Table 2.
Set of primers designed with the 1st approach (Fig. 1A) to amplify genomic regions with candidate SSRs in a broad range of Phytophthora species (Table 1).
| Forward primers(a) | Reverse primers(a) | SSRs(a) | Source(b) | |
| P. sojae | S1F ACGACGTGTCCAAGAACCAC |
S3R ATGTTGACCGTGTTCTGCTG |
(CCG)7;(AGC)4; (AGC)14 | scaffold_3: 1346836–1347814 |
| S4F AARATGACGTGGACKGAGAG |
S5R TGATSGTGGAGAARCTCATCT |
(AAC)14 | scaffold_14: 861958–862585 |
|
| S6F GGAGTTCGCCATCAACAACT |
S7R TCAGCTTCTGTCGRTCGAC |
(AAG)14 | scaffold_24: 159790–160289 |
|
| S8F YGYGTCTCGCCCAYGAC |
S9R GACGACACCGGSGAGAG |
(ACC)4;(AGC)4; (AGC)28; (AAC)4 | scaffold_76: 171071–172890 |
|
| S10F GCGSTACGAGACCTGGAC |
S11R GACTCRCCCTTCGACTCSTC |
(CAG)14 | ||
| S12F GGAGGCCGAGTCGGARTA |
S13R TAYTCCGACTCGGCCTCC |
(AGC)14 | scaffold_136: 56988–57479 |
|
| S14F GACGCMSYYGAGTGGAAAG |
S15R ATTTKGSACAGATACCGACG |
(AAG)15 | scaffold_65: 332082–332852 |
|
| S16F TCTACGTGAATGCCATGAGG |
S17R CGTTCAGCTTCTGTCGATCR |
(AAG)15 | scaffold_79: 50973–51428 |
|
| S18F YACCATCTCCAACCTGCTG |
S19R CACCACCTCGAGTAGCTCCC |
(AGC)7; (AGG)13 | scaffold_2: 1159730–1160958 |
|
| S19F GGGAGCTACTCGAGGTGGTG |
S20R TCGTCTCAATCTCKGACTGA |
(AGC)6 | ||
| S21F ATCTGGGCTTCCASGAGGT |
S22R CTGATCCTCCGCCACAY |
(AAG)12; (ATC)6; (ATC)4; (AAG)5 | scaffold_138: 18289–18854 |
|
| S23F GACTCGGACTCGGACGAC |
S25R CTCCTGCTCKTCTTTCAGGC |
(AGG)7; (AAG)10; (GAG)4; (AAG)12; (GAG)5; (AGA)6 | scaffold_90: 249340–250137 |
|
| S37R CTTRCCBTCCTTGTCCTTYT |
||||
| S27F GAAGCGCGGGCGWGT |
S31R TCCTCCTCTTCTTCTTCGTCW |
(AAG)4; (AGG)4; (ACG)4; (AGG)11 | scaffold_16: 680126–681136 |
|
| S31F WGACGAAGAAGAAGAGGAGGA |
S28R TCATTCATCAGCGTGTCRAT |
(GAG)4 | ||
| S34F ABGAWGACGABGAGGAVGAV |
||||
| S29F MGCAAGAAGGCGTCGTA |
S30R CCTTCATCATGAGCTTCTGG |
(AGG)4 (AAG)11 | scaffold_40: 353572–354360 |
|
| P. ramorum | R1F GYGGCGGTGGCTACAGYG |
R3R CTGCTGYTGCTGGTTGAAAG |
(ACC)4; (ACC)5; (ACC)4 | scaffold_23: 349447–350425 |
| R2F CTACTCSAGCCGCTACGC |
||||
| R3F CTTTCAACCAGCARCAGCAG |
R4R GTTCATCATGCCWCCCATR |
(AGC)8 | scaffold_23: 350406–351828 |
|
| R4F YATGGGWGGCATGATGAAC |
R5R AGGACCAGGAGATGGAGGAC |
(AGC)4; (AGC)12; (AGC)4 | ||
| R7F TGTTCCARACCCGCTTCC |
R8R CACCAAGCAGCACKCGC |
(ACG)9; (AAC)5; (AGC)10 | scaffold_10: 436897–437690 |
|
| R9R GGAACGCACCAAAGACGC |
||||
| R10F GGAGATGACGGAAGATGACG |
R11R CCATCGAARTACATSACACGA |
(AAGCC)4; (AGG)9; (AAG)7 | scaffold_5: 750031–750612 |
|
| R13F AAGTCGAAGCTCGTGGTSAC |
R14R GTATCCGCTGRAAGAGCGTC |
(AAG)10 | scaffold_78: 40203–40815 |
|
| R15F CCGGAGCGCGTGGA |
R16R GGTAGTTGAGCGGCTTCTTG |
(CCG)6 | scaffold_2778: 35–305 |
|
| R16F CAAGAAGCCGCTCAACTACC |
R17R TAACGGATCAGCTCTTGCTG |
(ATC)4; (AGG)8 | scaffold_2778: 286–1134 |
|
| P. infestans | I3F GCCTGTGGAYGAGAATGGYS |
I4R CAGATCCACGACACCRGGY |
(AAG)8 | Pi_002_41652 _Feb05 |
| I5F CATCAACAAGTGCTCGTWCS |
I6R TAGTCRAYGTTCTTGTTGTTCA |
(AGC)5; (AGC)8 | Supercont1.7 842678–843649 |
|
| I7F GHGTGGGCGAGTACTCCAAG |
I8R AAGCTGGCTATRWACACTGCCG |
(AG)9 | Supercont1.4 1481811–1482015 |
|
| I9F GCATYGGGTCGTTCCTGTA |
I10R AGHGTGCAGTACAGACCCGC |
(AAG)11 | Supercont1.5 1235771–1236143 |
|
| I11F TCGTCBGTGTCCTCBACGTC |
I12R ACCAGCATCTTRTTCTGRGCAG |
(ACC)8 | Supercont1.45 522394–522633 |
|
| I13F GTCTGCGCTGTCGGAACT |
I14R TRATGATGCGGTTCATCTCG |
(AAG)7; (AAG)4 | Supercont1.220 167896–168460 |
|
(a) = Primers are listed according to the localization in their respective genome projects (P. sojae, P. ramorum or P. infestans) and according to the flanked SSRs. In some circumstances, a pool of different primers was designed to amplify selected genomic regions from as many as possible Phytophthora species. Similarly, when target regions contained two or more SSRs and were too long to be amplified by a single amplification a pool of different primers was designed.
(b) = Gene sequences available at http://genome.jgi-psf.org/sojae1/sojae1.home.html (P. sojae), http://genome.jgi-psf.org/ramorum1/ramorum1.home.html (P. ramorum) and http://www.pfgd.org/ or http://www.broad.mit.edu/annotation/genome/phytophthora_infestans/Home.html (P. infestans).