Evaluation of different PCR-based DNA fingerprinting techniques for assessing the genetic variability of isolates of the fungus Epicoccum nigrum

Journal of Applied Microbiology

Volumn 87, Issue 6, 1999, Pages 898-906

  Arenal, F ^a   Platas, G ^a   Martin, J ^a   Salazar, O ^a   Pelaez F ^a  

^a Medical affairs Merck sharp and Dohme ltd   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ECOLOGY; POLYMERASE CHAIN REACTION;

DNA FINGERPRINTING; EPICOCCUM NIGRUM; FINGERPRINTING TECHNIQUES; GENETIC FINGERPRINTING; GENETIC VARIABILITY; GENETICS DIVERSITIES; MICROSATELLITES; MOLECULAR MARKER; PCR TECHNIQUES; SIMILARITY INDICES;

DNA SEQUENCES;

FUNGAL DNA;

DNA; FUNGUS; GENETIC VARIATION;

ACCURACY; ANALYTIC METHOD; ARTICLE; CONTROLLED STUDY; DNA FINGERPRINTING; EPICOCCUM NIGRUM; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; HYPHOMYCETES; INTERMETHOD COMPARISON; NONHUMAN; PHYLOGENY; STRAIN DIFFERENCE; VALIDATION PROCESS;

EPICOCCUM NIGRUM; FUNGI; HYPHOMYCETES;

EID: 0033381659     PISSN: 13645072     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2672.1999.00946.x     Document Type: Article

References (41)

1. Arenal, F., Platas, G., Monte, E. and Peláez, F. (1999) ITS sequencing supports that Epicoccum nigrum and Phoma epicoccina are the same biological species Mycological Research accepted for publication.
2. Bamford, P.C., Norris, G.L.F. and Ward, G. (1961) Flavipin production by Epicoccum spp. Transactions of the British Mycological Society 44, 354-356.
3. Bills, G.F., Platas, G., Peláex, P. and Masurekar, P. (1999) Reclassification of a Pneumocandin-producing anamorph, Glarea Lozoyensis gen. et sp. nov., previously identified as Zalerion arboricola. Mycological Research 103, 179-192.
4. Boland, G.J. and Inglis, G.D. (1989) Antagonism of white mold (Sclerotinia sclerotiorum) of bean by fungi from bean and rapeseed flowers. Canadian Journal of Botany 67, 1775-1781.
5. Brown, A.E., Finlay, R. and Ward, J. (1987) Antifungal compounds produced by Epicoccum purpurascens against soil-borne plant pathogenic fungi. Soil Biology and Biochemistry 19, 657-664.
6. Bruton, B.D., Redlin, S.C., Collins, J.K. and Sams, C.E. (1993) Post harvest decay of cantaloupe caused by Epicoccum nigrum. Plant Disease 77, 1060-1062.
7. Buscot, F., Wipf, D., Munch, J.C., Botton, B. and Martin, F. (1996) DNA polymorphism in morels: PCR/RFLP analysis of the ribosomal DNA spacers and microsatellite-primed PCR. Mycological Research 100, 63-71.
8. Cain, A.J. and Harrison, G.A. (1958) An analysis of the taxonomist's use of affinity. Proceedings of the Zoological Society of London 131, 85-98.
9. Chand, T. and Logan, C. (1984) Antagonists and parasites of Rhizoctonia solani and their efficacy in reducing stem canker of potato under controlled conditions. Transactions of the British Mycological Society 83, 107-112.
10. Domsch, K.H. and Gams, W. (1993) Compendium of Soil Fungi, vol. 1, Eching: Germany: IHW-Verlag.
11. Egger, K.N. and Sigler, L. (1993) Relatedness of the ericoid endophytes Scytalidium vaccinii and Hymoscyphus ericae inferred from analysis of ribosomal DNA. Mycologia 85, 219-230.
12. Felsenstein, J. (1993) PHVLIP (Phylogenetic Inference Package) Version 3.5c. Seattle: Department of Genetics, University of Washington.
13. Fouly, H.M., Wilkinson, H.T. and Chen, W. (1997) Restriction analysis of internal transcribed spacers and the small subunit gene of ribosomal DNA among four Gaeumannomyces species. Mycologia 89, 590-597.
14. Haemmerli, U.A., Brèndle, U.E., Petrini, O. and McDermott, J.M. (1992) Differentiation of isolates of Discula umbrinella (Teleomorph: apiognomonia errabunda) from beech chestnut, and oak using randomly amplified polymorphic DNA markers. Molecular Plant-Microbe Interactions 5, 479-483.
15. Harrington, F.A. and Potter, D. (1997) Phylogenetic relationships within Sarcoscypha based upon nucleotide sequences of the internal transcribed spacer of nuclear ribosomal DNA. Mycologia 89, 258-267.
16. Herrero, M.L. and Klemsdal, S.S. (1998) Identification of Pythium aphanidermatum using the RAPD technique. Mycological Research 102, 136 140.
17. Hirsch, C.F. and Sigmund, J.M. (1995) Use of PCR fingerprinting to differentiate bacteria for microbial products screening. Journal of Industrial Microbiology 15, 85 93.
18. Hseu, R.S., Wang, H.H., Wang, H.F. and Moncalvo, J.M. (1996) Differentiation and grouping of isolates of the Ganoderma lucidum complex by random amplified polymorphic DNA-PCR compared with grouping on the basis of internal transcribed spacer sequences. Applied and Environmental Microbiology 62, 1354-1363.
19. Julian, M.C., Acero, J., Salazar, O., Keijer, J. and Rubio, V. (1999) Mating type correlated molecular markers and demonstration of Heterokaryosis in the phytopathogenic fungus Thanatephorus cucumeris (Rizoctonia solani) AG 1 1C by AFLP DNA finger-printing analysis. Journal of Biotechnology 67, 49-56.
20. Longato, S. and Bonfante, P. (1997) Molecular identification of mycorrhizal fungi by direct amplification of microsatellite regions. Mycological Research 101, 425-432.
21. Madrigal, C., Pascual, S. and Melgarejo, P. (1994) Biological control of peach twig blight (Monilinia laxa) with Epicoccum nigrum. Plant Pathology 43, 554-561.
22. McCutcheon, T.L., Carroll, G.C. and Schwab, S. (1993) Genotypic diversity in populations of a fungal endophyte from Douglas fir. Mycologia 85, 180 186.
23. Moron, R., González, I. and Genilloud, O. (1999) New genus-specific primers for the identification of members of the genera Pseudonocardia and Saccharopolyspora. International Journal of Systematic Bacteriology. 49, 149-162.
24. Mueller, U.G., Lipari, S.E. and Milgroom, M.G. (1996) Amplified fragment length polymorphism (AFLP) fingerprinting of symbiotic fungi cultured by the fungus-growing ant Cyphomyrmex minutus. Molecular Ecology 5, 119-122.
25. Pei, M.H., Whelan, M.J., Halford, N.G. and Royle, DJ. (1997) Distinction between stem-and leaf-infecting forms of Melampsora rust on Salix viminalis using RAPD markers. Mycological Research 101, 7-10.
26. Peláez, F., Platas, G., Collado, J. and Díez, M.T. (1996) Infraspecific variation in two species of aquatic hyphomycetes assessed by RAPD analysis. Mycological Research 100, 831-837.
27. Raina, K., Jackson, N. and Chandlee, J.M. (1997) Detection of genetic variation in Sclerotinia homeocarpa isolates using RAPD analysis. Mycological Research 101, 585-590.
28. Rocijmans, H.J., DeHoog, G.S., Tan, C.S. and Figge, M.J. (1997) Molecular taxonomy and GC/MS of metabolites of Scytalidium hyalinum and Nattrassia mangiferae (Hendersonula toruloidea). Journal of Medical and Veterinary Mycology 35, 181-188.
29. Rohel, E., Couteaudier, Y., Papierok, B., Cavelier, N. and Dedryver, C.A. (1997) Ribosomal internal transcribed spacer size variation correlated with RAPD-PCR pattern polymorphisms in the entomopathogenic fungus Erynia neaphidis and some closely related species. Mycological Research 101, 573-579.
30. Sneath, P.H.A. and Sokal, R.R. (1973) Numerical Taxonomy. San Francisco, CA: W.H. Freeman and Co.
31. Stenlid, J., Karlsson, O. and Högberg, N. (1994) Intraspecific genetic variation in Heterobasidion annosum revealed by amplification of minisatellite DNA. Mycological Research 98, 57-63.
32. Tigano-Milani, M.S., Samson, R.A., Martins, I. and Sobral, B. (1995) DNA markers for differentiating isolates of Paecilomyces lilacinus. Microbiology 141, 239-245.
33. Vaneechoutte, M., Boerling, P., Tichy, H.V., Bannerman, E., Jäger, B. and Bille, J. (1998) Comparison of PCR-based DNA finger-printing techniques for the identification of Listeria species and their use for atypical Listeria isolates. International Journal of Systematic Bacteriology 48, 127-139.
34. Vos, P., Hogers, R., Bleeker, M., Reijans, M., Van de Lee, T., Hornes, M., Frijters, A. and Pot, J. (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research 23, 4407-4414.
35. Ward, E. and Akrofi, A.Y. (1994) Identification of fungi in the Gaeumannomyces-Phyalophora complex by RFLPs of PCR-amplified ribosomal DNAs. Mycological Research 98, 219-224.
36. Weising, K., Atkinson, R.G. and Gardner, R.C. (1995) Gcnomic fingerprinting by microsatellite-primed PCR: a critical evaluation. PCR methods and Applications 4, 249-255.
37. Welsh, J. and McClelland, M. (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Research 18, 7213-7218.
38. Welsh, J. and McClelland, M. (1991) Gcnomic fingerprints produced by PCR with consensus tRNA gene primers. Nucleic Acids Research 19, 861-866.
39. White, T.J., Bruns, T., Lee, S. and Taylor, J. (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR Protocols: A Guide to Methods and Amplifications, ed. Innis, M.A., Gelfand, D.H., Sninsky, J.J. and White, T.J., pp. 315-322. New York, NY: Academic Press.
40. Williams, J.G.K., Kubelik, A.R., Livak, K.L., Rafalski, J.A. and Tingey, S.V. (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research 18, 6531-6535.
41. Yan, Z.H., Rogers, S.O. and Wang, C.J.K. (1995) Assessment of Phialophora species based on ribosomal DNA internal transcribed spacers and morphology. Mycologia 87, 72-83.