1
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Schmey T, Tominello-Ramirez CS, Brune C, Stam R. Alternaria diseases on potato and tomato. MOLECULAR PLANT PATHOLOGY 2024; 25:e13435. [PMID: 38476108 DOI: 10.1111/mpp.13435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 03/14/2024]
Abstract
Alternaria spp. cause different diseases in potato and tomato crops. Early blight caused by Alternaria solani and brown spot caused by Alternaria alternata are most common, but the disease complex is far more diverse. We first provide an overview of the Alternaria species infecting the two host plants to alleviate some of the confusion that arises from the taxonomic rearrangements in this fungal genus. Highlighting the diversity of Alternaria fungi on both solanaceous hosts, we review studies investigating the genetic diversity and genomes, before we present recent advances from studies elucidating host-pathogen interactions and fungicide resistances. TAXONOMY Kingdom Fungi, Phylum Ascomycota, Class Dothideomycetes, Order Pleosporales, Family Pleosporaceae, Genus Alternaria. BIOLOGY AND HOST RANGE Alternaria spp. adopt diverse lifestyles. We specifically review Alternaria spp. that cause disease in the two solanaceous crops potato (Solanum tuberosum) and tomato (Solanum lycopersicum). They are necrotrophic pathogens with no known sexual stage, despite some signatures of recombination. DISEASE SYMPTOMS Symptoms of the early blight/brown spot disease complex include foliar lesions that first present as brown spots, depending on the species with characteristic concentric rings, which eventually lead to severe defoliation and considerable yield loss. CONTROL Good field hygiene can keep the disease pressure low. Some potato and tomato cultivars show differences in susceptibility, but there are no fully resistant varieties known. Therefore, the main control mechanism is treatment with fungicides.
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Affiliation(s)
- Tamara Schmey
- TUM School of Life Science Weihenstephan, Technical University of Munich, Freising, Germany
| | - Christopher S Tominello-Ramirez
- Department of Phytopathology and Crop Protection, Institute of Phytopathology, Christian Albrechts University, Kiel, Germany
| | - Carolin Brune
- TUM School of Life Science Weihenstephan, Technical University of Munich, Freising, Germany
| | - Remco Stam
- Department of Phytopathology and Crop Protection, Institute of Phytopathology, Christian Albrechts University, Kiel, Germany
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2
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Khayi S, Armitage AD, Gaboun F, Meftah-kadmiri I, Lahlali R, Fokar M, Mentag R. Chromosome-scale assembly uncovers genomic compartmentation of Fusarium oxysporum f. sp. albedinis, the causal agent of Bayoud disease in date palm. Front Microbiol 2023; 14:1268051. [PMID: 37886058 PMCID: PMC10599148 DOI: 10.3389/fmicb.2023.1268051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
Date palm (Phoenixdactylifera) is the most significant crop across North Africa and the Middle East. However, the crop faces a severe threat from Bayoud disease caused by the fungal pathogen Fusarium oxysporum f. sp. albedinis (FOA). FOA is a soil-borne fungus that infects the roots and vascular system of date palms, leading to widespread destruction of date palm plantations in North Africa over the last century. This is considered the most devastating pathogen of oasis agriculture in North Africa and responsible for loss of 13 million trees in Algeria and Morocco alone. In this study, we present a chromosome-scale high-quality genome assembly of the virulent isolate Foa 44, which provides valuable insights into understanding the genetic basis of Bayoud disease. The genome assembly consists of 11 chromosomes and 40 unplaced contigs, totalling 65,971,825 base pairs in size. It exhibits a GC ratio of 47.77% and a TE (transposable element) content of 17.30%. Through prediction and annotation, we identified 20,416 protein-coding genes. By combining gene and repeat densities analysis with alignment to Fusarium oxysporum f. sp. lycopersici (FOL) 4287 isolate genome sequence, we determined the core and lineage-specific compartments in Foa 44, shedding light on the genome structure of this pathogen. Furthermore, a phylogenomic analysis based on the 3,292 BUSCOs core genome revealed a distinct clade of FOA isolates within the Fusarium oxysporum species complex (FOSC). Notably, the genealogies of the five identified Secreted In Xylem (SIX) genes (1, 6, 9, 11 and 14) in FOA displayed a polyphyletic pattern, suggesting a horizontal inheritance of these effectors. These findings provide a valuable genomics toolbox for further research aimed at combatting the serious biotic constraints posed by FOA to date palm. This will pave the way for a deeper understanding of Bayoud disease and facilitate the development of effective diagnostic tools and control measures.
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Affiliation(s)
- Slimane Khayi
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Rabat, Morocco
| | - Andrew D. Armitage
- Natural Resources Institute, University of Greenwich, Chatham Maritime, Greenwich, United Kingdom
| | - Fatima Gaboun
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Rabat, Morocco
| | - Issam Meftah-kadmiri
- Plant and Microbial Biotechnology Center, Moroccan Foundation of Advanced Science Innovation and Research MAScIR, Ben Guerir, Morocco
- Plant and Soil Microbiome Sub-Program, AgroBioSciences, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Rachid Lahlali
- Phytopathology Unit, Department of Plant Protection, Ecole Nationale D’Agriculture de Meknes, Meknès, Morocco
- Plant Pathology Laboratory, AgroBioSciences, College of Sustainable Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Mohamed Fokar
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, United States
| | - Rachid Mentag
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Rabat, Morocco
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3
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Milner DS, Galindo LJ, Irwin NAT, Richards TA. Transporter Proteins as Ecological Assets and Features of Microbial Eukaryotic Pangenomes. Annu Rev Microbiol 2023; 77:45-66. [PMID: 36944262 DOI: 10.1146/annurev-micro-032421-115538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Here we review two connected themes in evolutionary microbiology: (a) the nature of gene repertoire variation within species groups (pangenomes) and (b) the concept of metabolite transporters as accessory proteins capable of providing niche-defining "bolt-on" phenotypes. We discuss the need for improved sampling and understanding of pangenome variation in eukaryotic microbes. We then review the factors that shape the repertoire of accessory genes within pangenomes. As part of this discussion, we outline how gene duplication is a key factor in both eukaryotic pangenome variation and transporter gene family evolution. We go on to outline how, through functional characterization of transporter-encoding genes, in combination with analyses of how transporter genes are gained and lost from accessory genomes, we can reveal much about the niche range, the ecology, and the evolution of virulence of microbes. We advocate for the coordinated systematic study of eukaryotic pangenomes through genome sequencing and the functional analysis of genes found within the accessory gene repertoire.
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Affiliation(s)
- David S Milner
- Department of Biology, University of Oxford, Oxford, United Kingdom;
| | | | - Nicholas A T Irwin
- Department of Biology, University of Oxford, Oxford, United Kingdom;
- Merton College, University of Oxford, Oxford, United Kingdom
| | - Thomas A Richards
- Department of Biology, University of Oxford, Oxford, United Kingdom;
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4
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Anderson VM, Wendt KL, Caughron JB, Matlock HP, Rangu N, Najar FZ, Miller AN, Luttenton MR, Cichewicz RH. Assessing Microbial Metabolic and Biological Diversity to Inform Natural Product Library Assembly. JOURNAL OF NATURAL PRODUCTS 2022; 85:1079-1088. [PMID: 35416663 DOI: 10.1021/acs.jnatprod.1c01197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The pressing need for novel chemical matter to support bioactive compound discovery has led natural product researchers to explore a wide range of source organisms and environments. One of the implicit guiding principles behind those efforts is the notion that sampling different environments is critical to accessing unique natural products. This idea was tested by comparing fungi from disparate biomes: aquatic sediments from Lake Michigan (USA) and terrestrial samples taken from the surrounding soils. Matched sets of Penicillium brevicompactum, Penicillium expansum, and Penicillium oxalicum from the two source environments were compared, revealing modest differences in physiological performance and chemical output. Analysis of LC-MS/MS-derived molecular feature data showed no source-dependent differences in chemical richness. High levels of scaffold homogeneity were also observed with 78-83% of scaffolds shared among the terrestrial and aquatic Penicillium spp. isolates. A comparison of the culturable fungi from the two biomes indicated that certain genera were more strongly associated with aquatic sediments (e.g., Trichoderma, Pseudeurotium, Cladosporium, and Preussia) versus the surrounding terrestrial environment (e.g., Fusarium, Pseudogymnoascus, Humicola, and Acremonium). Taken together, these results suggest that focusing efforts on sampling the microbial resources that are unique to an environment may have a more pronounced effect on enhancing the sought-after natural product diversity needed for chemical discovery and screening collections.
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Affiliation(s)
- Victoria M Anderson
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Karen L Wendt
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - James B Caughron
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Hagan P Matlock
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Nitin Rangu
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Fares Z Najar
- Chemistry and Biochemistry Bioinformatics Core, Department of Chemistry & Biochemistry, Stephenson Life Science Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Andrew N Miller
- Illinois Natural History Survey, University of Illinois Urbana-Champaign, Champaign, Illinois 61820, United States
| | - Mark R Luttenton
- R. B. Annis Water Resources Institute, Grand Valley State University, Muskegon, Michigan 49441, United States
| | - Robert H Cichewicz
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
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5
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Abstract
Alternaria alternata is a common species of fungus frequently isolated from plants as both an endophyte and a pathogen. Although the current definition of A. alternata rests on a foundation of morphological, genetic and genomic analyses, doubts persist regarding the scope of A. alternata within the genus due to the varied symbiotic interactions and wide host range observed in these fungi. These doubts may be due in large part to the history of unstable taxonomy in Alternaria, based on limited morphological characters for species delimitation and host specificity associated with toxins encoded by genes carried on conditionally dispensable chromosomes. This review explores the history of Alternaria taxonomy, focusing in particular on the use of nutritional mode and host associations in species delimitation, with the goal of evaluating A. alternata as it currently stands based on taxonomic best practice. Given the recombination detected among isolates of A. alternata, different symbiotic associations in this species should not be considered phylogenetically informative.
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Affiliation(s)
- Mara DeMers
- Plant and Microbial Biology Department, College of Biological Sciences, University of Minnesota, St. Paul, MN, USA
- *Correspondence: Mara DeMers,
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6
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Nagel JH, Wingfield MJ, Slippers B. Next-generation sequencing provides important insights into the biology and evolution of the Botryosphaeriaceae. FUNGAL BIOL REV 2021. [DOI: 10.1016/j.fbr.2021.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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7
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Dettman JR, Eggertson Q. Phylogenomic analyses of Alternaria section Alternaria: A high-resolution, genome-wide study of lineage sorting and gene tree discordance. Mycologia 2021; 113:1218-1232. [PMID: 34637684 DOI: 10.1080/00275514.2021.1950456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The genus Alternaria contains a diversity of saprobic and pathogenic species that can be found in a wide range of environments. Alternaria is currently divided into 26 subgeneric sections, and the "small-spored" Alternaria section Alternaria includes many species that are economically important agricultural pathogens. Recognizing that a stable framework for systematics and species identification is essential for management and regulation purposes, this section has experienced much taxonomic debate and systematic revision in recent years. Molecular phylogenetic studies have challenged the reliability of using morphological characteristics to differentiate Alternaria species but have also suggested that commonly used molecular markers for fungal phylogenetics may not be sufficiently informative at this taxonomic level. To allow the assessment of molecular variation and evolutionary history at a genome-wide scale, we present an overview and analysis of phylogenomic resources for Alternaria section Alternaria. We review the currently available genomic resources and report five newly sequenced genomes. We then perform multiple comparative genomic analyses, including macrosynteny assessment and inference of phylogenetic relationships using a variety of data sets and analysis methods. Fine-scale, genome-wide phylogenetic reconstruction revealed incomplete lineage sorting and the genomic distribution of gene/species tree discordance. Based on these patterns, we propose a list of candidate genes that may be developed into informative markers that are diagnostic for the main lineages. This overview identifies gaps in knowledge and can guide future genome sequencing efforts for this important group of plant pathogenic fungi.
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Affiliation(s)
- Jeremy R Dettman
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada
| | - Quinn Eggertson
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada
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8
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Vignolle GA, Schaffer D, Zehetner L, Mach RL, Mach-Aigner AR, Derntl C. FunOrder: A robust and semi-automated method for the identification of essential biosynthetic genes through computational molecular co-evolution. PLoS Comput Biol 2021; 17:e1009372. [PMID: 34570757 PMCID: PMC8476034 DOI: 10.1371/journal.pcbi.1009372] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/23/2021] [Indexed: 11/24/2022] Open
Abstract
Secondary metabolites (SMs) are a vast group of compounds with different structures and properties that have been utilized as drugs, food additives, dyes, and as monomers for novel plastics. In many cases, the biosynthesis of SMs is catalysed by enzymes whose corresponding genes are co-localized in the genome in biosynthetic gene clusters (BGCs). Notably, BGCs may contain so-called gap genes, that are not involved in the biosynthesis of the SM. Current genome mining tools can identify BGCs, but they have problems with distinguishing essential genes from gap genes. This can and must be done by expensive, laborious, and time-consuming comparative genomic approaches or transcriptome analyses. In this study, we developed a method that allows semi-automated identification of essential genes in a BGC based on co-evolution analysis. To this end, the protein sequences of a BGC are blasted against a suitable proteome database. For each protein, a phylogenetic tree is created. The trees are compared by treeKO to detect co-evolution. The results of this comparison are visualized in different output formats, which are compared visually. Our results suggest that co-evolution is commonly occurring within BGCs, albeit not all, and that especially those genes that encode for enzymes of the biosynthetic pathway are co-evolutionary linked and can be identified with FunOrder. In light of the growing number of genomic data available, this will contribute to the studies of BGCs in native hosts and facilitate heterologous expression in other organisms with the aim of the discovery of novel SMs. The discovery and description of novel fungal secondary metabolites promises novel antibiotics, pharmaceuticals, and other useful compounds. A way to identify novel secondary metabolites is to express the corresponding genes in a suitable expression host. Consequently, a detailed knowledge or an accurate prediction of these genes is necessary. In fungi, the genes are co-localized in so-called biosynthetic gene clusters. Notably, the clusters may also contain genes that are not necessary for the biosynthesis of the secondary metabolites, so-called gap genes. We developed a method to detect co-evolved genes within the clusters and demonstrated that essential genes are co-evolving and can thus be differentiated from the gap genes. This adds an additional layer of information, which can support researchers with their decisions on which genes to study and express for the discovery of novel secondary metabolites.
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Affiliation(s)
- Gabriel A. Vignolle
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Denise Schaffer
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Leopold Zehetner
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Robert L. Mach
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Astrid R. Mach-Aigner
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Christian Derntl
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
- * E-mail:
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9
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Crous P, Lombard L, Sandoval-Denis M, Seifert K, Schroers HJ, Chaverri P, Gené J, Guarro J, Hirooka Y, Bensch K, Kema G, Lamprecht S, Cai L, Rossman A, Stadler M, Summerbell R, Taylor J, Ploch S, Visagie C, Yilmaz N, Frisvad J, Abdel-Azeem A, Abdollahzadeh J, Abdolrasouli A, Akulov A, Alberts J, Araújo J, Ariyawansa H, Bakhshi M, Bendiksby M, Ben Hadj Amor A, Bezerra J, Boekhout T, Câmara M, Carbia M, Cardinali G, Castañeda-Ruiz R, Celis A, Chaturvedi V, Collemare J, Croll D, Damm U, Decock C, de Vries R, Ezekiel C, Fan X, Fernández N, Gaya E, González C, Gramaje D, Groenewald J, Grube M, Guevara-Suarez M, Gupta V, Guarnaccia V, Haddaji A, Hagen F, Haelewaters D, Hansen K, Hashimoto A, Hernández-Restrepo M, Houbraken J, Hubka V, Hyde K, Iturriaga T, Jeewon R, Johnston P, Jurjević Ž, Karalti İ, Korsten L, Kuramae E, Kušan I, Labuda R, Lawrence D, Lee H, Lechat C, Li H, Litovka Y, Maharachchikumbura S, Marin-Felix Y, Matio Kemkuignou B, Matočec N, McTaggart A, Mlčoch P, Mugnai L, Nakashima C, Nilsson R, Noumeur S, Pavlov I, Peralta M, Phillips A, Pitt J, Polizzi G, Quaedvlieg W, Rajeshkumar K, Restrepo S, Rhaiem A, Robert J, Robert V, Rodrigues A, Salgado-Salazar C, Samson R, Santos A, Shivas R, Souza-Motta C, Sun G, Swart W, Szoke S, Tan Y, Taylor J, Taylor P, Tiago P, Váczy K, van de Wiele N, van der Merwe N, Verkley G, Vieira W, Vizzini A, Weir B, Wijayawardene N, Xia J, Yáñez-Morales M, Yurkov A, Zamora J, Zare R, Zhang C, Thines M. Fusarium: more than a node or a foot-shaped basal cell. Stud Mycol 2021; 98:100116. [PMID: 34466168 PMCID: PMC8379525 DOI: 10.1016/j.simyco.2021.100116] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid genera (www.fusarium.org).
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Key Words
- Apiognomonia platani (Lév.) L. Lombard
- Atractium ciliatum Link
- Atractium pallidum Bonord.
- Calloria tremelloides (Grev.) L. Lombard
- Cephalosporium sacchari E.J. Butler
- Cosmosporella cavisperma (Corda) Sand.-Den., L. Lombard & Crous
- Cylindrodendrum orthosporum (Sacc. & P. Syd.) L. Lombard
- Dialonectria volutella (Ellis & Everh.) L. Lombard & Sand.-Den.
- Fusarium aeruginosum Delacr.
- Fusarium agaricorum Sarrazin
- Fusarium albidoviolaceum Dasz.
- Fusarium aleyrodis Petch
- Fusarium amentorum Lacroix
- Fusarium annuum Leonian
- Fusarium arcuatum Berk. & M.A. Curtis
- Fusarium aridum O.A. Pratt
- Fusarium armeniacum (G.A. Forbes et al.) L.W. Burgess & Summerell
- Fusarium arthrosporioides Sherb.
- Fusarium asparagi Delacr.
- Fusarium batatas Wollenw.
- Fusarium biforme Sherb.
- Fusarium buharicum Jacz. ex Babajan & Teterevn.-Babajan
- Fusarium cactacearum Pasin. & Buzz.-Trav.
- Fusarium cacti-maxonii Pasin. & Buzz.-Trav.
- Fusarium caudatum Wollenw.
- Fusarium cavispermum Corda
- Fusarium cepae Hanzawa
- Fusarium cesatii Rabenh.
- Fusarium citriforme Jamal.
- Fusarium citrinum Wollenw.
- Fusarium citrulli Taubenh.
- Fusarium clavatum Sherb.
- Fusarium coccinellum Kalchbr.
- Fusarium cromyophthoron Sideris
- Fusarium cucurbitae Taubenh.
- Fusarium cuneiforme Sherb.
- Fusarium delacroixii Sacc.
- Fusarium dimerum var. nectrioides Wollenw.
- Fusarium echinatum Sand.-Den. & G.J. Marais
- Fusarium epicoccum McAlpine
- Fusarium eucheliae Sartory, R. Sartory & J. Mey.
- Fusarium fissum Peyl
- Fusarium flocciferum Corda
- Fusarium gemmiperda Aderh.
- Fusarium genevense Dasz.
- Fusarium graminearum Schwabe
- Fusarium graminum Corda
- Fusarium heterosporioides Fautrey
- Fusarium heterosporum Nees & T. Nees
- Fusarium idahoanum O.A. Pratt
- Fusarium juruanum Henn.
- Fusarium lanceolatum O.A. Pratt
- Fusarium lateritium Nees
- Fusarium loncheceras Sideris
- Fusarium longipes Wollenw. & Reinking
- Fusarium lyarnte J.L. Walsh, Sangal., L.W. Burgess, E.C.Y. Liew & Summerell
- Fusarium malvacearum Taubenh.
- Fusarium martii f. phaseoli Burkh.
- Fusarium muentzii Delacr.
- Fusarium nigrum O.A. Pratt
- Fusarium oxysporum var. asclerotium Sherb.
- Fusarium palczewskii Jacz.
- Fusarium palustre W.H. Elmer & Marra
- Fusarium polymorphum Matr.
- Fusarium poolense Taubenh.
- Fusarium prieskaense G.J. Marais & Sand.-Den.
- Fusarium prunorum McAlpine
- Fusarium pusillum Wollenw.
- Fusarium putrefaciens Osterw.
- Fusarium redolens Wollenw.
- Fusarium reticulatum Mont.
- Fusarium rhizochromatistes Sideris
- Fusarium rhizophilum Corda
- Fusarium rhodellum McAlpine
- Fusarium roesleri Thüm.
- Fusarium rostratum Appel & Wollenw.
- Fusarium rubiginosum Appel & Wollenw.
- Fusarium rubrum Parav.
- Fusarium samoense Gehrm.
- Fusarium scirpi Lambotte & Fautrey
- Fusarium secalis Jacz.
- Fusarium spinaciae Hungerf.
- Fusarium sporotrichioides Sherb.
- Fusarium stercoris Fuckel
- Fusarium stilboides Wollenw.
- Fusarium stillatum De Not. ex Sacc.
- Fusarium sublunatum Reinking
- Fusarium succisae Schröt. ex Sacc.
- Fusarium tabacivorum Delacr.
- Fusarium trichothecioides Wollenw.
- Fusarium tritici Liebman
- Fusarium tuberivorum Wilcox & G.K. Link
- Fusarium tumidum var. humi Reinking
- Fusarium ustilaginis Kellerm. & Swingle
- Fusarium viticola Thüm.
- Fusarium werrikimbe J.L. Walsh, L.W. Burgess, E.C.Y. Liew & B.A. Summerell
- Fusarium willkommii Lindau
- Fusarium xylarioides Steyaert
- Fusarium zygopetali Delacr.
- Fusicolla meniscoidea L. Lombard & Sand.-Den.
- Fusicolla quarantenae J.D.P. Bezerra, Sand.-Den., Crous & Souza-Motta
- Fusicolla sporellula Sand.-Den. & L. Lombard
- Fusisporium andropogonis Cooke ex Thüm.
- Fusisporium anthophilum A. Braun
- Fusisporium arundinis Corda
- Fusisporium avenaceum Fr.
- Fusisporium clypeaster Corda
- Fusisporium culmorum Wm.G. Sm.
- Fusisporium didymum Harting
- Fusisporium elasticae Thüm.
- Fusisporium episphaericum Cooke & Ellis
- Fusisporium flavidum Bonord.
- Fusisporium hordei Wm.G. Sm.
- Fusisporium incarnatum Roberge ex Desm.
- Fusisporium lolii Wm.G. Sm.
- Fusisporium pandani Corda
- Gibberella phyllostachydicola W. Yamam.
- Hymenella aurea (Corda) L. Lombard
- Hymenella spermogoniopsis (Jul. Müll.) L. Lombard & Sand.-Den.
- Luteonectria Sand.-Den., L. Lombard, Schroers & Rossman
- Luteonectria albida (Rossman) Sand.-Den. & L. Lombard
- Luteonectria nematophila (Nirenberg & Hagedorn) Sand.-Den. & L. Lombard
- Macroconia bulbipes Crous & Sand.-Den.
- Macroconia phlogioides Sand.-Den. & Crous
- Menispora penicillata Harz
- Multi-gene phylogeny
- Mycotoxins
- Nectriaceae
- Neocosmospora
- Neocosmospora epipeda Quaedvl. & Sand.-Den.
- Neocosmospora floridana (T. Aoki et al.) L. Lombard & Sand.-Den.
- Neocosmospora merkxiana Quaedvl. & Sand.-Den.
- Neocosmospora neerlandica Crous & Sand.-Den.
- Neocosmospora nelsonii Crous & Sand.-Den.
- Neocosmospora obliquiseptata (T. Aoki et al.) L. Lombard & Sand.-Den.
- Neocosmospora pseudopisi Sand.-Den. & L. Lombard
- Neocosmospora rekana (Lynn & Marinc.) L. Lombard & Sand.-Den.
- Neocosmospora tuaranensis (T. Aoki et al.) L. Lombard & Sand.-Den.
- Nothofusarium Crous, Sand.-Den. & L. Lombard
- Nothofusarium devonianum L. Lombard, Crous & Sand.-Den.
- Novel taxa
- Pathogen
- Scolecofusarium L. Lombard, Sand.-Den. & Crous
- Scolecofusarium ciliatum (Link) L. Lombard, Sand.-Den. & Crous
- Selenosporium equiseti Corda
- Selenosporium hippocastani Corda
- Selenosporium sarcochroum Desm
- Selenosporium urticearum Corda.
- Setofusarium (Nirenberg & Samuels) Crous & Sand.-Den.
- Setofusarium setosum (Samuels & Nirenberg) Sand.-Den. & Crous.
- Sphaeria sanguinea var. cicatricum Berk.
- Sporotrichum poae Peck.
- Stylonectria corniculata Gräfenhan, Crous & Sand.-Den.
- Stylonectria hetmanica Akulov, Crous & Sand.-Den.
- Taxonomy
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Affiliation(s)
- P.W. Crous
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - L. Lombard
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - M. Sandoval-Denis
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, the Netherlands
| | - K.A. Seifert
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada
| | - H.-J. Schroers
- Plant Protection Department, Agricultural Institute of Slovenia, Hacquetova ulica 17, 1000, Ljubljana, Slovenia
| | - P. Chaverri
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
- Escuela de Biología and Centro de Investigaciones en Productos Naturales, Universidad de Costa Rica, San Pedro, Costa Rica
| | - J. Gené
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut i Institut d’Investigació Sanitària Pere Virgili (IISPV), Universitat Rovira i Virgili, 43201, Reus, Spain
| | - J. Guarro
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut i Institut d’Investigació Sanitària Pere Virgili (IISPV), Universitat Rovira i Virgili, 43201, Reus, Spain
| | - Y. Hirooka
- Department of Clinical Plant Science, Faculty of Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo, 184-8584, Japan
| | - K. Bensch
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - G.H.J. Kema
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - S.C. Lamprecht
- ARC-Plant Health and Protection, Private Bag X5017, Stellenbosch, 7599, Western Cape, South Africa
| | - L. Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - A.Y. Rossman
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR, 97330, USA
| | - M. Stadler
- Department of Microbial Drugs, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - R.C. Summerbell
- Sporometrics, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - J.W. Taylor
- Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA, 94720-3102, USA
| | - S. Ploch
- Senckenberg Biodiversity and Climate Research Center, Senckenberganlage 25, D-60325, Frankfurt am Main, Germany
| | - C.M. Visagie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, P. Bag X20, Hatfield, 0028, Pretoria, South Africa
| | - N. Yilmaz
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, P. Bag X20, Hatfield, 0028, Pretoria, South Africa
| | - J.C. Frisvad
- Department of Biotechnology and Biomedicine, DTU-Bioengineering, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - A.M. Abdel-Azeem
- Systematic Mycology Lab., Botany and Microbiology Department, Faculty of Science, Suez Canal University, Ismailia, 41522, Egypt
| | - J. Abdollahzadeh
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, P.O. Box 416, Sanandaj, Iran
| | - A. Abdolrasouli
- Department of Medical Microbiology, King's College Hospital, London, UK
- Department of Infectious Diseases, Imperial College London, London, UK
| | - A. Akulov
- Department of Mycology and Plant Resistance, V. N. Karazin Kharkiv National University, Maidan Svobody 4, 61022, Kharkiv, Ukraine
| | - J.F. Alberts
- Department of Food Science and Technology, Cape Peninsula University of Technology, P.O. Box 1906, Bellville, 7535, South Africa
| | - J.P.M. Araújo
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, USA
| | - H.A. Ariyawansa
- Department of Plant Pathology and Microbiology, College of Bio-Resources and Agriculture, National Taiwan University, No.1, Sec.4, Roosevelt Road, Taipei, 106, Taiwan, ROC
| | - M. Bakhshi
- Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), P.O. Box 19395-1454, Tehran, Iran
| | - M. Bendiksby
- Natural History Museum, University of Oslo, Norway
- Department of Natural History, NTNU University Museum, Trondheim, Norway
| | - A. Ben Hadj Amor
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - J.D.P. Bezerra
- Setor de Micologia/Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Rua 235 - s/n – Setor Universitário - CEP: 74605-050, Universidade Federal de Goiás/Federal University of Goiás, Goiânia, Brazil
| | - T. Boekhout
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - M.P.S. Câmara
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, 52171-900, PE, Brazil
| | - M. Carbia
- Departamento de Parasitología y Micología, Instituto de Higiene, Facultad de Medicina – Universidad de la República, Av. A. Navarro 3051, Montevideo, Uruguay
| | - G. Cardinali
- Department of Pharmaceutical Science, University of Perugia, Via Borgo 20 Giugno, 74 Perugia, Italy
| | - R.F. Castañeda-Ruiz
- Instituto de Investigaciones Fundamentales en Agricultura Tropical Alejandro de Humboldt (INIFAT), Académico Titular de la Academia de Ciencias de, Cuba
| | - A. Celis
- Grupo de Investigación Celular y Molecular de Microorganismos Patógenos (CeMoP), Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, 111711, Colombia
| | - V. Chaturvedi
- Mycology Laboratory, New York State Department of Health Wadsworth Center, Albany, NY, USA
| | - J. Collemare
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - D. Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchatel, CH-2000, Neuchatel, Switzerland
| | - U. Damm
- Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806, Görlitz, Germany
| | - C.A. Decock
- Mycothèque de l'Université catholique de Louvain (MUCL, BCCMTM), Earth and Life Institute – ELIM – Mycology, Université catholique de Louvain, Croix du Sud 2 bte L7.05.06, B-1348, Louvain-la-Neuve, Belgium
| | - R.P. de Vries
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - C.N. Ezekiel
- Department of Microbiology, Babcock University, Ilishan Remo, Ogun State, Nigeria
| | - X.L. Fan
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - N.B. Fernández
- Laboratorio de Micología Clínica, Hospital de Clínicas, Universidad de Buenos Aires, Buenos Aires, Argentina
- Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - E. Gaya
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK
| | - C.D. González
- Laboratorio de Salud de Bosques y Ecosistemas, Instituto de Conservación, Biodiversidad y Territorio, Facultad de Ciencias Forestales y Recursos Naturales, Universidad Austral de Chile, casilla 567, Valdivia, Chile
| | - D. Gramaje
- Institute of Grapevine and Wine Sciences (ICVV), Spanish National Research Council (CSIC)-University of La Rioja-Government of La Rioja, Logroño, 26007, Spain
| | - J.Z. Groenewald
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - M. Grube
- Institut für Biologie, Karl-Franzens-Universität Graz, Holteigasse 6, 8010, Graz, Austria
| | - M. Guevara-Suarez
- Applied genomics research group, Universidad de los Andes, Cr 1 # 18 a 12, Bogotá, Colombia
| | - V.K. Gupta
- Center for Safe and Improved Food, Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
- Biorefining and Advanced Materials Research Center, Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
| | - V. Guarnaccia
- Department of Agricultural, Forestry and Food Sciences (DISAFA), University of Torino, Largo P. Braccini 2, 10095, Grugliasco, TO, Italy
| | | | - F. Hagen
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - D. Haelewaters
- Research Group Mycology, Department of Biology, Ghent University, 35 K.L. Ledeganckstraat, 9000, Ghent, Belgium
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - K. Hansen
- Department of Botany, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden
| | - A. Hashimoto
- Microbe Division/Japan Collection of Microorganisms RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | | | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - V. Hubka
- Department of Botany, Charles University in Prague, Prague, Czech Republic
| | - K.D. Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chaing Rai, 57100, Thailand
| | - T. Iturriaga
- Cornell University, 334 Plant Science Building, Ithaca, NY, 14850, USA
| | - R. Jeewon
- Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Mauritius, Reduit, Mauritius
| | - P.R. Johnston
- Manaaki Whenua Landcare Research, Private Bag 92170, Auckland, 1142, New Zealand
| | - Ž. Jurjević
- EMSL Analytical, Inc., 200 Route 130 North, Cinnaminson, NJ, 08077, USA
| | - İ. Karalti
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Yeditepe University, Turkey
| | - L. Korsten
- Department of Plant and Soil Sciences, University of Pretoria, P. Bag X20 Hatfield, Pretoria, 0002, South Africa
| | - E.E. Kuramae
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, the Netherlands
- Institute of Environmental Biology, Ecology and Biodiversity, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - I. Kušan
- Laboratory for Biological Diversity, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia
| | - R. Labuda
- University of Veterinary Medicine, Vienna (VetMed), Institute of Food Safety, Food Technology and Veterinary Public Health, Veterinaerplatz 1, 1210 Vienna and BiMM – Bioactive Microbial Metabolites group, 3430 Tulln a.d. Donau, Austria
| | - D.P. Lawrence
- University of California, Davis, One Shields Ave., Davis, CA, 95616, USA
| | - H.B. Lee
- Department of Agricultural Biological Chemistry, College of Agriculture & Life Sciences, Chonnam National University, Yongbong-Dong 300, Buk-Gu, Gwangju, 61186, South Korea
| | - C. Lechat
- Ascofrance, 64 route de Chizé, 79360, Villiers-en-Bois, France
| | - H.Y. Li
- The Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Ministry of Agriculture, The Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Y.A. Litovka
- V.N. Sukachev Institute of Forest SB RAS, Laboratory of Reforestation, Mycology and Plant Pathology, Krasnoyarsk, 660036, Russia
- Reshetnev Siberian State University of Science and Technology, Department of Chemical Technology of Wood and Biotechnology, Krasnoyarsk, 660037, Russia
| | - S.S.N. Maharachchikumbura
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Y. Marin-Felix
- Department of Microbial Drugs, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - B. Matio Kemkuignou
- Department of Microbial Drugs, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - N. Matočec
- Laboratory for Biological Diversity, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia
| | - A.R. McTaggart
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, G.P.O. Box 267, Brisbane, 4001, Australia
| | - P. Mlčoch
- Department of Botany, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - L. Mugnai
- Department of Agricultural, Food, Environmental and Forestry Science and Technology (DAGRI), Plant Pathology and Entomology section, University of Florence, P.le delle Cascine 28, 50144, Firenze, Italy
| | - C. Nakashima
- Graduate school of Bioresources, Mie University, Kurima-machiya 1577, Tsu, Mie, 514-8507, Japan
| | - R.H. Nilsson
- Gothenburg Global Biodiversity Center at the Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30, Gothenburg, Sweden
| | - S.R. Noumeur
- Department of Microbiology and Biochemistry, Faculty of Natural and Life Sciences, University of Batna 2, Batna, 05000, Algeria
| | - I.N. Pavlov
- V.N. Sukachev Institute of Forest SB RAS, Laboratory of Reforestation, Mycology and Plant Pathology, Krasnoyarsk, 660036, Russia
- Reshetnev Siberian State University of Science and Technology, Department of Chemical Technology of Wood and Biotechnology, Krasnoyarsk, 660037, Russia
| | - M.P. Peralta
- Laboratorio de Micodiversidad y Micoprospección, PROIMI-CONICET, Av. Belgrano y Pje. Caseros, Argentina
| | - A.J.L. Phillips
- Universidade de Lisboa, Faculdade de Ciências, Biosystems and Integrative Sciences Institute (BioISI), Campo Grande, 1749-016, Lisbon, Portugal
| | - J.I. Pitt
- Microbial Screening Technologies, 28 Percival Rd, Smithfield, NSW, 2164, Australia
| | - G. Polizzi
- Dipartimento di Agricoltura, Alimentazione e Ambiente, sez. Patologia vegetale, University of Catania, Via S. Sofia 100, 95123 Catania, Italy
| | - W. Quaedvlieg
- Phytopathology, Van Zanten Breeding B.V., Lavendelweg 15, 1435 EW, Rijsenhout, the Netherlands
| | - K.C. Rajeshkumar
- National Fungal Culture Collection of India (NFCCI), Biodiversity and Palaeobiology (Fungi) Group, Agharkar Research Institute, Pune, Maharashtra, 411 004, India
| | - S. Restrepo
- Laboratory of Mycology and Phytopathology – (LAMFU), Department of Chemical and Food Engineering, Universidad de los Andes, Cr 1 # 18 a 12, Bogotá, Colombia
| | - A. Rhaiem
- Plant Pathology and Population Genetics, Laboratory of Microorganisms, National Gene Bank, Tunisia
| | | | - V. Robert
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - A.M. Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
| | - C. Salgado-Salazar
- USDA-ARS Mycology & Nematology Genetic Diversity & Biology Laboratory, Bldg. 010A, Rm. 212, BARC-West, 10300 Baltimore Ave, Beltsville, MD, 20705, USA
| | - R.A. Samson
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - A.C.S. Santos
- Departamento de Micologia Prof. Chaves Batista, Universidade Federal de Pernambuco, Centro de Biociências, Cidade Universitária, Av. Prof. Moraes Rego, s/n, Recife, PE, CEP: 50670-901, Brazil
| | - R.G. Shivas
- Centre for Crop Health, University of Southern Queensland, Toowoomba, 4350, Queensland, Australia
| | - C.M. Souza-Motta
- Departamento de Micologia Prof. Chaves Batista, Universidade Federal de Pernambuco, Centro de Biociências, Cidade Universitária, Av. Prof. Moraes Rego, s/n, Recife, PE, CEP: 50670-901, Brazil
| | - G.Y. Sun
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - W.J. Swart
- Faculty of Natural and Agricultural Sciences, Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | | | - Y.P. Tan
- Centre for Crop Health, University of Southern Queensland, Toowoomba, 4350, Queensland, Australia
- Queensland Plant Pathology Herbarium, Department of Agriculture and Fisheries, Dutton Park, Queensland, 4102, Australia
| | - J.E. Taylor
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, United Kingdom
| | - P.W.J. Taylor
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - P.V. Tiago
- Departamento de Micologia Prof. Chaves Batista, Universidade Federal de Pernambuco, Centro de Biociências, Cidade Universitária, Av. Prof. Moraes Rego, s/n, Recife, PE, CEP: 50670-901, Brazil
| | - K.Z. Váczy
- Food and Wine Research Institute, Eszterházy Károly University, 6 Leányka Street, H-3300, Eger, Hungary
| | | | - N.A. van der Merwe
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, P. Bag X20, Hatfield, 0028, Pretoria, South Africa
| | - G.J.M. Verkley
- Westerdijk Fungal Biodiversity Institute, 3508 AD, Utrecht, the Netherlands
| | - W.A.S. Vieira
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, 52171-900, PE, Brazil
| | - A. Vizzini
- Department of Life Sciences and Systems Biology, University of Torino and Institute for Sustainable Plant Protection (IPSP-SS Turin), C.N.R, Viale P.A. Mattioli, 25, I-10125, Torino, Italy
| | - B.S. Weir
- Manaaki Whenua Landcare Research, Private Bag 92170, Auckland, 1142, New Zealand
| | - N.N. Wijayawardene
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan, 655011, China
| | - J.W. Xia
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, China
| | - M.J. Yáñez-Morales
- Fitosanidad, Colegio de Postgraduados-Campus Montecillo, Montecillo-Texcoco, 56230 Edo. de Mexico, Mexico
| | - A. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstrasse 7 B, 38124, Braunschweig, Germany
| | - J.C. Zamora
- Museum of Evolution, Uppsala University, Norbyvägen 16, SE-752 36, Uppsala, Sweden
| | - R. Zare
- Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), P.O. Box 19395-1454, Tehran, Iran
| | - C.L. Zhang
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, China
| | - M. Thines
- Senckenberg Biodiversity and Climate Research Center, Senckenberganlage 25, D-60325, Frankfurt am Main, Germany
- Goethe-University Frankfurt am Main, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue Str. 13, D-60438, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany
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10
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Chauhan DS, Gupta P, Pottoo FH, Amir M. Secondary Metabolites in the Treatment of Diabetes Mellitus: A Paradigm Shift. Curr Drug Metab 2020; 21:493-511. [PMID: 32407267 DOI: 10.2174/1389200221666200514081947] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/07/2020] [Accepted: 03/10/2020] [Indexed: 01/09/2023]
Abstract
Diabetes mellitus (DM) is a chronic, polygenic and non-infectious group of diseases that occurs due to insulin resistance or its low production by the pancreas and is also associated with lifelong damage, dysfunction and collapse of various organs. Management of diabetes is quite complex having many bodily and emotional complications and warrants efficient measures for prevention and control of the same. As per the estimates of the current and future diabetes prevalence, around 425 million people were diabetic in 2017 which is anticipated to rise up to 629 million by 2045. Various studies have vaguely proven the fact that several vitamins, minerals, botanicals and secondary metabolites demonstrate hypoglycemic activity in vivo as well as in vitro. Flavonoids, anthocyanin, catechin, lipoic acid, coumarin metabolites, etc. derived from herbs were found to elicit a significant influence on diabetes. However, the prescription of herbal compounds depend on various factors, including the degree of diabetes progression, comorbidities, feasibility, economics as well as their ADR profile. For instance, cinnamon could be a more favorable choice for diabetic hypertensive patients. Diabecon®, Glyoherb® and Diabeta Plus® are some of the herbal products that had been launched in the market for the favorable or adjuvant therapy of diabetes. Moreover, Aloe vera leaf gel extract demonstrates significant activity in diabetes. The goal of this review was to inscribe various classes of secondary metabolites, in particular those obtained from plants, and their role in the treatment of DM. Recent advancements in recognizing the markers which can be employed for identifying altered metabolic pathways, biomarker discovery, limitations, metabolic markers of drug potency and off-label effects are also reviewed.
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Affiliation(s)
| | - Paras Gupta
- Department of Clinical Research, DIPSAR, Pushp Vihar Sec-3, New Dehli, India
| | - Faheem Hyder Pottoo
- Department of Pharmacology, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Mohd Amir
- Department of Natural Product & Alternative Medicine, College of Clinical Pharmacy, Imam Abdul Rahman Bin Faisal University, Dammam, 31441, Saudi Arabia
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11
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Abstract
Most genomes within the species complex of Fusarium oxysporum are organized into two compartments: the core chromosomes (CCs) and accessory chromosomes (ACs). As opposed to CCs, which are conserved and vertically transmitted to carry out essential housekeeping functions, lineage- or strain-specific ACs are believed to be initially horizontally acquired through unclear mechanisms. These two genomic compartments are different in terms of gene density, the distribution of transposable elements, and epigenetic markers. Although common in eukaryotes, the functional importance of ACs is uniquely emphasized among fungal species, specifically in relationship to fungal pathogenicity and their adaptation to diverse hosts. With a focus on the cross-kingdom fungal pathogen F. oxysporum, this review provides a summary of the differences between CCs and ACs based on current knowledge of gene functions, genome structures, and epigenetic signatures, and explores the transcriptional crosstalk between the core and accessory genomes.
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12
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Li J, Cornelissen B, Rep M. Host-specificity factors in plant pathogenic fungi. Fungal Genet Biol 2020; 144:103447. [PMID: 32827756 DOI: 10.1016/j.fgb.2020.103447] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 08/14/2020] [Accepted: 08/15/2020] [Indexed: 01/18/2023]
Abstract
Fortunately, no fungus can cause disease on all plant species, and although some plant-pathogenic fungi have quite a broad host range, most are highly limited in the range of plant species or even cultivars that they cause disease in. The mechanisms of host specificity have been extensively studied in many plant-pathogenic fungi, especially in fungal pathogens causing disease on economically important crops. Specifically, genes involved in host specificity have been identified during the last few decades. In this overview, we describe and discuss these host-specificity genes. These genes encode avirulence (Avr) proteins, proteinaceous host-specific toxins or secondary metabolites. We discuss the genomic context of these genes, their expression, polymorphism, horizontal transfer and involvement in pathogenesis.
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Affiliation(s)
- Jiming Li
- Molecular Plant Pathology, University of Amsterdam, Amsterdam 1098 XH, the Netherlands
| | - Ben Cornelissen
- Molecular Plant Pathology, University of Amsterdam, Amsterdam 1098 XH, the Netherlands
| | - Martijn Rep
- Molecular Plant Pathology, University of Amsterdam, Amsterdam 1098 XH, the Netherlands.
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13
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Shen Y, Nie J, Kuang L, Zhang J, Li H. DNA sequencing, genomes and genetic markers of microbes on fruits and vegetables. Microb Biotechnol 2020; 14:323-362. [PMID: 32207561 PMCID: PMC7936329 DOI: 10.1111/1751-7915.13560] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/01/2020] [Accepted: 03/02/2020] [Indexed: 12/20/2022] Open
Abstract
The development of DNA sequencing technology has provided an effective method for studying foodborne and phytopathogenic microorganisms on fruits and vegetables (F & V). DNA sequencing has successfully proceeded through three generations, including the tens of operating platforms. These advances have significantly promoted microbial whole‐genome sequencing (WGS) and DNA polymorphism research. Based on genomic and regional polymorphisms, genetic markers have been widely obtained. These molecular markers are used as targets for PCR or chip analyses to detect microbes at the genetic level. Furthermore, metagenomic analyses conducted by sequencing the hypervariable regions of ribosomal DNA (rDNA) have revealed comprehensive microbial communities in various studies on F & V. This review highlights the basic principles of three generations of DNA sequencing, and summarizes the WGS studies of and available DNA markers for major bacterial foodborne pathogens and phytopathogenic fungi found on F & V. In addition, rDNA sequencing‐based bacterial and fungal metagenomics are summarized under three topics. These findings deepen the understanding of DNA sequencing and its application in studies of foodborne and phytopathogenic microbes and shed light on strategies for the monitoring of F & V microbes and quality control.
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Affiliation(s)
- Youming Shen
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Jiyun Nie
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China.,College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lixue Kuang
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Jianyi Zhang
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Haifei Li
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
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14
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Multi-locus phylogeny and pathogenicity of Stemphylium species associated with legumes in Australia. Mycol Prog 2020. [DOI: 10.1007/s11557-020-01566-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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15
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Armitage AD, Cockerton HM, Sreenivasaprasad S, Woodhall J, Lane CR, Harrison RJ, Clarkson JP. Genomics Evolutionary History and Diagnostics of the Alternaria alternata Species Group Including Apple and Asian Pear Pathotypes. Front Microbiol 2020; 10:3124. [PMID: 32038562 PMCID: PMC6989435 DOI: 10.3389/fmicb.2019.03124] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 12/24/2019] [Indexed: 02/04/2023] Open
Abstract
The Alternaria section alternaria (Alternaria alternata species group) represents a diverse group of saprotroph, human allergens, and plant pathogens. Alternaria taxonomy has benefited from recent phylogenetic revision but the basis of differentiation between major phylogenetic clades within the group is not yet understood. Furthermore, genomic resources have been limited for the study of host-specific pathotypes. We report near complete genomes of the apple and Asian pear pathotypes as well as draft assemblies for a further 10 isolates representing Alternaria tenuissima and Alternaria arborescens lineages. These assemblies provide the first insights into differentiation of these taxa as well as allowing the description of effector and non-effector profiles of apple and pear conditionally dispensable chromosomes (CDCs). We define the phylogenetic relationship between the isolates sequenced in this study and a further 23 Alternaria spp. based on available genomes. We determine which of these genomes represent MAT1-1-1 or MAT1-2-1 idiomorphs and designate host-specific pathotypes. We show for the first time that the apple pathotype is polyphyletic, present in both the A. arborescens and A. tenuissima lineages. Furthermore, we profile a wider set of 89 isolates for both mating type idiomorphs and toxin gene markers. Mating-type distribution indicated that gene flow has occurred since the formation of A. tenuissima and A. arborescens lineages. We also developed primers designed to AMT14, a gene from the apple pathotype toxin gene cluster with homologs in all tested pathotypes. These primers allow identification and differentiation of apple, pear, and strawberry pathotypes, providing new tools for pathogen diagnostics.
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Affiliation(s)
- Andrew D. Armitage
- NIAB EMR, East Malling, United Kingdom
- Natural Resources Institute, University of Greenwich, Chatham Maritime, London, United Kingdom
| | | | | | - James Woodhall
- Parma Research and Extension Center, University of Idaho, Parma, ID, United States
| | | | | | - John P. Clarkson
- Warwick Crop Centre, University of Warwick, Warwick, United Kingdom
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16
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Rajarammohan S, Paritosh K, Pental D, Kaur J. Comparative genomics of Alternaria species provides insights into the pathogenic lifestyle of Alternaria brassicae - a pathogen of the Brassicaceae family. BMC Genomics 2019; 20:1036. [PMID: 31888481 PMCID: PMC6937934 DOI: 10.1186/s12864-019-6414-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 12/19/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alternaria brassicae, a necrotrophic pathogen, causes Alternaria Leaf Spot, one of the economically important diseases of Brassica crops. Many other Alternaria spp. such as A. brassicicola and A. alternata are known to cause secondary infections in the A. brassicae-infected Brassicas. The genome architecture, pathogenicity factors, and determinants of host-specificity of A. brassicae are unknown. In this study, we annotated and characterised the recently announced genome assembly of A. brassicae and compared it with other Alternaria spp. to gain insights into its pathogenic lifestyle. RESULTS We also sequenced the genomes of two A. alternata isolates that were co-infecting B. juncea using Nanopore MinION sequencing for additional comparative analyses within the Alternaria genus. Genome alignments within the Alternaria spp. revealed high levels of synteny between most chromosomes with some intrachromosomal rearrangements. We show for the first time that the genome of A. brassicae, a large-spored Alternaria species, contains a dispensable chromosome. We identified 460 A. brassicae-specific genes, which included many secreted proteins and effectors. Furthermore, we have identified the gene clusters responsible for the production of Destruxin-B, a known pathogenicity factor of A. brassicae. CONCLUSION The study provides a perspective into the unique and shared repertoire of genes within the Alternaria genus and identifies genes that could be contributing to the pathogenic lifestyle of A. brassicae.
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Affiliation(s)
- Sivasubramanian Rajarammohan
- Department of Genetics, University of Delhi , South Campus, New Delhi, 110021, India
- Present Address: National Agri-Food Biotechnology Institute, Mohali, India
| | - Kumar Paritosh
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| | - Deepak Pental
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| | - Jagreet Kaur
- Department of Genetics, University of Delhi , South Campus, New Delhi, 110021, India.
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17
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Ametrano CG, Grewe F, Crous PW, Goodwin SB, Liang C, Selbmann L, Lumbsch HT, Leavitt SD, Muggia L. Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota). IMA Fungus 2019; 10:19. [PMID: 32647623 PMCID: PMC7325674 DOI: 10.1186/s43008-019-0018-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/11/2019] [Indexed: 12/31/2022] Open
Abstract
Dothideomycetes is the most diverse fungal class in Ascomycota and includes species with a wide range of lifestyles. Previous multilocus studies have investigated the taxonomic and evolutionary relationships of these taxa but often failed to resolve early diverging nodes and frequently generated inconsistent placements of some clades. Here, we use a phylogenomic approach to resolve relationships in Dothideomycetes, focusing on two genera of melanized, extremotolerant rock-inhabiting fungi, Lichenothelia and Saxomyces, that have been suggested to be early diverging lineages. We assembled phylogenomic datasets from newly sequenced (4) and previously available genomes (238) of 242 taxa. We explored the influence of tree inference methods, supermatrix vs. coalescent-based species tree, and the impact of varying amounts of genomic data. Overall, our phylogenetic reconstructions provide consistent and well-supported topologies for Dothideomycetes, recovering Lichenothelia and Saxomyces among the earliest diverging lineages in the class. In addition, many of the major lineages within Dothideomycetes are recovered as monophyletic, and the phylogenomic approach implemented strongly supports their relationships. Ancestral character state reconstruction suggest that the rock-inhabiting lifestyle is ancestral within the class.
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Affiliation(s)
- Claudio G Ametrano
- Department of Life Sciences, University of Trieste, via Giorgieri 10, 34127 Trieste, Italy
| | - Felix Grewe
- Grainger Bioinformatics Center and Integrative Research Center, Science and Education, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605 USA
| | - Pedro W Crous
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85176, 3508 AD Utrecht, The Netherlands
| | - Stephen B Goodwin
- USDA-ARS, Crop Production and Pest Control Research Unit and Department of Botany and Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 USA
| | - Chen Liang
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109 China
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell' Università, 01100 Viterbo, Italy.,Italian National Antarctic Museum (MNA), Mycological Section, Genoa, Italy
| | - H Thorsten Lumbsch
- Grainger Bioinformatics Center and Integrative Research Center, Science and Education, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605 USA
| | - Steven D Leavitt
- Department of Biology and M.L. Bean Life Science Museum, Brigham Young University, 4102 Life Science Building, Provo, UT 84602 USA
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, via Giorgieri 10, 34127 Trieste, Italy
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18
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Ushijima K, Yamamoto M. A Sequence Resource of Autosomes and Additional Chromosomes in the Peach Pathotype of Alternaria alternata. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1273-1276. [PMID: 31125281 DOI: 10.1094/mpmi-04-19-0093-a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Alternaria alternata is a generally saprophytic fungus. Its genome consists of 10 autosomes, while some strains have one or two additional chromosomes, called a conditionally dispensable chromosome (CDC). A CDC is not required for reproduction but confers host-specific pathogenicity. We sequenced the genome of the peach pathotype of A. alternata using Nanopore and assembled it into 20 sequences. The 10 largest sequences corresponded to 10 gapless sequences of A. solani autosomes, and 1 sequence was a mitochondrial genome. Nine other sequences may be derived from CDCs because of lack of similarity with autosomes of other Alternaria spp. The sequence information could provide novel insights into genomes of Alternaria spp. and on the biosynthesis of a novel host-specific toxin in the peach pathotype of A. alternata.
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Affiliation(s)
- Koichiro Ushijima
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Mikihiro Yamamoto
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
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19
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Wang M, Fu H, Shen X, Ruan R, Rokas A, Li H. Genomic features and evolution of the conditionally dispensable chromosome in the tangerine pathotype of Alternaria alternata. MOLECULAR PLANT PATHOLOGY 2019; 20:1425-1438. [PMID: 31297970 PMCID: PMC6792136 DOI: 10.1111/mpp.12848] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The tangerine pathotype of the ascomycete fungus Alternaria alternata is the causal agent of citrus brown spot, which can result in significant losses of both yield and marketability for tangerines worldwide. A conditionally dispensable chromosome (CDC), which harbours the host-selective ACT toxin gene cluster, is required for tangerine pathogenicity of A. alternata. To understand the genetic makeup and evolution of the tangerine pathotype CDC, we isolated and sequenced the CDCs of the A. alternata Z7 strain and analysed the function and evolution of their genes. The A. alternata Z7 strain has two CDCs (~1.1 and ~0.8 Mb, respectively), and the longer Z7 CDC contains all but one contig of the shorter one. Z7 CDCs contain 254 predicted protein-coding genes, which are enriched in functional categories associated with 'metabolic process' (55 genes, P = 0.037). Relatively few of the CDC genes can be classified as carbohydrate-active enzymes (CAZymes) (4) and transporters (19) and none as kinases. Evolutionary analysis of the 254 CDC proteins showed that their evolutionary conservation tends to be restricted within the genus Alternaria and that the CDC genes evolve faster than genes in the essential chromosomes, likely due to fewer selective constraints. Interestingly, phylogenetic analysis suggested that four of the 25 genes responsible for the ACT toxin production were likely transferred from Colletotrichum (Sordariomycetes). Functional experiments showed that two of them are essential for the virulence of the tangerine pathotype of A. alternata. These results provide new insights into the function and evolution of CDC genes in Alternaria.
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Affiliation(s)
- Mingshuang Wang
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of BiotechnologyZhejiang UniversityHangzhou310058China
- Department of Biological SciencesVanderbilt UniversityNashvilleTN37235USA
- College of Life and Environmental SciencesHangzhou Normal UniversityHangzhou310036China
| | - Huilan Fu
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of BiotechnologyZhejiang UniversityHangzhou310058China
| | - Xing‐Xing Shen
- Department of Biological SciencesVanderbilt UniversityNashvilleTN37235USA
| | - Ruoxin Ruan
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of BiotechnologyZhejiang UniversityHangzhou310058China
- Hangzhou Academy of Agricultural SciencesHangzhou310024China
| | - Antonis Rokas
- Department of Biological SciencesVanderbilt UniversityNashvilleTN37235USA
| | - Hongye Li
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of BiotechnologyZhejiang UniversityHangzhou310058China
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20
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Weitemier K, Straub SC, Fishbein M, Bailey CD, Cronn RC, Liston A. A draft genome and transcriptome of common milkweed ( Asclepias syriaca) as resources for evolutionary, ecological, and molecular studies in milkweeds and Apocynaceae. PeerJ 2019; 7:e7649. [PMID: 31579586 PMCID: PMC6756140 DOI: 10.7717/peerj.7649] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/09/2019] [Indexed: 02/06/2023] Open
Abstract
Milkweeds (Asclepias) are used in wide-ranging studies including floral development, pollination biology, plant-insect interactions and co-evolution, secondary metabolite chemistry, and rapid diversification. We present a transcriptome and draft nuclear genome assembly of the common milkweed, Asclepias syriaca. This reconstruction of the nuclear genome is augmented by linkage group information, adding to existing chloroplast and mitochondrial genomic resources for this member of the Apocynaceae subfamily Asclepiadoideae. The genome was sequenced to 80.4× depth and the draft assembly contains 54,266 scaffolds ≥1 kbp, with N50 = 3,415 bp, representing 37% (156.6 Mbp) of the estimated 420 Mbp genome. A total of 14,474 protein-coding genes were identified based on transcript evidence, closely related proteins, and ab initio models, and 95% of genes were annotated. A large proportion of gene space is represented in the assembly, with 96.7% of Asclepias transcripts, 88.4% of transcripts from the related genus Calotropis, and 90.6% of proteins from Coffea mapping to the assembly. Scaffolds covering 75 Mbp of the Asclepias assembly formed 11 linkage groups. Comparisons of these groups with pseudochromosomes in Coffea found that six chromosomes show consistent stability in gene content, while one may have a long history of fragmentation and rearrangement. The progesterone 5β-reductase gene family, a key component of cardenolide production, is likely reduced in Asclepias relative to other Apocynaceae. The genome and transcriptome of common milkweed provide a rich resource for future studies of the ecology and evolution of a charismatic plant family.
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Affiliation(s)
- Kevin Weitemier
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA
| | | | - Mark Fishbein
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, OK, USA
| | - C. Donovan Bailey
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - Richard C. Cronn
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR, USA
| | - Aaron Liston
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR, USA
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21
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Rajarammohan S, Pental D, Kaur J. Near-Complete Genome Assembly of Alternaria brassicae-A Necrotrophic Pathogen of Brassica Crops. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:928-930. [PMID: 30920345 DOI: 10.1094/mpmi-03-19-0084-a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Alternaria brassicae, a necrotrophic fungal pathogen, causes Alternaria blight, an important disease of brassica crops. Although many Alternaria spp. have been sequenced, no genome information is available for A. brassicae, a monotypic lineage within the Alternaria genus. A highly contiguous genome assembly of A. brassicae has been generated using Nanopore MinION sequencing with an N50 of 2.98 Mb, yielding nine full chromosome-level sequences. This study adds to the current genomic resources available for the genus Alternaria and will provide opportunities for further analyses to unravel the mechanisms underlying pathogenicity of this important necrotrophic pathogen.
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Affiliation(s)
| | - Deepak Pental
- 2Centre for Genetic Manipulation of Crop Plants, University of Delhi - South Campus, Delhi, India
| | - Jagreet Kaur
- 1Department of Genetics, University of Delhi - South Campus, Delhi, India
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22
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Choudhary P, Chakdar H, Singh A, Kumar S, Singh SK, Aarthy M, Goswami SK, Srivastava AK, Saxena AK. Computational identification and antifungal bioassay reveals phytosterols as potential inhibitor of Alternaria arborescens. J Biomol Struct Dyn 2019; 38:1143-1157. [PMID: 30898083 DOI: 10.1080/07391102.2019.1597767] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Alternaria arborescens is a major pathogen for crops like tomato, tangerine and so on and its control is mostly dependent on the application of chemical agents. Plants as the sources of natural products are very attractive option for developing eco-friendly and natural antifungal agents. In this study, we modeled three-dimensional structure of chorismate synthase (CS) enzyme from A. arborescens. Docking studies of phytosterols, namely, γ-sitosterol and β-sitosterol, with CS showed them to be potential inhibitor of CS. To explore the stability and conformational flexibility of all the AaCS complex systems, molecular dynamics simulations were performed. None of the putative inhibitors as well as β- and γ-sitosterol showed interaction with the FMNH2 binding pocket of the tomato CS (major host of A. arborescens) indicating their suitability as antifungal compounds inhibiting the shikimate pathway without causing any harm to the host. An in vivo antifungal bioassay showed a significant reduction in fungal growth in the presence of β-sitosterol (500 ppm) which resulted in ∼23% and ∼17% reduction in fungal fresh and dry weight, respectively, at 8 days after inoculation. This study provides experimental evidence establishing natural sterols like β-sitosterol can be useful in curbing A. arborescens damage in an eco-friendly manner.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Prassan Choudhary
- Microbial Technology Unit, ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, India
| | - Hillol Chakdar
- Microbial Technology Unit, ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, India
| | - Arjun Singh
- Microbial Technology Unit, ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, India
| | - Sunil Kumar
- Microbial Technology Unit, ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, India
| | - Sanjeev Kumar Singh
- Department of Bioinformatics, Algappa University, Karaikudi, Tamil Nadu, India
| | - Murali Aarthy
- Department of Bioinformatics, Algappa University, Karaikudi, Tamil Nadu, India
| | - Sanjay Kumar Goswami
- Microbial Technology Unit, ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, India
| | - Alok Kumar Srivastava
- Microbial Technology Unit, ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, India
| | - Anil Kumar Saxena
- Microbial Technology Unit, ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, India
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23
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Yang N, Ma G, Chen K, Wu X. The Population Genetics of Alternaria tenuissima in Four Regions of China as Determined by Microsatellite Markers Obtained by Transcriptome Sequencing. Front Microbiol 2018; 9:2904. [PMID: 30559728 PMCID: PMC6287023 DOI: 10.3389/fmicb.2018.02904] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 11/13/2018] [Indexed: 12/02/2022] Open
Abstract
A total of 32,284 unigenes were obtained from the transcriptome of Alternaria tenuissima, a pathogenic fungus causing foliar disease in tomato, using next-generation sequencing (NGS) technology. In total, 24,670 unigenes were annotated using five databases, including NCBI non-redundant protein, Swiss-Prot, euKaryotic Orthologous Groups, Kyoto Encyclopedia of Genes and Genomes, and the Gene Ontology. A total of 1,140 simple sequence repeats were also identified for use as molecular markers. Sixteen of the simple sequence repeat loci were selected to study the population structure of A. tenuissima. A population genetic analysis of 191 A. tenuissima isolates, sampled from four geographic regions in China, indicated that A. tenuissima had a high level of genetic diversity, and that the selected simple sequence repeat markers could reliably capture the genetic variation. The null hypothesis of random mating was rejected for all four geographic regions in China. Isolation by distance was observed for the entire data set, but not within clusters, which is indicative of barriers to gene flow among geographic regions. The analyses of Bayesian and principal coordinates, however, did not separate four geographic regions into four separate genetic clusters. The different levels of historical migration rates suggest that isolation by distance did not represent a major biological obstacle to the spread of A. tenuissima. The potential epidemic spread of A. tenuissima in China may occur through the transport of plant products or other factors. The presented results provide a basis for a comprehensive understanding of the population genetics of A. tenuissima in China.
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Affiliation(s)
| | | | | | - Xuehong Wu
- College of Plant Protection, Department of Plant Pathology, China Agricultural University, Beijing, China
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24
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Bertazzoni S, Williams AH, Jones DA, Syme RA, Tan KC, Hane JK. Accessories Make the Outfit: Accessory Chromosomes and Other Dispensable DNA Regions in Plant-Pathogenic Fungi. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:779-788. [PMID: 29664319 DOI: 10.1094/mpmi-06-17-0135-fi] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Fungal pathogen genomes can often be divided into core and accessory regions. Accessory regions ARs) may be comprised of either ARs (within core chromosomes (CCs) or wholly dispensable (accessory) chromosomes (ACs). Fungal ACs and ARs typically accumulate mutations and structural rearrangements more rapidly over time than CCs and many harbor genes relevant to host-pathogen interactions. These regions are of particular interest in plant pathology and include host-specific virulence factors and secondary metabolite synthesis gene clusters. This review outlines known ACs and ARs in fungal genomes, methods used for their detection, their common properties that differentiate them from the core genome, and what is currently known of their various roles in pathogenicity. Reports on the evolutionary processes generating and shaping AC and AR compartments are discussed, including repeat induced point mutation and breakage fusion bridge cycles. Previously ACs have been studied extensively within key genera, including Fusarium, Zymoseptoria, and Alternaria, but are growing in frequency of observation and perceived importance across a wider range of fungal species. Recent advances in sequencing technologies permit affordable genome assembly and resequencing of populations that will facilitate further discovery and routine screening of ACs.
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Affiliation(s)
- Stefania Bertazzoni
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
| | - Angela H Williams
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
| | - Darcy A Jones
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
| | - Robert A Syme
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
| | - Kar-Chun Tan
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
| | - James K Hane
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
- 2 Curtin Institute for Computation, Curtin University, Perth, Western Australia, Australia
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25
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Wolters PJ, Faino L, van den Bosch TBM, Evenhuis B, Visser RGF, Seidl MF, Vleeshouwers VGAA. Gapless Genome Assembly of the Potato and Tomato Early Blight Pathogen Alternaria solani. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:692-694. [PMID: 29432053 DOI: 10.1094/mpmi-12-17-0309-a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The Alternaria genus consists of saprophytic fungi as well as plant-pathogenic species that have significant economic impact. To date, the genomes of multiple Alternaria species have been sequenced. These studies have yielded valuable data for molecular studies on Alternaria fungi. However, most of the current Alternaria genome assemblies are highly fragmented, thereby hampering the identification of genes that are involved in causing disease. Here, we report a gapless genome assembly of A. solani, the causal agent of early blight in tomato and potato. The genome assembly is a significant step toward a better understanding of pathogenicity of A. solani.
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Affiliation(s)
- Pieter J Wolters
- 1 Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Luigi Faino
- 2 Laboratory of Phytopathology, Wageningen University and Research
| | | | - Bert Evenhuis
- 4 Applied Arable and Vegetable Research, Wageningen University and Research, Edelhertweg 1, 8219 PH, Lelystad, The Netherlands
| | - Richard G F Visser
- 1 Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Michael F Seidl
- 2 Laboratory of Phytopathology, Wageningen University and Research
| | - Vivianne G A A Vleeshouwers
- 1 Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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Ekanayaka AH, Hyde KD, Jones EBG, Zhao Q. Taxonomy and phylogeny of operculate discomycetes: Pezizomycetes. FUNGAL DIVERS 2018. [DOI: 10.1007/s13225-018-0402-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Soyer JL, Balesdent MH, Rouxel T, Dean RA. To B or not to B: a tale of unorthodox chromosomes. Curr Opin Microbiol 2018; 46:50-57. [PMID: 29579575 DOI: 10.1016/j.mib.2018.01.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/19/2018] [Accepted: 01/24/2018] [Indexed: 01/21/2023]
Affiliation(s)
- Jessica L Soyer
- UMR BIOGER, INRA, AgroParisTech, Paris-Saclay University, Thiverval-Grignon, France
| | | | - Thierry Rouxel
- UMR BIOGER, INRA, AgroParisTech, Paris-Saclay University, Thiverval-Grignon, France
| | - Ralph A Dean
- Center for Integrated Fungal Research, North Carolina State University & Department of Entomology and Plant Pathology, North Carolina State University, United States.
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Geisen R, Touhami N, Schmidt-Heydt M. Mycotoxins as adaptation factors to food related environments. Curr Opin Food Sci 2017. [DOI: 10.1016/j.cofs.2017.07.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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29
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Ruiz-Ruano FJ, Cabrero J, López-León MD, Sánchez A, Camacho JPM. Quantitative sequence characterization for repetitive DNA content in the supernumerary chromosome of the migratory locust. Chromosoma 2017; 127:45-57. [PMID: 28868580 DOI: 10.1007/s00412-017-0644-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 08/23/2017] [Accepted: 08/24/2017] [Indexed: 12/23/2022]
Abstract
Repetitive DNA is a major component in most eukaryotic genomes but is ignored in most genome sequencing projects. Here, we report the quantitative composition in repetitive DNA for a supernumerary (B) chromosome, in the migratory locust (Locusta migratoria), by Illumina sequencing of genomic DNA from B-carrying and B-lacking individuals and DNA obtained from a microdissected B chromosome, as well as the physical mapping of some elements. B chromosome DNA of 94.9% was repetitive, in high contrast with the 64.1% of standard (A) chromosomes. B chromosomes are enriched in satellite DNA (satDNA) (65.2% of B-DNA), with a single satellite (LmiSat02-176) comprising 55% of the B. Six satDNAs were visualized by FISH on the B chromosome, and the only A chromosome carrying all these satellites was autosome 9, pointing to this chromosome, along with autosome 8 (which shares histone genes with the B) as putative ancestors of the B chromosome. We found several transposable elements (TEs) showing nucleotidic variation specific to B-carrying individuals, which was also present in B-carrying transcriptomes. Remarkably, an interstitial region of the B chromosome included a 17 kb chimera composed of 29 different TEs, suggesting reiterative TE insertion in this B chromosome region.
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Affiliation(s)
- Francisco J Ruiz-Ruano
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, 18071, Granada, Spain.
| | - Josefa Cabrero
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, 18071, Granada, Spain
| | - María Dolores López-León
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, 18071, Granada, Spain
| | - Antonio Sánchez
- Departamento de Biología Experimental, Universidad de Jaén, Jaén, Spain
| | - Juan Pedro M Camacho
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, 18071, Granada, Spain
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Meena M, Gupta SK, Swapnil P, Zehra A, Dubey MK, Upadhyay RS. Alternaria Toxins: Potential Virulence Factors and Genes Related to Pathogenesis. Front Microbiol 2017; 8:1451. [PMID: 28848500 PMCID: PMC5550700 DOI: 10.3389/fmicb.2017.01451] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 07/18/2017] [Indexed: 01/04/2023] Open
Abstract
Alternaria is an important fungus to study due to their different life style from saprophytes to endophytes and a very successful fungal pathogen that causes diseases to a number of economically important crops. Alternaria species have been well-characterized for the production of different host-specific toxins (HSTs) and non-host specific toxins (nHSTs) which depend upon their physiological and morphological stages. The pathogenicity of Alternaria species depends on host susceptibility or resistance as well as quantitative production of HSTs and nHSTs. These toxins are chemically low molecular weight secondary metabolites (SMs). The effects of toxins are mainly on different parts of cells like mitochondria, chloroplast, plasma membrane, Golgi complex, nucleus, etc. Alternaria species produce several nHSTs such as brefeldin A, tenuazonic acid, tentoxin, and zinniol. HSTs that act in very low concentrations affect only certain plant varieties or genotype and play a role in determining the host range of specificity of plant pathogens. The commonly known HSTs are AAL-, AK-, AM-, AF-, ACR-, and ACT-toxins which are named by their host specificity and these toxins are classified into different family groups. The HSTs are differentiated on the basis of bio-statistical and other molecular analyses. All these toxins have different mode of action, biochemical reactions and signaling mechanisms to cause diseases. Different species of Alternaria produced toxins which reveal its biochemical and genetic effects on itself as well as on its host cells tissues. The genes responsible for the production of HSTs are found on the conditionally dispensable chromosomes (CDCs) which have been well characterized. Different bio-statistical methods like basic local alignment search tool (BLAST) data analysis used for the annotation of gene prediction, pathogenicity-related genes may provide surprising knowledge in present and future.
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Affiliation(s)
- Mukesh Meena
- Department of Botany, Institute of Science, Banaras Hindu UniversityVaranasi, India
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Mehrabi R, Mirzadi Gohari A, Kema GHJ. Karyotype Variability in Plant-Pathogenic Fungi. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:483-503. [PMID: 28777924 DOI: 10.1146/annurev-phyto-080615-095928] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Recent advances in genetic and molecular technologies gradually paved the way for the transition from traditional fungal karyotyping to more comprehensive chromosome biology studies. Extensive chromosomal polymorphisms largely resulting from chromosomal rearrangements (CRs) are widely documented in fungal genomes. These extraordinary CRs in fungi generate substantial genome plasticity compared to other eukaryotic organisms. Here, we review the most recent findings on fungal CRs and their underlying mechanisms and discuss the functional consequences of CRs for adaptation, fungal evolution, host range, and pathogenicity of fungal plant pathogens in the context of chromosome biology. In addition to a complement of permanent chromosomes called core chromosomes, the genomes of many fungal pathogens comprise distinct unstable chromosomes called dispensable chromosomes (DCs) that also contribute to chromosome polymorphisms. Compared to the core chromosomes, the structural features of DCs usually differ for gene density, GC content, housekeeping genes, and recombination frequency. Despite their dispensability for normal growth and development, DCs have important biological roles with respect to pathogenicity in some fungi but not in others. Therefore, their evolutionary origin is also reviewed in relation to overall fungal physiology and pathogenicity.
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Affiliation(s)
- Rahim Mehrabi
- Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Amir Mirzadi Gohari
- Department of Plant Pathology, Faculty of Agricultural Sciences and Engineering, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
- Wageningen Plant Research, Wageningen University and Research, 6700AA Wageningen, The Netherlands;
| | - Gert H J Kema
- Wageningen Plant Research, Wageningen University and Research, 6700AA Wageningen, The Netherlands;
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Erlendson AA, Friedman S, Freitag M. A Matter of Scale and Dimensions: Chromatin of Chromosome Landmarks in the Fungi. Microbiol Spectr 2017; 5:10.1128/microbiolspec.FUNK-0054-2017. [PMID: 28752814 PMCID: PMC5536859 DOI: 10.1128/microbiolspec.funk-0054-2017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Indexed: 02/06/2023] Open
Abstract
Chromatin and chromosomes of fungi are highly diverse and dynamic, even within species. Much of what we know about histone modification enzymes, RNA interference, DNA methylation, and cell cycle control was first addressed in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Aspergillus nidulans, and Neurospora crassa. Here, we examine the three landmark regions that are required for maintenance of stable chromosomes and their faithful inheritance, namely, origins of DNA replication, telomeres and centromeres. We summarize the state of recent chromatin research that explains what is required for normal function of these specialized chromosomal regions in different fungi, with an emphasis on the silencing mechanism associated with subtelomeric regions, initiated by sirtuin histone deacetylases and histone H3 lysine 27 (H3K27) methyltransferases. We explore mechanisms for the appearance of "accessory" or "conditionally dispensable" chromosomes and contrast what has been learned from studies on genome-wide chromosome conformation capture in S. cerevisiae, S. pombe, N. crassa, and Trichoderma reesei. While most of the current knowledge is based on work in a handful of genetically and biochemically tractable model organisms, we suggest where major knowledge gaps remain to be closed. Fungi will continue to serve as facile organisms to uncover the basic processes of life because they make excellent model organisms for genetics, biochemistry, cell biology, and evolutionary biology.
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Affiliation(s)
- Allyson A. Erlendson
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331
| | - Steven Friedman
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331
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Vlaardingerbroek I, Beerens B, Schmidt SM, Cornelissen BJC, Rep M. Dispensable chromosomes in Fusarium oxysporum f. sp. lycopersici. MOLECULAR PLANT PATHOLOGY 2016; 17:1455-1466. [PMID: 27271322 PMCID: PMC6638487 DOI: 10.1111/mpp.12440] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 06/02/2016] [Accepted: 06/03/2016] [Indexed: 05/23/2023]
Abstract
The genomes of many filamentous fungi consist of a 'core' part containing conserved genes essential for normal development as well as conditionally dispensable (CD) or lineage-specific (LS) chromosomes. In the plant-pathogenic fungus Fusarium oxysporum f. sp. lycopersici, one LS chromosome harbours effector genes that contribute to pathogenicity. We employed flow cytometry to select for events of spontaneous (partial) loss of either the two smallest LS chromosomes or two different core chromosomes. We determined the rate of spontaneous loss of the 'effector' LS chromosome in vitro at around 1 in 35 000 spores. In addition, a viable strain was obtained lacking chromosome 12, which is considered to be a part of the core genome. We also isolated strains carrying approximately 1-Mb deletions in the LS chromosomes and in the dispensable core chromosome. The large core chromosome 1 was never observed to sustain deletions over 200 kb. Whole-genome sequencing revealed that some of the sites at which the deletions occurred were the same in several independent strains obtained for the two chromosomes tested, indicating the existence of deletion hotspots. For the core chromosome, this deletion hotspot was the site of insertion of the marker used to select for loss events. Loss of the core chromosome did not affect pathogenicity, whereas loss of the effector chromosome led to a complete loss of pathogenicity.
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Affiliation(s)
- Ido Vlaardingerbroek
- Molecular Plant PathologyUniversity of AmsterdamAmsterdam1098 XH, the Netherlands
| | - Bas Beerens
- Molecular Plant PathologyUniversity of AmsterdamAmsterdam1098 XH, the Netherlands
| | - Sarah M. Schmidt
- Molecular Plant PathologyUniversity of AmsterdamAmsterdam1098 XH, the Netherlands
| | | | - Martijn Rep
- Molecular Plant PathologyUniversity of AmsterdamAmsterdam1098 XH, the Netherlands
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Vanheule A, Audenaert K, Warris S, van de Geest H, Schijlen E, Höfte M, De Saeger S, Haesaert G, Waalwijk C, van der Lee T. Living apart together: crosstalk between the core and supernumerary genomes in a fungal plant pathogen. BMC Genomics 2016; 17:670. [PMID: 27552804 PMCID: PMC4994206 DOI: 10.1186/s12864-016-2941-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 07/14/2016] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Eukaryotes display remarkable genome plasticity, which can include supernumerary chromosomes that differ markedly from the core chromosomes. Despite the widespread occurrence of supernumerary chromosomes in fungi, their origin, relation to the core genome and the reason for their divergent characteristics are still largely unknown. The complexity of genome assembly due to the presence of repetitive DNA partially accounts for this. RESULTS Here we use single-molecule real-time (SMRT) sequencing to assemble the genome of a prominent fungal wheat pathogen, Fusarium poae, including at least one supernumerary chromosome. The core genome contains limited transposable elements (TEs) and no gene duplications, while the supernumerary genome holds up to 25 % TEs and multiple gene duplications. The core genome shows all hallmarks of repeat-induced point mutation (RIP), a defense mechanism against TEs, specific for fungi. The absence of RIP on the supernumerary genome accounts for the differences between the two (sub)genomes, and results in a functional crosstalk between them. The supernumerary genome is a reservoir for TEs that migrate to the core genome, and even large blocks of supernumerary sequence (>200 kb) have recently translocated to the core. Vice versa, the supernumerary genome acts as a refuge for genes that are duplicated from the core genome. CONCLUSIONS For the first time, a mechanism was determined that explains the differences that exist between the core and supernumerary genome in fungi. Different biology rather than origin was shown to be responsible. A "living apart together" crosstalk exists between the core and supernumerary genome, accelerating chromosomal and organismal evolution.
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Affiliation(s)
- Adriaan Vanheule
- Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Wageningen UR, Wageningen, The Netherlands
| | - Kris Audenaert
- Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | | | | | | | - Monica Höfte
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Sarah De Saeger
- Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Geert Haesaert
- Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Lu H, Quan H, Ren Z, Wang S, Xue R, Zhao B. The Genome of Undifilum oxytropis Provides Insights into Swainsonine Biosynthesis and Locoism. Sci Rep 2016; 6:30760. [PMID: 27477109 PMCID: PMC4967851 DOI: 10.1038/srep30760] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 07/08/2016] [Indexed: 01/15/2023] Open
Abstract
Undifilum oxytropis is a fungal endophyte of locoweeds. It produces swainsonine, which is the principal toxic ingredient of locoweeds. However, the genes, pathways and mechanisms of swainsonine biosynthesis are not known. In this study, the genome of U. oxytropis was firstly sequenced and assembled into a 70.05 megabases (Mb) draft genome, which encoded 11,057 protein-coding genes, and 54% of them were similar to current publicly available sequences. U. oxytropis genes were annotated and 164 putative genes were annotated into enzymes, such as Saccharopine dehydrogenase, Saccharopine oxidase, and Pyrroline-5-carboxylate reductase, hypothesized to be involved in the biosynthesis pathway of swainsonine. The genome sequence and gene annotation of U. oxytropis will provide new insights into functional analyses. The characterization of genes in swainsonine biosynthesis will greatly facilitate locoweed poisoning research and help direct locoism management.
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Affiliation(s)
- Hao Lu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Haiyun Quan
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhenhui Ren
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shuai Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ruixu Xue
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Baoyu Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
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Hou Y, Ma X, Wan W, Long N, Zhang J, Tan Y, Duan S, Zeng Y, Dong Y. Comparative Genomics of Pathogens Causing Brown Spot Disease of Tobacco: Alternaria longipes and Alternaria alternata. PLoS One 2016; 11:e0155258. [PMID: 27159564 PMCID: PMC4861331 DOI: 10.1371/journal.pone.0155258] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 04/26/2016] [Indexed: 12/30/2022] Open
Abstract
The genus Alternaria is a group of infectious/contagious pathogenic fungi that not only invade a wide range of crops but also induce severe allergic reactions in a part of the human population. In this study, two strains Alternaria longipes cx1 and Alternaria alternata cx2 were isolated from different brown spot lesions on infected tobacco leaves. Their complete genomes were sequenced, de novo assembled, and comparatively analyzed. Phylogenetic analysis revealed that A. longipes cx1 and A. alternata cx2 diverged 3.3 million years ago, indicating a recent event of speciation. Seventeen non-ribosomal peptide synthetase (NRPS) genes and 13 polyketide synthase (PKS) genes in A. longipes cx1 and 13 NRPS genes and 12 PKS genes in A. alternata cx2 were identified in these two strains. Some of these genes were predicted to participate in the synthesis of non-host specific toxins (non-HSTs), such as tenuazonic acid (TeA), alternariol (AOH) and alternariol monomethyl ether (AME). By comparative genome analysis, we uncovered that A. longipes cx1 had more genes putatively involved in pathogen-plant interaction, more carbohydrate-degrading enzymes and more secreted proteins than A. alternata cx2. In summary, our results demonstrate the genomic distinction between A. longipes cx1 and A. altenata cx2. They will not only improve the understanding of the phylogenetic relationship among genus Alternaria, but more importantly provide valuable genomic resources for the investigation of plant-pathogen interaction.
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Affiliation(s)
- Yujie Hou
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Xiao Ma
- Longrun Pu-erh Tea Academy, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Wenting Wan
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Ni Long
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Jing Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yuntao Tan
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Shengchang Duan
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yan Zeng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Science, Kunming, Yunnan, China
| | - Yang Dong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Biological Big Data College, Yunnan Agricultural University, Kunming, Yunnan, China
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Tymon LS, Cummings TF, Johnson DA. Pathogenicity and Aggressiveness of Three Alternaria spp. on Potato Foliage in the U.S. Northwest. PLANT DISEASE 2016; 100:797-801. [PMID: 30688619 DOI: 10.1094/pdis-08-15-0942-re] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Alternaria spp. were collected from potato foliage showing symptoms of early blight and brown spot in the Columbia Basin, WA and Bonners Ferry and Rupert, ID between 2009 and 2011. The aggressiveness of three Alternaria spp. on potato was quantified on nonwounded and wounded detached leaves of 'Russet Norkotah' potato; wounded detached leaves of 'Alturas', 'Ranger Russet', 'Russet Burbank', and 'Umatilla Russet'; and whole plants of Russet Norkotah. Mean infection frequencies (MIF) and area under the lesion expansion curve (AULEC) were significantly greater for Alternaria solani (P = 0.0072 and 0.0002, respectively) than for A. arborescens or A. arbusti on nonwounded leaves. Wounding of tissue significantly increased MIF and AULEC for A. arbusti (P = 0.008 and 0.0047, respectively) and AULEC for A. arborescens (P = 0.01) relative to nonwounded tissue. AULEC did not differ significantly among the three Alternaria spp. when inoculated onto wounded foliage of whole plants (P = 0.34); the AULEC of whole plants was positively and significantly correlated with AULEC on detached leaves (P = 0.03). Umatilla Russet was the most susceptible and Russet Burbank was the least susceptible based on MIF and AULEC for all three pathogen species. Results indicate that A. solani was the more aggressive pathogen of potato in the Columbia Basin, because both A. arborescens and A. arbusti require wounds and A. arbusti lesions do not expand significantly in comparison with A. solani or A. arborescens following inoculation.
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Affiliation(s)
- Lydia S Tymon
- Department of Plant Pathology, Washington State University, Pullman 99164
| | - Thomas F Cummings
- Department of Plant Pathology, Washington State University, Pullman 99164
| | - Dennis A Johnson
- Department of Plant Pathology, Washington State University, Pullman 99164
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Nagrale DT, Sharma L, Kumar S, Gawande SP. Recent Diagnostics and Detection Tools: Implications for Plant Pathogenic Alternaria and Their Disease Management. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27312-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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40
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Andam CP, Carver SM, Berthrong ST. Horizontal Gene Flow in Managed Ecosystems. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2015. [DOI: 10.1146/annurev-ecolsys-112414-054126] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Cheryl P. Andam
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115;
| | - Sarah M. Carver
- Central Research, The Kraft Heinz Company, Glenview, Illinois 60025;
| | - Sean T. Berthrong
- Department of Biological Sciences, Butler University, Indianapolis, Indiana 46208;
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Wang H, Sivonen K, Fewer DP. Genomic insights into the distribution, genetic diversity and evolution of polyketide synthases and nonribosomal peptide synthetases. Curr Opin Genet Dev 2015; 35:79-85. [PMID: 26605685 DOI: 10.1016/j.gde.2015.10.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 10/20/2015] [Accepted: 10/21/2015] [Indexed: 11/18/2022]
Abstract
Polyketides and nonribosomal peptides are important secondary metabolites that exhibit enormous structural diversity, have many pharmaceutical applications, and include a number of clinically important drugs. These complex metabolites are most commonly synthesized on enzymatic assembly lines of polyketide synthases and nonribosomal peptide synthetases. Genome-mining studies making use of the recent explosion in the number of genome sequences have demonstrated unexpected enzymatic diversity and greatly expanded the known distribution of these enzyme systems across the three domains of life. The wealth of data now available suggests that genome-mining efforts will uncover new natural products, novel biosynthetic mechanisms, and shed light on the origin and evolution of these important enzymes.
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Affiliation(s)
- Hao Wang
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, FIN-00014 Helsinki, Finland.
| | - Kaarina Sivonen
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, FIN-00014 Helsinki, Finland
| | - David P Fewer
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, FIN-00014 Helsinki, Finland
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Armitage AD, Barbara DJ, Harrison RJ, Lane CR, Sreenivasaprasad S, Woodhall JW, Clarkson JP. Discrete lineages within Alternaria alternata species group: Identification using new highly variable loci and support from morphological characters. Fungal Biol 2015; 119:994-1006. [DOI: 10.1016/j.funbio.2015.06.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 06/29/2015] [Accepted: 06/30/2015] [Indexed: 01/24/2023]
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Woudenberg J, Seidl M, Groenewald J, de Vries M, Stielow J, Thomma B, Crous P. Alternaria section Alternaria: Species, formae speciales or pathotypes? Stud Mycol 2015; 82:1-21. [PMID: 26951037 PMCID: PMC4774270 DOI: 10.1016/j.simyco.2015.07.001] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The cosmopolitan fungal genus Alternaria consists of multiple saprophytic and pathogenic species. Based on phylogenetic and morphological studies, the genus is currently divided into 26 sections. Alternaria sect. Alternaria contains most of the small-spored Alternaria species with concatenated conidia, including important plant, human and postharvest pathogens. Species within sect. Alternaria have been mostly described based on morphology and / or host-specificity, yet molecular variation between them is minimal. To investigate whether the described morphospecies within sect. Alternaria are supported by molecular data, whole-genome sequencing of nine Alternaria morphospecies supplemented with transcriptome sequencing of 12 Alternaria morphospecies as well as multi-gene sequencing of 168 Alternaria isolates was performed. The assembled genomes ranged in size from 33.3-35.2 Mb within sect. Alternaria and from 32.0-39.1 Mb for all Alternaria genomes. The number of repetitive sequences differed significantly between the different Alternaria genomes; ranging from 1.4-16.5 %. The repeat content within sect. Alternaria was relatively low with only 1.4-2.7 % of repeats. Whole-genome alignments revealed 96.7-98.2 % genome identity between sect. Alternaria isolates, compared to 85.1-89.3 % genome identity for isolates from other sections to the A. alternata reference genome. Similarly, 1.4-2.8 % and 0.8-1.8 % single nucleotide polymorphisms (SNPs) were observed in genomic and transcriptomic sequences, respectively, between isolates from sect. Alternaria, while the percentage of SNPs found in isolates from different sections compared to the A. alternata reference genome was considerably higher; 8.0-10.3 % and 6.1-8.5 %. The topology of a phylogenetic tree based on the whole-genome and transcriptome reads was congruent with multi-gene phylogenies based on commonly used gene regions. Based on the genome and transcriptome data, a set of core proteins was extracted, and primers were designed on two gene regions with a relatively low degree of conservation within sect. Alternaria (96.8 and 97.3 % conservation). Their potential discriminatory power within sect. Alternaria was tested next to nine commonly used gene regions in sect. Alternaria, namely the SSU, LSU, ITS, gapdh, rpb2, tef1, Alt a 1, endoPG and OPA10-2 gene regions. The phylogenies from the two gene regions with a relatively low conservation, KOG1058 and KOG1077, could not distinguish the described morphospecies within sect. Alternaria more effectively than the phylogenies based on the commonly used gene regions for Alternaria. Based on genome and transcriptome comparisons and molecular phylogenies, Alternaria sect. Alternaria consists of only 11 phylogenetic species and one species complex. Thirty-five morphospecies, which cannot be distinguished based on the multi-gene phylogeny, are synonymised under A. alternata. By providing guidelines for the naming and identification of phylogenetic species in Alternaria sect. Alternaria, this manuscript provides a clear and stable species classification in this section.
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Affiliation(s)
- J.H.C. Woudenberg
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - M.F. Seidl
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - J.Z. Groenewald
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - M. de Vries
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - J.B. Stielow
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - B.P.H.J. Thomma
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - P.W. Crous
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
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Pusztahelyi T, Holb IJ, Pócsi I. Secondary metabolites in fungus-plant interactions. FRONTIERS IN PLANT SCIENCE 2015; 6:573. [PMID: 26300892 PMCID: PMC4527079 DOI: 10.3389/fpls.2015.00573] [Citation(s) in RCA: 254] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 07/13/2015] [Indexed: 05/18/2023]
Abstract
Fungi and plants are rich sources of thousands of secondary metabolites. The genetically coded possibilities for secondary metabolite production, the stimuli of the production, and the special phytotoxins basically determine the microscopic fungi-host plant interactions and the pathogenic lifestyle of fungi. The review introduces plant secondary metabolites usually with antifungal effect as well as the importance of signaling molecules in induced systemic resistance and systemic acquired resistance processes. The review also concerns the mimicking of plant effector molecules like auxins, gibberellins and abscisic acid by fungal secondary metabolites that modulate plant growth or even can subvert the plant defense responses such as programmed cell death to gain nutrients for fungal growth and colonization. It also looks through the special secondary metabolite production and host selective toxins of some significant fungal pathogens and the plant response in form of phytoalexin production. New results coming from genome and transcriptional analyses in context of selected fungal pathogens and their hosts are also discussed.
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Affiliation(s)
- Tünde Pusztahelyi
- Central Laboratory, Faculty of Agricultural and Food Sciences and Environmental Management, University of DebrecenDebrecen, Hungary
| | - Imre J. Holb
- Faculty of Agricultural and Food Sciences and Environmental Management, Institute of Horticulture, University of DebrecenDebrecen, Hungary
- Department of Plant Pathology, Centre for Agricultural Research, Plant Protection Institute, Hungarian Academy of SciencesDebrecen, Hungary
| | - István Pócsi
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of DebrecenDebrecen, Hungary
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Thynne E, McDonald MC, Solomon PS. Phytopathogen emergence in the genomics era. TRENDS IN PLANT SCIENCE 2015; 20:246-255. [PMID: 25682011 DOI: 10.1016/j.tplants.2015.01.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 01/13/2015] [Accepted: 01/19/2015] [Indexed: 06/04/2023]
Abstract
Phytopathogens are a global threat to plant agriculture and biodiversity. The genomics era has lead to an exponential rise in comparative gene and genome studies of both economically significant and insignificant microorganisms. In this review we highlight some recent comparisons and discuss how they identify shared genes or genomic regions associated with host virulence. The two major mechanisms of rapid genome adaptation - horizontal gene transfer and hybridisation - are reviewed and we consider how intra-specific pan-genome sequences encode alternative host specificity. We also discuss the power that access to expansive gene databases provides in aiding the study of phytopathogen emergence. These databases can rapidly enable the identification of an unknown pathogen and its origin, as well as genomic adaptations required for emergence.
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Affiliation(s)
- Elisha Thynne
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, 2601, ACT, Australia
| | - Megan C McDonald
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, 2601, ACT, Australia
| | - Peter S Solomon
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, 2601, ACT, Australia.
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Dang HX, Pryor B, Peever T, Lawrence CB. The Alternaria genomes database: a comprehensive resource for a fungal genus comprised of saprophytes, plant pathogens, and allergenic species. BMC Genomics 2015; 16:239. [PMID: 25887485 PMCID: PMC4387663 DOI: 10.1186/s12864-015-1430-7] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/02/2015] [Indexed: 12/19/2022] Open
Abstract
Background Alternaria is considered one of the most common saprophytic fungal genera on the planet. It is comprised of many species that exhibit a necrotrophic phytopathogenic lifestyle. Several species are clinically associated with allergic respiratory disorders although rarely found to cause invasive infections in humans. Finally, Alternaria spp. are among the most well known producers of diverse fungal secondary metabolites, especially toxins. Description We have recently sequenced and annotated the genomes of 25 Alternaria spp. including but not limited to many necrotrophic plant pathogens such as A. brassicicola (a pathogen of Brassicaceous crops like cabbage and canola) and A. solani (a major pathogen of Solanaceous plants like potato and tomato), and several saprophytes that cause allergy in human such as A. alternata isolates. These genomes were annotated and compared. Multiple genetic differences were found in the context of plant and human pathogenicity, notably the pro-inflammatory potential of A. alternata. The Alternaria genomes database was built to provide a public platform to access the whole genome sequences, genome annotations, and comparative genomics data of these species. Genome annotation and comparison were performed using a pipeline that integrated multiple computational and comparative genomics tools. Alternaria genome sequences together with their annotation and comparison data were ported to Ensembl database schemas using a self-developed tool (EnsImport). Collectively, data are currently hosted using a customized installation of the Ensembl genome browser platform. Conclusion Recent efforts in fungal genome sequencing have facilitated the studies of the molecular basis of fungal pathogenicity as a whole system. The Alternaria genomes database provides a comprehensive resource of genomics and comparative data of an important saprophytic and plant/human pathogenic fungal genus. The database will be updated regularly with new genomes when they become available. The Alternaria genomes database is freely available for non-profit use at http://alternaria.vbi.vt.edu.
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Affiliation(s)
- Ha X Dang
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA. .,Current address: Department of Internal Medicine, Division of Oncology, and The Genome Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - Barry Pryor
- Department of Plant Sciences, University of Arizona, Tucson, Arizona, 85721, USA.
| | - Tobin Peever
- Department of Plant Pathology, Washington State University, Pullman, Washington, 99164, USA.
| | - Christopher B Lawrence
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA. .,Department of Plant Pathology, Washington State University, Pullman, Washington, 99164, USA.
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Dang HX, Pryor B, Peever T, Lawrence CB. The Alternaria genomes database: a comprehensive resource for a fungal genus comprised of saprophytes, plant pathogens, and allergenic species. BMC Genomics 2015; 16:239. [PMID: 25887485 DOI: 10.1186/s12864-015-1430-7/figures/5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/02/2015] [Indexed: 05/25/2023] Open
Abstract
BACKGROUND Alternaria is considered one of the most common saprophytic fungal genera on the planet. It is comprised of many species that exhibit a necrotrophic phytopathogenic lifestyle. Several species are clinically associated with allergic respiratory disorders although rarely found to cause invasive infections in humans. Finally, Alternaria spp. are among the most well known producers of diverse fungal secondary metabolites, especially toxins. DESCRIPTION We have recently sequenced and annotated the genomes of 25 Alternaria spp. including but not limited to many necrotrophic plant pathogens such as A. brassicicola (a pathogen of Brassicaceous crops like cabbage and canola) and A. solani (a major pathogen of Solanaceous plants like potato and tomato), and several saprophytes that cause allergy in human such as A. alternata isolates. These genomes were annotated and compared. Multiple genetic differences were found in the context of plant and human pathogenicity, notably the pro-inflammatory potential of A. alternata. The Alternaria genomes database was built to provide a public platform to access the whole genome sequences, genome annotations, and comparative genomics data of these species. Genome annotation and comparison were performed using a pipeline that integrated multiple computational and comparative genomics tools. Alternaria genome sequences together with their annotation and comparison data were ported to Ensembl database schemas using a self-developed tool (EnsImport). Collectively, data are currently hosted using a customized installation of the Ensembl genome browser platform. CONCLUSION Recent efforts in fungal genome sequencing have facilitated the studies of the molecular basis of fungal pathogenicity as a whole system. The Alternaria genomes database provides a comprehensive resource of genomics and comparative data of an important saprophytic and plant/human pathogenic fungal genus. The database will be updated regularly with new genomes when they become available. The Alternaria genomes database is freely available for non-profit use at http://alternaria.vbi.vt.edu .
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Affiliation(s)
- Ha X Dang
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA.
- Current address: Department of Internal Medicine, Division of Oncology, and The Genome Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - Barry Pryor
- Department of Plant Sciences, University of Arizona, Tucson, Arizona, 85721, USA.
| | - Tobin Peever
- Department of Plant Pathology, Washington State University, Pullman, Washington, 99164, USA.
| | - Christopher B Lawrence
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA.
- Department of Plant Pathology, Washington State University, Pullman, Washington, 99164, USA.
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Wisecaver JH, Rokas A. Fungal metabolic gene clusters-caravans traveling across genomes and environments. Front Microbiol 2015; 6:161. [PMID: 25784900 PMCID: PMC4347624 DOI: 10.3389/fmicb.2015.00161] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 02/11/2015] [Indexed: 11/13/2022] Open
Abstract
Metabolic gene clusters (MGCs), physically co-localized genes participating in the same metabolic pathway, are signature features of fungal genomes. MGCs are most often observed in specialized metabolism, having evolved in individual fungal lineages in response to specific ecological needs, such as the utilization of uncommon nutrients (e.g., galactose and allantoin) or the production of secondary metabolic antimicrobial compounds and virulence factors (e.g., aflatoxin and melanin). A flurry of recent studies has shown that several MGCs, whose functions are often associated with fungal virulence as well as with the evolutionary arms race between fungi and their competitors, have experienced horizontal gene transfer (HGT). In this review, after briefly introducing HGT as a source of gene innovation, we examine the evidence for HGT's involvement on the evolution of MGCs and, more generally of fungal metabolism, enumerate the molecular mechanisms that mediate such transfers and the ecological circumstances that favor them, as well as discuss the types of evidence required for inferring the presence of HGT in MGCs. The currently available examples indicate that transfers of entire MGCs have taken place between closely related fungal species as well as distant ones and that they sometimes involve large chromosomal segments. These results suggest that the HGT-mediated acquisition of novel metabolism is an ongoing and successful ecological strategy for many fungal species.
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Affiliation(s)
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University Nashville, TN, USA
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Affiliation(s)
- Krishna Kant Sharma
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
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50
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Galazka JM, Freitag M. Variability of chromosome structure in pathogenic fungi--of 'ends and odds'. Curr Opin Microbiol 2014; 20:19-26. [PMID: 24835423 PMCID: PMC4133287 DOI: 10.1016/j.mib.2014.04.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 04/22/2014] [Indexed: 01/19/2023]
Abstract
Chromatin structure can affect the organization and maintenance of chromosomes. Recent discoveries in several filamentous fungi suggest mechanisms for the clustering and co-regulation of secondary metabolite genes or pathogenicity islands. An extreme case of this may be fungal 'accessory', 'conditionally dispensable', or 'supernumerary' chromosomes that often confer beneficial traits. Fungal supernumerary chromosomes may be derived by similar mechanisms as animal or plant B chromosomes, and we thus propose that this term should be reconsidered to capture the wide variety of fungal accessory chromosomes. In some fungi, both the 'ends' of chromosomes and these 'odd B chromosomes are enriched with a silencing histone modification, H3 lysine 27 trimethylation (H3K27me3), suggesting parallel mechanisms in evolving subtelomeric or B-chromosomal pathogenicity islands and secondary metabolite clusters (SMCs).
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Affiliation(s)
- Jonathan M Galazka
- Department of Biochemistry and Biophysics, Center of Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, United States
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Center of Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, United States.
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