New Virus Genomes Discovered Via a Systematic Analysis of Fungal Public Transcriptomes
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
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. -
Kitahara Et at AVIROL.Pdf
Title A unique mitovirus from Glomeromycota, the phylum of arbuscular mycorrhizal fungi Author(s) Kitahara, Ryoko; Ikeda, Yoji; Shimura, Hanako; Masuta, Chikara; Ezawa, Tatsuhiro Archives of Virology, 159(8), 2157-2160 Citation https://doi.org/10.1007/s00705-014-1999-1 Issue Date 2014-08 Doc URL http://hdl.handle.net/2115/59807 Rights The final publication is available at Springer via http://dx.doi.org/10.1007/s00705-014-1999-1 Type article (author version) File Information Kitahara_et_at_AVIROL.pdf Instructions for use Hokkaido University Collection of Scholarly and Academic Papers : HUSCAP Arch Virol, accepted for publication: Jan 21 2014 DOI: 10.1007/s00705-014-1999-1 Title: A unique mitovirus from Glomeromycota, the phylum of arbuscular mycorrhizal fungi Authors: Ryoko Kitahara, Yoji Ikeda, Hanako Shimura, Chikara Masuta, and Tatsuhiro Ezawa*. Address: Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589 Japan Authors for correspondence: Tatsuhiro Ezawa Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589 Japan Tel +81-11-706-3845; Fax +81-11-706-3845 Email [email protected] No. of table: N/A No. of figure: two No. of color figure for online publication: one (Fig. 1) Supplementary information: three figures and one table Kitahara et al. 1 Abstract 2 3 Arbuscular mycorrhizal (AM) fungi that belong to the phylum Glomeromycota associate 4 with most land plants and supply mineral nutrients to the host plants. One of the four viral 5 segments found by deep-sequencing of dsRNA in the AM fungus Rhizophagus clarus strain 6 RF1 showed similarity to mitoviruses and is characterized in this report. -
Distribution of Methionine Sulfoxide Reductases in Fungi and Conservation of the Free- 2 Methionine-R-Sulfoxide Reductase in Multicellular Eukaryotes
bioRxiv preprint doi: https://doi.org/10.1101/2021.02.26.433065; this version posted February 27, 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 Distribution of methionine sulfoxide reductases in fungi and conservation of the free- 2 methionine-R-sulfoxide reductase in multicellular eukaryotes 3 4 Hayat Hage1, Marie-Noëlle Rosso1, Lionel Tarrago1,* 5 6 From: 1Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, 7 Marseille, France. 8 *Correspondence: Lionel Tarrago ([email protected]) 9 10 Running title: Methionine sulfoxide reductases in fungi 11 12 Keywords: fungi, genome, horizontal gene transfer, methionine sulfoxide, methionine sulfoxide 13 reductase, protein oxidation, thiol oxidoreductase. 14 15 Highlights: 16 • Free and protein-bound methionine can be oxidized into methionine sulfoxide (MetO). 17 • Methionine sulfoxide reductases (Msr) reduce MetO in most organisms. 18 • Sequence characterization and phylogenomics revealed strong conservation of Msr in fungi. 19 • fRMsr is widely conserved in unicellular and multicellular fungi. 20 • Some msr genes were acquired from bacteria via horizontal gene transfers. 21 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.02.26.433065; this version posted February 27, 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. -
Phaeoseptaceae, Pleosporales) from China
Mycosphere 10(1): 757–775 (2019) www.mycosphere.org ISSN 2077 7019 Article Doi 10.5943/mycosphere/10/1/17 Morphological and phylogenetic studies of Pleopunctum gen. nov. (Phaeoseptaceae, Pleosporales) from China Liu NG1,2,3,4,5, Hyde KD4,5, Bhat DJ6, Jumpathong J3 and Liu JK1*,2 1 School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, P.R. China 2 Guizhou Key Laboratory of Agricultural Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang 550006, P.R. China 3 Faculty of Agriculture, Natural Resources and Environment, Naresuan University, Phitsanulok 65000, Thailand 4 Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand 5 Mushroom Research Foundation, Chiang Rai 57100, Thailand 6 No. 128/1-J, Azad Housing Society, Curca, P.O., Goa Velha 403108, India Liu NG, Hyde KD, Bhat DJ, Jumpathong J, Liu JK 2019 – Morphological and phylogenetic studies of Pleopunctum gen. nov. (Phaeoseptaceae, Pleosporales) from China. Mycosphere 10(1), 757–775, Doi 10.5943/mycosphere/10/1/17 Abstract A new hyphomycete genus, Pleopunctum, is introduced to accommodate two new species, P. ellipsoideum sp. nov. (type species) and P. pseudoellipsoideum sp. nov., collected from decaying wood in Guizhou Province, China. The genus is characterized by macronematous, mononematous conidiophores, monoblastic conidiogenous cells and muriform, oval to ellipsoidal conidia often with a hyaline, elliptical to globose basal cell. Phylogenetic analyses of combined LSU, SSU, ITS and TEF1α sequence data of 55 taxa were carried out to infer their phylogenetic relationships. The new taxa formed a well-supported subclade in the family Phaeoseptaceae and basal to Lignosphaeria and Thyridaria macrostomoides. -
Newsletter of Feb
V OMPHALINISSN 1925-1858 Vol. V, No 2 Newsletter of Feb. 28, 2014 OMPHALINA OMPHALINA, newsletter of Foray Newfoundland & Labrador, has no fi xed schedule of publication, and no promise to appear again. Its primary purpose is to serve as a conduit of information to registrants of the upcoming foray and secondarily as a communications tool with members. Issues of OMPHALINA are archived in: is an amateur, volunteer-run, community, Library and Archives Canada’s Electronic Collection <http://epe. not-for-profi t organization with a mission to lac-bac.gc.ca/100/201/300/omphalina/index.html>, and organize enjoyable and informative amateur Centre for Newfoundland Studies, Queen Elizabeth II Library mushroom forays in Newfoundland and (printed copy also archived) <http://collections.mun.ca/cdm4/ description.php?phpReturn=typeListing.php&id=162>. Labrador and disseminate the knowledge gained. The content is neither discussed nor approved by the Board of Directors. Therefore, opinions expressed do not represent the views of the Board, Webpage: www.nlmushrooms.ca the Corporation, the partners, the sponsors, or the members. Opinions are solely those of the authors and uncredited opinions solely those of the Editor. ADDRESS Foray Newfoundland & Labrador Please address comments, complaints, contributions to the self-appointed Editor, Andrus Voitk: 21 Pond Rd. Rocky Harbour NL seened AT gmail DOT com, A0K 4N0 CANADA … who eagerly invites contributions to OMPHALINA, dealing with any aspect even remotely related to mushrooms. E-mail: info AT nlmushrooms DOT ca Authors are guaranteed instant fame—fortune to follow. Authors retain copyright to all published material, and BOARD OF DIRECTORS CONSULTANTS submission indicates permission to publish, subject to the usual editorial decisions. -
Fungal Planet Description Sheets: 716–784 By: P.W
Fungal Planet description sheets: 716–784 By: P.W. Crous, M.J. Wingfield, T.I. Burgess, G.E.St.J. Hardy, J. Gené, J. Guarro, I.G. Baseia, D. García, L.F.P. Gusmão, C.M. Souza-Motta, R. Thangavel, S. Adamčík, A. Barili, C.W. Barnes, J.D.P. Bezerra, J.J. Bordallo, J.F. Cano-Lira, R.J.V. de Oliveira, E. Ercole, V. Hubka, I. Iturrieta-González, A. Kubátová, M.P. Martín, P.-A. Moreau, A. Morte, M.E. Ordoñez, A. Rodríguez, A.M. Stchigel, A. Vizzini, J. Abdollahzadeh, V.P. Abreu, K. Adamčíková, G.M.R. Albuquerque, A.V. Alexandrova, E. Álvarez Duarte, C. Armstrong-Cho, S. Banniza, R.N. Barbosa, J.-M. Bellanger, J.L. Bezerra, T.S. Cabral, M. Caboň, E. Caicedo, T. Cantillo, A.J. Carnegie, L.T. Carmo, R.F. Castañeda-Ruiz, C.R. Clement, A. Čmoková, L.B. Conceição, R.H.S.F. Cruz, U. Damm, B.D.B. da Silva, G.A. da Silva, R.M.F. da Silva, A.L.C.M. de A. Santiago, L.F. de Oliveira, C.A.F. de Souza, F. Déniel, B. Dima, G. Dong, J. Edwards, C.R. Félix, J. Fournier, T.B. Gibertoni, K. Hosaka, T. Iturriaga, M. Jadan, J.-L. Jany, Ž. Jurjević, M. Kolařík, I. Kušan, M.F. Landell, T.R. Leite Cordeiro, D.X. Lima, M. Loizides, S. Luo, A.R. Machado, H. Madrid, O.M.C. Magalhães, P. Marinho, N. Matočec, A. Mešić, A.N. Miller, O.V. Morozova, R.P. Neves, K. Nonaka, A. Nováková, N.H. -
Next-Generation Sequencing Reveals an Extraordinary Virus with Multiple Genomic Co
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 30 March 2018 doi:10.20944/preprints201803.0271.v1 Peer-reviewed version available at Viruses 2018, 10, 260; doi:10.3390/v10050260 1 Blackcurrant leaf chlorosis associated virus: next-generation sequencing 2 reveals an extraordinary virus with multiple genomic components including 3 evidence of circular RNA 4 5 Delano James*, James Phelan and Daniel Sanderson 6 Sidney Laboratory, Centre for Plant Health, Canadian Food Inspection Agency, 8801 East 7 Saanich Road, North Saanich, British Columbia, V8L 1H3, Canada; 8 [email protected] (J.P.); [email protected] (D.S.) 9 *Correspondence: [email protected]; Tel.: 1 250 363 6650; FAX: 1 250 363 6661 10 11 Abstract: Blackcurrant leaf chlorosis associated virus (BCLCaV) was detected recently by next- 12 generation sequencing (NGS) and proposed as a new and distinct species in the genus 13 Idaeovirus. Genomic components of BCLCaV that were detected and confirmed include: 1) 14 RNA-1 that is monocistronic and encodes the replicase complex; 2) a bicistronic RNA-2 that 15 encodes a movement protein (MP) and the coat protein (CP) of the virus, with open reading 16 frames (ORF) that overlap by a single adenine (A) nucleotide (nt) representing the third position 17 of an opal stop codon of the MP ORF2a and the first position of the start codon of the CP 18 ORF2b; 3) a subgenomic form of RNA-2 (RNA-3) that contains ORF2b; and 4) a concatenated 19 form of RNA-2 that consists of a complementary and inverted RNA-3 conjoined to the full- 20 length RNA-2. -
Molecular Systematics of the Marine Dothideomycetes
available online at www.studiesinmycology.org StudieS in Mycology 64: 155–173. 2009. doi:10.3114/sim.2009.64.09 Molecular systematics of the marine Dothideomycetes S. Suetrong1, 2, C.L. Schoch3, J.W. Spatafora4, J. Kohlmeyer5, B. Volkmann-Kohlmeyer5, J. Sakayaroj2, S. Phongpaichit1, K. Tanaka6, K. Hirayama6 and E.B.G. Jones2* 1Department of Microbiology, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand; 2Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Paholyothin Road, Khlong 1, Khlong Luang, Pathum Thani, 12120, Thailand; 3National Center for Biothechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, MSC 6510, Bethesda, Maryland 20892-6510, U.S.A.; 4Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, U.S.A.; 5Institute of Marine Sciences, University of North Carolina at Chapel Hill, Morehead City, North Carolina 28557, U.S.A.; 6Faculty of Agriculture & Life Sciences, Hirosaki University, Bunkyo-cho 3, Hirosaki, Aomori 036-8561, Japan *Correspondence: E.B. Gareth Jones, [email protected] Abstract: Phylogenetic analyses of four nuclear genes, namely the large and small subunits of the nuclear ribosomal RNA, transcription elongation factor 1-alpha and the second largest RNA polymerase II subunit, established that the ecological group of marine bitunicate ascomycetes has representatives in the orders Capnodiales, Hysteriales, Jahnulales, Mytilinidiales, Patellariales and Pleosporales. Most of the fungi sequenced were intertidal mangrove taxa and belong to members of 12 families in the Pleosporales: Aigialaceae, Didymellaceae, Leptosphaeriaceae, Lenthitheciaceae, Lophiostomataceae, Massarinaceae, Montagnulaceae, Morosphaeriaceae, Phaeosphaeriaceae, Pleosporaceae, Testudinaceae and Trematosphaeriaceae. Two new families are described: Aigialaceae and Morosphaeriaceae, and three new genera proposed: Halomassarina, Morosphaeria and Rimora. -
Two Pleosporalean Root-Colonizing Fungi, Fuscosphaeria Hungarica Gen
Mycological Progress (2021) 20:39–50 https://doi.org/10.1007/s11557-020-01655-8 ORIGINAL ARTICLE Two pleosporalean root-colonizing fungi, Fuscosphaeria hungarica gen. et sp. nov. and Delitschia chaetomioides, from a semiarid grassland in Hungary Alexandra Pintye1 & Dániel G. Knapp2 Received: 15 May 2020 /Revised: 14 November 2020 /Accepted: 29 November 2020 # The Author(s) 2020 Abstract In this study, we investigated two unidentified lineages of root-colonizing fungi belonging to the order Pleosporales (Dothideomycetes), which were isolated from Festuca vaginata (Poaceae), a dominant grass species in the semiarid sandy grass- lands of Hungary. For molecular phylogenetic studies, seven loci (internal transcribed spacer, partial large subunit and small subunit region of nrRNA, partial transcription elongation factor 1-α, RNA polymerase II largest subunit, RNA polymerase II second largest subunit, and ß-tubulin genes) were amplified and sequenced. Based on morphology and multilocus phylogenetic analyses, we found that one lineage belonged to Delitschia chaetomioides P. Karst. (Delitschiaceae), and the isolates of the other lineage represented a novel monotypic genus in the family Trematosphaeriaceae (suborder Massarineae). For this lineage, we proposed a new genus, Fuscosphaeria, represented by a single species, F. hungarica. In both lineages, only immature and degenerated sporocarps could be induced. These were sterile, black, globose, or depressed globose structures with numerous mycelioid appendages submerged in culture media or on the -
Taxonomic Revision of True Morels (<I>Morchella</I>) in Canada And
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln U.S. Department of Agriculture: Agricultural Publications from USDA-ARS / UNL Faculty Research Service, Lincoln, Nebraska 2012 Taxonomic revision of true morels (Morchella) in Canada and the United States Michael Kuo Eastern Illinois University Damon R. Dewsbury University of Toronto Kerry O'Donnell USDA-ARS M. Carol Carter Stephen A. Rehner USDA-ARS, [email protected] See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/usdaarsfacpub Kuo, Michael; Dewsbury, Damon R.; O'Donnell, Kerry; Carter, M. Carol; Rehner, Stephen A.; Moore, John David; Moncalvo, Jean-Marc; Canfield, Stephen A.; Stephenson, Steven L.; Methven, Andrew S.; and Volk, Thomas J., "Taxonomic revision of true morels (Morchella) in Canada and the United States" (2012). Publications from USDA-ARS / UNL Faculty. 1564. https://digitalcommons.unl.edu/usdaarsfacpub/1564 This Article is brought to you for free and open access by the U.S. Department of Agriculture: Agricultural Research Service, Lincoln, Nebraska at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Publications from USDA-ARS / UNL Faculty by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Michael Kuo, Damon R. Dewsbury, Kerry O'Donnell, M. Carol Carter, Stephen A. Rehner, John David Moore, Jean-Marc Moncalvo, Stephen A. Canfield, Steven L. Stephenson, Andrew S. Methven, and Thomas J. Volk This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/ usdaarsfacpub/1564 Mycologia, 104(5), 2012, pp. 1159–1177. DOI: 10.3852/11-375 # 2012 by The Mycological Society of America, Lawrence, KS 66044-8897 Taxonomic revision of true morels (Morchella) in Canada and the United States Michael Kuo M. -
Diversity and Evolution of Viral Pathogen Community in Cave Nectar Bats (Eonycteris Spelaea)
viruses Article Diversity and Evolution of Viral Pathogen Community in Cave Nectar Bats (Eonycteris spelaea) Ian H Mendenhall 1,* , Dolyce Low Hong Wen 1,2, Jayanthi Jayakumar 1, Vithiagaran Gunalan 3, Linfa Wang 1 , Sebastian Mauer-Stroh 3,4 , Yvonne C.F. Su 1 and Gavin J.D. Smith 1,5,6 1 Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; [email protected] (D.L.H.W.); [email protected] (J.J.); [email protected] (L.W.); [email protected] (Y.C.F.S.) [email protected] (G.J.D.S.) 2 NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 119077, Singapore 3 Bioinformatics Institute, Agency for Science, Technology and Research, Singapore 138671, Singapore; [email protected] (V.G.); [email protected] (S.M.-S.) 4 Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore 5 SingHealth Duke-NUS Global Health Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore 168753, Singapore 6 Duke Global Health Institute, Duke University, Durham, NC 27710, USA * Correspondence: [email protected] Received: 30 January 2019; Accepted: 7 March 2019; Published: 12 March 2019 Abstract: Bats are unique mammals, exhibit distinctive life history traits and have unique immunological approaches to suppression of viral diseases upon infection. High-throughput next-generation sequencing has been used in characterizing the virome of different bat species. The cave nectar bat, Eonycteris spelaea, has a broad geographical range across Southeast Asia, India and southern China, however, little is known about their involvement in virus transmission. -
Molecular Identification and Characterization of Two Rubber Dandelion
Molecular Identification and Characterization of Two Rubber Dandelion Amalgaviruses Archives of Virology – Annotated Sequence Record Humberto Debat1*, Zinan Luo, Brian J. Iaffaldano, Xiaofeng Zhuang, Katrina Cornish 2 1 Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), 11 de setiembre 4755, Córdoba, Argentina, X5020ICA. 2 Department of Horticulture and Crop Science, The Ohio State University, Ohio Agricultural Research and Development Center, Williams Hall, 1680 Madison Avenue, Wooster, OH 44691. * Corresponding author: Humberto Debat, [email protected], Tel: +54 9 351 4973636, Fax: +54 9 351 4974330 Abstract The Amalgaviridae family is composed of persistent viruses that share the genome architecture of Totiviridae and gene evolutionary resemblance to Partitiviridae. A single Amalgavirus genus has been assigned to this family, harboring only four recognized species, corresponding to plant infecting viruses with dsRNA monopartite genomes of ca. 3.4 kb. Here, we present the genomic identification and characterization of two novel Amalgavirus detected in Rubber dandelion (Taraxacum kok-saghyz). The sequenced isolates presented a 3,409 and 3,413 nt long genome, harbouring two partially overlapping ORFs encoding a putative coat protein and an RNA-dependent RNA polymerase (RdRP). Multiple independent RNAseq data suggest that the identified viruses have a differential distribution and low relative RNA levels in infected plants. Virus presence was not associated with any apparent symptoms on the plant host. We propose the name rubber dandelion latent virus 1 & 2 to the detected Amalgavirus. Annotated sequence record Natural rubber is an essential material to the manufacture of 50,000 different rubber and latex products.