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Spatial and temporal differences in the community structure of endophytic fungi in the carnivorous plant Pinguicula moranensis (Lentibulariaceae). FUNGAL ECOL 2021. [DOI: 10.1016/j.funeco.2021.101087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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2
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Rokni N, Akbar Sadati SA, Safaie N, Ebrahimi MA, Samimifar M. Assessment of genetic relatedness among commercial and wild strains of Agaricus bisporus using repetitive extragenic palindromic sequences and polymerase chain reaction. MYCOSCIENCE 2019. [DOI: 10.1016/j.myc.2019.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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3
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Babu BK, Saxena AK, Srivastava AK, Arora DK. Identification and detection of Macrophomina phaseolina by using species-specific oligonucleotide primers and probe. Mycologia 2017. [DOI: 10.1080/15572536.2007.11832511] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | | | | | - Dilip K. Arora
- National Bureau of Agriculturally Important Microorganisms(NBAIM), Mau Nath Bhanjan, Post bag no.-6, Uttar Pradesh-275101, India
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Dos Santos TT, de Souza Leite T, de Queiroz CB, de Araújo EF, Pereira OL, de Queiroz MV. High genetic variability in endophytic fungi from the genus Diaporthe isolated from common bean (Phaseolus vulgaris L.) in Brazil. J Appl Microbiol 2016; 120:388-401. [PMID: 26541097 DOI: 10.1111/jam.12985] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 08/26/2015] [Accepted: 09/07/2015] [Indexed: 01/11/2023]
Abstract
AIMS The goals of the present study were to identify, to analyse the phylogenetic relations and to evaluate the genetic variability in Diaporthe endophytic isolates from common bean. METHODS AND RESULTS Diaporthe sp., D. infecunda and D. phaseolorum strains were identified using multilocus phylogeny (rDNA ITS region; EF1-α, β-tubulin, and calmodulin genes). IRAP (Inter-Retrotransposon Amplified Polymorphism) and REMAP (Retrotransposon-Microsatellite Amplified Polymorphism) molecular markers reveal the existence of high genetic variability, especially among D. infecunda isolates. CONCLUSIONS It was concluded that the multilocus phylogenetic approach was more effective than individual analysis of ITS sequences, in identifying the isolates to species level, and that IRAP and REMAP markers can be used for studying the genetic variability in the genus Diaporthe particularly at the intraspecific level. SIGNIFICANCE AND IMPACT OF THE STUDY The combined use of molecular tools such as multilocus phylogenetic approach and molecular markers, as performed in this study, is the best way to distinguish endophytic strains of Diaporthe isolated from common bean (Phaseolus vulgaris L.).
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Affiliation(s)
- T T Dos Santos
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Brazil.,Instituto de Ciências e Tecnologia das Águas, Universidade Federal do Oeste do Pará, Santarém, Brazil
| | - T de Souza Leite
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Brazil
| | - C B de Queiroz
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Brazil
| | - E F de Araújo
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Brazil
| | - O L Pereira
- Department of Phytopathology, Universidade Federal de Viçosa, Viçosa, Brazil
| | - M V de Queiroz
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Brazil
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Mishra RK, Pandey BK, Pathak N, Zeeshan M. BOX-PCR- and ERIC-PCR-based genotyping and phylogenetic correlation among Fusarium oxysporum isolates associated with wilt disease in Psidium guajava L. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2015. [DOI: 10.1016/j.bcab.2014.09.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Xu Z, Ali Z, Hou X, Li H, Yi J, Abbasi P. Characterization of Chinese eggplant isolates of the fungal pathogen Verticillium dahliae from different geographic origins. GENETICS AND MOLECULAR RESEARCH 2013; 12:183-95. [DOI: 10.4238/2013.january.24.11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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8
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Letourneau A, Seena S, Marvanová L, Bärlocher F. Potential use of barcoding to identify aquatic hyphomycetes. FUNGAL DIVERS 2010. [DOI: 10.1007/s13225-009-0006-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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9
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Pazoutová S. Genetic variation of Phoma sorghina isolates from Southern Africa and Texas. Folia Microbiol (Praha) 2009; 54:217-29. [PMID: 19649739 DOI: 10.1007/s12223-009-0035-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Revised: 03/30/2009] [Indexed: 10/20/2022]
Abstract
Genetic variability of Phoma sorghina, a ubiquitous facultative phytopathogen, was investigated on 41 isolates cultivated from surface-sterilized sorghum grains originating from South Africa and Texas; pearl millet isolates from Namibia were also included. Most of the isolates from Texas produced intense red pigments, especially on Czapek-Dox agar plates. Many African isolates formed conspicuous dark radial substrate hyphae with intercalated chlamydospores on oatmeal plates. Conidial dimensions and shape were very variable (mean lengths 4.5-5.7 microm). Haplotypes were defined based on 53 markers from banding patterns obtained with rep-PCR (primers: M13core, ERIC IR). The shared geographic origin was partially reflected in the clades of the haplotype phylogram. The values of G(ST) were intermediate; 16-37 % of the variation was found between the populations. Nm values of gene flow were 0.84-1.15. Average gene diversity H(E) was moderate (0.256). Sequences of ITS-rDNA were obtained from 21 isolates. Allele 1 was found in 9 isolates scattered throughout the clades, allele 2 occurred in 6 isolates (5 of them from the same clade), alleles 3 and 4 were shared by two isolates each and two isolates were unique. Alleles 1 and 2 were also found among highly related sequences from GenBank. All shared an 8-bp deletion near the 5' end of ITS2 that was not found in any other Phoma/Didymella species and which may be a typical marker for P. sorghina. Among related species, members of legume-associated Ascochyta/Didymella complex, Epicoccum spp., D. applanata and P. glomerata were found.
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Affiliation(s)
- S Pazoutová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Prague, Czech Republic.
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10
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Production of extracellular enzymes by different isolates of Pochonia chlamydosporia. ACTA ACUST UNITED AC 2009; 113:867-76. [DOI: 10.1016/j.mycres.2009.04.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Revised: 03/22/2009] [Accepted: 04/21/2009] [Indexed: 11/22/2022]
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Manzanilla-López RH, Clark IM, Atkins SD, Hirsch PR, Kerry BR. Rapid and reliable DNA extraction and PCR fingerprinting methods to discriminate multiple biotypes of the nematophagous fungus Pochonia chlamydosporia isolated from plant rhizospheres. Lett Appl Microbiol 2008; 48:71-6. [PMID: 19018961 DOI: 10.1111/j.1472-765x.2008.02489.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS To develop a simple, rapid, reliable protocol producing consistent polymerase chain reaction (PCR) fingerprints of Pochonia chlamydosporia var. chlamydosporia biotypes for analysing different fungal isolates during co-infection of plants and nematodes. METHODS AND RESULTS DNA extracted from different P. chlamydosporia biotypes was fingerprinted using enterobacterial repetitive intragenic consensus (ERIC)-PCR. Four extraction methods (rapid alkaline lysis; microLYSIS-PLUS; DNeasy; FTA cards) gave consistent results within each protocol but these varied between protocols. Reproducible fingerprints were obtained only if DNA was extracted from fresh fungal cultures that were free of agar. Some DNA degradation occurred during storage, except with the FTA cards, used with this fungus for the first time, which provide a method for long-term archiving. Rapid alkaline lysis and ERIC-PCR identified fungal isolates from root and nematode egg surfaces when plants were treated with different combinations of fungal biotypes; the dominant biotype isolated from the rhizosphere was not always the most abundant in eggs. CONCLUSIONS ERIC-PCR fingerprinting can reliably detect and identify different P. chlamydosporia biotypes. It is important to use fresh mycelium and the same DNA isolation method throughout each study. SIGNIFICANCE AND IMPACT OF THE STUDY This evaluation of methods to assess genetic diversity and identify specific P. chlamydosporia biotypes is relevant to other mycelial fungi.
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Affiliation(s)
- R H Manzanilla-López
- Nematode Interactions Unit, Department of Plant Pathology and Microbiology, Rothamsted Research, Harpenden, Hertfordshire, UK.
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Siqueira JF, Rôças IN. Exploiting Molecular Methods to Explore Endodontic Infections: Part 1—Current Molecular Technologies for Microbiological Diagnosis. J Endod 2005; 31:411-23. [PMID: 15917679 DOI: 10.1097/01.don.0000157989.44949.26] [Citation(s) in RCA: 149] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Endodontic infections have been traditionally studied by culture-dependent methods. However, as with other areas of clinical microbiology, culture-based investigations are plagued by significant problems, including the probable involvement of viable but uncultivable micro-organisms with disease causation and inaccurate microbial identification. Innumerous molecular technologies have been used for microbiological diagnosis in clinical microbiology, but only recently some of these techniques have been applied in endodontic microbiology research. This paper intended to review the main molecular methods that have been used or have the potential to be used in the study of endodontic infections. Moreover, advantages and limitations of current molecular techniques when compared to conventional methods for microbial identification are also discussed.
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Affiliation(s)
- J F Siqueira
- Department of Endodontics, Estácio de Sá University, Rio de Janeiro, Rio de Janeiro, Brazil.
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Ciancio A, Loffredo A, Paradies F, Turturo C, Sialer MF. Detection of Meloidogyne incognita and Pochonia chlamydosporia by fluorogenic molecular probes. ACTA ACUST UNITED AC 2005. [DOI: 10.1111/j.1365-2338.2005.00794.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Tymon AM, Pell JK. ISSR, ERIC and RAPD techniques to detect genetic diversity in the aphid pathogen Pandora neoaphidis. ACTA ACUST UNITED AC 2005; 109:285-93. [PMID: 15912945 DOI: 10.1017/s0953756204001807] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The entomopathogenic fungus Pandora neoaphidis is an important natural enemy of aphids. ISSR, ERIC (Enterobacterial Repetitive Intergenic Consensus) and RAPD PCR-based DNA fingerprint analyses were undertaken to study intra-specific variation amongst 30 isolates of P. neoaphidis worldwide, together with six closely related species of Entomophthorales. All methods yielded scorable binary characters, and distance matrices were constructed from both individual and combined data sets. Neighbour-joining was used to construct consensus phylogenetic trees which showed that although P. neoaphidis isolates were highly polymorphic they separated into a monophyletic group compared with the other Entomophthorales tested. Three distinct subclades were found, with UK isolates occupying two of these. No specific correlation with aphid host species was established for any of the isolates apart from those in one cluster which contained isolates obtained from nettle aphid, Microlophium carnosum. ERIC, ISSR and RAPD analysis allowed the rapid genetic characterisation and differentiation of isolates with the generation of potential isolate- and cluster specific-diagnostic DNA markers.
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Affiliation(s)
- Anna M Tymon
- Plant and Invertebrate Ecology Division, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
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Tymon AM, Shah PA, Pell JK. PCR-based molecular discrimination of Pandora neoaphidis isolates from related entomopathogenic fungi and development of species-specific diagnostic primers. ACTA ACUST UNITED AC 2004; 108:419-33. [PMID: 15209282 DOI: 10.1017/s0953756204009694] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Studies were performed to assess the genetic variation amongst isolates of the aphid-pathogenic fungus Pandora neoaphidis (syn. Erynia neoaphidis). 37 isolates were examined, from a range of pest and non-pest aphid species, as well as 21 from eight other entomophthoralean species. Universal primers were used to amplify the ITS rDNA regions and all of the species tested produced discrete ITS groups, with the exception of Conidiobolus spp. Neighbour-joining analysis of the ITS2 regions from P. neoaphidis, P. kondoiensis and Zoophthora radicans demonstrated that these three species formed distinct groups with sequence identities of 58-82% between the groups. An ITS size of ca 1,100 bp was diagnostic for P. neoaphidis, while ca 1,450 bp was characteristic of P. kondoiensis. ITS-RFLP analysis failed to yield intraspecific polymorphisms in any of the P. neoaphidis isolates screened, although it was useful in distinguishing between different entomophthoralean species. Some intraspecific variation in the ITS region was detected in a number of isolates of Z. radicans and Conidiobolus spp. We propose that two isolates previously identified as P. neoaphidis based on conidia morphology, are actually P. kondoiensis based on molecular studies. Sequencing analysis of the complete ITS region from P. neoaphidis and P. kondoiensis allowed species-specific primers to be developed for P. neoaphidis and P. kondoiensis. These were used to screen aphids infected in laboratory bioassays and from field-collected samples, without prior isolation of the fungus. The primers are useful tools for quantifying the epizootiology of P. neoaphidis in aphid populations, as well as assessing competitive interactions between these two species.
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MESH Headings
- Animals
- Aphids/microbiology
- Base Sequence
- DNA Primers
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Entomophthorales/genetics
- Entomophthorales/isolation & purification
- Image Processing, Computer-Assisted
- Molecular Sequence Data
- Phylogeny
- Polymerase Chain Reaction
- Polymorphism, Restriction Fragment Length
- RNA/chemistry
- RNA/genetics
- RNA, Mitochondrial
- RNA, Ribosomal, 5.8S/chemistry
- RNA, Ribosomal, 5.8S/genetics
- Sequence Alignment
- Sequence Analysis, DNA
- Species Specificity
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Affiliation(s)
- Anna M Tymon
- Plant and Invertebrate Ecology Division, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK.
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Mauchline TH, Kerry BR, Hirsch PR. The biocontrol fungus Pochonia chlamydosporia shows nematode host preference at the infraspecific level. ACTA ACUST UNITED AC 2004; 108:161-9. [PMID: 15119353 DOI: 10.1017/s095375620300889x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A RAPD-PCR assay was developed and used to test for competitive variability in growth of the nematode biological control fungus Pochonia chlamydosporia. Saprophytic competence in soil with or without tomato plants was examined in three isolates of the fungus: RES 280 (J), originally isolated from potato cyst nematode (PCN) cysts; RES 200 (I) and RES 279 (S), both originally isolated from root knot nematode (RKN) eggs. Viable counts taken at 70 d indicated that I was the best saprophyte followed by S, with J the poorest. RAPD-PCR analysis of colonies from mixed treatments revealed that there was a cumulative effect of adding isolates to the system. This suggested that the isolates did not interact and that they may occupy separate niches in soil and the rhizosphere. To investigate parasitic ability, soils were seeded with two isolates of the fungus: J and S, singly or in combination. Tomato or potato plants were grown in these soils: free of nematodes, or inoculated with PCN or RKN, and incubated for 77 d. The abundance of the PCN isolate J in PCN cysts was significantly greater than that of the RKN isolate S but in RKN egg masses, S was significantly more abundant than J. RAPD-PCR analysis of colonies from mixed treatments confirmed that J was more abundant than S in PCN cysts whereas the converse was observed on RKN egg masses. This substantiates the phenomenon of nematode host preference at the infraspecific level of P. chlamydosporia and highlights its relevance for biological control of plant parasitic nematodes.
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Stadler M, Tichy HV, Katsiou E, Hellwig V. Chemotaxonomy of Pochonia and other conidial fungi with Verticillium-like anamorphs. Mycol Prog 2003. [DOI: 10.1007/s11557-006-0048-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Atkins SD, Hidalgo-Diaz L, Clark IM, Morton CO, de Oca NM, Gray PA, Kerry BR. Approaches for monitoring the release of Pochonia chlamydosporia var. catenulata, a biocontrol agent of root-knot nematodes. MYCOLOGICAL RESEARCH 2003; 107:206-12. [PMID: 12747332 DOI: 10.1017/s095375620300724x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Pochonia chlamydosporia var. catenulata is a potential biocontrol agent against root-knot nematodes. Diagnosis of isolates has relied on morphological identification, and is both time-consuming and difficult. beta-tubulin primers have been developed for the identification of this fungus that were specific enough to distinguish between varieties of the fungus within the same species. Separate primers have been developed for the specific detection of P. chlamydosporia var. catenulata based on ITS sequences, which were able to detect the fungus in soil from various sites in Cuba where the biocontrol agent had been added. When the PCR diagnosis was combined with serial dilution of soil samples on selective medium, colonies were rapidly identified. The fungus was still present, albeit at low densities, in soils inoculated five years previously. The development of a baiting method allowed quick in situ screening of the isolates' ability to infect nematode eggs, and when combined with PCR diagnosis both varieties of the fungus could be detected in infected eggs. RFLP analysis of ITS sequences from P. chlamydosporia provided an extra level of discrimination between isolates.
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Affiliation(s)
- Simon D Atkins
- Nematode Interaction Unit, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK.
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Atkins SD, Hidalgo-Diaz L, Kalisz H, Mauchline TH, Hirsch PR, Kerry BR. Development of a new management strategy for the control of root-knot nematodes (Meloidogyne spp) in organic vegetable production. PEST MANAGEMENT SCIENCE 2003; 59:183-189. [PMID: 12587872 DOI: 10.1002/ps.603] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The nematophagous fungus, Pochonia chlamydosporia (Goddard) Zare & Gams, has been investigated as a potential biological control agent for use in integrated pest management strategies for Meloidogyne incognita (Kof & White) Chitwood in vegetable crops. The release of the fungus as a biological control agent requires a diagnostic method to monitor its spread in the environment and to gain knowledge of its ecology. Only molecular methods are sufficiently discriminating to enable the detection of specific isolates of fungi in soil. A method to extract DNA from soil was developed to increase the efficacy of PCR-based diagnostic tests that use specific primers. A selected isolate of P chlamydosporia var catenulata was applied at densities similar to those that occur naturally in nematode-suppressive soils. The fungus significantly reduced nematode infestations in soil following a tomato crop, in a strategy that combined the use of the fungus with crop rotation. The survival of the fungus in soil was also examined in controlled conditions in which it remained in soil in densities significantly greater than its original application rate for at least 5 months. Hence, it seems that populations of this fungus may be built up in soil and have significant effects on the regulation of root-knot nematode populations.
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Affiliation(s)
- Simon D Atkins
- Nematode Interactions Unit, IACR-Rothamsted, Harpenden, Herts AL5 2JQ, UK
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Morton CO, Mauchline TH, Kerry BR, Hirsch PR. PCR-based DNA fingerprinting indicates host-related genetic variation in the nematophagous fungus Pochonia chlamydosporia. MYCOLOGICAL RESEARCH 2003; 107:198-205. [PMID: 12747331 DOI: 10.1017/s0953756203007251] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The mitosporic fungus Pochonia chlamydosporia is a potential biocontrol agent for cyst (Heterodera spp. and Globodera spp.) and root knot (Meloidogyne spp.) nematodes, which are important agricultural plant pests. 54 isolates from diverse geographical regions and several nematode hosts were used in this study. Genetic variation was examined using enterobacterial repetitive intergenic consensus (ERIC) primed PCR and sequences from the internal transcribed spacer (ITS) rRNA region. ERIC PCR yielded 35 scorable binary characters from all the fungi tested and cluster analysis of the data showed that isolates from cyst nematodes were more genetically variable than those from root knot nematodes. The ITS regions were highly conserved, the only significant difference being an extra thymidine in isolates from Meloidogyne spp. Assays with nematode eggs indicated that isolates differ in their ability to infect different nematode genera. The results indicate host related variation in P. chlamydosporia. This finding has significant implications for the application of P. chlamydosporia as a biocontrol agent.
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Affiliation(s)
- C Oliver Morton
- Nematode Interactions Unit, IACR-Rothamsted, Harpenden, Hertfordshire AL5 2JQ, UK.
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de Arruda MCC, Ferreira MASV, Miller RNG, Resende MLV, Felipe MSS. Nuclear and mitochondrial rDNA variability in Crinipellis perniciosa from different geographic origins and hosts. MYCOLOGICAL RESEARCH 2003; 107:25-37. [PMID: 12735241 DOI: 10.1017/s0953756202006895] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Genetic variability in Crinipellis perniciosa, the causal organism of witches' broom disease in Theobroma cacao, was determined in strains originating from T. cacao and other susceptible host species Heteropterys acutifolia and Solanum lycocarpum in Brazil, in order to clarify host specificity and geographical variability. RFLP analysis of the ribosomal DNA ITS regions (rDNA ITS), and the mitochondrial DNA small subunit ribosomal DNA gene (mtDNA SSU rDNA) did not reveal any genetic variability in 120 tested strains, possibly serving only as species level markers. Genetic variability was observed in the ribosomal DNA IGS spacer region, in terms of IGS size, RFLPs and sequence data. Phylogenetic analyses (using CLUSTAL W, PHYLIP and TREEVIEW) indicated considerable differences between C. perniciosa strains from T. cacao and those from H. acutifolia (85-86%) and S. lycocarpum (95-96%). Sequence differences also indicated that C. perniciosa from T. cacao in Bahia is less variable (98%) when compared to the pathogen on T. cacao in Amazonas (97-98%), perhaps reflecting a recent introduction to T. cacao in Bahia.
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Morton CO, Hirsch PR, Peberdy JP, Kerry BR. Cloning of and genetic variation in protease VCP1 from the nematophagous fungus Pochonia chlamydosporia. MYCOLOGICAL RESEARCH 2003; 107:38-46. [PMID: 12735242 DOI: 10.1017/s0953756202007050] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The fungus Pochonia chlamydosporia is a biocontrol agent with commercial potential for root knot and cyst nematodes. It produces an alkaline serine protease, VCP1, during infection of nematode eggs. The gene encoding VCP1 was sequenced and the sequences of cDNAs from six isolates from different nematode hosts were compared. The gene encoding VCP1 was similar to PR1 from Metarhizium anisopliae with similar regulatory elements. Comparison of translated cDNA sequences revealed two amino acid polymorphisms at positions 65 and 99, indicating a difference between isolates from cyst and root nematodes. The positions and nature of the polymorphisms indicated that the two forms of VCP1 might have different properties and this was tested with five chromogenic polypeptide substrates. Enzyme assays revealed the two forms differed in their abilities to utilise Succ-Ala-Ala-Pro-Phe-pNa and Succ-Ala-Val-Pro-Phe-pNa, suggesting different amino acid affinities at the S3 binding region. This indicates host related genetic variation in VCP1 between isolates of P. chlamydosporia isolated from different nematode hosts, which might contribute to host preference. Such differences may be important in future exploitation of P. chlamydosporia as a nematode biocontrol agent.
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Affiliation(s)
- C Oliver Morton
- Nematode Interactions Unit, IACR-Rothamsted, Harpenden, Herts AL5 2JQ, UK.
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Muthumeenakshi S, Goldstein AL, Stewart A, Whipps JM. Molecular studies on intraspecific diversity and phylogenetic position of Coniothyrium minitans. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s0953-7562(08)61968-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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McDonald JG, Wong E, White GP. Differentiation of Tilletia Species by rep-PCR Genomic Fingerprinting. PLANT DISEASE 2000; 84:1121-1125. [PMID: 30831905 DOI: 10.1094/pdis.2000.84.10.1121] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The potential of repetitive-sequence-based polymerase chain reaction (rep-PCR) fingerprinting of fungal genomic DNA as a rapid and simple alternative to random amplified polymorphic DNA (RAPD) analysis in the study of phylogenetic relationships, and also as a diagnostic method, was investigated with species of Tilletia. DNA primers (BOX, ERIC, and REP) corresponding to conserved repetitive element motifs, originally described in prokaryotes, were used to generate genomic fingerprints of T. indica, T. walkeri, T. controversa, T. laevis, T. tritici, T. goloskokovii, T. barclayana, and members of the T. fusca complex. Computer-assisted analysis of the database of combined fingerprints clearly distinguished each taxon and indicated phylo-genetic relationships consistent with previously reported RAPD analyses. There were three main clusters with isolates showing 35 to 40% similarity. Group 1 included T. indica and T. walkeri; group 2 included members of the T. fusca complex, as well as T. controversa, T. laevis, T. tritici, and T. goloskokovii; and group 3 included only T. barclayana. If, as is likely, the conserved repetitive element motifs on which this technique is based are widespread or universal in fungal species, rep-PCR shows strong potential, not only as a simple generic taxonomic tool, but also as a diagnostic method.
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Affiliation(s)
- J G McDonald
- Centre for Plant Quarantine Pests, Canadian Food Inspection Agency, 3851 Fallowfield Rd., Nepean, Ontario, K2H 8P9
| | - E Wong
- Centre for Plant Quarantine Pests, Canadian Food Inspection Agency, 3851 Fallowfield Rd., Nepean, Ontario, K2H 8P9
| | - G P White
- Centre for Plant Quarantine Pests, Canadian Food Inspection Agency, 3851 Fallowfield Rd., Nepean, Ontario, K2H 8P9
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Kerry BR. Rhizosphere Interactions and the Exploitation of Microbial Agents for the Biological Control of Plant-Parasitic Nematodes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2000; 38:423-441. [PMID: 11701849 DOI: 10.1146/annurev.phyto.38.1.423] [Citation(s) in RCA: 133] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A range of specialist and generalist microorganisms in the rhizosphere attacks plant-parasitic nematodes. Plants have a profound effect on the impact of this microflora on the regulation of nematode populations by influencing both the dynamics of the nematode host and the structure and dynamics of the community of antagonists and parasites in the rhizosphere. In general, those organisms that have a saprophytic phase in their life cycle are most affected by environmental conditions in the rhizosphere, but effects on obligate parasites have also been recorded. Although nematodes influence the colonization of roots by pathogenic and beneficial microorganisms, little is known of such interactions with the natural enemies of nematodes in the rhizosphere. As nematodes influence the quantity and quality of root exudates, they are likely to affect the physiology of those microorganisms in the rhizosphere; such changes may be used as signals for nematode antagonists and parasites. Successful biological control strategies will depend on a thorough understanding of these interactions at the population, organismal, and molecular scale.
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Affiliation(s)
- B R Kerry
- Entomology and Nematology Department, IACR-Rothamsted, Harpenden, Hertfordshire, AL5 2JQ, United Kingdom; e-mail:
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Segregation and recombination of PCR based markers in sexual progeny of Phaeosphaeria species. ACTA ACUST UNITED AC 2000. [DOI: 10.1017/s095375620000246x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Detection of the nematophagous fungus Verticillium chlamydosporium in nematode-infested plant roots using PCR. ACTA ACUST UNITED AC 2000. [DOI: 10.1017/s0953756299001483] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Genetic relationships of pathogenic Typhula species assessed by RAPD, ITS-RFLP and ITS sequencing. ACTA ACUST UNITED AC 2000. [DOI: 10.1017/s0953756299001033] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Toda T, Hyakumachi M, Arora DK. Genetic relatedness among and within different Rhizoctonia solani anastomosis groups as assessed by RAPD, ERIC and REP-PCR. Microbiol Res 1999. [DOI: 10.1016/s0944-5013(99)80022-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Pecchia S, Mercatelli E, Vannacci G. PCR amplification and characterization of the intergenic spacer region of the ribosomal DNA in Pyrenophora graminea. FEMS Microbiol Lett 1998; 166:21-7. [PMID: 9741081 DOI: 10.1111/j.1574-6968.1998.tb13178.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Successful amplification of the whole intergenic spacer region of the nuclear ribosomal repeat (IGS) in Pyrenophora graminea was obtained with a PCR-based assay. Single amplification products showed length differences. Depending on the length of the IGS-PCR product, ca. 3.8 or 4.4 kb, two groups of isolates could be identified. The RFLP patterns of isolates obtained with the 6-base cutting enzymes Apal, BglII, DraI, EcoRV, HindIII and SacI were similar within each group and different between the two groups. Restriction patterns of IGS-PCR products digested with the 4-base cutting enzyme AluI were polymorphic among isolates in spite of their IGS-PCR product length. In order to characterize the long and short IGS-PCR products the restriction map is shown. The long product shows an additional HindIII site and a BglII site that is lacking in the short product. However, the latter shows a SacI site that is not present in the long IGS-PCR product. Therefore, the described PCR-RFLP analysis of the IGS appears to be a useful tool to resolve genetic variation between P. graminea isolates.
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Affiliation(s)
- S Pecchia
- Dipartimento di Coltivazione e Difesa delle Specie Legnose, Università degli Studi di Pisa, Italy.
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