A database to support plant pest diagnostic activities

List of primers included in the Fungi Methodology pages

The Fungi database contains various loci for different organism groups, amplified in some cases by different primers. The table below summarizes this data and is provided as a useful overview. The primers are not guaranteed to work for all species or strains of the given organism group, or within other groups not explicitly mentioned next to the primer. Hyperlinks are provided to the cited manuscripts.

LocusPrimer nameDirectionSequence (5'-3')ReferenceUsed in Organism group
5.8S nrRNA gene with the two flanking internal transcribed spacers (ITS)ITS-4ReverseTCC TCC GCT TAT TGA TAT GCWhite et al. (1990)All
ITS-5ForwardGGA AGT AAA AGT CGT AAC AAG GWhite et al. (1990)All
ITS1FForwardCTT GGT CAT TTA GAG GAA GTA AGardes & Bruns (1993)All
LR5ReverseTCC TGA GGG AAA CTT CGVilgalys & Hester (1990)All
V9GForwardTTA CGT CCC TGC CCT TTG TAde Hoog and Gerrits van den Ende (1998)All
Intergenic Spacer 1 of nRNA operon (IGS1)LR12RForwardCTG AAC GCC TCT AAG TCA GAAVilgalys lab, Duke UniversityPhytophthora, Puccinia, Verticillium
Seq5SReverseCAG ATC AGA CGG GAT GCG GTWoodhall et al. (2007)Phytophthora, Puccinia, Verticillium
Partial 18S ribosomal RNA gene (SSU)NS1ForwardGTA GTC ATA TGC TTG TCT CWhite et al. (1990)Colletotrichum, Phoma
NS4ReverseCTT CCG TCA ATT CCT TTA AGWhite et al. (1990)Colletotrichum, Phoma
Partial 28S ribosomal RNA gene (LSU)LR0RForwardGTA CCC GCT GAA CTT AAG CRehner & Samuels (1994)Colletotrichum, Mycosphaerella, Phoma, Phyllosticta
LR5ReverseTCC TGA GGG AAA CTT CGVilgalys & Hester (1990)Colletotrichum, Melampsora, Mycosphaerella, Phyllosticta, Puccinia, Stenocarpella, Thecaphora, Verticillium
LR7ReverseTAC TAC CAC CAA GAT CTVilgalys & Hester (1990)Phoma
LSU1FdForwardGRA TCA GGT AGG RAT ACC CGCrous et al. (2009)Melampsora, Mycosphaerella, Phyllosticta, Puccinia, Stenocarpella, Thecaphora, Verticillium
Partial actin gene (ACT)ACT-512FForwardATG TGC AAG GCC GGT TTC GCCarbone & Kohn (1999)Colletotrichum, Mycosphaerella, Phyllosticta, Phoma, Verticillium
ACT-783RReverseTAC GAG TCC TTC TGG CCC ATCarbone & Kohn (1999)Colletotrichum, Phyllosticta, Phoma, Verticillium
ACT2RdReverseARR TCR CGD CCR GCC ATG TCGroenewald et al. (2013) & Quaedvlieg et al. (2011)Mycosphaerella
Partial apurinic DNA lyase gene (APN2)Apn1W1FForwardATG GAG CAC AAA AAC GAA CACrouch et al. (2009)Colletotrichum
Apn1W1RReverseGCG GAG CAG AGG ATG TAG TCCrouch et al. (2009)Colletotrichum
Partial beta-tubulin gene (Tub2)Bt-2bReverseACC CTC AGT GTA GTG ACC CTT GGCGlass & Donaldson (1995)Colletotrichum
Btub_F1ForwardGCC AAG TTC TGG GAG GTC ATCBlair et al. (2008)Phytophthora
T1ForwardAAC ATG CGT GAG ATT GTA AGTO’Donnell & Cigelnik (1997)Colletotrichum, Mycosphaerella
T2ReverseTAG TGA CCC TTG GCC CAG TTGO’Donnell & Cigelnik (1997)Colletotrichum
TUB2Fd (=BT2Fd)ForwardGTB CAC CTY CAR ACC GGY CAR TGGroenewald et al. (2013) & Woudenberg et al. (2009)Colletotrichum, Mycosphaerella, Phoma
TUB4Rd (=BT4R)ReverseCCR GAY TGR CCR AAR ACR AAG TTG TCGroenewald et al. (2013) & Woudenberg et al. (2009)Colletotrichum, Mycosphaerella, Phoma
TUBUR1 (= BTubR1)ReverseCCT GGT ACT GCT GGT ACT CAGKroon et al. (2004)Phytophthora
Partial calmodulin gene (CAL)CAL-228FForwardGAG TTC AAG GAG GCC TTC TCC CCarbone & Kohn (1999)Colletotrichum, Mycosphaerella, Phoma, Verticillium
CAL-235FForwardTTC AAG GAG GCC TTC TCC CTC TTQuaedvlieg et al. (2012)Mycosphaerella
CAL-737RReverseCAT CTT TCT GGC CAT CAT GGCarbone & Kohn (1999)Colletotrichum, Phoma, Verticillium
CAL2RdReverseTGR TCN GCC TCD CGG ATC ATC TCGroenewald et al. (2013) & Quaedvlieg et al. (2011)Mycosphaerella
CL1ForwardGAR TWC AAG GAG GCC TTC TCO’Donnell et al. (2000)Colletotrichum
CL1CForwardGAA TTC AAG GAG GCC TTC TCWeir et al. (2012)Colletotrichum
CL2AReverseTTT TTG CAT CAT GAG TTG GACO’Donnell et al. (2000)Colletotrichum
CL2CReverseCTT CTG CAT CAT GAG CTG GACWeir et al. (2012)Colletotrichum
Partial chitin synthase 1 gene (CHS-1)CHS-354RReverseTGG AAG AAC CAT CTG TGA GAG TTGCarbone & Kohn (1999)Colletotrichum, Phoma
CHS-79FForwardTGG GGC AAG GAT GCT TGG AAG AAGCarbone & Kohn (1999)Colletotrichum, Phoma
Partial cytochrome oxidase 1 (CO1)Cox1MlpAFForwardTAA GAT GAC TTT ATA GTA CCA AFeau et al. (2009)Melampsora
Cox1MlpARReverseGCT CCT ACC ATT ACM GFeau et al. (2009)Melampsora
OomCoxI-LevloReverseCYT CHG GRT GWC CRA AAA ACC AAARobideau et al. (2011)Phytophthora
OomCoxI-LevupForwardTCA WCW MGA TGG CTT TTT TCA ACRobideau et al. (2011)Phytophthora
PezizFForwardTCA GGR TTA YTA GGW ACA GCA TTTNguyen & Seifert (2008)Verticillium
PezizRReverseACC TCA GGR TGY CCG AAG AATNguyen & Seifert (2008)Verticillium
Partial cytochrome oxidase 2 (COX2)FM75ForwardCCT TGG CAA TTA GGA TTT CAA GATMartin & Tooley (2003)Phytophthora
FM78ReverseACA AAT TTC ACT ACA TTG TCCMartin & Tooley (2003)Phytophthora
Partial glutamine synthetase gene (GS)GSF1ForwardATG GCC GAG TAC ATC TGGStephenson et al. (1997)Colletotrichum
GSF3ForwardGCC GGT GGA GGA ACC GTC GWeir et al. (2012)Colletotrichum
GSR1ReverseGAA CCG TCG AAG TTC CAGStephenson et al. (1997)Colletotrichum
GSR2ReverseGAA CCG TCG AAG TTC CACWeir et al. (2012)Colletotrichum
Partial glyceraldehyde-3- phosphate dehydrogenase gene (GAPDH)GDFForwardGCC GTC AAC GAC CCC TTC ATT GATempleton et al. (1992)Colletotrichum
GDF1ForwardGCC GTC AAC GAC CCC TTC ATT GAGuerber et al. (2003)Colletotrichum, Phyllosticta
GDRReverseGGG TGG AGT CGT ACT TGA GCA TGTTempleton et al. (1992)Colletotrichum
GDR1ReverseGGG TGG AGT CGT ACT TGA GCA TGTGuerber et al. (2003)Colletotrichum
Gpd1-LMForwardATT GGC CGC ATC GTC TTC CGC AAMyllys et al. (2002)Phyllosticta
Gpd2-LMReverseCCC ACT CGT TGT CGT ACC AMyllys et al. (2002)Phyllosticta
GPDHR2ReverseCTC RGM RGC RGC CTT GAT GGGlienke et al. (2011)Phyllosticta
Partial histone H3 gene (HIS3)CYLH3FForwardAGG TCC ACT GGT GGC AAGCrous et al. (2004)Colletotrichum
CYLH3RReverseAGC TGG ATG TCC TTG GAC TGCrous et al. (2004)Colletotrichum
Partial manganese superoxide dismutase gene (SOD2)SOD507FForwardATG GCA GCC TTT CCG TTG AGA TACCrouch et al. (2006)Colletotrichum
SOD507RReverseAGT TGA CAT GAA GCC ACC TAC AGCCrouch et al. (2006)Colletotrichum
SOD625FForwardGCC CAC AGT ACA TAT TGC CTA AGCCrouch et al. (2006)Colletotrichum
SOD625RReverseTCA TCC CGG GAG CCA GAA AAC CTCrouch et al. (2006)Colletotrichum
SODglo2-FForwardCAG ATC ATG GAG CTG CAC CAMoriwaki & Tsukiboshi (2009)Colletotrichum
SODglo2-RReverseTAG TAC GCG TGC TCG GAC ATMoriwaki & Tsukiboshi (2009)Colletotrichum
Partial mating type locus gene (MAT1-2)Mat1M72FForwardACG GCA AAC GGC TCA GGG AGT GCrouch et al. (2009)Colletotrichum
Mat1M72RReverseAAT GCC GAG TCC CAC GAG GTT CGCrouch et al. (2009)Colletotrichum
Partial Ras-related protein gene (Ypt1)Ypt1FForwardCGA CCA TYG GYG TKG ACT TTChen & Roxby (1996)Phytophthora
Ypt5RReverseGCA GCT TGT TSA CGT TCT CRSchena & Cooke (2006)Phytophthora
Partial RNA polymerase II largest subunit (RPB1)RPB1-Af (=RPB1-Ac)ForwardGAR TGY CCD GGD CAY TTY GGStiller & Hall (1997), modification by Giho SungPhoma
RPB1-CrReverseCCN GCD ATN TCR TTR TCC ATR TAMatheny et al (2002), modification by Giho SungPhoma
Partial RNA polymerase II second largest subunit (RPB2)fRPB2-414RReverseACM ANN CCC CAR TGN GWR TTR TGQuaedvlieg et al. (2011)Mycosphaerella
fRPB2-5FForwardGAY GAY MGW GAT CAY TTY GGLiu et al. (1999)Colletotrichum, Mycosphaerella
fRPB2-7RReverseCCC ATW GCY TGC TTM CCC ATLiu et al. (1999)Colletotrichum
Partial translation elongation factor 1-alpha gene (TEF)EF-2ReverseGGA RGT ACC AGT SAT CAT GTTO'Donnell et al. (1998)Monilinia, Mycosphaerella, Phyllosticta, Stenocarpella
EF1-728FForwardCAT CGA GAA GTT CGA GAA GGCarbone & Kohn (1999)Monilinia, Mycosphaerella, Phyllosticta, Stenocarpella
EF1-986RReverseTAC TTG AAG GAA CCC TTA CCCarbone & Kohn (1999)Monilinia, Mycosphaerella, Phyllosticta, Stenocarpella
EFCF1ForwardAGT GCG GTG GTA TCG ACA AGJones et al. (2011)Ceratocystis
EFCF2ReverseTGC TCA CGG GTC TGG CCA TOliveira et al. (2015)Ceratocystis
EFCF6ReverseCAT GTC ACG GAC GGC GAA ACJones et al. (2011)Ceratocystis
ELONGF1 (=EF1AF)ForwardTCA CGA TCG ACA TTG CCC TGKroon et al. (2004)Phytophthora
ELONGR1 (=EF1AR)ReverseACG GCT CGA GGA TGA CCA TGKroon et al. (2004)Phytophthora
TEF1-983F (=EF1-983F)ForwardGCY CCY GGH CAY CGT GAY TTY ATThe Hibbett lab primer protocols
TEF1-2218R (=EF1-2218R)ReverseAT GAC ACC RAC RGC RAC RGT YTGThe Hibbett lab primer protocols