Phylogenetic analysis and Real Time PCR detection of a presumbably undescribed Peronospora species on sweet basil and sage

Mycological Research

Volumn 109, Issue 11, 2005, Pages 1276-1287

  Belbahri, Lassaad ^a   Calmin, Gautier ^a   Pawlowski, Jan ^b   Lefort, Francois ^a  

^a UNIVERSITY OF APPLIED SCIENCES WESTERN SWITZERLAND   (Switzerland)

^b UNIVERSITY OF GENEVA   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL DNA; RIBOSOMAL SPACER DNA; RNA 18S; RNA 28S;

FUNGAL DISEASE; FUNGUS; PHYLOGENETICS; POLYMERASE CHAIN REACTION;

ARTICLE; BASIL; BAYES THEOREM; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; NUCLEOTIDE SEQUENCE; PERONOSPORA; PHYLOGENY; POLYMERASE CHAIN REACTION; SALVIA OFFICINALIS; SEQUENCE ALIGNMENT; SWITZERLAND;

BASE SEQUENCE; BAYES THEOREM; DNA, FUNGAL; DNA, RIBOSOMAL SPACER; OCIMUM BASILICUM; PERONOSPORA; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 18S; RNA, RIBOSOMAL, 28S; SALVIA OFFICINALIS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SWITZERLAND;

LAMIACEAE; MAGNOLIOPHYTA; MENTA; MENTHA; OCIMUM; OCIMUM BASILICUM; PERONOSPORA; PERONOSPORA FARINOSA; PERONOSPORA LAMII; SALVIA;

EID: 26244465164     PISSN: 09537562     EISSN: None     Source Type: Journal    
DOI: 10.1017/S0953756205003928     Document Type: Article

References (54)

1. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25: 3389-3402.
2. Angiosperm Phylogeny Group (1998) An ordinal classification for the families of flowering plants. Annals of the Missouri Botanical Garden 85: 531-553.
3. Bentley, J. I. (1980) Downy mildew (Peronospora lamii) on Lamium maculatum. Plant Pathology 29: 201-202.
4. Bonants, P., de Weerdt, M. H., van Gent Pelzer, M., Lacourt, I., Cooke, D. & Duncan, J. (1997) Detection and identification of Phytophthora fragariae Hickman by the polymerase chain reaction. European Journal of Plant Pathology 103: 345-355.
5. Boonham, N., Walsh, K., Preston, S., North, J., Smith, P. & Barker, I. (2002) The detection of tuber necrotic isolates of Potato virus Y, and the accurate discrimination of PVY(O), PVY(N) and PVY(C) strains using RT-PCR. Journal of Virological Methods 102: 103-112.
6. Boonham, N., Perez, L. G., Mendez, M. S., Peralta, E. L., Blockley, A., Walsh, K., Barker, I. & Mumford, R. A. (2004) Development of a real-time RT-PCR assay for the detection of potato spindle tuber viroid. Journal of Virological Methods 116: 139-146.
7. Brouwer, M., Lievens, B., van Hemelrijck, W., van den Ackerveken, G., Cammue, B. P. & Thomma, B. P. (2003) Quantification of disease progression of several microbial pathogens on Arabidopsis thaliana using real-time fluorescence PCR. FEMS Microbiology Letters 228: 241-248.
8. Burdon, J. J. & Silk, J. (1997) Sources and patterns of diversity in plant pathogenic fungi. Phytopathology 87: 664-669.
9. Byrne, J. (2000) Downy mildew on Lamium. Michigan State University's Landscape Crop Advisory Team Alert 15: 1.
10. Byrne, J. (2001) Downy mildew on Salvia. Michigan State University's Greehouse Alert 9: 1.
11. Constantinescu, O. & Fatehi, J. (2002) Peronospora-like fungi (Chromista, Peronosporales) parasitic on Brassicaceae and related hosts. Nova Hedwigia 74: 291-338.
12. Cooke, D. E. L., Drenth, A., Duncan, J. M., Wagels, G. & Brasier, C. M. (2000) A molecular phylogeny of Phytophthora and related oomycetes. Fungal Genetics and Biology 30: 17-32.
13. Crawford, A. R., Bassam, B. J., Drenth, A., Maclean, D. J. & Irwin, J. A. G. (1996) Evolutionary relationships among Phytophthora species deduced from rDNA sequence analysis. Mycological Research 100: 437-443.
14. De Cock, A. W. A. M. & Lévesque, A. (2004) New species of Pythium and Phytophthora. Studies in Mycology 50: 481-487.
15. De Cock, A. W. A. M., Quail, A., Descalzo, R., Mayes, C. & Lévesque, C. A. (1998). Identification and detection of Pythium species by reverse dot blot hybridization. Proceedings of the International Congress of Plant Pathology, Edinburgh, UK. Aug. 1998: 3.3.26.
16. Gamliel, A. & Yarden, O. (1998) Diversification of diseases affecting herb crops in Israel accompanies the increase in herb crop production. Phytoparasitica 26: 1-6.
17. Galtier, N., Gouy, M. & Gautier, C. (1996) SEAVIEW and PHYLO_WIN, two graphic tools for sequence alignment and molecular phylogeny. Computer Applications in Bioscience 12: 543-548.
18. Garibaldi, A., Minuto, A., Minuto, G. & Gullino, M. L. (2004) First report of downy mildew on basil (Ocimum basilicum) in Italy. Plant Disease 84: 1154.
19. Guindon, S. & Gascuel, O. (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology 52: 696-704.
20. Gumedzoe, M. Y. D., Hemou, P., Lepage, A. & Lecat, N. (1998) Inventaire et identification de Peronospora lamii (Al. Br.) de By, agent causal du mildiou du basilic (Ocimum basilicum) dans les exploitations de Gyma Cultures. Les VIIIe Journées Scientifiques de l'Université du Bénin, 11-15 mai 1998, Lomé, Bénin.
21. Hall, G. (1996) Modern approaches to species concepts in downy mildews. Plant Pathology 45: 1009-1026.
22. Hansford, C. G. (1933) Annual report of the mycologist. Review of Applied Mycology 12: 421-422.
23. Hasegawa, M., Kishino, H. & Yano, T.-A. (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22: 160-174.
24. Heller, W. & Baroffio, C. (2003) Le mildiou (Peronospora lamii) du basilic progresse! Der Gemüsebau/Le Maraîcher 8: 12-13.
25. Hill, C. F., Pearson, H. G. & Gill, G. S. C. (2004) Peronospora dianthi and Peronospora lamii, two downy mildews recently detected in New Zealand. New Zealand Plant Protection 57: 348.
26. Holcomb, G. E. (2000) First report of downy mildew caused by Peronospora lamii on Salvia Splendens and Salvia coccinea. Plant Disease 84: 1154.
27. Holland, P. M., Abramson, R. D., Watson, R. & Gelfand, D. H. (1991) Detection of specific polymerase chain reaction product by utilizing the 5′-3′ exonuclease activity of Thermus aquaticus DNA polymerase. Proceedings of the National Academy of Sciences, USA 88: 357-362.
28. Huelsenbeck, J. P. & Ronquist, F. (2001) MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17: 754-755.
29. Ivors, K., Wilkinson, C. & Garbelotto, M. (2003) Nested TaqMan PCR for detection of Phytophthora ramorum in environmental plant samples. Mycological Society of America/British Mycological Society Joint Meeting, 26-31 July, Asilomar Conference Center, California, US.
30. Klassen, W. (2002) Some exotic pathogens of plants which threaten horticultural production and trade in southern Florida. In Major Production Problems affecting Miami-Dade Agriculture and Emerging Technological Developments (R. L. Degner, T. J. Stevens & K. L. Morgan, eds): 29-31. Florida Agricultural Market Research Center, Miami.
31. Kokko, H., Virtaharju, O., Karenlempi, S., Cooke, D. E. L., Williams, N. A. & Williamson, B. (1999) Downy mildew (Peronospora rubi) in Rubus arcticus: a threat to commercial berry production in Finland. Acta Horticultural 505: 137-141.
32. Korimbocus, J., Coates, D., Barker, I. & Boonham, N. (2002) Improved detection of Sugarcane yellow leaf virus using a real-time fluorescent (TaqMan) RT-PCR assay. Journal of Virological Methods 103: 109-120.
33. Lanave, C., Preparata, G., Saccone, C. & Serio, G. (1984) A new method for calculating evolutionary substitution rates. Journal of Molecular Evolution 20: 86-93.
34. Leahy, R. (2001) Peronospora lamii A. Braun, downy mildew collected at a nursery in Tampa. Triology (Plant Pathology section): 40: 1.
35. Lefort, F., Gigon, V. & Amos, B. (2003) Le mildiou s'étend. Déjà détecté dans de nombreux pays européens, Peronospora lamii responsable du mildiou du basilic, a été observé en Suisse dans la région lémanique. Réussir Fruits et Légumes 223: 66.
36. Lindqvist, H., Koponen, H. & Valkonen, J. P. T. (1998) Peronospora sparsa on cultivated Rubus arcticus and its detection by PCR based on ITS sequences. Plant Disease 82: 1304-1311.
37. Lindqvist-Kreuze, H., Koponen, H. & Valkonen, J. P. T. (2002) Variability of Peronospora sparsa (syn.P. rubi) in Finland as measured by amplified fragment length polymorphism. European Journal of Plant Pathology 108: 327-335.
38. Mackay, I. M., Arden, K. E. & Nitsche, A. (2002) Real-time PCR in virology. Nucleic Acids Research 30: 1292-1305.
39. Martini, P., Rapetti, S., Bozzano, G. & Bassetti, G. (2003) Segnalazione in Italia di Peronospora lamii su basilico (Ocimum basilicum L.). Atti del Convegno 'Problemi fitopatologici emergenti e implicazioni per la difesa delle colture', Sanremo IM 27-29 novembre 2003: 79-82.
40. McMillan, R. T. jr & Graves, W. R. (1994) First report of downy mildew of Salvia in Florida. Plant Disease 78: 317.
41. Minuto, A., Pensa, P. & Garibaldi, A. (1999) Peronospora lamii, nuovo parassita fogliara della salvia, Colture-Protette 28: 63-64.
42. Morrison, T. B., Weis, J. J. & Wittwer, C. T. (1998) Quantification of low-copy transcripts by continuous SYBR Green I monitoring during amplification. Biotechniques 24: 954-962.
43. Müller, J. (1999) Peronospora swinglei-ein neuer Falscher Mehltaupilz für die Tschechische Republik. Czech Mycology 51: 185-191.
44. Mumford, R. A., Walsh, K., Barker, I. K. & Boonham, N. (2000) Detection of Potato mop top virus and Tobacco rattle virus using a multiplex real-time fluorescent reverse transcription polymerase chain reaction assay. Phytopathology 90: 448-453.
45. Plenk, A. (2002) Peronospora lamii A. Braun, eine noch in Österreich seltene Krankheit an Salvia officinalis. Fachgruppe Phytomedizin, Austrian Association of Agricultural Research Institutions, ALVA Tagung 2002: 1.
46. Rodriguez, F., Oliver, J. F., Martin, A. & Medina, J. R. (1990) The general stochastic model of nucleotide substitution. Journal of Theoretical Biology 142: 485-501.
47. Scott, J. B., Hay, F. S. & Wilson, C. R. (2004) Phylogenetic analysis of the downy mildew pathogen of oilseed poppy in Tasmania, and its detection by PCR. Mycological Research 108: 198-205.
48. Spencer, D. M. (1981) The Downy Mildews. Academic Press, London.
49. Tyagi, S. & Kramer, F. R. (1996) Molecular beacons: probes that fluoresce upon hybridization. Nature Biotechnology 14: 303-308.
50. Voglmayr, H. (2003) Phylogenetic relationships of Peronospora and related genera based on nuclear ribosomal ITS sequences. Mycological Research 107: 1-11.
51. Voltolina, G. (2001) Sclarea sclarea L. Veneto Agricoltura Piante Officinale 2: 1-12.
52. Whitcombe, D., Theaker, J., Guy, S. P., Brown, T. & Little, S. (1999) Detection of PCR products using self-probing amplicons and flourescence. Nature Biotechnology 17: 804-807.
53. White, T. J., Burns, T., Lee, S. & Taylor, J. (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR Protocols: a guide to methods and applications (M. A. Innis, D. H. Gelfand, J. J. Sinsky & T. J. White, eds): 315-322. Academic Press, San Diego.
54. Wittwer, C. T., Herrmann, M. G., Moss, A. A. & Rasmussen, R. P. (1997) Continuous fluorescence monitoring of rapid cycle DNA amplification. BioTechniques 22: 130-138.