Clarification on Host Range of Didymella Pinodes the Causal
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Biology and Recent Developments in the Systematics of Phoma, a Complex Genus of Major Quarantine Significance Reviews, Critiques
Fungal Diversity Reviews, Critiques and New Technologies Reviews, Critiques and New Technologies Biology and recent developments in the systematics of Phoma, a complex genus of major quarantine significance Aveskamp, M.M.1*, De Gruyter, J.1, 2 and Crous, P.W.1 1CBS Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands 2Plant Protection Service (PD), P.O. Box 9102, 6700 HC Wageningen, The Netherlands Aveskamp, M.M., De Gruyter, J. and Crous, P.W. (2008). Biology and recent developments in the systematics of Phoma, a complex genus of major quarantine significance. Fungal Diversity 31: 1-18. Species of the coelomycetous genus Phoma are ubiquitously present in the environment, and occupy numerous ecological niches. More than 220 species are currently recognised, but the actual number of taxa within this genus is probably much higher, as only a fraction of the thousands of species described in literature have been verified in vitro. For as long as the genus exists, identification has posed problems to taxonomists due to the asexual nature of most species, the high morphological variability in vivo, and the vague generic circumscription according to the Saccardoan system. In recent years the genus was revised in a series of papers by Gerhard Boerema and co-workers, using culturing techniques and morphological data. This resulted in an extensive handbook, the “Phoma Identification Manual” which was published in 2004. The present review discusses the taxonomic revision of Phoma and its teleomorphs, with a special focus on its molecular biology and papers published in the post-Boerema era. Key words: coelomycetes, Phoma, systematics, taxonomy. -
A Mechanistic Weather-Driven Model for Ascochyta Rabiei Infection and Disease Development in Chickpea
plants Article A Mechanistic Weather-Driven Model for Ascochyta rabiei Infection and Disease Development in Chickpea Irene Salotti and Vittorio Rossi * Department of Sustainable Crop Production (DI.PRO.VES.), Università Cattolica del Sacro Cuore, Via E. Parmense 84, 29122 Piacenza, Italy; [email protected] * Correspondence: [email protected] Abstract: Ascochyta blight caused by Ascochyta rabiei is an important disease of chickpea. By using systems analysis, we retrieved and analyzed the published information on A. rabiei to develop a mechanistic, weather-driven model for the prediction of Ascochyta blight epidemics. The ability of the model to predict primary infections was evaluated using published data obtained from trials conducted in Washington (USA) in 2004 and 2005, Israel in 1996 and 1998, and Spain from 1988 to 1992. The model showed good accuracy and specificity in predicting primary infections. The probability of correctly predicting infections was 0.838 and the probability that there was no infection when not predicted was 0.776. The model’s ability to predict disease progress during the growing season was also evaluated by using data collected in Australia from 1996 to 1998 and in Southern Italy in 2019; a high concordance correlation coefficient (CCC = 0.947) between predicted and observed data was obtained, with an average distance between real and fitted data of root mean square error (RMSE) = 0.103, indicating that the model was reliable, accurate, and robust in predicting seasonal dynamics of Ascochyta blight epidemics. The model could help growers schedule fungicide treatments to control Ascochyta blight on chickpea. Citation: Salotti, I.; Rossi, V. -
Taxonomy and Multigene Phylogenetic Evaluation of Novel Species in Boeremia and Epicoccum with New Records of Ascochyta and Didymella (Didymellaceae)
Mycosphere 8(8): 1080–1101 (2017) www.mycosphere.org ISSN 2077 7019 Article Doi 10.5943/mycosphere/8/8/9 Copyright © Guizhou Academy of Agricultural Sciences Taxonomy and multigene phylogenetic evaluation of novel species in Boeremia and Epicoccum with new records of Ascochyta and Didymella (Didymellaceae) Jayasiri SC1,2, Hyde KD2,3, Jones EBG4, Jeewon R5, Ariyawansa HA6, Bhat JD7, Camporesi E8 and Kang JC1 1 Engineering and Research Center for Southwest Bio-Pharmaceutical Resources of National Education Ministry of China, Guizhou University, Guiyang, Guizhou Province 550025, P.R. China 2Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand 3World Agro forestry Centre East and Central Asia Office, 132 Lanhei Road, Kunming 650201, P. R. China 4Botany and Microbiology Department, College of Science, King Saud University, Riyadh, 1145, Saudi Arabia 5Department of Health Sciences, Faculty of Science, University of Mauritius, Reduit, Mauritius 6Department of Plant Pathology and Microbiology, College of BioResources and Agriculture, National Taiwan University, No.1, Sec.4, Roosevelt Road, Taipei 106, Taiwan, ROC. 7No. 128/1-J, Azad Housing Society, Curca, P.O. Goa Velha, 403108, India 89A.M.B. Gruppo Micologico Forlivese “Antonio Cicognani”, Via Roma 18, Forlì, Italy; A.M.B. CircoloMicologico “Giovanni Carini”, C.P. 314, Brescia, Italy; Società per gliStudiNaturalisticidella Romagna, C.P. 144, Bagnacavallo (RA), Italy *Correspondence: [email protected] Jayasiri SC, Hyde KD, Jones EBG, Jeewon R, Ariyawansa HA, Bhat JD, Camporesi E, Kang JC 2017 – Taxonomy and multigene phylogenetic evaluation of novel species in Boeremia and Epicoccum with new records of Ascochyta and Didymella (Didymellaceae). -
Draft Genome Sequencing and Secretome Analysis of Fungal
www.nature.com/scientificreports OPEN Draft genome sequencing and secretome analysis of fungal phytopathogen Ascochyta Received: 28 October 2015 Accepted: 04 April 2016 rabiei provides insight into the Published: 19 April 2016 necrotrophic effector repertoire Sandhya Verma, Rajesh Kumar Gazara, Shadab Nizam, Sabiha Parween, Debasis Chattopadhyay & Praveen Kumar Verma Constant evolutionary pressure acting on pathogens refines their molecular strategies to attain successful pathogenesis. Recent studies have shown that pathogenicity mechanisms of necrotrophic fungi are far more intricate than earlier evaluated. However, only a few studies have explored necrotrophic fungal pathogens. Ascochyta rabiei is a necrotrophic fungus that causes devastating blight disease of chickpea (Cicer arietinum). Here, we report a 34.6 megabase draft genome assembly of A. rabiei. The genome assembly covered more than 99% of the gene space and 4,259 simple sequence repeats were identified in the assembly. A total of 10,596 high confidence protein-coding genes were predicted which includes a large and diverse inventory of secretory proteins, transporters and primary and secondary metabolism enzymes reflecting the necrotrophic lifestyle ofA. rabiei. A wide range of genes encoding carbohydrate- active enzymes capable for degradation of complex polysaccharides were also identified. Comprehensive analysis predicted a set of 758 secretory proteins including both classical and non-classical secreted proteins. Several of these predicted secretory proteins showed high cysteine content and numerous tandem repeats. Together, our analyses would broadly expand our knowledge and offer insights into the pathogenesis and necrotrophic lifestyle of fungal phytopathogens. Chickpea (Cicer arietinum L.), an important high-protein source, is an annual legume crop grown worldwide. -
Inventory and Review of Quantitative Models for Spread of Plant Pests for Use in Pest Risk Assessment for the EU Territory1
EFSA supporting publication 2015:EN-795 EXTERNAL SCIENTIFIC REPORT Inventory and review of quantitative models for spread of plant pests for use in pest risk assessment for the EU territory1 NERC Centre for Ecology and Hydrology 2 Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, OX10 8BB, UK ABSTRACT This report considers the prospects for increasing the use of quantitative models for plant pest spread and dispersal in EFSA Plant Health risk assessments. The agreed major aims were to provide an overview of current modelling approaches and their strengths and weaknesses for risk assessment, and to develop and test a system for risk assessors to select appropriate models for application. First, we conducted an extensive literature review, based on protocols developed for systematic reviews. The review located 468 models for plant pest spread and dispersal and these were entered into a searchable and secure Electronic Model Inventory database. A cluster analysis on how these models were formulated allowed us to identify eight distinct major modelling strategies that were differentiated by the types of pests they were used for and the ways in which they were parameterised and analysed. These strategies varied in their strengths and weaknesses, meaning that no single approach was the most useful for all elements of risk assessment. Therefore we developed a Decision Support Scheme (DSS) to guide model selection. The DSS identifies the most appropriate strategies by weighing up the goals of risk assessment and constraints imposed by lack of data or expertise. Searching and filtering the Electronic Model Inventory then allows the assessor to locate specific models within those strategies that can be applied. -
Reference Genome Assembly for Australian Ascochyta Rabiei Isolate Arme14
GENOME REPORT Reference Genome Assembly for Australian Ascochyta rabiei Isolate ArME14 Ramisah Mohd Shah,†,1 Angela H. Williams,†,‡ James K. Hane,*,† Julie A. Lawrence,* Lina M. Farfan-Caceres,* Johannes W. Debler,* Richard P. Oliver,†,‡ and Robert C. Lee*,2 *Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia, †Murdoch University, Murdoch, WA, Australia, and ‡Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia ORCID IDs: 0000-0003-0196-0022 (A.H.W.); 0000-0002-7651-0977 (J.K.H.); 0000-0002-3604-051X (J.W.D.); 0000-0001-7290-4154 (R.P.O.); 0000-0002-4174-7042 (R.C.L.) ABSTRACT Ascochyta rabiei is the causal organism of ascochyta blight of chickpea and is present in KEYWORDS chickpea crops worldwide. Here we report the release of a high-quality PacBio genome assembly for the PacBio Australian A. rabiei isolate ArME14. We compare the ArME14 genome assembly with an Illumina assembly for Pleosporales Indian A. rabiei isolate, ArD2. The ArME14 assembly has gapless sequences for nine chromosomes with Dothideomycetes telomere sequences at both ends and 13 large contig sequences that extend to one telomere. The total plant pathogen length of the ArME14 assembly was 40,927,385 bp, which was 6.26 Mb longer than the ArD2 assembly. chickpea Division of the genome by OcculterCut into GC-balanced and AT-dominant segments reveals 21% of the genome contains gene-sparse, AT-rich isochores. Transposable elements and repetitive DNA sequences in the ArME14 assembly made up 15% of the genome. A total of 11,257 protein-coding genes were predicted compared with 10,596 for ArD2. -
Molecular Phylogeny of Phoma and Allied Anamorph Genera: Towards a Reclassification of the Phoma Complex
mycological research 113 (2009) 508–519 journal homepage: www.elsevier.com/locate/mycres Molecular phylogeny of Phoma and allied anamorph genera: Towards a reclassification of the Phoma complex Johannes DE GRUYTERa,b,*, Maikel M. AVESKAMPa, Joyce H. C. WOUDENBERGa, Gerard J. M. VERKLEYa, Johannes Z. GROENEWALDa, Pedro W. CROUSa aCBS Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands bPlant Protection Service, P.O. Box 9102, 6700 HC Wageningen, The Netherlands article info abstract Article history: The present generic concept of Phoma is broadly defined, with nine sections being recog- Received 2 July 2008 nised based on morphological characters. Teleomorph states of Phoma have been described Received in revised form in the genera Didymella, Leptosphaeria, Pleospora and Mycosphaerella, indicating that Phoma 19 December 2008 anamorphs represent a polyphyletic group. In an attempt to delineate generic boundaries, Accepted 8 January 2009 representative strains of the various Phoma sections and allied coelomycetous genera were Published online 18 January 2009 included for study. Sequence data of the 18S nrDNA (SSU) and the 28S nrDNA (LSU) regions Corresponding Editor: of 18 Phoma strains included were compared with those of representative strains of 39 al- David L. Hawksworth lied anamorph genera, including Ascochyta, Coniothyrium, Deuterophoma, Microsphaeropsis, Pleurophoma, Pyrenochaeta, and 11 teleomorph genera. The type species of the Phoma sec- Keywords: tions Phoma, Phyllostictoides, Sclerophomella, Macrospora and Peyronellaea grouped in a sub- Ascochyta clade in the Pleosporales with the type species of Ascochyta and Microsphaeropsis. The new Coelomycetes family Didymellaceae is proposed to accommodate these Phoma sections and related ana- Coniothyrium morph genera. -
Comparative Mapping of Disease Resistance Genes in Lathyrus Spp
Comparative mapping of disease resistance genes in Lathyrus spp. using model legume genetic information Nuno Felipe Alves de Almeida Dissertation presented to obtain the Ph.D degree in Biology Instituto de Tecnologia Química e Biológica António Xavier | Universidade Nova de Lisboa Oeiras, July, 2015 PhD Supervisors Maria Carlota Vaz Patto, PhD Diego Rubiales, PhD The work presented in this thesis was performed mainly at: Under the supervision of Maria Carlota Vaz Patto, PhD Under the supervision of Diego Rubiales, PhD The student, Nuno Felipe Alves de Almeida received financial support from Fundação para a Ciência e Tecnologia and Fundo Social Europeu in the scope of Quadro Comunitário de Apoio through the PhD Fellowship SFRH/BD/44357/2008. iii ISBN: 978-989-20-5841-2 Table of Contents LIST OF FIGURES .............................................................................. XIII LIST OF TABLES ................................................................................ XV LIST OF ADDITIONAL FILES .............................................................. XVII ACKNOWLEDGMENTS / AGRADECIMENTOS ......................................... XIX RESUMO .......................................................................................... XXI ABSTRACT ...................................................................................... XXV LIST OF ABBREVIATIONS ................................................................. XXIX CHAPTER 1 - GENERAL INTRODUCTION ................................................. 1 1.1. Introduction -
International Legume Society 2015
LEGUME PERSPECTIVES Where the global pulse beats mightiest Echoes of VI IFLRC + VII ICLGG in Saskatoon The journal of the International Legume Society Issue 7 • April 2015 IMPRESSUM ISSN Publishing Director 2340-1559 (electronic issue) Diego Rubiales CSIC, Institute for Sustainable Agriculture Quarterly publication Córdoba, Spain January, April, July and October [email protected] (additional issues possible) Editor-in-Chief Published by Carlota Vaz Patto International Legume Society (ILS) Instituto de Tecnologia Química e Biológica António Xavier (Universidade Nova de Lisboa) Co-published by Oeiras, Portugal CSIC, Institute for Sustainable Agriculture, Córdoba, Spain [email protected] Instituto de Tecnologia Química e Biológica António Xavier (Universidade Nova de Lisboa), Oeiras, Portugal Technical Editor Institute of Field and Vegetable Crops, Novi Sad, Serbia Aleksandar Mikić Institute of Field and Vegetable Crops Office and subscriptions Novi Sad, Serbia CSIC, Institute for Sustainable Agriculture [email protected] International Legume Society Apdo. 4084, 14080 Córdoba, Spain Front cover art: Phone: +34957499215 • Fax: +34957499252 EELG: Earth ElectroLegumoGram [email protected] by Aleksandar Mikić Assistant Editors Mike Ambrose Ramakrishnan Nair John Innes Centre, Norwich, UK AVRDC - The World Vegetable Center, Shanhua, Taiwan Paolo Annicchiarico Pádraig O‟Kiely Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Teagasc, Grange, Ireland Centro di Ricerca per le Produzioni Foraggere e Lattiero-Casearie, -
Challenges with Managing Disease Complexes During Application Of
Challenges with Managing Disease Complexes during Application of Different Measures Against Foliar Diseases of Field Pea Martin John Barbetti, Tanveer N., Ian Pritchard, Jay-Ram Lamichhane, Jean-Noël Aubertot, David Camilo Corrales Munoz, Ming Pei You To cite this version: Martin John Barbetti, Tanveer N., Ian Pritchard, Jay-Ram Lamichhane, Jean-Noël Aubertot, et al.. Challenges with Managing Disease Complexes during Application of Different Measures Against Foliar Diseases of Field Pea. Plant Disease, American Phytopathological Society, In press, 30 p. hal-02937483 HAL Id: hal-02937483 https://hal.inrae.fr/hal-02937483 Submitted on 14 Sep 2020 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 Page 1 of 29 Challenges with Managing Disease Complexes during Application of Different Measures Against Foliar Diseases of Field Pea Martin J. Barbetti 1,†, Tanveer N. Khan 1, Ian Pritchard 2, Jay Ram Lamichhane 3, Jean-Noël Aubertot 3, David Camilo Corrales 3, Ming Pei You 1 1 School of Agriculture and Environment and UWA Institute of Agriculture, seeking The University of Western Australia, WA, 6009, Australia 2 Department of Primary Industry and Regional Development, Northam, WA 6401, Australia 3 INRAE, Université Fédérale de Toulouse, UMR AGIR, CS52627, F-31326 Castanet-Tolosan Cedex, France † Corresponding author: M.J. -
A Polyphasic Approach to Characterise Phoma and Related Pleosporalean Genera
available online at www.studiesinmycology.org StudieS in Mycology 65: 1–60. 2010. doi:10.3114/sim.2010.65.01 Highlights of the Didymellaceae: A polyphasic approach to characterise Phoma and related pleosporalean genera M.M. Aveskamp1, 3*#, J. de Gruyter1, 2, J.H.C. Woudenberg1, G.J.M. Verkley1 and P.W. Crous1, 3 1CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; 2Dutch Plant Protection Service (PD), Geertjesweg 15, 6706 EA Wageningen, The Netherlands; 3Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands *Correspondence: Maikel M. Aveskamp, [email protected] #Current address: Mycolim BV, Veld Oostenrijk 13, 5961 NV Horst, The Netherlands Abstract: Fungal taxonomists routinely encounter problems when dealing with asexual fungal species due to poly- and paraphyletic generic phylogenies, and unclear species boundaries. These problems are aptly illustrated in the genus Phoma. This phytopathologically significant fungal genus is currently subdivided into nine sections which are mainly based on a single or just a few morphological characters. However, this subdivision is ambiguous as several of the section-specific characters can occur within a single species. In addition, many teleomorph genera have been linked to Phoma, three of which are recognised here. In this study it is attempted to delineate generic boundaries, and to come to a generic circumscription which is more correct from an evolutionary point of view by means of multilocus sequence typing. Therefore, multiple analyses were conducted utilising sequences obtained from 28S nrDNA (Large Subunit - LSU), 18S nrDNA (Small Subunit - SSU), the Internal Transcribed Spacer regions 1 & 2 and 5.8S nrDNA (ITS), and part of the β-tubulin (TUB) gene region. -
Microplastics Accumulate Fungal Pathogens in Terrestrial Ecosystems
www.nature.com/scientificreports OPEN Microplastics accumulate fungal pathogens in terrestrial ecosystems Gerasimos Gkoutselis1,5, Stephan Rohrbach2,5, Janno Harjes1, Martin Obst3, Andreas Brachmann4, Marcus A. Horn2* & Gerhard Rambold1* Microplastic (MP) is a pervasive pollutant in nature that is colonised by diverse groups of microbes, including potentially pathogenic species. Fungi have been largely neglected in this context, despite their afnity for plastics and their impact as pathogens. To unravel the role of MP as a carrier of fungal pathogens in terrestrial ecosystems and the immediate human environment, epiplastic mycobiomes from municipal plastic waste from Kenya were deciphered using ITS metabarcoding as well as a comprehensive meta-analysis, and visualised via scanning electron as well as confocal laser scanning microscopy. Metagenomic and microscopic fndings provided complementary evidence that the terrestrial plastisphere is a suitable ecological niche for a variety of fungal organisms, including important animal and plant pathogens, which formed the plastisphere core mycobiome. We show that MPs serve as selective artifcial microhabitats that not only attract distinct fungal communities, but also accumulate certain opportunistic human pathogens, such as cryptococcal and Phoma-like species. Therefore, MP must be regarded a persistent reservoir and potential vector for fungal pathogens in soil environments. Given the increasing amount of plastic waste in terrestrial ecosystems worldwide, this interrelation may have severe consequences for the trans-kingdom and multi-organismal epidemiology of fungal infections on a global scale. Plastic waste, an inevitable and inadvertent marker of the Anthropocene, has become a ubiquitous pollutant in nature1. Plastics can therefore exert negative efects on biota in both, aquatic and terrestrial ecosystems.