 1: [email protected] 19 Corresponding author 2: [email protected] 20 21 22 #Present address: Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 23 Hamburg 22607, Germany 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.03.14.435335; this version posted March 14, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 24 Abstract 25 Marine algae viruses are important for controlling microorganism communities in the marine 26 ecosystem, and played a fundamental role during the early events of viral evolution.
    [Show full text]
  • Complete Genome Sequence of a Novel Dsrna Mycovirus Isolated from the Phytopathogenic Fungus Fusarium Oxysporum F
    Complete genome sequence of a novel dsRNA mycovirus isolated from the phytopathogenic fungus Fusarium oxysporum f. sp. dianthi. Carlos G. Lemus-Minor1, M. Carmen Cañizares2, María D. García-Pedrajas2, Encarnación Pérez- Artés1,* 1Department of Crop Protection, Instituto de Agricultura Sostenible, IAS-CSIC, Alameda del Obispo s/n. Apdo 4084, 14080 Córdoba, Spain. 2Instituto de Hortofruticultura Subtropical y Mediterránea ‘‘La Mayora’’, Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental ‘‘La Mayora’’, 29750 Algarrobo-Costa, Málaga, Spain. *Corresponding author Encarnación Pérez-Artés. e-mail: [email protected] Phone: +34 957 49 92 23 Fax: +34 957 49 92 52 Abstract A novel double-stranded RNA (dsRNA) mycovirus, designated Fusarium oxysporum f. sp. dianthi mycovirus 1 (FodV1), was isolated from a strain of the phytopathogenic fungus F. oxysporum f. sp. dianthi. The FodV1 genome has four dsRNA segments designated, from the largest to the smallest one, dsRNA 1, 2 3, and 4. Each one of these segments contained a single open reading frame (ORF). DsRNA 1 (3555 bp) and dsRNA 3 (2794 bp) encoded a putative RNA-dependent RNA polymerase (RdRp) and a putative coat protein (CP), respectively. Whereas dsRNA 2 (2809 bp) and dsRNA 4 (2646 bp) ORFs encoded hypothetical proteins (named P2 and P4, respectively) with unknown functions. Analysis of its genomic structure, homology searches of the deducted amino acid sequences, and phylogenetic analysis all indicated that FodV1 is a new member of the Chrysoviridae family. This is the first report of the complete genomic characterization of a mycovirus identified in the plant pathogenic species Fusarium oxysporum.
    [Show full text]
  • Detection and Characterization of a Novel Marine Birnavirus Isolated from Asian Seabass in Singapore
    Chen et al. Virology Journal (2019) 16:71 https://doi.org/10.1186/s12985-019-1174-0 RESEARCH Open Access Detection and characterization of a novel marine birnavirus isolated from Asian seabass in Singapore Jing Chen1†, Xinyu Toh1†, Jasmine Ong1, Yahui Wang1, Xuan-Hui Teo1, Bernett Lee2, Pui-San Wong3, Denyse Khor1, Shin-Min Chong1, Diana Chee1, Alvin Wee1, Yifan Wang1, Mee-Keun Ng1, Boon-Huan Tan3 and Taoqi Huangfu1* Abstract Background: Lates calcarifer, known as seabass in Asia and barramundi in Australia, is a widely farmed species internationally and in Southeast Asia and any disease outbreak will have a great economic impact on the aquaculture industry. Through disease investigation of Asian seabass from a coastal fish farm in 2015 in Singapore, a novel birnavirus named Lates calcarifer Birnavirus (LCBV) was detected and we sought to isolate and characterize the virus through molecular and biochemical methods. Methods: In order to propagate the novel birnavirus LCBV, the virus was inoculated into the Bluegill Fry (BF-2) cell line and similar clinical signs of disease were reproduced in an experimental fish challenge study using the virus isolate. Virus morphology was visualized using transmission electron microscopy (TEM). Biochemical analysis using chloroform and 5-Bromo-2′-deoxyuridine (BUDR) sensitivity assays were employed to characterize the virus. Next-Generation Sequencing (NGS) was also used to obtain the virus genome for genetic and phylogenetic analyses. Results: The LCBV-infected BF-2 cell line showed cytopathic effects such as rounding and granulation of cells, localized cell death and detachment of cells observed at 3 to 5 days’ post-infection.
    [Show full text]
  • The LUCA and Its Complex Virome in Another Recent Synthesis, We Examined the Origins of the Replication and Structural Mart Krupovic , Valerian V
    PERSPECTIVES archaea that form several distinct, seemingly unrelated groups16–18. The LUCA and its complex virome In another recent synthesis, we examined the origins of the replication and structural Mart Krupovic , Valerian V. Dolja and Eugene V. Koonin modules of viruses and posited a ‘chimeric’ scenario of virus evolution19. Under this Abstract | The last universal cellular ancestor (LUCA) is the most recent population model, the replication machineries of each of of organisms from which all cellular life on Earth descends. The reconstruction of the four realms derive from the primordial the genome and phenotype of the LUCA is a major challenge in evolutionary pool of genetic elements, whereas the major biology. Given that all life forms are associated with viruses and/or other mobile virion structural proteins were acquired genetic elements, there is no doubt that the LUCA was a host to viruses. Here, by from cellular hosts at different stages of evolution giving rise to bona fide viruses. projecting back in time using the extant distribution of viruses across the two In this Perspective article, we combine primary domains of life, bacteria and archaea, and tracing the evolutionary this recent work with observations on the histories of some key virus genes, we attempt a reconstruction of the LUCA virome. host ranges of viruses in each of the four Even a conservative version of this reconstruction suggests a remarkably complex realms, along with deeper reconstructions virome that already included the main groups of extant viruses of bacteria and of virus evolution, to tentatively infer archaea. We further present evidence of extensive virus evolution antedating the the composition of the virome of the last universal cellular ancestor (LUCA; also LUCA.
    [Show full text]
  • Exposure Pathways to High-Consequence Pathogens in the Wastewater Collection and Treatment Systems
    See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/326786071 Exposure Pathways to High-Consequence Pathogens in the Wastewater Collection and Treatment Systems Technical Report · July 2018 DOI: 10.13140/RG.2.2.14738.15043 CITATIONS READS 0 608 2 authors: Sandip Chattopadhyay Sarah Taft United States Environmental Protection Agency United States Environmental Protection Agency 74 PUBLICATIONS 435 CITATIONS 17 PUBLICATIONS 170 CITATIONS SEE PROFILE SEE PROFILE Some of the authors of this publication are also working on these related projects: Exposure Assessment of Livestock Carcass Management Options During Emergencies View project Waste Management - Encapsulation of Contaminated Wastes View project All content following this page was uploaded by Sandip Chattopadhyay on 02 August 2018. The user has requested enhancement of the downloaded file. EPA/600/R-18/221 | July 2018 www.epa.gov/homeland-security-research Exposure Pathways to High-Consequence Pathogens in the Wastewater Collection and Treatment Systems Office of Research and Development Homeland Security Research Program EPA/600/R-18/221 July 2018 Exposure Pathways to High-Consequence Pathogens in the Wastewater Collection and Treatment Systems by Sandip Chattopadhyay, Ph.D. Sarah Taft, Ph.D. Threat and Consequence Assessment Division National Homeland Security Research Center Cincinnati, OH 45268 Contract No. EP-C-14-001 to ICF under Work Assignment 40 U.S. Environmental Protection Agency Project Officer Office of Research and Development Homeland Security Research Program Cincinnati, OH 45268 Disclaimer The U.S. Environmental Protection Agency (EPA) through its Office of Research and Development funded and managed the research described here under Contract No.
    [Show full text]