Detection of a Conspecific Mycovirus in Two Closely Related Native And
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The Phylogenetic Relationships of Torrendiella and Hymenotorrendiella Gen
Phytotaxa 177 (1): 001–025 ISSN 1179-3155 (print edition) www.mapress.com/phytotaxa/ PHYTOTAXA Copyright © 2014 Magnolia Press Article ISSN 1179-3163 (online edition) http://dx.doi.org/10.11646/phytotaxa.177.1.1 The phylogenetic relationships of Torrendiella and Hymenotorrendiella gen. nov. within the Leotiomycetes PETER R. JOHNSTON1, DUCKCHUL PARK1, HANS-OTTO BARAL2, RICARDO GALÁN3, GONZALO PLATAS4 & RAÚL TENA5 1Landcare Research, Private Bag 92170, Auckland, New Zealand. 2Blaihofstraße 42, D-72074 Tübingen, Germany. 3Dpto. de Ciencias de la Vida, Facultad de Biología, Universidad de Alcalá, P.O.B. 20, 28805 Alcalá de Henares, Madrid, Spain. 4Fundación MEDINA, Microbiología, Parque Tecnológico de Ciencias de la Salud, 18016 Armilla, Granada, Spain. 5C/– Arreñales del Portillo B, 21, 1º D, 44003, Teruel, Spain. Corresponding author: [email protected] Abstract Morphological and phylogenetic data are used to revise the genus Torrendiella. The type species, described from Europe, is retained within the Rutstroemiaceae. However, Torrendiella species reported from Australasia, southern South America and China were found to be phylogenetically distinct and have been recombined in the newly proposed genus Hymenotorrendiel- la. The Hymenotorrendiella species are distinguished morphologically from Rutstroemia in having a Hymenoscyphus-type rather than Sclerotinia-type ascus apex. Zoellneria, linked taxonomically to Torrendiella in the past, is genetically distinct and a synonym of Chaetomella. Keywords: ascus apex, phylogeny, taxonomy, Hymenoscyphus, Rutstroemiaceae, Sclerotiniaceae, Zoellneria, Chaetomella Introduction Torrendiella was described by Boudier and Torrend (1911), based on T. ciliata Boudier in Boudier and Torrend (1911: 133), a species reported from leaves, and more rarely twigs, of Rubus, Quercus and Laurus from Spain, Portugal and the United Kingdom (Graddon 1979; Spooner 1987; Galán et al. -
Origin, Adaptation and Evolutionary Pathways of Fungal Viruses
Virus Genes 16:1, 119±131, 1998 # 1998 Kluwer Academic Publishers, Boston. Manufactured in The Netherlands. Origin, Adaptation and Evolutionary Pathways of Fungal Viruses SAID A. GHABRIAL Department of Plant Pathology, University of Kentucky, Lexington, KY, USA Abstract. Fungal viruses or mycoviruses are widespread in fungi and are believed to be of ancient origin. They have evolved in concert with their hosts and are usually associated with symptomless infections. Mycoviruses are transmitted intracellularly during cell division, sporogenesis and cell fusion, and they lack an extracellular phase to their life cycles. Their natural host ranges are limited to individuals within the same or closely related vegetative compatibility groups. Typically, fungal viruses are isometric particles 25±50 nm in diameter, and possess dsRNA genomes. The best characterized of these belong to the family Totiviridae whose members have simple undivided dsRNA genomes comprised of a coat protein (CP) gene and an RNA dependent RNA polymerase (RDRP) gene. A recently characterized totivirus infecting a ®lamentous fungus was found to be more closely related to protozoan totiviruses than to yeast totiviruses suggesting these viruses existed prior to the divergence of fungi and protozoa. Although the dsRNA viruses at large are polyphyletic, based on RDRP sequence comparisons, the totiviruses are monophyletic. The theory of a cellular self-replicating mRNA as the origin of totiviruses is attractive because of their apparent ancient origin, the close relationships among their RDRPs, genome simplicity and the ability to use host proteins ef®ciently. Mycoviruses with bipartite genomes ( partitiviruses), like the totiviruses, have simple genomes, but the CP and RDRP genes are on separate dsRNA segments. -
Residual Effects Caused by a Past Mycovirus Infection in Fusarium Circinatum
Article Residual Effects Caused by a Past Mycovirus Infection in Fusarium circinatum Cristina Zamora-Ballesteros 1,2,* , Brenda D. Wingfield 3 , Michael J. Wingfield 3, Jorge Martín-García 1,2 and Julio J. Diez 1,2 1 Sustainable Forest Management Research Institute, University of Valladolid—INIA, 34004 Palencia, Spain; [email protected] (J.M.-G.); [email protected] (J.J.D.) 2 Department of Vegetal Production and Forest Resources, University of Valladolid, 34004 Palencia, Spain 3 Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa; brenda.wingfi[email protected] (B.D.W.); Mike.Wingfi[email protected] (M.J.W.) * Correspondence: [email protected] Abstract: Mycoviruses are known to be difficult to cure in fungi but their spontaneous loss occurs commonly. The unexpected disappearance of mycoviruses can be explained by diverse reasons, from methodological procedures to biological events such as posttranscriptional silencing machinery. The long-term effects of a virus infection on the host organism have been well studied in the case of human viruses; however, the possible residual effect on a fungus after the degradation of a mycovirus is unknown. For that, this study analyses a possible residual effect on the transcriptome of the pathogenic fungus Fusarium circinatum after the loss of the mitovirus FcMV1. The mycovirus that previously infected the fungal isolate was not recovered after a 4-year storage period. Only 14 genes were determined as differentially expressed and were related to cell cycle regulation and amino acid metabolism. The results showed a slight acceleration in the metabolism of the host that had lost the mycovirus by the upregulation of the genes involved in essential functions for fungal development. -
Soybean Thrips (Thysanoptera: Thripidae) Harbor Highly Diverse Populations of Arthropod, Fungal and Plant Viruses
viruses Article Soybean Thrips (Thysanoptera: Thripidae) Harbor Highly Diverse Populations of Arthropod, Fungal and Plant Viruses Thanuja Thekke-Veetil 1, Doris Lagos-Kutz 2 , Nancy K. McCoppin 2, Glen L. Hartman 2 , Hye-Kyoung Ju 3, Hyoun-Sub Lim 3 and Leslie. L. Domier 2,* 1 Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA; [email protected] 2 Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Urbana, IL 61801, USA; [email protected] (D.L.-K.); [email protected] (N.K.M.); [email protected] (G.L.H.) 3 Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 300-010, Korea; [email protected] (H.-K.J.); [email protected] (H.-S.L.) * Correspondence: [email protected]; Tel.: +1-217-333-0510 Academic Editor: Eugene V. Ryabov and Robert L. Harrison Received: 5 November 2020; Accepted: 29 November 2020; Published: 1 December 2020 Abstract: Soybean thrips (Neohydatothrips variabilis) are one of the most efficient vectors of soybean vein necrosis virus, which can cause severe necrotic symptoms in sensitive soybean plants. To determine which other viruses are associated with soybean thrips, the metatranscriptome of soybean thrips, collected by the Midwest Suction Trap Network during 2018, was analyzed. Contigs assembled from the data revealed a remarkable diversity of virus-like sequences. Of the 181 virus-like sequences identified, 155 were novel and associated primarily with taxa of arthropod-infecting viruses, but sequences similar to plant and fungus-infecting viruses were also identified. -
Hymenoscyphus Fraxineus
Hymenoscyphus fraxineus Synonyms: Chalara fraxinea Kowalski (anamorph), Hymenoscyphus pseudoalbidus (teleomorph). Common Name(s) Ash dieback, ash decline Type of Pest Fungal pathogen Taxonomic Position Class: Leotiomycetes, Order: Helotiales, Family: Helotiaceae Reason for Inclusion in Figure 1. Mature Fraxinus excelsior showing Manual extensive shoot, twig, and branch dieback. CAPS Target: AHP Prioritized Epicormic shoot formation is also present. Photo Pest List – 2010-2016 credit: Andrin Gross. Background An extensive dieback of ash (Fig. 1) was observed from 1996 to 2006 in Lithuania and Poland. Trees were dying in all age classes, irrespective of site conditions and regeneration conditions. A fungus, described as a new species Chalara fraxinea, was isolated from shoots and some roots (Kowalski, 2006). The fungal pathogen varied from other species of Chalara by its small, short cylindrical conidia extruded in chains or in slimy droplets, morphological features of the phialophores, and by colony characteristics. Initial taxonomic studies concerning Chalara fraxinea established that its perfect state was the ascomycete Hymenoscyphus albidus (Gillet) W. Phillips, a fungus that has been known from Europe since 1851. Kowalski and Holdenrieder (2009b) provide a description and photographs of the teleomorphic state, Hymenoscyphus albidus. A molecular taxonomic study of Hymenoscyphus albidus indicated that there was significant evidence for the existence of two morphologically very similar taxa, H. albidus, and a new species, Hymenoscyphus pseudoalbidus (Queloz et al., 2010). Furthermore, studies suggested that H. albidus was likely a non-pathogenic species, whereas H. pseudoalbidus was the virulent species responsible for the current ash dieback epidemic in Europe (Queloz et al., 2010). A survey in Denmark showed that expansion of H. -
Taxonomic Study of Lambertella (Rutstroemiaceae, Helotiales) and Allied Substratal Stroma Forming Fungi from Japan
Taxonomic Study of Lambertella (Rutstroemiaceae, Helotiales) and Allied Substratal Stroma Forming Fungi from Japan 著者 趙 彦傑 内容記述 この博士論文は全文公表に適さないやむを得ない事 由があり要約のみを公表していましたが、解消した ため、2017年8月23日に全文を公表しました。 year 2014 その他のタイトル 日本産Lambertella属および基質性子座を形成する 類縁属の分類学的研究 学位授与大学 筑波大学 (University of Tsukuba) 学位授与年度 2013 報告番号 12102甲第6938号 URL http://hdl.handle.net/2241/00123740 Taxonomic Study of Lambertella (Rutstroemiaceae, Helotiales) and Allied Substratal Stroma Forming Fungi from Japan A Dissertation Submitted to the Graduate School of Life and Environmental Sciences, the University of Tsukuba in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Agricultural Science (Doctoral Program in Biosphere Resource Science and Technology) Yan-Jie ZHAO Contents Chapter 1 Introduction ............................................................................................................... 1 1–1 The genus Lambertella in Rutstroemiaceae .................................................................... 1 1–2 Taxonomic problems of Lambertella .............................................................................. 5 1–3 Allied genera of Lambertella ........................................................................................... 7 1–4 Objectives of the present research ................................................................................. 12 Chapter 2 Materials and Methods ............................................................................................ 17 2–1 Collection and isolation -
Ancient Recombination Events and the Origins of Hepatitis E Virus Andrew G
Kelly et al. BMC Evolutionary Biology (2016) 16:210 DOI 10.1186/s12862-016-0785-y RESEARCH ARTICLE Open Access Ancient recombination events and the origins of hepatitis E virus Andrew G. Kelly, Natalie E. Netzler and Peter A. White* Abstract Background: Hepatitis E virus (HEV) is an enteric, single-stranded, positive sense RNA virus and a significant etiological agent of hepatitis, causing sporadic infections and outbreaks globally. Tracing the evolutionary ancestry of HEV has proved difficult since its identification in 1992, it has been reclassified several times, and confusion remains surrounding its origins and ancestry. Results: To reveal close protein relatives of the Hepeviridae family, similarity searching of the GenBank database was carried out using a complete Orthohepevirus A, HEV genotype I (GI) ORF1 protein sequence and individual proteins. The closest non-Hepeviridae homologues to the HEV ORF1 encoded polyprotein were found to be those from the lepidopteran-infecting Alphatetraviridae family members. A consistent relationship to this was found using a phylogenetic approach; the Hepeviridae RdRp clustered with those of the Alphatetraviridae and Benyviridae families. This puts the Hepeviridae ORF1 region within the “Alpha-like” super-group of viruses. In marked contrast, the HEV GI capsid was found to be most closely related to the chicken astrovirus capsid, with phylogenetic trees clustering the Hepeviridae capsid together with those from the Astroviridae family, and surprisingly within the “Picorna-like” supergroup. These results indicate an ancient recombination event has occurred at the junction of the non-structural and structure encoding regions, which led to the emergence of the entire Hepeviridae family. -
Metatranscriptomic Reconstruction Reveals RNA Viruses with the Potential to Shape Carbon Cycling in Soil
Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil Evan P. Starra, Erin E. Nucciob, Jennifer Pett-Ridgeb, Jillian F. Banfieldc,d,e,f,g,1, and Mary K. Firestoned,e,1 aDepartment of Plant and Microbial Biology, University of California, Berkeley, CA 94720; bPhysical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550; cDepartment of Earth and Planetary Science, University of California, Berkeley, CA 94720; dEarth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; eDepartment of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720; fChan Zuckerberg Biohub, San Francisco, CA 94158; and gInnovative Genomics Institute, Berkeley, CA 94720 Contributed by Mary K. Firestone, October 25, 2019 (sent for review May 16, 2019; reviewed by Steven W. Wilhelm and Kurt E. Williamson) Viruses impact nearly all organisms on Earth, with ripples of influ- trophic levels (18). This phenomenon, termed “the viral shunt” (18, ence in agriculture, health, and biogeochemical processes. However, 19), is thought to sustain up to 55% of heterotrophic bacterial very little is known about RNA viruses in an environmental context, production in marine systems (20). However, some organic parti- and even less is known about their diversity and ecology in soil, 1 of cles released through viral lysis aggregate and sink to the deep the most complex microbial systems. Here, we assembled 48 indi- ocean, where they are sequestered from the atmosphere (21). Most vidual metatranscriptomes from 4 habitats within a planted soil studies investigating viral impactsoncarboncyclinghavefocused sampled over a 22-d time series: Rhizosphere alone, detritosphere on DNA phages, while the extent and contribution of RNA viruses alone, rhizosphere with added root detritus, and unamended soil (4 on carbon cycling remains unclear in most ecosystems. -
A Review Paper on Mycoviruses Aqleem Abbas* College of Plant Science and Technology, HZAU Wuhan, China
atholog P y & nt a M Abbas, J Plant Pathol Microbiol 2016, 7:12 l i P c f r o o b DOI: 10.4172/2157-7471.1000390 l i Journal of a o l n o r g u y o J ISSN: 2157-7471 Plant Pathology & Microbiology Review ArticleArticle Open Access A Review Paper on Mycoviruses Aqleem Abbas* College of Plant Science and Technology, HZAU Wuhan, China Abstract Mycoviruses are very significant viruses, which are found to be infecting fungi. These Mycoviruses require the living cells of their hosts for replicate like the plant and animal viruses. The genome of Mycoviruses mostly consist of double stranded RNA (dsRNA) and least of Mycoviruses genome consist of positive, single stranded RNA (-ssRNA). Moreover, DNA Mycoviruses have been reported recently. These viruses have been detected in almost all fungal phylum but still most of the Mycoviruses remain unknown. Mycoviruses are important in a sense that they mostly remain silent and rarely develop symptom in their hosts. Some Mycoviruses have been reported which are causing irregular growth, abnormal pigmentation and some are involved in changing their host sexual reproduction. For the management of Plant diseases, the importance of Mycoviruses arises because of their most significant effect that is they reduced virulence of their host. Technically the reduced virulence is called hypovirulence. This hypovirulence phenomena has increased importance of Mycoviruses because it has the potential to reduce the crop losses and forests caused by their hosts which are plant pathogenic fungi. In this review, I explore different aspects and importance of Mycoviruses. -
Towards a Unified Paradigm for Sequencebased Identification of Fungi
Received Date : 10-May-2013 Revised Date : 08-Jul-2013 Accepted Date : 17-Jul-2013 Article type : Opinion Towards a unified paradigm for sequence-based identification of Fungi Authors Urmas Kõljalg1, 2, R. Henrik Nilsson3, Kessy Abarenkov2, Leho Tedersoo2, Andy FS Taylor4, 5, Mohammad Bahram1, Scott T. Bates6, Thomas D. Bruns7, Johan Bengtsson-Palme8, Tony Martin Callaghan9, Brian Douglas9, Tiia Drenkhan10, Ursula Eberhardt11, Margarita Dueñas12, Tine Grebenc13, Gareth W. Griffith9, Martin Hartmann14, 15, Paul M. Kirk16, Petr Kohout1, 17, Ellen Article 3 18 19 12 20 Larsson , Björn D. Lindahl , Robert Lücking , María P. Martín , P. Brandon Matheny , Nhu H. Nguyen7, Tuula Niskanen21, Jane Oja1, Kabir G. Peay22, Ursula Peintner23, Marko Peterson1, Kadri Põldmaa1, Lauri Saag1, Irja Saar1, Arthur Schüßler24, James A. Scott25, Carolina Senés24, Matthew E. Smith26, Ave Suija1, D. Lee Taylor27, M. Teresa Telleria12, Michael Weiß28, Karl- Henrik Larsson29. 1 Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, 51005 Tartu, Estonia. 2 Natural History Museum, University of Tartu, Vanemuise 46, 51014 Tartu, Estonia. 3 Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-40530 Göteborg, Sweden. 4 The James Hutton Institute, Craigiebuckler, Aberdeen, AB15 8QH, Scotland, UK. 5 Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UU, UK. This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: Accepted 10.1111/mec.12481 This article is protected by copyright. -
Discovery of New Mycoviral Genomes Within Publicly Available Fungal Transcriptomic Datasets
bioRxiv preprint doi: https://doi.org/10.1101/510404; this version posted January 3, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Discovery of new mycoviral genomes within publicly available fungal transcriptomic datasets 1 1 1,2 1 Kerrigan B. Gilbert , Emily E. Holcomb , Robyn L. Allscheid , James C. Carrington * 1 Donald Danforth Plant Science Center, Saint Louis, Missouri, USA 2 Current address: National Corn Growers Association, Chesterfield, Missouri, USA * Address correspondence to James C. Carrington E-mail: [email protected] Short title: Virus discovery from RNA-seq data bioRxiv preprint doi: https://doi.org/10.1101/510404; this version posted January 3, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Abstract The distribution and diversity of RNA viruses in fungi is incompletely understood due to the often cryptic nature of mycoviral infections and the focused study of primarily pathogenic and/or economically important fungi. As most viruses that are known to infect fungi possess either single-stranded or double-stranded RNA genomes, transcriptomic data provides the opportunity to query for viruses in diverse fungal samples without any a priori knowledge of virus infection. Here we describe a systematic survey of all transcriptomic datasets from fungi belonging to the subphylum Pezizomycotina. -
Molecular Characterization of a Novel Mycovirus Isolated from Rhizoctonia Solani AG-1 IA 9-11
Molecular characterization of a novel mycovirus isolated from Rhizoctonia solani AG-1 IA 9-11 Yang Sun Yunnan Agricultural University Yan qiong Li Kunming University Wen han Dong Yunnan Agricultural University Ai li Sun Yunnan Agricultural University Ning wei Chen Yunnan Agricultural University Zi fang Zhao Yunnan Agricultural University Yong qing Li Zhaotong Plant Protection and Quarantine Station Gen hua Yang ( [email protected] ) Yunnan Agricultural University https://orcid.org/0000-0003-3322-1558 Cheng yun Li Yunnan Agricultural University Research Article Keywords: SMC, PRK, RT-like super family, RsRV-HN008, RdRp Posted Date: May 19th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-520549/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/9 Abstract The complete genome of the dsRNA virus isolated from Rhizoctonia solani AG-1 IA 9–11 (designated as Rhizoctonia solani dsRNA virus 11, RsRV11 ) were determined. The RsRV11 genome was 9,555 bp in length, contained three conserved domains, SMC, PRK and RT-like super family, and encoded two non- overlapping open reading frames (ORFs). ORF1 potentially coded for a 204.12 kDa predicted protein, which shared low but signicant amino acid sequence identities with the putative protein encoded by Rhizoctonia solani RNA virus HN008 (RsRV-HN008) ORF1. ORF2 potentially coded for a 132.41 kDa protein which contained the conserved motifs of the RNA-dependent RNA polymerase (RdRp). Phylogenetic analysis indicated that RsRV11 was clustered with RsRV-HN008 in a separate clade independent of other virus families. It implies that RsRV11, along with RsRV-HN008 possibly a new fungal virus taxa closed to the family Megabirnaviridae, and RsRV11 is a new member of mycoviruses.