TABLE 2. Primers and probes used for polymerase chain reaction assays targeting Phytophthora spp. and P. ramorum   

Name

Primer sequence

Region

Notes

Universal to Phytophthora species

Oom-Btub-up415 F

Oom(Ph)-Btub-lo954 R

Oom(Ph)-Btub-up901 F

Oom-Btub-lo1401 R


5′-CGCATCAACGTGTACTACAA-3′

5′-GCACACCAGGTGGTTC-3′

5′-TACGACATTTGCTTCCG-3′

5′-CGCTTGAACATCTCCTGG-3′

β-tubulin

β-tubulin

≈539 bp
 

≈500 bp

Universal to Phytophthora species
UN-UP18S42 F

OOM-LO5.8S47 R

OOM-UP5.8S-55 F

UN-LO28S22 R


5′-CGTAACAAGGTTTCCGTAGGTGAAC-3′

5′-ATTACGTATCGCAGTTCGCAG-3′

5′-TGCGATACGTAATGCGAATT-3′

5′-GTTTCTTTTCCTCCGCTTATTGATATG-3′


ITS
 

ITS


≈350 bp
 

≈650 bp

Universal to Phytophthora species
Phy_elicitor1 F

Phy_elicitor2 R


5′-GCCCTCGTCGGCTCCAC-3′

5′-GTGAACACGTTGAGTACCAGGC-3′


Elicitin


≈300 bp

Specific to P. ramorum

Phy_ram_482U_LNA F

Phy_ram_653L_LNA R

ITSPrim622U F

ITSPrimer755L R

Prameli 102U F

Prameli259L R

5′-GGCGCTGTACGACATTTG-3′
5′-ACGCGGGAACGGAATCAA-3′
5′-AATGACTGGTGAACCGTAGCTG-3
5′-CGAAGCCGCCAACACAAG-3′
5′-TTCAACCAGTGCGCGACC-3′
5′-GGCACAGTCAGCTCGCAGTC-3′

 

β-tubulin

ITS


Elicitin

LNA modified
171 bp

133 bp


157 bp

Beacon4. Beta tub F

[6~FAM]CGGGCTCGGACATAGCGGCGCACACCAGCCCG[Dabcyl]

β-tubulin

 

    TaqMan probes

TaqMan581L R

TaqManITSGB651L R

Taq195eli R


[6~FAM]CGTGGTGATGCCGGACATAGCG[BHQ1~Q]

[6~FAM]AACACCGTCGATTCAAAAGCCAAGC[BHQ1~Q]

[6~FAM]CCGTGGACGCGCACATGAGCGAGTAC[BHQ1~Q


β-tubulin

ITS

Elicitin