Real-time assays for detection of Phytophthora spp. and identification of an avr3a gene variant

Armstrong MR, Whisson SC, Pritchard L, Bos JIB et al (2005) An ancestral oomycete locus contains late blight avirulence gene Avr3a, encoding a protein that is recognized in the host cytoplasm. Proc Natl Acad Sci USA 102:7766–7771 Ausubel FM, Brent R, Kingston RE, Moore DD, Seidmann JG, Struhl K (1990) Current protocols in molecular biology, vol 3. Wiley, New York, p A.3–D.1 Baka ZAM (1997) Mating type, nuclear DNA content and isozyme analysis of Egyptian isolates of Phytophthora infestans. Folia Microb 42:613–620 Beketova MP, Sokolova EA, Malyuchenko OP, Alekseev YI, Kuznetsova MA, Kozlovsky BE, Rogozina EV, Khavkin EE (2014) On molecular identification of Phytophthora infestans genotypes. Rus Agric Sci 40:435–438 Clément JAJ, Baldwin TK, Magalon H, Glais I, Gracianne C, Andrivon D, Jacquot E (2013) Specific detection and quantification of virulent/avirulent Phytophthora infestans isolates using a real-time PCR assay that targets polymorphisms of the Avr3a gene. Lett Appl Microb 56:322–332 Cooke DEL, Cano LM, Raffaele S, Bain RA, Cooke LR, Etherington GJ et al (2012) Genome analyses of an aggressive and invasive lineage of the Irish potato famine pathogen. PLoS Pathol 8:e1002940 Drenth A, Guest DI (2004) Principles of Phytophthora disease management. In: Drenth A, Guest DI (eds) Diversity and management of Phytophthora in Southeast Asia, ACIAR Monograph, vol 114. Australian Centre for International Agricultural Research, Canberra, Australia, pp 154–160 El-Ganainy S, Ahmed Y, Soliman M, Ismail A, Tohamy A, Randall E, Cooke D (2016) A shift in the population of Phytophthora infestans on Egyptian potato crops. Phytopathology 106:140 El-Korany AE (2008) Occurrence of oospores of Phytophthora infestans in the field and under controlled conditions. J Agric Environ Sci Alex Univ 7:31–52 Ersek T, Schoelz JE, English JT (1994) PCR amplification of species-specific DNA sequences can distinguish among Phytophthora species. Appl Environ Microb 60:2616–2621 Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95e98 Judelson HS, Tooley PW (2000) Enhanced polymerase chain reaction methods for detecting and quantifying Phytophthora infestans in plants. Phytopathology 90:1112–1119 Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic Press, New York, pp 21–132 Meszka B, Michalecka M (2016) Identification of Phytophthora spp. isolated from plants and soil samples on strawberry plantations in Poland. J Plant Dis Prot 123:29–36 Murry MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucl Acids Res 8:4321–4325 Ristaino JB (2002) Tracking historic migrations of the Irish potato famine pathogen, Phytophthora infestans. Microb Infect 4:1369–1377 Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425 Scibetta S, Schena L, Chimento A, Cacciola SO, Cooke DEL (2012) A molecular method to assess Phytophthora diversity in environmental samples. J Microb Methods 88:356–368 Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729 Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 25:4876–4882 Wilfinger WW, Mackey K, Chomczynski P (1997) Effect of pH and ionic strength on the spectrophotometric assessment of nucleic acid purity. Biotechniques 22:474–478