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.
| Locus | Primer name | Direction | Sequence (5'-3') | Reference | Used in Organism group |
|---|---|---|---|---|---|
| 5.8S nrRNA gene with the two flanking internal transcribed spacers (ITS) | ITS-4 | Reverse | TCC TCC GCT TAT TGA TAT GC | White et al. (1990) | All |
| ITS-5 | Forward | GGA AGT AAA AGT CGT AAC AAG G | White et al. (1990) | All | |
| ITS1F | Forward | CTT GGT CAT TTA GAG GAA GTA A | Gardes & Bruns (1993) | All | |
| LR5 | Reverse | TCC TGA GGG AAA CTT CG | Vilgalys & Hester (1990) | All | |
| V9G | Forward | TTA CGT CCC TGC CCT TTG TA | de Hoog and Gerrits van den Ende (1998) | All | |
| Intergenic Spacer 1 of nRNA operon (IGS1) | LR12R | Forward | CTG AAC GCC TCT AAG TCA GAA | Vilgalys lab, Duke University | Phytophthora, Puccinia, Verticillium |
| Seq5S | Reverse | CAG ATC AGA CGG GAT GCG GT | Woodhall et al. (2007) | Phytophthora, Puccinia, Verticillium | |
| Partial 18S ribosomal RNA gene (SSU) | NS1 | Forward | GTA GTC ATA TGC TTG TCT C | White et al. (1990) | Colletotrichum, Phoma |
| NS4 | Reverse | CTT CCG TCA ATT CCT TTA AG | White et al. (1990) | Colletotrichum, Phoma | |
| Partial 28S ribosomal RNA gene (LSU) | LR0R | Forward | GTA CCC GCT GAA CTT AAG C | Rehner & Samuels (1994) | Colletotrichum, Mycosphaerella, Phoma, Phyllosticta |
| LR5 | Reverse | TCC TGA GGG AAA CTT CG | Vilgalys & Hester (1990) | Colletotrichum, Melampsora, Mycosphaerella, Phyllosticta, Puccinia, Stenocarpella, Thecaphora, Verticillium | |
| LR7 | Reverse | TAC TAC CAC CAA GAT CT | Vilgalys & Hester (1990) | Phoma | |
| LSU1Fd | Forward | GRA TCA GGT AGG RAT ACC CG | Crous et al. (2009) | Melampsora, Mycosphaerella, Phyllosticta, Puccinia, Stenocarpella, Thecaphora, Verticillium | |
| Partial actin gene (ACT) | ACT-512F | Forward | ATG TGC AAG GCC GGT TTC GC | Carbone & Kohn (1999) | Colletotrichum, Mycosphaerella, Phyllosticta, Phoma, Verticillium |
| ACT-783R | Reverse | TAC GAG TCC TTC TGG CCC AT | Carbone & Kohn (1999) | Colletotrichum, Phyllosticta, Phoma, Verticillium | |
| ACT2Rd | Reverse | ARR TCR CGD CCR GCC ATG TC | Groenewald et al. (2013) & Quaedvlieg et al. (2011) | Mycosphaerella | |
| Partial apurinic DNA lyase gene (APN2) | Apn1W1F | Forward | ATG GAG CAC AAA AAC GAA CA | Crouch et al. (2009) | Colletotrichum |
| Apn1W1R | Reverse | GCG GAG CAG AGG ATG TAG TC | Crouch et al. (2009) | Colletotrichum | |
| Partial beta-tubulin gene (Tub2) | Bt-2b | Reverse | ACC CTC AGT GTA GTG ACC CTT GGC | Glass & Donaldson (1995) | Colletotrichum |
| Btub_F1 | Forward | GCC AAG TTC TGG GAG GTC ATC | Blair et al. (2008) | Phytophthora | |
| T1 | Forward | AAC ATG CGT GAG ATT GTA AGT | O’Donnell & Cigelnik (1997) | Colletotrichum, Mycosphaerella | |
| T2 | Reverse | TAG TGA CCC TTG GCC CAG TTG | O’Donnell & Cigelnik (1997) | Colletotrichum | |
| TUB2Fd (=BT2Fd) | Forward | GTB CAC CTY CAR ACC GGY CAR TG | Groenewald et al. (2013) & Woudenberg et al. (2009) | Colletotrichum, Mycosphaerella, Phoma | |
| TUB4Rd (=BT4R) | Reverse | CCR GAY TGR CCR AAR ACR AAG TTG TC | Groenewald et al. (2013) & Woudenberg et al. (2009) | Colletotrichum, Mycosphaerella, Phoma | |
| TUBUR1 (= BTubR1) | Reverse | CCT GGT ACT GCT GGT ACT CAG | Kroon et al. (2004) | Phytophthora | |
| Partial calmodulin gene (CAL) | CAL-228F | Forward | GAG TTC AAG GAG GCC TTC TCC C | Carbone & Kohn (1999) | Colletotrichum, Mycosphaerella, Phoma, Verticillium |
| CAL-235F | Forward | TTC AAG GAG GCC TTC TCC CTC TT | Quaedvlieg et al. (2012) | Mycosphaerella | |
| CAL-737R | Reverse | CAT CTT TCT GGC CAT CAT GG | Carbone & Kohn (1999) | Colletotrichum, Phoma, Verticillium | |
| CAL2Rd | Reverse | TGR TCN GCC TCD CGG ATC ATC TC | Groenewald et al. (2013) & Quaedvlieg et al. (2011) | Mycosphaerella | |
| CL1 | Forward | GAR TWC AAG GAG GCC TTC TC | O’Donnell et al. (2000) | Colletotrichum | |
| CL1C | Forward | GAA TTC AAG GAG GCC TTC TC | Weir et al. (2012) | Colletotrichum | |
| CL2A | Reverse | TTT TTG CAT CAT GAG TTG GAC | O’Donnell et al. (2000) | Colletotrichum | |
| CL2C | Reverse | CTT CTG CAT CAT GAG CTG GAC | Weir et al. (2012) | Colletotrichum | |
| Partial chitin synthase 1 gene (CHS-1) | CHS-354R | Reverse | TGG AAG AAC CAT CTG TGA GAG TTG | Carbone & Kohn (1999) | Colletotrichum, Phoma |
| CHS-79F | Forward | TGG GGC AAG GAT GCT TGG AAG AAG | Carbone & Kohn (1999) | Colletotrichum, Phoma | |
| Partial cytochrome oxidase 1 (CO1) | Cox1MlpAF | Forward | TAA GAT GAC TTT ATA GTA CCA A | Feau et al. (2009) | Melampsora |
| Cox1MlpAR | Reverse | GCT CCT ACC ATT ACM G | Feau et al. (2009) | Melampsora | |
| OomCoxI-Levlo | Reverse | CYT CHG GRT GWC CRA AAA ACC AAA | Robideau et al. (2011) | Phytophthora | |
| OomCoxI-Levup | Forward | TCA WCW MGA TGG CTT TTT TCA AC | Robideau et al. (2011) | Phytophthora | |
| PezizF | Forward | TCA GGR TTA YTA GGW ACA GCA TTT | Nguyen & Seifert (2008) | Verticillium | |
| PezizR | Reverse | ACC TCA GGR TGY CCG AAG AAT | Nguyen & Seifert (2008) | Verticillium | |
| Partial cytochrome oxidase 2 (COX2) | FM75 | Forward | CCT TGG CAA TTA GGA TTT CAA GAT | Martin & Tooley (2003) | Phytophthora |
| FM78 | Reverse | ACA AAT TTC ACT ACA TTG TCC | Martin & Tooley (2003) | Phytophthora | |
| Partial glutamine synthetase gene (GS) | GSF1 | Forward | ATG GCC GAG TAC ATC TGG | Stephenson et al. (1997) | Colletotrichum |
| GSF3 | Forward | GCC GGT GGA GGA ACC GTC G | Weir et al. (2012) | Colletotrichum | |
| GSR1 | Reverse | GAA CCG TCG AAG TTC CAG | Stephenson et al. (1997) | Colletotrichum | |
| GSR2 | Reverse | GAA CCG TCG AAG TTC CAC | Weir et al. (2012) | Colletotrichum | |
| Partial glyceraldehyde-3- phosphate dehydrogenase gene (GAPDH) | GDF | Forward | GCC GTC AAC GAC CCC TTC ATT GA | Templeton et al. (1992) | Colletotrichum |
| GDF1 | Forward | GCC GTC AAC GAC CCC TTC ATT GA | Guerber et al. (2003) | Colletotrichum, Phyllosticta | |
| GDR | Reverse | GGG TGG AGT CGT ACT TGA GCA TGT | Templeton et al. (1992) | Colletotrichum | |
| GDR1 | Reverse | GGG TGG AGT CGT ACT TGA GCA TGT | Guerber et al. (2003) | Colletotrichum | |
| Gpd1-LM | Forward | ATT GGC CGC ATC GTC TTC CGC AA | Myllys et al. (2002) | Phyllosticta | |
| Gpd2-LM | Reverse | CCC ACT CGT TGT CGT ACC A | Myllys et al. (2002) | Phyllosticta | |
| GPDHR2 | Reverse | CTC RGM RGC RGC CTT GAT GG | Glienke et al. (2011) | Phyllosticta | |
| Partial histone H3 gene (HIS3) | CYLH3F | Forward | AGG TCC ACT GGT GGC AAG | Crous et al. (2004) | Colletotrichum |
| CYLH3R | Reverse | AGC TGG ATG TCC TTG GAC TG | Crous et al. (2004) | Colletotrichum | |
| Partial manganese superoxide dismutase gene (SOD2) | SOD507F | Forward | ATG GCA GCC TTT CCG TTG AGA TAC | Crouch et al. (2006) | Colletotrichum |
| SOD507R | Reverse | AGT TGA CAT GAA GCC ACC TAC AGC | Crouch et al. (2006) | Colletotrichum | |
| SOD625F | Forward | GCC CAC AGT ACA TAT TGC CTA AGC | Crouch et al. (2006) | Colletotrichum | |
| SOD625R | Reverse | TCA TCC CGG GAG CCA GAA AAC CT | Crouch et al. (2006) | Colletotrichum | |
| SODglo2-F | Forward | CAG ATC ATG GAG CTG CAC CA | Moriwaki & Tsukiboshi (2009) | Colletotrichum | |
| SODglo2-R | Reverse | TAG TAC GCG TGC TCG GAC AT | Moriwaki & Tsukiboshi (2009) | Colletotrichum | |
| Partial mating type locus gene (MAT1-2) | Mat1M72F | Forward | ACG GCA AAC GGC TCA GGG AGT G | Crouch et al. (2009) | Colletotrichum |
| Mat1M72R | Reverse | AAT GCC GAG TCC CAC GAG GTT CG | Crouch et al. (2009) | Colletotrichum | |
| Partial Ras-related protein gene (Ypt1) | Ypt1F | Forward | CGA CCA TYG GYG TKG ACT TT | Chen & Roxby (1996) | Phytophthora |
| Ypt5R | Reverse | GCA GCT TGT TSA CGT TCT CR | Schena & Cooke (2006) | Phytophthora | |
| Partial RNA polymerase II largest subunit (RPB1) | RPB1-Af (=RPB1-Ac) | Forward | GAR TGY CCD GGD CAY TTY GG | Stiller & Hall (1997), modification by Giho Sung | Phoma |
| RPB1-Cr | Reverse | CCN GCD ATN TCR TTR TCC ATR TA | Matheny et al (2002), modification by Giho Sung | Phoma | |
| Partial RNA polymerase II second largest subunit (RPB2) | fRPB2-414R | Reverse | ACM ANN CCC CAR TGN GWR TTR TG | Quaedvlieg et al. (2011) | Mycosphaerella |
| fRPB2-5F | Forward | GAY GAY MGW GAT CAY TTY GG | Liu et al. (1999) | Colletotrichum, Mycosphaerella | |
| fRPB2-7R | Reverse | CCC ATW GCY TGC TTM CCC AT | Liu et al. (1999) | Colletotrichum | |
| Partial translation elongation factor 1-alpha gene (TEF) | EF-2 | Reverse | GGA RGT ACC AGT SAT CAT GTT | O'Donnell et al. (1998) | Monilinia, Mycosphaerella, Phyllosticta, Stenocarpella |
| EF1-728F | Forward | CAT CGA GAA GTT CGA GAA GG | Carbone & Kohn (1999) | Monilinia, Mycosphaerella, Phyllosticta, Stenocarpella | |
| EF1-986R | Reverse | TAC TTG AAG GAA CCC TTA CC | Carbone & Kohn (1999) | Monilinia, Mycosphaerella, Phyllosticta, Stenocarpella | |
| EFCF1 | Forward | AGT GCG GTG GTA TCG ACA AG | Jones et al. (2011) | Ceratocystis | |
| EFCF2 | Reverse | TGC TCA CGG GTC TGG CCA T | Oliveira et al. (2015) | Ceratocystis | |
| EFCF6 | Reverse | CAT GTC ACG GAC GGC GAA AC | Jones et al. (2011) | Ceratocystis | |
| ELONGF1 (=EF1AF) | Forward | TCA CGA TCG ACA TTG CCC TG | Kroon et al. (2004) | Phytophthora | |
| ELONGR1 (=EF1AR) | Reverse | ACG GCT CGA GGA TGA CCA TG | Kroon et al. (2004) | Phytophthora | |
| TEF1-983F (=EF1-983F) | Forward | GCY CCY GGH CAY CGT GAY TTY AT | The Hibbett lab primer protocols | Phoma | |
| TEF1-2218R (=EF1-2218R) | Reverse | AT GAC ACC RAC RGC RAC RGT YTG | The Hibbett lab primer protocols | Phoma |