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 Molecular Plant Pathology 7:365-379. (pdf of reprint)

Schena L, Cooke DE. 2006 Assessing the potential of regions of the nuclear and mitochondrial genome to develop a J. Microbiological Methods 67:70-85. (pdf of reprint)

Schena, L., Duncan, J.M., 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 Pathology 57:64-75.

            The ras-related Ypt-1 gene has several conserved exons separated by variable introns that exhibit enough variation to be useful for development of Phytophthora species-specific diagnostic markers.  Conserved sequences in exon 3 and 6 were used to develop a Phytophthora genus-specific primer pair (Yph1F and Yph2R) that generated an amplicon ranging in size from 419-478 bp depending on the species (this primer pair did not amplify 9 Pythium spp. that were tested; Schena et al. 2008).  Nested within this amplicon and based on sequence differences in introns 3, 4, and 5 the species-specific primers were developed.  Species-specific amplicons range in size from 73 to 258 bp.  Depending on the concentration of target sequences present in the plant tissue the amplification can either be nested with the Phytophthora genus specific primers used in the first amplification followed by the species-specific primer pair (for samples with low pathogen DNA concentrations) or the species specific primers can be used in a single amplification round.

Real-time PCR TaqMan diagnostic markers have been developed for P. ramorum, P. kernoviae, P. citricola and P. quercina. 

Real-time SYBR green diagnostic markers have been developed for P. cactorum, P. cambivora, P. cinnamomi, P. citricola, P. europaea. P. ilicis, P. inundata, P. kernoviae, P. lateralis, P. megasperma, P. nemorosa, P. pseudosyringae, P. psychrophila, P. quercina, and P. ramorum.

Sequence alignments and the location of species-specific primers used in the work by Schena et al. (2008) can be downloaded (contributed by Leonardo Schena).   It would be advisable to check GenBank for additional sequences that may have been deposited since this alignment was made.

From Schena et al. 2006



From Schena et al. 2006 

From Schena et al. 2008



From Schena et al. 2008