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Table 3 Accession numbers and SSRs for GenBank deposited sequences http://www.ncbi.nlm.nih.gov/ amplified from 16 Phytophthora species (Table 1) using primers designed on P. sojae with the first approach (Fig.1A).

From: Use of genome sequence data in the design and testing of SSR markers for Phytophthora species

Phytoph. species SELECTED PRIMERS(a)
  S1F-S3R S4F-S5R S6F-S7R S10F-11R S16F-17R S18F-19R S19F-20R S21F-22R S23F-S25R(1) (2)S31F-28R S27F-S31R S29F-S30R
P. alni subsp. alni SCRP2 NS++ 58°C/1.7 mM* EF216617 No SSR 58°C/1.0 mM* EF216607 (aac)4 58°C/1.7 mM* EF216602 (agc)6 58°C/1.0 mM* NS++ 55°C/1.7 mM* NA+ EF216590 No SSR 58°C/1.0 mM* EF216580 (aag)5 (agg)5 (aag)4 (aag)6 (agg)5 58°C/1.0 mM* EF216565 (agg)7 (aag)10 (agg)16 (aag)12 (aag)4 58°C/1.0 mM* NS++ 58°C/1.0 mM* EF216555 (aag)8 (agg)4 (agg)4 (aag)5 (agg)4 (aag)4 (aag)5 58°C/1.0 mM* EF216552 (aag)8 58°C/1.0 mM*
P. cambiv. SCRP67 NS++ 58°C/1.7 mM* EF216618 No SSR 58°C/1.0 mM* EF216606 (aac)4 58°C/1.7 mM* EF216601 (agc)4 (cg)5 58°C/1.0 mM* EF216593 No SSR 55°C/1.7 mM* NS++ 58°C/1.0 mM* NS++ 58°C/1.0 mM* EF216581 (agg)4 (aag)5 (aag)4 58°C/1.0 mM* EF216569 (agg)10 (aag)10 (agg)9 (aag)12 (agg)4 (agg)7 58°C/1.0 mM* NA+ NA+ EF216551 (aag)8 58°C/1.0 mM*
P. cinnam. SCRP115 NA+ NA+ NA+ NS++ 58°C/1.0 mM* NS++ 55°C/1.7 mM* NA+ NA+ NS++ 58°C/1.0 mM* NA+ NA+ NA+ EF2165 (aag)8 (agg)5 (aag)9 58°C/1.0 mM*
P. citricola SCRP130 NA+ EF216619 No SSR 58°C/1.0 mM* NA+ NA+ NA+ NA+ NA+ NS++ 58°C/1.0 mM* NA+ NS++ 58°C/1.0 mM* NA+ EF216553 (aag)7 (aag)7 58°C/1.0 mM*
P. europaea SCRP622 NS++ 58°C/1.0 mM* EF216616 (acg)4 58°C/1.0 mM* EF216605 No SSR 58°C/1.7 mM* EF216600 No SSR 58°C/1.0 mM* NS++ 55°C/1.7 mM* NS++ 55°C/1.7 mM* EF216589 No SSR 58°C/1.0 mM* EF216576 (aag)4 58°C/1.0 mM* EF216568 (agg)9 (aag)10 (aag)7 (agg)4 (aag)6 (agg)4 (agg)4 58°C/1.0 mM* NA+ NA+ EF21655054 (aag)9 58°C/1.0 mM*
P. fragariae var.rubi SCRP333 NA+ NA+ NS++ 58°C/1.7 mM* NS++ 58°C/1.0 mM* EF216594 (aac)4 55°C/1.7 mM* NA+ EF216584 No SSR 58°C/1.0 mM* NA+ NA+ NA+ NS++ 60°C/0.7 mM* EF216542 (aag)7 (aag)8 58°C/1.0 mM*
P. ilicis SCRP377 NS++ 58°C/1.7 mM* EF216608 (ccg)4 58°C/1.0 mM* NA+ NS++ 58°C/1.0 mM* NS++ 55°C/1.7 mM* NA+ NA+ NA+ EF216575 No SSR 58°C/1.0 mM* NA+ NS++ 60°C/0.7 mM* EF216543 (aag)5 58°C/1.0 mM*
P. infestans sc 03.26.3.3 NA+ EF216615 No SSR 58°C/1.0 mM* NA+ NA+ NS++ 55°C/1.7 mM* NA+ NA+ NA+ NA+ EF216560 No SSR 58°C/1.0 mM* NA+ NS++ 58°C/1.0 mM*
P. inundata SCRP644 EF216624 No SSR 58°C/1.0 mM* EF216614 No SSR 58°C/1.0 mM* NA+ EF216599 No SSR 58°C/1.0 mM* NS++ 55°C/1.7 mM* NA+ EF216588 No SSR 58°C/1.0 mM* NA+ NA+ NS++ 58°C/0.7 mM* NS++ 60°C/0.7 mM* EF216549 (aag)8 58°C/1.0 mM*
P. lateralis SCRP390 NS++ 58°C/1.0 mM* EF216611 No SSR 58°C/1.0 mM* EF216604 (ac)5 58°C/1.7 mM* EF216598 (agc)4 58°C/1.0 mM* NS++ 55°C/1.7 mM* EF216592 (acg)4 (agc)4 58°C/1.0 mM* EF216587 No SSR 58°C/1.0 mM* EF216579 (aag)5 58°C/1.0 mM* EF216564 (agg)5 (aag)4 (aag)6 (agg)4 58°C/1.0 mM* EF216556 (agg)4 58°C/0.7 mM* NS++ 60°C/0.7 mM* EF216548 (aag)5 (aag)9 58°C/1.0 mM*
P. nemor. SCRP910 NA+ EF216613 (ccg)4 58°C/1.0 mM* NA+ EF216597 No SSR 58°C/1.0 mM* NA+ NS++ 55°C/1.7 mM* NA+ NA+ EF216572 No SSR 58°C/1.0 mM* EF216559 No SSR 58°C/1.0 mM* NA+ EF216547 (aag)5 58°C/1.0 mM*
P. pseudos. SCRP674 EF216622 No SSR 58°C/1.0 mM* NS++ 58°C/1.0 mM* NS++ 58°C/1.7 mM* EF216596 No SSR 58°C/1.0 mM* NA+ NA+ NA+ NA+ EF216573 No SSR 58°C/1.0 mM* EF216557 (agg)14 58°C/1.0 mM* NS++ 60°C/0.7 mM* EF216546 (aag)4 58°C/1.0 mM*
P. psychro. SCRP630 EF216623 (agc)4 58°C/1.0 mM* EF216612 (ccg)4 58°C/1.0 mM* NA+ NA+ NA+ NA+ NA+ NS++ 58°C/1.0 mM* EF216574 No SSR 58°C/1.0 mM* EF216558 (agg)6 (agg)4 (aag)4 (agg)4 58°C/0.7 mM* NS++ 60°C/0.7 mM* EF216545 (aag)4 58°C/1.0 mM*
P. quercina SCRP541 EF216621 (agc)5 58°C/1.0 mM* NA+ NA+ NA+ NA+ NA+ NA+ NS++ 58°C/1.0 mM* EF216563 (aag)10 (aag)5 58°C/1.0 mM* EF216561 (agg)4 58°C/1.0 mM* NA+ EF216544 (aag)7 58°C/1.0 mM*
P. ramorum SCRP911 EF216620 No SSR 58°C/1.0 mM* EF216610 (acc)4 58°C/1.0 mM* EF216603 No SSR 55°C/1.7 mM* NS++ 58°C/1.0 mM* EF216595 No SSR 55°C/1.7 mM* EF216591 No SSR 58°C/1.0 mM* EF216586 No SSR 58°C/1.0 mM* EF216578 (aag)4 (atc)4 (aag)5 (aag)5 58°C/1.0 mM* EF216562 (aag)4 (agg)4 (aag)7 58°C/1.0 mM* NS++ 58°C/0.7 mM* NA+ EF216540 (aag)4 58°C/1.0 mM*
P. sojae SCRP555 NA+ EF216609 (aac)14 58°C/1.0 mM* NS++ 58°C/1.7 mM* NS++ 58°C/1.0 mM* EF382779 No SSR 55°C/1.7 mM* NA+ EF216585 (agc)6 58°C/1.0 mM* EF216577 (aag)12 (atc)6 (atc)4 (aag)5 58°C/1.0 mM* NS++ 58°C/0.7 mM* NS++ 58°C/0.7 mM* NA+ EF216541 (agg)4 (aag)11 58°C/1.0 mM*
  1. (a) = Primers listed in Table 2 and not reported in this table are those that did not produce any reliable sequence (see text).
  2. (1) = Primer S25R was replaced by primer S37R for P. nemorosa, P. pseudosyringae, P. psychrophila, and P. ilicis.
  3. (2) = Primer S31F was replaced by primer S34F for P. alni, P. citricola, P. infestans, P. nemorosa, and P. quercina.
  4. NA+ = Isolate-primer combinations that did not produce any amplification or produced complex profiles (two or more fragments).
  5. NS++ = Isolate-primer combinations for which single PCR bands were obtained but direct sequencing did not produce reliable results.
  6. °C/mM* = Selected annealing temperature (°C) and MgCl2 concentration (mM) in PCR reactions.