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Huang CH, Chang MT, Huang L. Species identification of Wickerhamomyces anomalus and related taxa using β-tubulin (β-tub) DNA barcode marker. Yeast 2012; 29:531-5. [PMID: 23172674 DOI: 10.1002/yea.2933] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 10/08/2012] [Indexed: 01/14/2023] Open
Abstract
Wickerhamomyces anomalus is used in food and feed processing, although the species has been reported as an opportunistic human pathogen, predominantly in neonates. Neither phenotypic nor the most frequently applied genotypic marker (D1/D2 LSU ribosomal DNA) provide sufficient resolution for accurate identification of this yeast. In this study, the β-tubulin gene was used for species identification by direct DNA sequencing and as marker in a species-specific PCR assay. The results showed that all examined W. anomalus strains were clearly distinguished from the closely related species by comparative sequence analysis of the β-tubulin gene. In addition, the species-specific primers were also developed based on the β-tubulin gene, which was employed for polymerase chain reaction with the template DNA of Wickerhamomyces strains. A single 218 bp species-specific band was found only in W. anomalus. Our data indicate that the phylogenetic relationships between these strains are easily resolved by sequencing of the β-tubulin gene and combined with species-specific PCR assay.
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Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Centre, Food Industry Research and Development Institute, Hsinchu, Taiwan, Republic of China.
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Malkus A, Reszka E, Chang CJ, Arseniuk E, Chang PFL, Ueng PP. Sequence diversity of beta-tubulin (tubA) gene in Phaeosphaeria nodorum and P. avenaria. FEMS Microbiol Lett 2005; 249:49-56. [PMID: 15972251 DOI: 10.1016/j.femsle.2005.05.049] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2004] [Revised: 04/12/2005] [Accepted: 05/28/2005] [Indexed: 11/20/2022] Open
Abstract
Full-length coding sequences of the beta-tubulin gene (tubA) were PCR-amplified and sequenced from 42 Phaeosphaeria isolates, including 16 P. nodorum and 23 P. avenaria species from cereals, two Polish isolates from rye (Secale cereale L.), and one isolate from dallis grass (Paspalum dilatatum Poir). A tubA gene of size 1556bp was identified in wheat- and barley-biotype P. nodorum (PN-w and PN-b), P. avenaria f. sp. avenaria (Paa), homothallic P. avenaria f. sp. triticea (P.a.t.) (Pat1) and the P.a.t. isolate (Pat3) from the State of Washington. The tubA gene length polymorphisms were detected in two P.a.t. isolates (Pat2) from foxtail barley (Hordeum jubatum L.), one from dallis grass and two Polish isolates from rye. These size differences were due to the variation of intron lengths among these three Phaeosphaeria species. All Phaeosphaeria isolates have identical 1344bp exons that can be translated into a 447 amino acid beta-tubulin. Like glyceraldehyde-3-phosphate dehydrogenase, the beta-tubulin amino acid sequence was identical in all Phaeosphaeria species used in this study, with the exception of the two Pat2 isolates. Six amino acid differences were evident in the beta-tubulin of these Pat2 isolates.
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Affiliation(s)
- Arkadiusz Malkus
- Department of Plant Pathology, Plant Breeding and Acclimatization Institute, Radzikow, Poland
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Peres NAR, Souza NL, Peever TL, Timmer LW. Benomyl Sensitivity of Isolates of Colletotrichum acutatum and C. gloeosporioides from Citrus. PLANT DISEASE 2004; 88:125-130. [PMID: 30812417 DOI: 10.1094/pdis.2004.88.2.125] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Postbloom fruit drop (PFD) of citrus, caused by Colletotrichum acutatum, produces orange-brown lesions on petals and results in premature fruit drop and the retention of calyces. C. gloeosporioides is common in groves and causes postharvest anthracnose on fruit. Both diseases are controlled effectively by the fungicide benomyl in research fields and commercial orchards. Highly sensitive and resistant isolates of C. gloeosporioides were found, whereas all isolates of C. acutatum tested were moderately resistant. In preliminary studies conducted in vitro with three isolates of each, mycelial growth of sensitive isolates of C. gloeosporioides was inhibited completely by benomyl (Benlate 50 WP) at 1.0 μg/ml, whereas resistant isolates grew well at 10 μg/ml. Growth of all isolates of C. acutatum was inhibited by about 55% at 0.1 μg/ml and by 80% at 1.0 μg/ml. Spore germination of C. acutatum was inhibited more at 0.1 μg/ml than at 1.0 μg/ml or higher concentrations. In all, 20 isolates of C. acutatum from 17 groves and 20 isolates of C. gloeosporioides from 7 groves were collected from locations with different histories of benomyl usage in São Paulo, Brazil, and Florida, United States. Benomyl at 1.0 μg/ml completely inhibited growth of 133 isolates of C. gloeosporioides, with the exception of 7 isolates that were highly resistant to the fungicide, whereas all isolates of C. acutatum were only partially inhibited at 0.1 and 1.0 μg/ml. Analysis of variance indicated that the sensitivity of the isolates of C. acutatum was not affected by benomyl usage or grove of origin, and country of origin had only minor effects. No highly resistant or sensitive isolate of C. acutatum was recovered. Partial sequencing of the β-tubulin gene did not reveal nucleotide substitutions in codons 198 or 200 in C. acutatum that usually are associated with benomyl resistance in other fungi.
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Affiliation(s)
| | - N L Souza
- Professor, Universidade Estadual Paulista, FCA, Botucatu, SP, 18603-970, Brazil
| | - T L Peever
- Assistant Professor, Washington State University, Pullman 99164-6430
| | - L W Timmer
- Professor, University of Florida, Citrus Research and Education Center, Lake Alfred 33850
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Abstract
Fungi (kingdom Mycota) and oomycetes (kingdom Stramenopila, phylum Oomycota) are crucially important in the nutrient cycles of the world. Their interactions with plants sometimes benefit and sometimes act to the detriment of humans. Many fungi establish ecologically vital mutualisms, such as in mycorrhizal fungi that enhance nutrient acquisition, and endophytes that combat insects and other herbivores. Other fungi and many oomycetes are plant pathogens that devastate natural and agricultural populations of plant species. Studies of fungal and oomycete evolution were extraordinarily difficult until the advent of molecular phylogenetics. Over the past decade, researchers applying these new tools to fungi and oomycetes have made astounding new discoveries, among which is the potential for interspecific hybridization. Consequences of hybridization among pathogens include adaptation to new niches such as new host species, and increased or decreased virulence. Hybrid mutualists may also be better adapted to new hosts and can provide greater or more diverse benefits to host plants.
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Affiliation(s)
- C L Schardl
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky 40546-0091, USA.
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Talhinhas P, Sreenivasaprasad S, Neves-Martins J, Oliveira H. Genetic and Morphological Characterization of Colletotrichum acutatum Causing Anthracnose of Lupins. PHYTOPATHOLOGY 2002; 92:986-996. [PMID: 18944024 DOI: 10.1094/phyto.2002.92.9.986] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
ABSTRACT Anthracnose, caused by Colletotrichum sp., is a serious problem of lupins (Lupinus spp.) worldwide. Morphological characters and molecular markers were used to characterize 43 Colletotrichum isolates from lupins, 8 isolates from other hosts, and 18 reference isolates representing related Colletotrichum spp., to assess the pathogen diversity and resolve its taxonomy. All lupin Colletotrichum isolates tested positive with C. acutatum-specific polymerase chain reaction (PCR) and did not test positive with C. gloeosporioides-specific PCR. Spore shape and colony diameter as well as insensitivity to benomyl grouped the lupin anthracnose isolates closer to C. acutatum than to C. gloeosporioides. Analysis of internal transcribed spacer (ITS) sequences of 57 Colletotrichum isolates grouped all lupin isolates with C. acutatum and distinct from C. gloeosporioides. Further, tub2 and his4 sequences revealed groups concordant with ITS, reducing the excessive dependence on the latter. Arbitrarily primed-PCR and amplified fragment length polymorphism analyses revealed intraspecific subgroups, but neither was useful to decipher species level relationships. ITS, tub2, and his4 results strongly support designating lupin anthracnose pathogen as C. acutatum or its subspecies. Most Colletotrichum isolates from lupins from worldwide locations are genetically homogeneous and form a distinct subgroup within C. acutatum. Present results also underline the potential of the C. acutatum-specific PCR for routine pathogen diagnosis.
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Characterisation of a β-tubulin gene from Melampsora lini and comparison of fungal β-tubulin genes. ACTA ACUST UNITED AC 2001. [DOI: 10.1017/s0953756201004245] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Perfect SE, Hughes HB, O'Connell RJ, Green JR. Colletotrichum: A model genus for studies on pathology and fungal-plant interactions. Fungal Genet Biol 1999; 27:186-98. [PMID: 10441444 DOI: 10.1006/fgbi.1999.1143] [Citation(s) in RCA: 196] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Species of Colletotrichum use diverse strategies for invading host tissue, ranging from intracellular hemibiotrophy to subcuticular intramural necrotrophy. In addition, these pathogens develop a series of specialized infection structures, including germ tubes, appressoria, intracellular hyphae, and secondary necrotrophic hyphae. Colletotrichum species provide excellent models for studying the molecular basis of infection structure differentiation and fungal-plant interactions. In this review we cover the various stages of the infection processes of Colletotrichum species, including spore adhesion and germination, germ tube and appressorium differentiation and functions, and biotrophic and necrotrophic development. The contribution of molecular, biochemical, and immunological approaches to the identification of genes and proteins relevant to each stage of fungal development will be considered. As well as reviewing results from several groups, we also describe our own work on the hemibiotrophic pathogen, C. lindemuthianum.
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Affiliation(s)
- S E Perfect
- School of Biological Sciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
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Yan K, Dickman MB. Isolation of a beta-tubulin gene from Fusarium moniliforme that confers cold-sensitive benomyl resistance. Appl Environ Microbiol 1996; 62:3053-6. [PMID: 8702300 PMCID: PMC168094 DOI: 10.1128/aem.62.8.3053-3056.1996] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
A beta-tubulin gene from a UV-irradiated benomyl-resistant mutant of Fusarium moniliforme was isolated, cloned, and sequenced. The gene encodes a 446-amino-acid polypeptide with homology to other fungal beta-tubulins. RNA blot analysis showed expression of the gene during vegetative growth and conidial germination but no expression during conidiation. A point mutation, which likely confers benomyl resistance, has been identified in the cloned gene; this mutation results in a single amino acid substitution of asparagine for tyrosine at position 50. Expression of benomyl resistance in the mutant was also cold sensitive. Sexual crosses betweeen the mutant and a wild-type strain indicated cosegregation of benomyl resistance and cold sensitivity.
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Affiliation(s)
- K Yan
- Department of Plant Pathology, University of Nebraska, Lincoln 68583-0722, USA
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Buhr TL, Dickman MB. Isolation, characterization, and expression of a second beta-tubulin-encoding gene from Colletotrichum gloeosporioides f. sp. aeschynomene. Appl Environ Microbiol 1994; 60:4155-9. [PMID: 7993097 PMCID: PMC201950 DOI: 10.1128/aem.60.11.4155-4159.1994] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Colletotrichum gloeosporioides f. sp. aeschynomene is a fungal plant pathogen of Aeschynomene virginica. A beta-tubulin-encoding gene (TUB2) from this pathogen was cloned and sequenced. The deduced amino acid sequence of TUB2 had a high degree of homology to other fungal beta-tubulins. A portion of TUB2 from a benomyl-resistant C. gloeosporioides f. sp. aeschynomene mutant was also cloned and sequenced. A point mutation resulting in a glutamic acid-to-lysine substitution at amino acid 198 likely confers benomyl resistance. The mutation is relevant for use as a selectable marker in developing a gene transfer system in C. gloeosporioides f. sp. aeschynomene. Northern (RNA) hybridizations with C. gloeosporioides f. sp. aeschynomene TUB2 and another C. gloeosporioides f. sp. aeschynomene beta-tubulin-encoding gene (TUB1) as probes showed differential expression of these genes in different cell types.
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Affiliation(s)
- T L Buhr
- Department of Plant Pathology, University of Nebraska, Lincoln 68583-0722
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Nowak C, Kück U. Development of an homologous transformation system for Acremonium chrysogenum based on the beta-tubulin gene. Curr Genet 1994; 25:34-40. [PMID: 8082163 DOI: 10.1007/bf00712964] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The beta-tubulin gene was isolated from the filamentous fungus Acremonium chrysogenum using a heterologous gene probe to screen an A. chrysogenum lambda library. Sequencing of the A. chrysogenum gene revealed a mosaic gene which contains five exons and four intervening sequences. The exons encode for a polypeptide of 447 amino-acid residues which showed a high degree of similarity when compared with amino-acid sequences from beta-tubulins of other eukaryotes. The introns are characterized by typical consensus sequences found in intervening sequences from other filamentous fungi. In-vitro mutagenesis of codon 167 of the beta-tubulin gene resulted in the substitution of a phenylalanine by a tyrosine in the corresponding polypeptide sequence. The mutated gene was used successfully in the transformation and co-transformation of A. chrysogenum to benomyl resistance. The molecular analysis of transformants provided evidence that they contain the mutated beta-tubulin gene in addition to the wild-type gene, as was proved by Southern-hybridization analysis and direct sequencing of PCR amplification products.
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Affiliation(s)
- C Nowak
- Lehrstuhl für Allgemeine Botanik, Ruhr-Universität Bochum, Germany
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