Fungal cultures and isolation of fungal DNA
P. azadirachate isolates used in this study were isolated from infected neem seeds and twig material (Table 1) as described by Sateesh  and maintained on PDA slants at 4o C until use. Other fungal isolates were collected from different sources (Table 2).
For isolation of DNA from fungal isolates, five mm diameter agar plug containing mycelia was inoculated in 250 ml conical flasks containing 100 ml of potato dextrose broth and incubated at 25±1°C for 10 days in alternate period of bright light and dark. DNA was extracted from 100 mg of the dried mycelium, ground in liquid nitrogen using mortar and pestle according to the procedure described by Raedor and Broda  and slightly modified by Chowdappa et al. . DNA was stored at -20ºC until further use. DNA concentration, yield and quality parameters based on absorbance at 260 and 280nm (A260/280 ratio) was estimated.
PCR amplification of ITS region and sequencing
DNA from all the isolates of P. azadirachtae was amplified by PCR with ITS1 and ITS4 primers as described by White et al. . The PCR products were outsourced for sequencing (Bioserve Technologies, Hyderabad, www.bioserveindia.com). The sequences were queried in BLAST search (www.ncbi.nlm.nih.gov) to confirm that it has homology identical to the previously reported rDNA sequences of Phomopsis. The ITS sequences of all the isolates were deposited in the GenBank (www.ncbi.nlm.nih.gov) with accession numbers as mentioned in the table1.
Validation of genus specific primers
The genus specific primers reported earlier in the literature, Phf/Phr  and PF1/PF2  were validated using DNA of ten different Phomopsis species (Table 2) including P. azadirachate. The PCR conditions were same as described by Prasad et al.  and Girish et al. .
Design of P. azadirachtae specific primers
A pair of P. azadirachtae specific primers, referred to as PA primers were designed from the ITS region of rDNA of the P. azadirachtae isolates. ITS sequences of P. azadirachtae isolates along with other Phomopsis species available in Genbank were aligned through Clustal W in Bioedit version 220.127.116.11. The forward primer PAF (5’- CCCTAGGGGGCCCCTCGG-3’) and the reverse primer PAR (5’-AGGGCCTGCTTTTGGGT-3’) were designed manually from the region conserved to P. azadirachtae and variable in other Phomopsis species. The Primers were checked for hairpin formation, Self-dimer, Hetero-dimer, G/C content and melting temperature using oligoAnalyzer 3.1 software (http://eu.idtdna.com/analyzer/applications/oligoanalyzer/).
Development of PCR assay specific for P. azadirachtae
The annealing temperature of PAF/PAR primer was determined by performing a gradient PCR between the annealing temperatures of 55°C - 65°C with the following conditions. PCR was performed in 50 μl reaction volume consisting of 1µl of template DNA, 5 μl 10x PCR buffer, 40.75 μl sterile distilled water, 1 μl 2.0 mM dNTPs, 1μl each of 50 pM primers...