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Baró Robaina Y, Schuster C, Castañeda-Ruiz RF, Gato Cárdenas Y, Márquez Gutiérrez ME, Ponce de la Cal A, Leclerque A. Metarhizium caribense sp. nov., a Novel Species of Entomopathogenic Metarhizium Fungi Associated with Weevils Impairing Coffee, Sugar Cane and Sweet Potato Cultivation. J Fungi (Basel) 2024; 10:612. [PMID: 39330372 PMCID: PMC11433170 DOI: 10.3390/jof10090612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 08/06/2024] [Accepted: 08/25/2024] [Indexed: 09/28/2024] Open
Abstract
(1) Background: Insect pathogenic fungi of the genus Metarhizium are under study and in application as highly solicited, more eco-system friendly substitutes for chemical insecticides in many countries and in different agricultural contexts. In Cuba and Florida, Metarhizium strains have previously been isolated from economically important coffee and sugar cane pests. (2) Methods: Unambiguous species delineation within the Metarhizium anisopliae species complex is methodologically challenging. Recently, a species-discriminating PCR approach has been developed based on ribosomal intergenic spacer (rIGS) sequences that covered the prominent four "PARB" species within the complex. This approach is combined here with further genetic markers and is extended to a further species. (3) Results: Metarhizium isolates from Cuba, found to be more naturally associated with the coffee berry borer, Hypothenemus hampei, were morphologically, microscopically and molecular taxonomically characterized. Multilocus sequence analysis based on 5TEF, MzIGS3 and rIGS markers delineated these weevil-associated strains from all previously established Metarhizium species. (4) Conclusions: The isolates under study represent a new fungal taxon proposed to be designated Metarhizium caribense. The rIGS-based species-discriminating diagnostic PCR is a suitable tool for the identification of new Metarhizium species and can be productively combined to approaches using further genetic markers.
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Affiliation(s)
| | - Christina Schuster
- Department of Biology, Technische Universität Darmstadt (TUDa), Schnittspahnstraße 10, 64287 Darmstadt, Germany
| | | | | | | | | | - Andreas Leclerque
- Department of Biology, Technische Universität Darmstadt (TUDa), Schnittspahnstraße 10, 64287 Darmstadt, Germany
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Manfrino R, Gutierrez A, Ben Gharsa H, Schuster C, López Lastra C, Leclerque A. Molecular taxonomic characterization and infra-specific diversity of entomopathogenic Beauveria bassiana fungi from Argentina. Fungal Biol 2024; 128:1800-1805. [PMID: 38796264 DOI: 10.1016/j.funbio.2024.04.003] [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] [Received: 09/23/2023] [Revised: 04/05/2024] [Accepted: 04/22/2024] [Indexed: 05/28/2024]
Abstract
It has been the aim of this study to molecular-taxonomically identify 15 Beauveria isolates collected from different geographical regions and insect hosts in Argentina and to investigate the levels of inter- and intra-specific diversity across this set of isolates. Based on phylogenetic analyses of EF1A-RPB1-RPB2 concatenated genes and BLOC markers, all Beauveria strains were identify as Beauveria bassiana. Within the B. bassiana clades of both phylogenies, isolates from Argentina were not clustered according to geographic origin or host. The 15 fungal isolates were further analyzed by PCR amplification of the intron insertion hot spot region of the nuclear 28S rRNA encoding sequence. By intron sequence and position, seven different group-I intron combinations termed variants A, B1, B2, C, D, E and F were found in the 15 isolates under study. Variants B1/B2 consisting of a single 28Si2 intron were found in ten isolates, whereas variant A occurred twice and variants C through F were unique across the set of isolates under study. The determination of the different introns and intron combinations in the 28S rRNA gene is a powerful tool for achieving infraspecific differentiation of B. bassiana isolates from Argentina.
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Affiliation(s)
- Romina Manfrino
- IDICAL-Instituto de Investigación de la Cadena Láctea, CONICET-Consejo Nacional de Investigaciones Científicas y Técnicas, INTA-Instituto Nacional de Tecnología Agropecuaria, Rafaela, 2300, Santa Fe, Argentina.
| | - Alejandra Gutierrez
- CEPAVE-Centro de Estudios Parasitológicos y de Vectores, Consejo Nacional de Investigaciones Científicas y Técnicas, UNLP-Universidad Nacional de La Plata, La Plata, 1900, Buenos Aires, Argentina
| | - Haifa Ben Gharsa
- Insect-Associated Microorganisms and Microbial Control, Department of Biology, Technische Universität Darmstadt, 64287, Darmstadt, Germany
| | - Christina Schuster
- Insect-Associated Microorganisms and Microbial Control, Department of Biology, Technische Universität Darmstadt, 64287, Darmstadt, Germany
| | - Claudia López Lastra
- CEPAVE-Centro de Estudios Parasitológicos y de Vectores, Consejo Nacional de Investigaciones Científicas y Técnicas, UNLP-Universidad Nacional de La Plata, La Plata, 1900, Buenos Aires, Argentina
| | - Andreas Leclerque
- Insect-Associated Microorganisms and Microbial Control, Department of Biology, Technische Universität Darmstadt, 64287, Darmstadt, Germany.
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Mantzoukas S, Koutsogeorgiou EI, Lagogiannis I, Gogolashvili N, Fifis GT, Navrozidis EI, Thomidis T, Andreadis SS. Effect of Entomopathogenic Fungi to Eggs and Nymphs Survival of Halyomorpha halys (Hemiptera: Pentatomidae) Under Laboratory Conditions. Curr Microbiol 2023; 81:48. [PMID: 38141115 DOI: 10.1007/s00284-023-03547-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/31/2023] [Indexed: 12/24/2023]
Abstract
Halyomorpha halys (Stål) (Hemiptera: Pentatomidae) is becoming a major pest of Greece's agricultural production, including tree fruit. Until now, the control of this pest has been based on conventional methods, with the application of chemical insecticides being the primary option. However, the wide distribution of H. halys, in combination with the large area of tree fruit production in Greece, raise the need for alternative control methods. In this study, we investigated the possibility of implementing microbial control agents for managing H. halys. Eggs and nymphs of H. halys were treated with 15 native entomopathogenic fungal isolates and their virulence was evaluated in the laboratory. After treatment, egg hatching time was recorded for 7 days and ranged from 4.5 to 7.0 days. Nymphal survival was recorded daily for 7 days following application and ranged from 2.1 to 6.6 days for second instar nymphs and 3.7 to 6.8 days for fourth instar ones. Beauveria varroae isolate displayed the highest toxicity to all H. halys stages that were tested and could be considered a promising biocontrol agent of this insect. Please check and confirm that the authors and their respective affiliations have been correctly identified and amend if necessary.οκ.
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Affiliation(s)
- Spiridon Mantzoukas
- Department of Agriculture, University of Ioannina, 45100, Ioannina, Arta, Greece.
- School of Science and Technology, Hellenic Open University, Patra, Greece.
| | - Eleni I Koutsogeorgiou
- Laboratory of Applied Zoology and Parasitology, School of Agriculture, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
- Institute of Plant Breeding and Genetic Resources, Directorate General of Agricultural Research, Hellenic Agricultural Organization «Dimitra», PO Box 60458, 57001, Thermi, Greece
| | - Ioannis Lagogiannis
- Institute of Industrial and Forage Crops, Department of Plant Protection, Directorate General of Agricultural Research, Hellenic Agricultural Organization «Dimitra», 26442, Patras, Greece
| | - Nikoloz Gogolashvili
- Department of Agriculture, School of Geosciences, International Hellenic University, 57400, Sindos, Greece
| | - Georgios T Fifis
- Department of Agriculture, School of Geosciences, International Hellenic University, 57400, Sindos, Greece
| | - Emmanuel I Navrozidis
- Department of Agriculture, School of Geosciences, International Hellenic University, 57400, Sindos, Greece
| | - Thomas Thomidis
- Department of Nutritional Sciences & Dietetics, School of Health Sciences, International Hellenic University, 57400, Sindos, Greece
| | - Stefanos S Andreadis
- Institute of Plant Breeding and Genetic Resources, Directorate General of Agricultural Research, Hellenic Agricultural Organization «Dimitra», PO Box 60458, 57001, Thermi, Greece.
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Schuster C, Baró Robaina Y, Ben Gharsa H, Bobushova S, Manfrino RG, Gutierrez AC, Lopez Lastra CC, Doolotkeldieva T, Leclerque A. Species Discrimination within the Metarhizium PARB Clade: Ribosomal Intergenic Spacer (rIGS)-Based Diagnostic PCR and Single Marker Taxonomy. J Fungi (Basel) 2023; 9:996. [PMID: 37888252 PMCID: PMC10607842 DOI: 10.3390/jof9100996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 10/28/2023] Open
Abstract
(1) Background: The entomopathogenic fungus Metarhizium anisopliae sensu lato forms a species complex, comprising a tight cluster made up of four species, namely M. anisopliae sensu stricto, M. pinghaense, M. robertsii and M. brunneum. Unambiguous species delineation within this "PARB clade" that enables both the taxonomic assignment of new isolates and the identification of potentially new species is highly solicited. (2) Methods: Species-discriminating primer pairs targeting the ribosomal intergenic spacer (rIGS) sequence were designed and a diagnostic PCR protocol established. A partial rIGS sequence, referred to as rIGS-ID800, was introduced as a molecular taxonomic marker for PARB species delineation. (3) Results: PARB species from a validation strain set not implied in primer design were clearly discriminated using the diagnostic PCR protocol developed. Using rIGS-ID800 as a single sequence taxonomic marker gave rise to a higher resolution and statistically better supported delineation of PARB clade species. (4) Conclusions: Reliable species discrimination within the Metarhizium PARB clade is possible through both sequencing-independent diagnostic PCR and sequencing-dependent single marker comparison, both based on the rIGS marker.
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Affiliation(s)
- Christina Schuster
- Department of Biology, Technische Universität Darmstadt (TUDa), Schnittspahnstraße 10, 64287 Darmstadt, Germany; (Y.B.R.)
| | - Yamilé Baró Robaina
- Department of Biology, Technische Universität Darmstadt (TUDa), Schnittspahnstraße 10, 64287 Darmstadt, Germany; (Y.B.R.)
- Plant Health Research Institute (INISAV), 110 Str. 514, Havana 11600, Cuba
| | - Haifa Ben Gharsa
- Department of Biology, Technische Universität Darmstadt (TUDa), Schnittspahnstraße 10, 64287 Darmstadt, Germany; (Y.B.R.)
| | - Saikal Bobushova
- Faculty of Agriculture, Kyrgyz-Turkish Manas University, 56 Chyngyz Aitmatov Avenue, Bishkek 720038, Kyrgyzstan
| | - Romina Guadalupe Manfrino
- Department of Biology, Technische Universität Darmstadt (TUDa), Schnittspahnstraße 10, 64287 Darmstadt, Germany; (Y.B.R.)
- Centro de Estudios Parasitólogicos y de Vectores (CEPAVE), CONICET-Consejo Nacional de Investigaciones Científicas y Técnicas, UNLP-Universidad Nacional de La Plata, La Plata 1900, Argentina
| | - Alejandra C. Gutierrez
- Centro de Estudios Parasitólogicos y de Vectores (CEPAVE), CONICET-Consejo Nacional de Investigaciones Científicas y Técnicas, UNLP-Universidad Nacional de La Plata, La Plata 1900, Argentina
| | - Claudia C. Lopez Lastra
- Centro de Estudios Parasitólogicos y de Vectores (CEPAVE), CONICET-Consejo Nacional de Investigaciones Científicas y Técnicas, UNLP-Universidad Nacional de La Plata, La Plata 1900, Argentina
| | - Tinatin Doolotkeldieva
- Faculty of Agriculture, Kyrgyz-Turkish Manas University, 56 Chyngyz Aitmatov Avenue, Bishkek 720038, Kyrgyzstan
| | - Andreas Leclerque
- Department of Biology, Technische Universität Darmstadt (TUDa), Schnittspahnstraße 10, 64287 Darmstadt, Germany; (Y.B.R.)
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Pérez-Rodríguez A, Duarte-Escalante E, Frías-De-León MG, Acosta Altamirano G, Meraz-Ríos B, Martínez-Herrera E, Arenas R, Reyes-Montes MDR. Phenotypic and Genotypic Identification of Dermatophytes from Mexico and Central American Countries. J Fungi (Basel) 2023; 9:jof9040462. [PMID: 37108916 PMCID: PMC10143779 DOI: 10.3390/jof9040462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Dermatophytes are fungi included in the genera Trichophyton, Microsporum, Epidermophyton, Nannizzia, Paraphyton, Lophophyton, and Arthroderma. Molecular techniques have contributed to faster and more precise identification, allowing significant advances in phylogenetic studies. This work aimed to identify clinical isolates of dermatophytes through phenotypic (macro- and micromorphology and conidia size) and genotypic methods (sequences of ITS regions, genes of β tubulin (BT2), and elongation factor α (Tef-1α)) and determine the phylogenetic relationships between isolates. Ninety-four dermatophyte isolates from Costa Rica, Guatemala, Honduras, Mexico, and the Dominican Republic were studied. The isolates presented macro- and micromorphology and conidia size described for the genera Trichophyton, Microsporum, and Epidermophyton. Genotypic analysis classified the isolates into the genera Trichophyton (63.8%), Nannizzia (25.5%), Arthroderma (9.6%), and Epidermophyton (1.1%). The most frequent species were T. rubrum (26 isolates, 27.6%), T. interdigitale (26 isolates, 27.6%), and N. incurvata (11 isolates, 11.7%), N. gypsea and A. otae (nine isolates, 9.6%), among others. The genotypic methods clarified the taxonomic status of closely related species. For instance, the ITS and BT2 markers of T. rubrum/T. violaceum did not differ but the Tef-1α gene did. On the other hand, the three markers differed in T. equinum/T. tonsurans. Therefore, the ITS, BT2, and Tef-1α genes are useful for typing in phylogenetic analyses of dermatophytes, with Tef-1α being the most informative locus. It should be noted that isolate MM-474 was identified as T. tonsurans when using ITS and Tef-1α, but when using BT2, it was identified as T. rubrum. On the other hand, no significant difference was found when comparing the methods for constructing phylogenies, as the topologies were similar.
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Affiliation(s)
- Angélica Pérez-Rodríguez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria No. 3000, Mexico City 04510, Mexico
| | - Esperanza Duarte-Escalante
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria No. 3000, Mexico City 04510, Mexico
| | - María Guadalupe Frías-De-León
- Hospital Regional de Alta Especialidad de Ixtapaluca, Carretera Federal México-Puebla Km. 34.5, Pueblo de Zoquiapan, Ixtapaluca 56530, Mexico
| | - Gustavo Acosta Altamirano
- Hospital Regional de Alta Especialidad de Ixtapaluca, Carretera Federal México-Puebla Km. 34.5, Pueblo de Zoquiapan, Ixtapaluca 56530, Mexico
| | - Beatriz Meraz-Ríos
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria No. 3000, Mexico City 04510, Mexico
- Hospital Regional de Alta Especialidad de Ixtapaluca, Carretera Federal México-Puebla Km. 34.5, Pueblo de Zoquiapan, Ixtapaluca 56530, Mexico
| | - Erick Martínez-Herrera
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, Mexico City 11340, Mexico
| | - Roberto Arenas
- Departamento de Dermatología, Sección de Micología, Hospital General Dr. Manuel Gea González, Mexico City 10480, Mexico
| | - María Del Rocío Reyes-Montes
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria No. 3000, Mexico City 04510, Mexico
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Intragenomic variation in nuclear ribosomal markers and its implication in species delimitation, identification and barcoding in fungi. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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7
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Theelen B, Christinaki AC, Dawson TL, Boekhout T, Kouvelis VN. Comparative analysis of Malassezia furfur mitogenomes and the development of a mitochondria-based typing approach. FEMS Yeast Res 2021; 21:6375414. [PMID: 34562093 PMCID: PMC8510979 DOI: 10.1093/femsyr/foab051] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/29/2021] [Indexed: 12/24/2022] Open
Abstract
Malassezia furfur is a yeast species belonging to Malasseziomycetes, Ustilaginomycotina and Basidiomycota that is found on healthy warm-blooded animal skin, but also involved in various skin disorders like seborrheic dermatitis/dandruff and pityriasis versicolor. Moreover, Malassezia are associated with bloodstream infections, Crohn's disease and pancreatic carcinoma. Recent advances in Malassezia genomics and genetics have focused on the nuclear genome. In this work, we present the M. furfur mitochondrial (mt) genetic heterogenicity with full analysis of 14 novel and six available M. furfur mt genomes. The mitogenome analysis reveals a mt gene content typical for fungi, including identification of variable mt regions suitable for intra-species discrimination. Three of them, namely the trnK–atp6 and cox3–nad3 intergenic regions and intron 2 of the cob gene, were selected for primer design to identify strain differences. Malassezia furfur strains belonging to known genetic variable clusters, based on AFLP and nuclear loci, were assessed for their mt variation using PCR amplification and sequencing. The results suggest that these mt regions are excellent molecular markers for the typing of M. furfur strains and may provide added value to nuclear regions when assessing evolutionary relationships at the intraspecies level.
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Affiliation(s)
- Bart Theelen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Anastasia C Christinaki
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.,Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15701, Greece
| | - Thomas L Dawson
- Agency for Science, Technology, and Research (A∗STAR), Skin Research Institute of Singapore (SRIS), 11 Mandalay Rd, #17-01, Singapore 308232, Singapore.,Center for Cell Death, Injury and Regeneration, Departments of Drug Discovery and Biomedical Sciences and Biochemistry and Molecular Biology, Medical University of South Carolina, 280 Calhoun St, Charleston, SC, 29425, USA
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Vassili N Kouvelis
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15701, Greece
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8
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Hilje-Rodríguez I, Albertazzi FJ, Rivera-Coto G, Molina-Bravo R. A multiplex qPCR TaqMan-assay to detect fungal antagonism between Trichoderma atroviride (Hypocreaceae) and Botrytis cinerea (Sclerotiniaceae) in blackberry fruits using a de novo tef1-α- and an IGS-sequence based probes. BIOTECHNOLOGY REPORTS 2020; 27:e00447. [PMID: 32528864 PMCID: PMC7276392 DOI: 10.1016/j.btre.2020.e00447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/07/2020] [Accepted: 03/19/2020] [Indexed: 11/29/2022]
Abstract
Quantitative polymerase chain reactions specifically detect Trichoderma atroviride. The method uses a probe based on the tef-1α for the detection. The method simultaneously detects T. atroviride and Botrytis cinerea in blackberries.
The aim of this study was to design a Trichoderma atroviride-specific qPCR oligo set, evaluate its specificity, and standardize a methodology that quantifies antagonism against Botrytis cinerea in blackberry fruits (Rubus adenotrichos Schltdl.). Primers and probe were designed based on the nuclear translation elongation factor 1-alpha (tef1-α) of T. atroviride. A commercial IGS-based oligo set was used to quantify B. cinerea. The specificity of the designed oligo set, along with ITS-based oligo sets, was assessed using other Trichoderma species and B. cinerea. Multiplex qPCR assays were performed using DNA from B. cinerea, T. atroviride, and blackberries inoculated with these fungi. Assays with the tef1-α oligo set showed high sensitivity and reproducibility. In inoculated fruits, T. atroviride and B. cinerea were quantified simultaneously, including in symptomless tissues. This work standardized a qPCR methodology that specifically targets a T. atroviride isolate. This newly-designed qPCR oligo set could be useful in future biological control programs.
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Affiliation(s)
- Irena Hilje-Rodríguez
- Escuela de Ciencias Agrarias, Universidad Nacional, Apartado Postal 86-3000, Heredia, Costa Rica
- Corresponding author.
| | - Federico J. Albertazzi
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, Apartado Postal 11501-2060, San José, Costa Rica
| | - German Rivera-Coto
- Escuela de Ciencias Agrarias, Universidad Nacional, Apartado Postal 86-3000, Heredia, Costa Rica
| | - Ramón Molina-Bravo
- Escuela de Ciencias Agrarias, Universidad Nacional, Apartado Postal 86-3000, Heredia, Costa Rica
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9
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Kortsinoglou AM, Saud Z, Eastwood DC, Butt TM, Kouvelis VN. The mitochondrial genome contribution to the phylogeny and identification of Metarhizium species and strains. Fungal Biol 2020; 124:845-853. [PMID: 32948272 DOI: 10.1016/j.funbio.2020.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/24/2020] [Indexed: 12/31/2022]
Abstract
The genus Metarhizium is composed of entomopathogenic fungal biological control agents (BCAs) used for invertebrate pest control. The phylogenetic relationships of species within this genus are still under scrutiny as several cryptic species can be found. In this work, the mitochondrial (mt) genome of Metarhizium brunneum ARSEF 4556 was fully sequenced and a comparative genome analysis was conducted with 7 other available mt genomes, belonging to 5 Metarhizium species: M. anisopliae, M. brunneum, M. robertsii, M. guizhouense and M. majus. Results showed that Metarhizium demonstrates greater conserved stability than other fungal mt genomes. Furthermore, this analysis located 7 diverse regions in both intergenic domains and gene fragments which were ideal for species/strain discrimination. The sequencing of these regions revealed several SNPs among 38 strains tested, 11 of which were uncharacterized. Single gene phylogenies presented variable results which may be used further for intra-species discrimination. Phylogenetic trees based on the concatenation of mt domains and the nuclear ITS1-5.8S-ITS2 region showed discrimination of the species studied and allowed the identification of uncharacterized strains. These were mostly placed within species M. anisopliae and M. brunneum. Five strains clustered together in a clade related to M. brunneum, suggesting that they comprise a cryptic species.
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Affiliation(s)
- Alexandra M Kortsinoglou
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece.
| | - Zack Saud
- Department of Biosciences, College of Science, Swansea University, Singleton Park, Swansea, SA2 8PP, Wales, United Kingdom.
| | - Dan C Eastwood
- Department of Biosciences, College of Science, Swansea University, Singleton Park, Swansea, SA2 8PP, Wales, United Kingdom.
| | - Tariq M Butt
- Department of Biosciences, College of Science, Swansea University, Singleton Park, Swansea, SA2 8PP, Wales, United Kingdom.
| | - Vassili N Kouvelis
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece.
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10
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Malarczyk D, Panek J, Frąc M. Alternative Molecular-Based Diagnostic Methods of Plant Pathogenic Fungi Affecting Berry Crops-A Review. Molecules 2019; 24:molecules24071200. [PMID: 30934757 PMCID: PMC6479758 DOI: 10.3390/molecules24071200] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/14/2019] [Accepted: 03/23/2019] [Indexed: 01/01/2023] Open
Abstract
Increasing consumer awareness of potentially harmful pesticides used in conventional agriculture has prompted organic farming to become notably more prevalent in recent decades. Central European countries are some of the most important producers of blueberries, raspberries and strawberries in the world and organic cultivation methods for these fruits have a significant market share. Fungal pathogens are considered to be the most significant threat to organic crops of berries, causing serious economic losses and reducing yields. In order to ameliorate the harmful effects of pathogenic fungi on cultivations, the application of rapid and effective identification methods is essential. At present, various molecular methods are applied for fungal species recognition, such as PCR, qPCR, LAMP and NGS.
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Affiliation(s)
- Dominika Malarczyk
- Institute of Agrophysics, Polish Academy of Sciences, 20-290 Lublin, Poland.
| | - Jacek Panek
- Institute of Agrophysics, Polish Academy of Sciences, 20-290 Lublin, Poland.
| | - Magdalena Frąc
- Institute of Agrophysics, Polish Academy of Sciences, 20-290 Lublin, Poland.
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11
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Nishi O, Sato H. Isolation of Metarhizium spp. from rhizosphere soils of wild plants reflects fungal diversity in soil but not plant specificity. Mycology 2019; 10:22-31. [PMID: 30834149 PMCID: PMC6394287 DOI: 10.1080/21501203.2018.1524799] [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: 06/18/2018] [Accepted: 09/12/2018] [Indexed: 01/21/2023] Open
Abstract
Understanding the abundance and diversity of fungal entomopathogens associated with plant species is critical for improving their field efficacy as microbial insecticides. Metarhizium is a cosmopolitan entomopathogenic fungus, with some species in this genus showing rhizosphere competencies. This study sought to determine the abundance and diversity of Metarhizium spp. in rhizosphere soils of wild plants in a field in Japan. Metarhizium spp. were detected in 76.2% of 151 rhizosphere soil samples collected from 41 plant species using a plating method. The mean density of Metarhizium spp. in rhizosphere soils was 1.2 × 104 colony forming units/g soil [base 10 logarithm of the mean = 4.06 (S.D. = 0.88)]. There was no significant difference in the densities and detection rates between Asteraceae and Poaceae as well as among two aster and one grass species. The fungal isolates were identified as five species, of which M. pingshaense was the most frequently detected and abundant species. No significant specific associations were recognised between the isolated Metarhizium spp. and the examined aster and grass species. Our findings demonstrated the high occurrence and abundance of M. pingshaense in rhizosphere soils of wild plants at the sampling site irrespective of host plant taxa.
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Affiliation(s)
- Oumi Nishi
- Research Fellowship for Young Scientists, Japan Society for the Promotion of Science, Tokyo, Japan
- Forest Entomology Division, Forestry and Forest Products Research Institute, Tsukuba city, Japan
| | - Hiroki Sato
- Forest Entomology Division, Forestry and Forest Products Research Institute, Tsukuba city, Japan
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Mayerhofer J, Lutz A, Dennert F, Rehner SA, Kepler RM, Widmer F, Enkerli J. A species-specific multiplexed PCR amplicon assay for distinguishing between Metarhizium anisopliae, M. brunneum, M. pingshaense and M. robertsii. J Invertebr Pathol 2019; 161:23-28. [PMID: 30641044 DOI: 10.1016/j.jip.2019.01.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 01/07/2019] [Accepted: 01/09/2019] [Indexed: 02/01/2023]
Abstract
The fungal species Metarhizium pingshaense, M. anisopliae, M. robertsii, and M. brunneum, a monophyletic group informally referred to as the PARB species complex, are well known facultative entomopathogens, including many commercialized strains used for biological pest control. Accurate and expedient species identification of Metarhizium isolates represents an important first step when addressing ecological as well as application-related questions involving these fungi. To this end, a species-specific multiplexed polymerase chain reaction (PCR) assay was developed for identification and discrimination among Metarhizium PARB complex species, based on unique sequence signature differences within the nuclear ribosomal intergenic spacer (rIGS) and nuclear intergenic spacer regions MzFG546 and MzIGS2. Species-specificities of the four primer pairs were assessed following a three-step approach including: (1) in silico verification of sequence signatures by BLASTN searches against publically available genome and amplicon sequence data, (2) corroboration of assay specificity and robustness by performing test PCR amplifications against a taxonomically curated reference strain collection of 68 Metarhizium strains representing 12 species, and (3) testing against a field collection of 19 unknown Metarhizium isolates from soil of a Swiss meadow. The specificity of these four primer pairs provide an efficient means to detect and discriminate PARB species in studies targeting ecological aspects of indigenous isolates, as well as efficacy, persistence and potential non-target effects of applied biocontrol strains.
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Affiliation(s)
| | - Andy Lutz
- Molecular Ecology, Agroscope, 8046 Zurich, Switzerland
| | - Francesca Dennert
- Molecular Ecology, Agroscope, 8046 Zurich, Switzerland; Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - Stephen A Rehner
- Systematic Mycology and Nematology Genomic Diversity and Biology Laboratory, USDA-ARS, Beltsville, MD 20705-2350, USA
| | - Ryan M Kepler
- Systematic Mycology and Nematology Genomic Diversity and Biology Laboratory, USDA-ARS, Beltsville, MD 20705-2350, USA
| | - Franco Widmer
- Molecular Ecology, Agroscope, 8046 Zurich, Switzerland
| | - Jürg Enkerli
- Molecular Ecology, Agroscope, 8046 Zurich, Switzerland.
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Pecchia S, Da Lio D. Development of a rapid PCR-Nucleic Acid Lateral Flow Immunoassay (PCR-NALFIA) based on rDNA IGS sequence analysis for the detection of Macrophomina phaseolina in soil. J Microbiol Methods 2018; 151:118-128. [PMID: 29959955 DOI: 10.1016/j.mimet.2018.06.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/22/2018] [Accepted: 06/26/2018] [Indexed: 11/30/2022]
Abstract
The 'Nucleic Acid Lateral Flow Immunoassay' (NALFIA) using a generic 'Lateral Flow Device' (LFD), combined with PCR employing labelled primers (PCR-NALFIA), enables to circumvent the use of electrophoresis, making the diagnostic procedure more rapid and easier. If the specific amplicon is present in the sample, a coloured band, with an intensity proportional to the amplicon concentration, will develop on the LFD strip in addition to the control band. Species-specific primers for M. phaseolina based on the rDNA intergenic spacer (IGS) were developed and their specificity was checked and confirmed using 20 isolates of M. phaseolina and other 16 non-target fungi. A DNA extraction protocol based on a bead-beating technique using silica beads, skimmed milk and PVP was also developed. The M. phaseolina specific primers MP102F/MP102R, 5' labelled with biotin and FITC respectively, were used in the PCR-NALFIA assay to identify the pathogen starting from mycelium or microsclerotia. Microsclerotia of M. phaseolina (1, 10, 100 and 200) were manipulated under a stereomicroscope and their DNA was extracted using microsclerotia alone or mixed with different types of soil. The resulting DNA, used for the PCR-NALFIA assay, provided positive results for all the samples tested. A semi-quantitative grey-scale reference card based on the PCR-NALFIA assay using intervals corresponding to microsclerotia soil number was developed. For this purpose, the normalized pixel grey volumes obtained after a densitometric analysis of the test line intensity generated by the LFD dipsticks were used.
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Affiliation(s)
- Susanna Pecchia
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy.
| | - Daniele Da Lio
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
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14
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Nishi O, Iiyama K, Yasunaga-Aoki C, Shimizu S. Species associations and distributions of soil entomopathogenic fungi Metarhizium spp. in Japan. Mycology 2017; 8:308-317. [PMID: 30123651 PMCID: PMC6059053 DOI: 10.1080/21501203.2017.1386244] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 09/26/2017] [Indexed: 11/14/2022] Open
Abstract
Metarhizium Sorokīn (Hypocreales: Clavicipitaceae) is a genus of facultative parasites of insects found in soils from various environments and is used for pest management. Understanding the habitat selection of Metarhizium spp. is critical to improve the efficacy and persistence of these fungi as microbial insecticides. This study sought to determine the habitat preferences of Metarhizium spp. in Japan. We identified 302 isolates of Metarhizium spp. as eight species by a combination of PCR–RFLP and phylogenetic analysis of DNA sequences. M. pingshaense was the predominant species in Japan and was most frequently isolated from both forest and agricultural environments. On the other hand, M. brunneum and M. pemphigi were comparatively restricted to forest environments. A similar species association was detected in a small area that was intensively investigated, where 7 species including 14 genotypes were isolated from soil. The results of this study have revealed different habitat preferences among Metarhizium spp. in Japan.
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Affiliation(s)
- Oumi Nishi
- Forest Entomology Division, Forestry and Forest Products Research Institute, Tsukuba City, Japan.,Research Fellowship for Young Scientists, Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo, Japan.,Laboratory of Insect Pathology and Microbial Control, Institute of Biological Control, Kyushu University, Higashi-ku, Fukuoka City, Japan
| | - Kazuhiro Iiyama
- Laboratory of Insect Pathology and Microbial Control, Institute of Biological Control, Kyushu University, Higashi-ku, Fukuoka City, Japan
| | - Chisa Yasunaga-Aoki
- Laboratory of Insect Pathology and Microbial Control, Institute of Biological Control, Kyushu University, Higashi-ku, Fukuoka City, Japan
| | - Susumu Shimizu
- Nishi-Nippon Junior College, Chuo-ku, Fukuoka City, Japan
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15
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Bischoff JF, Rehner SA, Humber RA. A multilocus phylogeny of the Metarhizium anisopliae lineage. Mycologia 2017; 101:512-30. [PMID: 19623931 DOI: 10.3852/07-202] [Citation(s) in RCA: 304] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Joseph F. Bischoff
- Animal and Plant Health Inspection Service, USDA, Beltsville, Maryland 20705-2350
| | - Stephen A. Rehner
- Systematic Mycology and Microbiology Laboratory, USDA-ARS, Beltsville, Maryland 20705-2350
| | - Richard A. Humber
- USDA-ARS, RW Holley Center for Agriculture and Health, Ithaca, New York 14853-2901
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16
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Yu JM, Cafarov IH, Babadoost M. Morphology, Molecular Identity, and Pathogenicity of Verticillium dahliae and V. longisporum Associated with Internally Discolored Horseradish Roots. PLANT DISEASE 2016; 100:749-757. [PMID: 30688617 DOI: 10.1094/pdis-08-15-0846-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
During 2008 to 2009, 255 isolates of Verticillium were obtained from internally discolored horseradish roots collected from California, Illinois, and Ontario. Twenty representative isolates were selected according to morphological features and geographic origin for further characterization. Based on the conidial size, the isolates were divided into two groups: Verticillium dahliae (4.4 ± 1.23 μm) and V. longisporum (7.8 ± 1.76 μm). Genetic diversity of the isolates was determined by sequence analysis of the internal transcribed spacer (ITS) and two mitochondrial genes (cytochrome oxidase subunit III [cox3] and NADH dehydrogenase subunit I [nad1]). Based on ITS analysis, Verticillium isolates were divided into two clades: V. dahliae and V. longisporum. However five isolates of V. longisporum (identified based on conidial size) were clustered with a V. dahliae clade, whereas the other five isolates formed a distinct V. longisporum clade. Combined analysis of the mitochondrial genes cox3 and nad1 showed that the two genetic clades of V. longisporum in ITS region analysis corresponded to the previously reported V. longisporum lineage A1/D3 and A1/D2. Pathogenicity tests revealed that all tested Verticillium isolates caused internal discoloration of horseradish roots, and there were no significant differences in either incidence or severity of root discoloration among the genetic groups.
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Affiliation(s)
- Jun Myoung Yu
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station 77843-2133
| | - Ibrahim H Cafarov
- Department of Plant Protection, Azerbaijan State Agricultural University, Ganja AZ 2000, Azerbaijan
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17
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Nishi O, Iiyama K, Yasunaga-Aoki C, Shimizu S. Phylogenetic status and pathogenicity of Metarhizium majus isolated from a fruit beetle larva in Japan. Mycol Prog 2015. [DOI: 10.1007/s11557-015-1082-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Papaioannou IA, Dimopoulou CD, Typas MA. "Cryptic" group-I introns in the nuclear SSU-rRNA gene of Verticillium dahliae. Curr Genet 2013; 60:135-48. [PMID: 24258678 DOI: 10.1007/s00294-013-0417-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 10/24/2013] [Accepted: 11/06/2013] [Indexed: 11/30/2022]
Abstract
Group-I introns are widespread--though irregularly distributed--in eukaryotic organisms, and they have been extensively used for discrimination and phylogenetic analyses. Within the Verticillium genus, which comprises important phytopathogenic fungi, a group-I intron was previously identified in the SSU-rRNA (18S) gene of only V. longisporum. In this work, we aimed at elucidating the SSU-located intron distribution in V. dahliae and other Verticillium species, and the assessment of heterogeneity regarding intron content among rDNA repeats of fungal strains. Using conserved PCR primers for the amplification of the SSU gene, a structurally similar novel intron (sub-group IC1) was detected in only a few V. dahliae isolates. However, when intron-specific primers were used for the screening of a diverse collection of Verticillium isolates that originally failed to produce intron-containing SSU amplicons, most were found to contain one or both intron types, at variable rDNA repeat numbers. This marked heterogeneity was confirmed with qRT-PCR by testing rDNA copy numbers (varying from 39 to 70 copies per haploid genome) and intron copy ratios in selected isolates. Our results demonstrate that (a) IC1 group-I introns are not specific to V. longisporum within the Verticillium genus, (b) V. dahliae isolates of vegetative compatibility groups (VCGs) 4A and 6, which bear the novel intron at most of their rDNA repeats, are closely related, and (c) there is considerable intra-genomic heterogeneity for the presence or absence of introns among the ribosomal repeats. These findings underline that distributions of introns in the highly heterogeneous repetitive rDNA complex should always be verified with sensitive methods to avoid misleading conclusions for the phylogeny of fungi and other organisms.
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Affiliation(s)
- Ioannis A Papaioannou
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece
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Papaioannou IA, Dimopoulou CD, Typas MA. Structural and phylogenetic analysis of the rDNA intergenic spacer region of Verticillium dahliae. FEMS Microbiol Lett 2013; 347:23-32. [PMID: 23841495 DOI: 10.1111/1574-6968.12215] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 07/08/2013] [Accepted: 07/08/2013] [Indexed: 12/31/2022] Open
Abstract
The nuclear ribosomal intergenic spacer (IGS) region was structurally analyzed and exploited for molecular discrimination and phylogenetic analysis of vegetative compatibility groups (VCGs) of Verticillium dahliae. A structural study of 201 available IGS sequences of the fungus was performed, and four classes of ubiquitous repetitive elements, organized in higher-order repetitive structures or composite blocks, were detected in a variable IGS subregion. This subregion was amplified from an international collection of 59 V. dahliae isolates covering all VCGs, together with nine representative V. albo-atrum and V. longisporum isolates, and sequenced. Structural and phylogenetic analyses of the sequences of this polymorphic IGS subregion were consistently informative and allowed the identification of two main lineages in V. dahliae, that is, clade I including VCGs 1A, 1B, 2A, 4B, and 3 and clade II containing VCGs 2B, 4A, and 6. Analysis of IGS sequences proved a highly suitable molecular tool for (a) rapid interspecific differentiation, (b) intraspecific discrimination among VCGs of V. dahliae, facilitating high-throughput VCG confirmation and prediction/profiling, and (c) phylogenetic analysis within and among V. dahliae VCGs.
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Affiliation(s)
- Ioannis A Papaioannou
- Department of Genetics & Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
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20
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González D. Identification, molecular characterization, and evolution of group I introns at the expansion segment D11 of 28S rDNA in Rhizoctonia species. Fungal Biol 2013; 117:623-37. [PMID: 24012302 DOI: 10.1016/j.funbio.2013.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 06/03/2013] [Accepted: 06/19/2013] [Indexed: 10/26/2022]
Abstract
The nuclear ribosomal DNA of Rhizoctonia species is polymorphic in terms of the nucleotide composition and length. Insertions of 349-410 nucleotides in length with characteristics of group I introns were detected at a single insertion point at the expansion segment D11 of 28S rDNA in 12 out of 64 isolates. Eleven corresponded to Rhizoctonia solani (teleomorph: Thanatephorous) and one (AG-Q) to Rhizoctonia spp. (teleomorph: Ceratobasidium). Sequence data showed that all but AG-Q contained conserved DNA catalytic core regions (P, Q, R, and S) essential for selfsplicing. The predicted secondary structure revealed that base-paired helices corresponded to subgroup IC1. Isolates from same anastomosis group and even subgroups within R. solani were variable with regard to possession of introns. Phylogenetic analyses indicated that introns were vertically transmitted. Unfortunately, sequence data from the conserved region from all 64 isolates were not useful for delimiting species. Analyses with IC1 introns at same insertion point, of both Ascomycota and Basidiomycota indicated the possibility of horizontal transfer at this site. The present study uncovered new questions on evolutionary pattern of change of these introns within Rhizoctonia species.
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Affiliation(s)
- Dolores González
- Instituto de Ecología, A.C., Red de Biodiversidad y Sistemática, Carretera Antigua a Coatepec No. 351, El Haya, Xalapa 91070, Veracruz, Mexico.
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21
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Mirete S, Patiño B, Jurado M, Vázquez C, González-Jaén MT. Structural variation and dynamics of the nuclear ribosomal intergenic spacer region in key members of the Gibberella fujikuroi species complex. Genome 2013; 56:205-13. [PMID: 23706073 DOI: 10.1139/gen-2013-0008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The intergenic spacer (IGS) region of the ribosomal DNA was cloned and sequenced in eight species within the Gibberella fujikuroi species complex with anamorphs in the genus Fusarium, a group that includes the most relevant toxigenic species. DNA sequence analyses revealed two categories of repeated elements: long repeats and short repeats of 125 and 8 bp, respectively. Long repeats were present in two copies and were conserved in all the species analyzed, whereas different numbers of short repeat elements were observed, leading to species-specific IGS sequences with different length. In Fusarium subglutinans and Fusarium nygamai, these differences seemed to be the result of duplication and deletion events. Here, we propose a model based on unequal crossing over that can explain these processes. The partial IGS sequence of 22 Fusarium proliferatum isolates was also obtained to study variation at the intraspecific level. The results revealed no differences in terms of number or pattern of repeated elements and detected frequent gene conversion events. These results suggest that the homogenization observed at the intraspecific level might not be achieved primarily by unequal crossing-over events but rather by processes associated with recombination such as gene conversion events.
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Affiliation(s)
- Salvador Mirete
- Department of Molecular Evolution, Centro de Astrobiología, CSIC-INTA, Torrejón de Ardoz, 28850 Madrid, Spain.
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Krimitzas A, Pyrri I, Kouvelis VN, Kapsanaki-Gotsi E, Typas MA. A phylogenetic analysis of Greek isolates of Aspergillus species based on morphology and nuclear and mitochondrial gene sequences. BIOMED RESEARCH INTERNATIONAL 2013; 2013:260395. [PMID: 23762830 PMCID: PMC3665174 DOI: 10.1155/2013/260395] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 04/09/2013] [Indexed: 12/13/2022]
Abstract
Aspergillus species originating from Greece were examined by morphological and molecular criteria to explore the diversity of this genus. The phylogenetic relationships of these species were determined using sequences from the ITS and IGS region of the nuclear rRNA gene complex, two nuclear genes ( β -tubulin (benA) and RNA polymerase II second largest subunit (rpb2)) and two mitochondrial genes (small rRNA subunit (rns) and cytochrome oxidase subunit I (cox1)) and, where available, related sequences from databases. The morphological characters of the anamorphs and teleomorphs, and the single gene phylogenetic trees, differentiated and placed the species examined in the well-supported sections of Aenei, Aspergillus, Bispori, Candidi, Circumdati, Clavati, Cremei, Flavi, Flavipedes, Fumigati, Nidulantes, Nigri, Restricti, Terrei, Usti, and Zonati, with few uncertainties. The combined use of the three commonly employed nuclear genes (benA, rpb2, and ITS), the IGS region, and two less often used mitochondrial gene sequences (rns and cox1) as a single unit resolved several taxonomic ambiguities. A phylogenetic tree was inferred using Neighbour-Joining, Maximum Parsimony, and Bayesian methods. The strains examined formed seven well-supported clades within the genus Aspergillus. Altogether, the concatenated nuclear and mitochondrial sequences offer additional tools for an improved understanding of phylogenetic relationships within this genus.
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Affiliation(s)
- Antonios Krimitzas
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistemiopolis, 15701 Athens, Greece
| | - Ioanna Pyrri
- Department of Ecology and Systematics, Faculty of Biology, National and Kapodistrian University of Athens, Panepistemiopolis, 15784 Athens, Greece
| | - Vassili N. Kouvelis
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistemiopolis, 15701 Athens, Greece
| | - Evangelia Kapsanaki-Gotsi
- Department of Ecology and Systematics, Faculty of Biology, National and Kapodistrian University of Athens, Panepistemiopolis, 15784 Athens, Greece
| | - Milton A. Typas
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistemiopolis, 15701 Athens, Greece
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A PCR-based tool for cultivation-independent detection and quantification of Metarhizium clade 1. J Invertebr Pathol 2011; 108:106-14. [DOI: 10.1016/j.jip.2011.07.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 07/22/2011] [Accepted: 07/23/2011] [Indexed: 11/19/2022]
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24
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Complete Sructure of Nuclear rDNA of the Obligate Plant Parasite Plasmodiophora brassicae: Intraspecific Polymorphisms in the Exon and Group I Intron of the Large Subunit rDNA. Protist 2011; 162:423-34. [DOI: 10.1016/j.protis.2011.02.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Accepted: 02/25/2011] [Indexed: 11/20/2022]
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25
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Zhao G, Li J, Chen F, Zou F, Yang J, Sugiyama H, Xu M, Lin Q, Lin R, Zhu X. Variability in intron sequences of housekeeping and antigen-coding genes among Schistosoma japonicum isolates in mainland China. Parasitol Int 2011; 60:170-4. [DOI: 10.1016/j.parint.2011.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Revised: 01/11/2011] [Accepted: 01/26/2011] [Indexed: 10/18/2022]
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26
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Garrido-Jurado I, Márquez M, Ortiz-Urquiza A, Santiago-Álvarez C, Iturriaga EA, Quesada-Moraga E, Monte E, Hermosa R. Genetic analyses place most Spanish isolates of Beauveria bassiana in a molecular group with word-wide distribution. BMC Microbiol 2011; 11:84. [PMID: 21521527 PMCID: PMC3111375 DOI: 10.1186/1471-2180-11-84] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Accepted: 04/26/2011] [Indexed: 11/17/2022] Open
Abstract
Background The entomopathogenic anamorphic fungus Beauveria bassiana is currently used as a biocontrol agent (BCA) of insects. Fifty-seven Beauveria bassiana isolates -53 from Spain- were characterized, integrating group I intron insertion patterns at the 3'-end of the nuclear large subunit ribosomal gene (LSU rDNA) and elongation factor 1-alpha (EF1-α) phylogenetic information, in order to assess the genetic structure and diversity of this Spanish collection of B. bassiana. Results Group I intron genotype analysis was based on the four highly conserved insertion sites of the LSU (Ec2653, Ec2449, Ec2066, Ec1921). Of the 16 possible combinations/genotypes, only four were detected, two of which were predominant, containing 44 and 9 members out of 57 isolates, respectively. Interestingly, the members of the latter two genotypes showed unique differences in their growth temperatures. In follow, EF1-α phylogeny served to classify most of the strains in the B. bassiana s.s. (sensu stricto) group and separate them into 5 molecular subgroups, all of which contained a group I intron belonging to the IC1 subtype at the Ec1921 position. A number of parameters such as thermal growth or origin (host, geographic location and climatic conditions) were also examined but in general no association could be found. Conclusion Most Spanish B. bassiana isolates (77.2%) are grouped into a major phylogenetic subgroup with word-wide distribution. However, high phylogenetic diversity was also detected among Spanish isolates from close geographic zones with low climatic variation. In general, no correlation was observed between the molecular distribution and geographic origin or climatic characteristics where the Spanish B. bassiana isolates were sampled.
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Affiliation(s)
- Inmaculada Garrido-Jurado
- Centro Hispano-Luso de Investigaciones Agrarias (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Río Duero 12, Campus de Villamayor, 37185 Salamanca, Spain
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Li Y, Cai SH. Sensitive and rapid detection of the insect pathogenic fungus Metarhizium anisopliae var. anisopliae by loop-mediated isothermal amplification. Curr Microbiol 2011; 62:1400-4. [PMID: 21274713 DOI: 10.1007/s00284-011-9872-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2011] [Accepted: 01/11/2011] [Indexed: 10/18/2022]
Abstract
A set of six specific primers was designed by targeting intergenic spacer region (IGS) sequences. With Bst DNA polymerase, the products could be clearly amplified for 60 min at 62 °C in a simple water bath. The sensitivity of the loop-mediated isothermal amplification (LAMP) for detecting Metarhizium anisopliae var. anisopliae was about 0.01 pg fungal DNA per reaction (equivalent to 27 conidia). LAMP products could be judged with agar gel or naked eye after addition of SYBR Green I. There were no cross reactions with other fungal isolates indicating high specificity of the LAMP. The LAMP could detect the presence of M. anisopliae var. anisopliae from soil. The detection limits for M. anisopliae var. anisopliae of LAMP reaction was 50 conidia per reaction in soil.
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Affiliation(s)
- Ya Li
- Agricultural College, Guangdong Ocean University, Zhanjiang, China
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O'Donnell K, Gueidan C, Sink S, Johnston PR, Crous PW, Glenn A, Riley R, Zitomer NC, Colyer P, Waalwijk C, Lee TVD, Moretti A, Kang S, Kim HS, Geiser DM, Juba JH, Baayen RP, Cromey MG, Bithell S, Sutton DA, Skovgaard K, Ploetz R, Corby Kistler H, Elliott M, Davis M, Sarver BAJ. A two-locus DNA sequence database for typing plant and human pathogens within the Fusarium oxysporum species complex. Fungal Genet Biol 2009; 46:936-48. [PMID: 19715767 DOI: 10.1016/j.fgb.2009.08.006] [Citation(s) in RCA: 170] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Revised: 08/14/2009] [Accepted: 08/18/2009] [Indexed: 12/20/2022]
Abstract
We constructed a two-locus database, comprising partial translation elongation factor (EF-1alpha) gene sequences and nearly full-length sequences of the nuclear ribosomal intergenic spacer region (IGS rDNA) for 850 isolates spanning the phylogenetic breadth of the Fusarium oxysporum species complex (FOSC). Of the 850 isolates typed, 101 EF-1alpha, 203 IGS rDNA, and 256 two-locus sequence types (STs) were differentiated. Analysis of the combined dataset suggests that two-thirds of the STs might be associated with a single host plant. This analysis also revealed that the 26 STs associated with human mycoses were genetically diverse, including several which appear to be nosocomial in origin. A congruence analysis, comparing partial EF-1alpha and IGS rDNA bootstrap consensus, identified a significant number of conflicting relationships dispersed throughout the bipartitions, suggesting that some of the IGS rDNA sequences may be non-orthologous. We also evaluated enniatin, fumonisin and moniliformin mycotoxin production in vitro within a phylogenetic framework.
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Affiliation(s)
- Kerry O'Donnell
- Microbial Genomics Research Unit, Agricultural Research Service, US Department of Agriculture, Peoria, IL 61604, USA.
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Variability of the Mitochondrial SSU rDNA of Nomuraea Species and Other Entomopathogenic Fungi from Hypocreales. Mycopathologia 2008; 167:145-54. [DOI: 10.1007/s11046-008-9157-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2008] [Accepted: 09/10/2008] [Indexed: 11/25/2022]
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Kouvelis VN, Sialakouma A, Typas MA. Mitochondrial gene sequences alone or combined with ITS region sequences provide firm molecular criteria for the classification of Lecanicillium species. ACTA ACUST UNITED AC 2008; 112:829-44. [PMID: 18501578 DOI: 10.1016/j.mycres.2008.01.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Revised: 01/11/2008] [Accepted: 01/24/2008] [Indexed: 11/18/2022]
Abstract
The recent revision of Verticillium sect. Prostrata led to the introduction of the genus Lecanicillium, which comprises the majority of the entomopathogenic strains. Sixty-five strains previously classified as Verticillium lecanii or Verticillium sp. from different geographical regions and hosts were examined and their phylogenetic relationships were determined using sequences from three mitochondrial (mt) genes [the small rRNA subunit (rns), the NADH dehydrogenase subunits 1 (nad1) and 3 (nad3)] and the ITS region. In general, single gene phylogenetic trees differentiated and placed the strains examined in well-supported (by BS analysis) groups of L. lecanii, L. longisporum, L. muscarium, and L. nodulosum, although in some cases a few uncertainties still remained. nad1 was the most informative single gene in phylogenetic analyses and was also found to contain group I introns with putative open reading frames (ORFs) encoding for GIY-YIG endonucleases. The combined use of mt gene sequences resolved taxonomic uncertainties arisen from ITS analysis and, alone or in combination with ITS sequences, helped in placing uncharacterised Verticillium lecanii and Verticillium sp. firmly into Lecanicillium species. Combined gene data from all the mt genes and all the mt genes and the ITS region together, were very similar. Furthermore, a relaxed correlation with host specificity -- at least for Homoptera -- was indicated for the rns and the combined mt gene sequences. Thus, the usefulness of mt gene sequences as a convenient molecular tool in phylogenetic studies of entomopathogenic fungi was demonstrated.
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Affiliation(s)
- Vassili N Kouvelis
- Department of Genetics and Biotechnology, Faculty of Biology, University of Athens, Panepistemiopolis, Athens, Greece
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Kouvelis VN, Ghikas DV, Edgington S, Typas MA, Moore D. Molecular characterization of isolates of Beauveria bassiana obtained from overwintering and summer populations of Sunn Pest (Eurygaster integriceps). Lett Appl Microbiol 2008; 46:414-20. [PMID: 18290810 DOI: 10.1111/j.1472-765x.2008.02331.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIM To examine whether isolates of the entomopathogenic fungus Beauveria bassiana are more closely associated to their summer hosts compared with overwintering hosts, with recently developed molecular tools based on mitochondrial regions. METHODS AND RESULTS Primers for the traditional ITS1-5.8S-ITS2 region and two mitochondrial intergenic regions, namely, nad3-atp9 and atp6-rns, were used. All amplified products were sequenced, aligned and Neighbour-Joining (NJ), parsimony and Bayesian phylogenetic inference analyses were performed. The isolates examined were grouped with very good support into three distinct groups, two of them showed geographical correlation, but no clear association to their host. CONCLUSIONS The mitochondrial intergenic regions used were more informative than the nuclear ITS1-5.8S-ITS2 sequences. The sequence variability observed, that allowed the phylogenetic placement of the isolates into distinct groups, depended on the geographical origin of the isolates and can be exploited for designing group-specific and isolate-specific primers for their genetic fingerprinting. No clear associations with summer Sunn Pest populations were observed. SIGNIFICANCE AND IMPACT OF THE STUDY Studies on the genetic variability of biocontrol agents like B. bassiana are indispensable for the development of molecular tools for their future monitoring.
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Affiliation(s)
- V N Kouvelis
- Department of Genetics and Biotechnology, Faculty of Biology, University of Athens, Athens, Greece
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Yanaka-Schäfer FY, Dall'Onder LP, Panichi MC, Mendes RG, Fagundes NJ, Bandinelli JB, Bogo MR. Sequence analysis of the rDNA intergenic spacer of Metarhizium strains isolated in Brazil. Genet Mol Biol 2008. [DOI: 10.1590/s1415-47572008000100020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
| | | | | | | | - Nelson J.R. Fagundes
- Pontifícia Universidade Católica do Rio Grande do Sul, Brazil; Universidade Federal do Rio Grande do Sul, Brazil
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Chilvers MI, du Toit LJ, Akamatsu H, Peever TL. A Real-Time, Quantitative PCR Seed Assay for Botrytis spp. that Cause Neck Rot of Onion. PLANT DISEASE 2007; 91:599-608. [PMID: 30780707 DOI: 10.1094/pdis-91-5-0599] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A real-time fluorescent polymerase chain reaction (PCR) assay was developed using SYBR Green chemistry to quantify the Botrytis spp. associated with onion (Allium cepa) seed that are also able to induce neck rot of onion bulbs, i.e., B. aclada, B. allii, and B. byssoidea. The nuclear ribosomal intergenic spacer (IGS) regions of target and nontarget Botrytis spp. were sequenced, aligned, and used to design a primer pair specific to B. aclada, B. allii, and B. byssoidea. Primers and amplification parameters were optimized to avoid amplifying the related species B. cinerea, B. porri, and B. squamosa, as well as Sclerotinia sclerotiorum and isolates of 15 other fungal species commonly found associated with onion seed. The primers reliably detected 10 fg of genomic DNA per PCR reaction extracted from pure cultures of B. aclada and B. allii. Conventional assays of surface-disinfested and nondisinfested seed on an agar medium were used to determine the incidence of neck rot Botrytis spp. associated with each of 23 commercial onion seed lots, and the real-time PCR assay was used to determine the quantity of DNA of neck rot Botrytis spp. in each seed lot. A linear relationship could not be found between the incidence of seed infected with the neck rot Botrytis spp. using the conventional agar seed assays and the quantity of DNA of the neck rot Botrytis spp. detected by the real-time PCR assay. However, the real-time PCR assay appeared to be more sensitive than the conventional agar assay, allowing detection of neck rot Botrytis spp. in 5 of the 23 seed lots that tested negative using the conventional agar seed assay.
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Affiliation(s)
| | | | | | - Tobin L Peever
- Associate Professor, Washington State University, Department of Plant Pathology, Pullman 99164-6430
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Márquez M, Iturriaga EA, Quesada-Moraga E, Santiago-Álvarez C, Monte E, Hermosa R. Detection of potentially valuable polymorphisms in four group I intron insertion sites at the 3'-end of the LSU rDNA genes in biocontrol isolates of Metarhizium anisopliae. BMC Microbiol 2006; 6:77. [PMID: 16978412 PMCID: PMC1578565 DOI: 10.1186/1471-2180-6-77] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2006] [Accepted: 09/15/2006] [Indexed: 11/10/2022] Open
Abstract
Background The entomopathogenic anamorphic fungus Metarhizum anisopliae is currently used as a biocontrol agent (BCA) of insects. In the present work, we analyzed the sequence data obtained from group I introns in the large subunit (LSU) of rDNA genes with a view to determining the genetic diversity present in an autochthonous collection of twenty-six M. anisopliae isolates selected as BCAs. Results DNA fragments corresponding to the 3'-end of the nuclear LSU rDNA genes of 26 M. anisopliae isolates were amplified by PCR. The amplicon sizes ranged from 0.8 to 3.4-kb. Four intron insertion sites, according to Escherichia coli J01695 numbering, were detected- Ec1921, Ec2066, Ec2449 and Ec2563- after sequencing and analysis of the PCR products. The presence/absence of introns allowed the 26 isolates to be distributed into seven genotypes. Nine of the isolates tested showed no introns, 4 had only one, 3 two, and 10 displayed three introns. The most frequent insertion sites were Ec1921 and Ec2449. Of the 26 isolates, 11 showed insertions at Ec2563 and a 1754-bp sequence was observed in ten of them. The most-parsimonious (MP) tree obtained from parsimony analysis of the introns revealed a main set containing four-groups that corresponded to the four insertion sites. Conclusion Four insertion sites of group I introns in the LSU rDNA genes allowed the establishment of seven genotypes among the twenty-six biocontrol isolates of M. anisopliae. Intron insertions at the Ec2563 site were observed for first time in this species.
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Affiliation(s)
- Marcela Márquez
- Centro Hispano-Luso de Investigaciones Agrarias (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental lab 208, Plaza Doctores de la Reina s/n, 37007 Salamanca, Spain
- Area de Genética. Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental lab 324, Plaza Doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Enrique A Iturriaga
- Area de Genética. Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental lab 324, Plaza Doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Enrique Quesada-Moraga
- Departamento de Ciencias y Recursos Agrícolas y Forestales, Universidad de Córdoba, Edificio C4 Celestino Mutis, Campus Rabanales, 14071 Córdoba, Spain
| | - Cándido Santiago-Álvarez
- Departamento de Ciencias y Recursos Agrícolas y Forestales, Universidad de Córdoba, Edificio C4 Celestino Mutis, Campus Rabanales, 14071 Córdoba, Spain
| | - Enrique Monte
- Centro Hispano-Luso de Investigaciones Agrarias (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental lab 208, Plaza Doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Rosa Hermosa
- Centro Hispano-Luso de Investigaciones Agrarias (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental lab 208, Plaza Doctores de la Reina s/n, 37007 Salamanca, Spain
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Pantou MP, Kouvelis VN, Typas MA. The complete mitochondrial genome of the vascular wilt fungus Verticillium dahliae: a novel gene order for Verticillium and a diagnostic tool for species identification. Curr Genet 2006; 50:125-36. [PMID: 16733756 DOI: 10.1007/s00294-006-0079-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2006] [Revised: 04/18/2006] [Accepted: 04/20/2006] [Indexed: 10/24/2022]
Abstract
The complete sequence (27,184 bp) of the mitochondrial (mt) genome of the phytopathogenic fungus Verticillium dahliae has been determined. It contains 14 protein-coding genes related to oxidative phosphorylation, two rRNA genes and a set of 25 tRNA genes. A single intron, that harbors an intronic ORF coding for a putative ribosomal protein (rps), is located within the large rRNA gene (rnl). Gene order comparisons of V. dahliae mtDNA and complete mt genomes of Pezizomycotina revealed four units of synteny for Sordariomycetes, namely rnl-trn ((11-12))-nad2-nad3, nad4L-nad5-cob-cox1, nad1-nad4-atp8-atp6 and rns-trn ((1-5))-cox3-trn ((1-5))-nad6-trn ((2-5)). These four units, in different combinations, merged to single continuous unit in the orders of Hypocreales and Sordariales. V. dahliae (Phyllachorales) and all members of the genus showed a unique feature which is the translocation of the nad1-nad4-atp8-atp6-rns-cox3-nad6 region in between genes nad3 and atp9 of the Hypocreales mtDNA gene order. Analysis of mt intergenic sequences of Verticillium species permitted the design of a species-specific primer allowing the discrimination of V. longisporum against V. dahliae and V. albo-atrum. By considering the protein-coding gene sequences as one unit, a phylogenetic comparison with representatives of Ascomycota complete mtDNA was performed.
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Affiliation(s)
- Malena P Pantou
- Department of Genetics and Biotechnology, Faculty of Biology, University of Athens, Panepistemiopolis, Greece
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36
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Ghikas DV, Kouvelis VN, Typas MA. The complete mitochondrial genome of the entomopathogenic fungus Metarhizium anisopliae var. anisopliae: gene order and trn gene clusters reveal a common evolutionary course for all Sordariomycetes, while intergenic regions show variation. Arch Microbiol 2006; 185:393-401. [PMID: 16552580 DOI: 10.1007/s00203-006-0104-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2005] [Revised: 02/08/2006] [Accepted: 02/27/2006] [Indexed: 11/24/2022]
Abstract
The mitochondrial genome (mtDNA) of the entomopathogenic fungus Metarhizium anisopliae var. anisopliae, with a total size of 24,673 bp, was one of the smallest known mtDNAs of Pezizomycotina. It contained the 14 typical genes coding for proteins related to oxidative phosphorylation, the two rRNA genes, a single intron that harbored an intronic ORF coding for a putative ribosomal protein (rps) within the large rRNA gene (rnl), and a set of 24 tRNA genes which recognized codons for all amino acids, except proline and valine. Gene order comparison with all known mtDNAs of Sordariomycetes illustrated a highly conserved genome organization for all the protein- and rRNA-coding genes, as well as three clusters of tRNA genes. By considering all mitochondrial essential protein-coding genes as one unit a phylogenetic study of these small genomes strongly supported the common evolutionary course of Sordariomycetes (100% bootstrap support) and highlighted the advantages of analyzing small genomes (mtDNA) over single genes. In addition, comparative analysis of three intergenic regions demonstrated sequence variability that can be exploited for intra- and inter-specific identification of Metarhizium.
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Affiliation(s)
- Dimitri V Ghikas
- Department of Genetics and Biotechnology, Faculty of Biology, University of Athens, Panepistemiopolis, 15701 Athens, Greece
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37
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Pantou MP, Strunnikova OK, Shakhnazarova VY, Vishnevskaya NA, Papalouka VG, Typas MA. Molecular and immunochemical phylogeny of Verticillium species. ACTA ACUST UNITED AC 2005; 109:889-902. [PMID: 16175791 DOI: 10.1017/s0953756205003345] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
21 strains with all typical morphological characteristics of eight Verticillium species (Phyllachorales) were studied in this work, together with representatives from four Hypocreales species (11 strains), that were previously classified as members of the genus. The PCR products from two nuclear genes, i.e. the ITS1-5.8S-ITS2 region and RNA polymerase II largest subunit gene (rpb1), together with four mitochondrial genes, i.e. the small ribosomal rRNA subunit (rns), the two NADH dehydrogenase subunit genes (nad1 and nad3), and the cytochrome oxidase subunit III gene (cox3) were sequenced and analyzed. Similarly, antibodies raised against one strain of each of the species examined (V. nubilum and V. theobromae excluded) were used against the proteins of all other strains. The number and relative area of precipitates formed after crossed electrophoreses served to estimate the degree of immunochemical relatedness. Combined molecular and immunochemical data clarified the phylogenetic relationships of all true Verticillium species and provided a convincing insight into the evolutionary relation of the sect. Nigrescentia with members of the sect. Verticillium and sect. Prostrata that until recently were included in Verticillium.
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Affiliation(s)
- Malena P Pantou
- Department of Genetics and Biotechnology, Faculty of Biology, University of Athens, Panepistemiopolis, Athens TK15701, Greece
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Suarez MB, Walsh K, Boonham N, O'Neill T, Pearson S, Barker I. Development of real-time PCR (TaqMan) assays for the detection and quantification of Botrytis cinerea in planta. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2005; 43:890-9. [PMID: 16198585 DOI: 10.1016/j.plaphy.2005.07.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2005] [Revised: 06/20/2005] [Accepted: 07/13/2005] [Indexed: 05/04/2023]
Abstract
Real-time PCR assays based on TaqMan chemistry have been developed for the detection and quantification of Botrytis cinerea, suitable for a wide range of different host plant species. Assays were designed to the beta-tubulin gene, the intergenic spacer (IGS) region of the nuclear ribosomal DNA and also to a previously published, species-specific sequence characterised amplified region (SCAR) marker; the assays were compared to a published method based on SYBR Green I technology. The assays designed to the IGS region and SCAR marker proved to be highly specific for B. cinerea but assays designed to the beta-tubulin gene and the previously published assay designed to the cutinase-A gene both cross-react with B. fabae. The assay designed to the IGS region was the most sensitive and was able to reliably detect and quantify as little as 20 fg of B. cinerea DNA. The method incorporates the detection of a gene from the plant host to compensate for variations in extraction efficiency and size of sample tested. The assays designed were used to follow the progression of infection of B. cinerea in plant material inoculated with spores to the point of symptom induction. They should be ideally suited to investigating infection processes in-planta and could be used to investigate aspects of infection/plant pathogenesis, by B. cinerea and are particularly suited to the detection and quantification of the pathogen prior to the development of symptoms.
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Affiliation(s)
- M Belen Suarez
- Central Science Laboratory, Sand Hutton, York, YO41 1LZ, United Kingdom
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Hong SG, Liu D, Pryor BM. Restriction mapping of the IGS region in Alternaria spp. reveals variable and conserved domains. ACTA ACUST UNITED AC 2005; 109:87-95. [PMID: 15736866 DOI: 10.1017/s0953756204001388] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Accurate identification of Alternaria spp. is dependent upon the production of diagnostic morphological characters under defined cultural conditions and the proper assessment of character variation. This process is often compromised by variation in laboratory facilities and technical expertise. To assist taxon identification and phylogenetic studies, restriction site information from the intergenic spacer (IGS) region of nuclear rDNA was evaluated. Restriction maps were constructed from 15 species of Alternaria and Stemphylium botryosum (telemorph Pleospora herbarum) for 11 restriction enzymes using a new method for restriction mapping based on differential priming of IGS amplicons. IGS fragment size varied among species from 2.2-3.9 kb. Based upon restriction site homology among closely-related and more distantly related species, the IGS region could be divided into conserved and variable domains. The conserved domain was approximately 0.75 kb in size and was located at the 3' end of the IGS region. Restriction site homology within this region was very high, especially among closely related taxa. The remainder of the region comprised the variable domain, which encompassed considerable differences in size and restriction sites among taxa. The presence or absence of restriction sites among taxa was analyzed using methods of neighbor-joining. Phylogenetic relationships based on this method were concordant with those previously resolved based upon other methods and other genomic regions.
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Affiliation(s)
- Soon Gyu Hong
- Division of Plant Pathology and Microbiology, Department of Plant Sciences, College of Agriculture and Life Sciences, University of Arizona, Forbes 204, P.O. Box 210036, Tucson, Arizona 85721, USA
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Roberts DW, St Leger RJ. Metarhizium spp., cosmopolitan insect-pathogenic fungi: mycological aspects. ADVANCES IN APPLIED MICROBIOLOGY 2004; 54:1-70. [PMID: 15251275 DOI: 10.1016/s0065-2164(04)54001-7] [Citation(s) in RCA: 247] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Donald W Roberts
- Department of Biology, Utah State University, Logan, Utah 84322-5305, USA
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Hughes WOH, Thomsen L, Eilenberg J, Boomsma JJ. Diversity of entomopathogenic fungi near leaf-cutting ant nests in a neotropical forest, with particular reference to Metarhizium anisopliae var. anisopliae. J Invertebr Pathol 2004; 85:46-53. [PMID: 14992860 DOI: 10.1016/j.jip.2003.12.005] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2003] [Accepted: 12/12/2003] [Indexed: 11/24/2022]
Abstract
We investigated the prevalence of entomopathogenic fungi associated with leaf-cutting ant colonies in a small area of tropical forest in Panama. There was a high abundance of Metarhizium anisopliae var. anisopliae near the colonies. Beauveria bassiana was also detected in the soil, Aspergillus flavus in dump material, and six Camponotus atriceps ants were found infected with Cordyceps sp. Based on a partial sequence of the IGS region, almost all of the M. anisopliae var. anisopliae isolates fell within one of the three main clades of M. anisopliae var. anisopliae, but with there still being considerable diversity within this clade. The vast majority of leaf-cutting ants collected were not infected by any entomopathogenic fungi. While leaf-cutting ants at this site must, therefore, regularly come into contact with a diversity of entomopathogenic fungi, they do not appear to be normally infected by them.
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Affiliation(s)
- W O H Hughes
- Department of Population Ecology, Zoological Institute, University of Copenhagen, Universitetsparken 15, Copenhagen 2100, Denmark.
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42
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Wang C, Li Z, Typas MA, Butt TM. Nuclear large subunit rDNA group I intron distribution in a population of Beauveria bassiana strains: phylogenetic implications. ACTA ACUST UNITED AC 2004; 107:1189-200. [PMID: 14635767 DOI: 10.1017/s0953756203008505] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Four group I introns, designated Bb1, Bb2, Bb3 and Bb4, were identified in the entomopathogenic hyphomycete Beauveria bassiana. Sequence analyses of these introns verified that they were invariably inserted at specific target sequences after conserved positions Ec2563, Ec2449, Ec2066 and Ec1921 of the large nuclear subunit (LSU) rDNA 3'-end. Secondary structure modelling confirmed that Bb1 and Bb3 belonged to subgroup IE while Bb2 and Bb4 belonged to subgroup IC1. Intron presence, distribution and size-variation were studied in a population of 125 B. bassiana strains using site-specific primers. Nucleotide sequences and secondary structures were compared and showed considerable variations usually at P1, P6 and P9 helices, but concomitantly, high homology between members of the same site-specific group. Intron distribution studies revealed that few (7.2%) strains were intron-less, most contained one (28%), two (48%) or three (16%) introns, while only one strain contained all four introns. Bb4-like introns (Ec1921) were the most abundant (86.4%), whereas the other three introns were evenly represented (ca 30%) in the B. bassiana population. Analysis of intron genotype distribution indicated a tenuous dependence upon geographic origin or insect host species. Phylogenetic analysis of all B. bassiana LSU introns and their close relatives from other entomopathogenic fungi showed a strong correlation between specific insertion sites and intron subgroups, fully supported by corresponding clades, suggesting common ancestry of the site specific LSU introns.
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Affiliation(s)
- Chengshu Wang
- School of Biological Sciences, University of Wales Swansea, SA2 8PP, UK
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Gibb EA, Hausner G. A group I intron-like sequence in the nuclear small ribosomal subunit gene of the ophiostomatoid fungus Gondwanamyces proteae. ACTA ACUST UNITED AC 2003; 107:1442-50. [PMID: 15000245 DOI: 10.1017/s0953756203008773] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
During a phylogenetic study of ophiostomatoid fungi, a group I intron-like sequence was noted in the SSU rDNA gene of Gondwanamyces proteae. Secondary structure and sequence characteristics assigned the intron to the I E class. We then examined 27 related Group I-like sequences deposited in GenBank, and as a result 15 additional and previously uncategorized I E rDNA introns were identified. This study, with other recent publications, suggests that the I E class might represent a major family of group I introns that are located within the nuclear SSU and, to some extent LSU, genes in fungi.
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Affiliation(s)
- Ewan A Gibb
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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