Development of a multiplex assay for genus- and species-specific detection of phytophthora based on differences in mitochondrial gene order

Phytopathology

Volumn 104, Issue 7, 2014, Pages 733-748

  Bilodeau, Guillaume J ^a   Martin, Frank N ^a   Coffey, Michael D ^b   Blomquist, Cheryl L ^c  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c CALIFORNIA DEPARTMENT OF FOOD AND AGRICULTURE   (United States)

Author keywords

Real time PCR

Indexed keywords

MITOCHONDRIAL DNA; PRIMER DNA; RIBOSOMAL SPACER DNA; SPACER DNA;

ARTICLE; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; GENETIC MARKER; GENETICS; ISOLATION AND PURIFICATION; METHODOLOGY; MULTIPLEX POLYMERASE CHAIN REACTION; PARASITOLOGY; PHYLOGENY; PHYTOPHTHORA; PLANT; PLANT DISEASE; REAL TIME POLYMERASE CHAIN REACTION; REAL-TIME PCR; SENSITIVITY AND SPECIFICITY; SPECIES DIFFERENCE; VALIDATION STUDY;

REAL-TIME PCR;

DNA PRIMERS; DNA, INTERGENIC; DNA, MITOCHONDRIAL; DNA, RIBOSOMAL SPACER; GENETIC MARKERS; MULTIPLEX POLYMERASE CHAIN REACTION; PHYLOGENY; PHYTOPHTHORA; PLANT DISEASES; PLANTS; REAL-TIME POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

EID: 84902265424     PISSN: 0031949X     EISSN: None     Source Type: Journal    
DOI: 10.1094/PHYTO-09-13-0263-R     Document Type: Article

References (47)

1. Afonina, I., Ankoudinova, I., Mills, A., Lokhov, S., Huynh, P., and Mahoney, W. 2007. Primers with 5′ flaps improve real-time PCR. Biotechniques 43:770, 772, 774
2. Arif, M., and Ochoa-Corona, F. M. 2012. Comparative assessment of 5′ A/T-rich overhang sequences with optimal and sub-optimal primers to increase PCR yields and sensitivity. Mol. Biotechnol. 55:17-26
3. Bezuidenhout, C. M., Denman, S., Kirk, S. A., Botha, W. J., Mostert, L., and McLeod, A. 2010. Phytophthora taxa associated with cultivated Agathosma, with emphasis on the P. citricola complex and P. capensis sp. nov. Persoonia: Mol. Phylogeny Evol. Fungi 25:32-49
4. Bilodeau, G., Koike, S. T., Uribe, P., and Martin, F. N. 2012. Development of an assay for rapid detection and quantification of Verticillium dahliae in soil. Phytopathology 102:331-343
5. Bilodeau, G., Pelletier, G., Pelletier, F., Lévesque, C. A., and Hamelin, R. C. 2009. Multiplex real-time polymerase chain reaction (PCR) for detection of Phytophthora ramorum, the causal agent of sudden oak death. Can. J. Plant Pathol. 31:195-210
6. Bilodeau, G. J., Levesque, C. A., de Cock, A. W. A. M., Duchaine, C., Briere, S., Uribe, P., Martin, F. N., and Hamelin, R. C. 2007. Molecular detection of Phytophthora ramorum by real-time polymerase chain reaction using TaqMan, SYBR Green, and molecular beacons. Phytopathology 97:632-642 (Pubitemid 46652631)
7. Blair, J. E., Coffey, M. D., and Martin, F. N. 2012. Species tree estimation for the late blight pathogen, Phytophthora infestans, and close relatives. PLoS One 7:e37003. Online publication. doi:37010.31371/journal/ pone.0037003
8. Blair, J. E., Coffey, M. D., Park, S. Y., Geiser, D. M., and Kang, S. C. 2008. A multi-locus phylogeny for Phytophthora utilizing markers derived from complete genome sequences. Fungal Genet. Biol. 45:266-277
9. Brasier, C. M. 2007. Phytophthora biodiversity: how many Phytophthora species are there? Pages 101-115 in: U.S. Dep. Agric. For. Serv. Pac. Southwest Res. Stn. E. M. Goheen and S. J. Frankel, eds. Proceedings of the Fourth Union of Forest Research Organization (IUFRO) Working Party 507.02.09. Gen. Tech. Rep. PSW-GTR-221
10. Brasier, C. M., Beales, P. A., Kirk, S. A., Denman, S., and Rose, J. 2005. Phytophthora kernoviae sp. nov., an invasive pathogen causing bleeding stem lesions on forest trees and foliar necrosis of ornamentals in the UK. Mycol. Res. 109:853-859 (Pubitemid 41215784)
11. Brasier, C. M., Cooke, D. E. L., and Duncan, J. M. 1999. Origin of a new Phytophthora pathogen through interspecific hybridization. Proc. Natl. Acad. Sci. USA 96:5878-5883 (Pubitemid 29234712)
12. Butler, D. K., and Metzenberg, R. L. 1989. Premeiotic change of nucleolous organizer size in Neurospora. Genetics 122:783-791
13. Chen, W., Djama, Z. R., Coffey, M. D., Martin, F. N., Bilodeau, G. J., Radmer, L., Denton, G., and Lévesque, C. A. 2012. Membrane-based oligonucleotide array developed from multiple markers for the detection of many Phytophthora species. Phytopathology 103:43-54
14. Dorak, M. T. 2006. Real-Time PCR. E. Owen and M. T. Dorak, eds. Taylor & Francis, Oxford
15. Garbelotto, M., Davidson, J. M., Ivors, K., Maloney, P. E., Huberli, D., Koike, S. T., and D. M. Rizzo 2003. Non-oak native plants are main hosts for sudden oak death pathogen in California. Calif. Agric. 57:18-23
16. Garbelotto, M., Rizzo, D. M., Hayden, K., Meija-Chang, M., Davidson, J. M., and Tjosvold, S. 2002. Phytophthora ramorum and sudden oak death in California: III. Preliminary studies in pathogen genetics. U. S. Dep. Agric. For. Serv. Gen. Tech. Rep. PSW-GTR-184:765-774
17. Goss, E. M., Cardenas, M. C., Myers, K., Forbes, G. A., Fry, W. E., Restrepo, S., and Grunwald, N. J. 2011. The plant pathogen Phytophthora andina emerged via hybridization of an unknown Phytophthora species and the Irish potato famine pathogen, P. infestans. PLoS One 6:e24543
18. Goss, E. M., Larsen, M., Chastagner, G. A., Givens, D. R., Grünwald, N. J., and Howlett, B. J. 2009. Population genetic analysis infers migration pathways of Phytophthora ramorum in US nurseries. PLoS Pathog. 5:e1000583
19. Hall, T. A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41:95-98
20. Heid, C., Stevens, J., Livak, K., and Williams, P. 1996. Real-time quantitative PCR. Genome Res. 6:986-994
21. Hong, C., Gallegly, M. E., Richardson, P. A., and Kong, P. 2011. Phytophthora pini Leonian resurrected to distinct species status. Mycologia 103:351-360
22. Hong, C. X., Gallegly, M. E., Browne, G. T., Bhat, R. G., Richardson, P. A., and Kong, P. 2009. The avocado subgroup of Phytophthora citricola constitutes a distinct species, Phytophthora mengei sp. nov. Mycologia 101:833-840
23. Ioos, R., Andrieux, A., Marcais, B., and Frey, P. 2006. Genetic characterization of the natural hybrid species Phytophthora alni as inferred from nuclear and mitochondrial DNA analyses. Fungal Genet. Biol. 43:511- 529 (Pubitemid 43744481)
24. Jeffers, S. N., and Martin, S. B. 1986. Comparison of two media selective for Phytophthora and Pythium species. Plant Dis. 70:1038-1043
25. Jung, T., and Burgess, T. I. 2009. Re-evaluation of Phytophthora citricola isolates from multiple woody hosts in Europe and North America reveals a new species, Phytophthora plurivora sp. nov. Persoonia 22:95-110
26. Kox, L. F. F., van Brouwershaven, I. R., van de Vossenberg, B., van den Beld, H. E., Bonants, P. J. M., and de Gruyter, J. 2007. Diagnostic values and utility of immunological, morphological, and molecular methods for in planta detection of Phytophthora ramorum. Phytopathology 97:1119- 1129 (Pubitemid 47441526)
27. Kroon, L. P. N. M., Brouwer, H., de Cock, A. W. A. M., and Govers, F. 2012. The genus Phytophthora anno 2012. Phytopathology 102:348-364
28. Maleszka, R., and Clark-Walker, G. D. 1993. Yeasts have a four-fold variation in ribosomal DNA copy number. Yeast 9:53-58 (Pubitemid 23043245)
29. Man-in-'t-Veld, W. A., Cock, A. W. A. M., and Summerbell, R. C. 2007. Natural hybrids of resident and introduced Phytophthora species proliferating on multiple new hosts. Eur. J. Plant Pathol. 117:25-33
30. Martin, F. N. 2000. Phylogenetic relationships among some Pythium species inferred from sequence analysis of the mitochondrially encoded cytochrome oxidase II gene. Mycologia 92:711-727
31. Martin, F. N. 2009. Pythium genetics. Pages 213-223 in: Oomycete Genetics and Genomics. K. Lamour and S. Kamoun, eds. John Wiley and Sons, Hoboken, NJ
32. Martin, F. N., Abad, Z. G., Balci, Y., and Ivors, K. 2012. Identification and detection of Phytophthora: reviewing our progress, identifying our needs. Plant Dis. 96:1080-1103
33. Martin, F. N., Bensasson, D., Tyler, B. M., and Boore, J. L. 2007. Mitochondrial genome sequences and comparative genomics of Phytophthora ramorum and P. sojae. Curr. Genet. 51:285-296 (Pubitemid 46605317)
34. Martin, F. N., Tooley, P. W., and Blomquist, C. 2004. Molecular detection of Phytophthora ramorum, the causal agent of sudden oak death in California, and two additional species commonly recovered from diseased plant material. Phytopathology 94:621-631 (Pubitemid 38681971)
35. Nirenberg, H. I., Gerlach, W. F., and Graefenhan, T. 2009. Phytophthora × pelgrandis, a new natural hybrid pathogenic to Pelargonium grandiflorum hort. Mycologia 101:220-231
36. Pasero, P., and Marilly, M. 1993. Size variation rDNA clusters in the yeasts Saccharomyces cerevisiae and Saccharomyces pombe. Mol. Gen. Genet. 236:448-452 (Pubitemid 23055590)
37. Pukkila, P. J., and Skrzynia, C. 1993. Frequent changes in the number of reiterated ribosomal RNA genes throughout the lifecycle of the basidiomycete Coprinus cinereus. Genetics 133:203-211 (Pubitemid 23033476)
38. Rizzo, D. M., and Garbelotto, M. 2003. Sudden oak death: endangering California and Oregon forest ecosystems. Front. Ecol. Environ. 1:197- 204
39. Rustchenko-Bulgac, E. P., Curran, T., and Sherman, F. 1993. Variation in the number of ribosomal DNA subunits in morphological mutants and normal strains of Candida albicans and in normal strains of Saccharomyces cerevisiae. J. Bacteriol. 175:7189-7199 (Pubitemid 23339295)
40. Schena, L., Duncan, J. M., and Cooke, D. E. L. 2008. Development and application of a PCR-based 'molecular tool box' for the identification of Phytophthora species damaging forests and natural ecosystems Plant Pathol. 57:64-75
41. Schena, L., Hughes, K. J. D., and Cooke, D. E. L. 2006. Detection and quantification of Phytophthora ramorum, P. kernoviae, P. citricola and P. quercina in symptomatic leaves by multiplex real-time PCR. Mol. Plant Pathol. 7:365-379
42. Scott, P. M., Burgess, T. I., Barber, P. A., Shearer, B. L., Stukely, M. J. C., Hardy, G. E. S. J., and Jung, T. 2009. Phytophthora multivora sp. nov., a new species recovered from declining Eucalyptus, Banksia, Agonis and other plant species in Western Australia. Persoonia 22:1-13
43. Sikora, K., Verstappen, E., Mendes, O., Schoen, C., Ristaino, J., and Bonants, P. 2012. A universal microarray detection method for identification of multiple Phytophthora spp. using padlock probes. Phytopathology 102:635-645
44. Spies, C. F. J., Mazzola, M., and McLeod, A. 2011. Characterisation and detection of Pythium and Phytophthora species associated with grapevines in South Africa. Eur. J. Plant Pathol. 131:103-119
45. Tooley, P. W., Martin, F. N., Carras, M. M., and Frederick, R. D. 2006. Real-time fluorescent polymerase chain reaction detection of Phytophthora ramorum and Phytophthora pseudosyringae using mitochondrial gene regions. Phytopathology 96:336-345
46. USDA-APHIS 2004. Sudden oak death: Phytophthora ramorum. In: Pest Detection and Management Programs. L. Levy and V. Mavrodieva, eds. USDA Animal Plant Health Inspection Service, USA
47. White, T. J., Bruns, T. D., Lee, S. B., and Taylor, J. W. 1990. Amplification and direct sequencing of fungal ribosomal RNA Genes for phylogenetics. Pages 315-322 in: PCR Protocols: A Guide to Methods and Applications - A Laboratory Manual. N. Innis, D. Gelfand, J. Sninsky, and T. White, eds. Academic Press, New York