Skip to main content

Advertisement

Table 4 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. ramorum with the first approach (Fig. 1A).

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

Phytophthora species SELECTED PRIMERS(a)
  (1)R1F-R3R R3F-R4R R4F-R5R R7F-9R(2) R10F-R11R R13F-R14R R16F-R17R
P. alni subsp. alni SCRP2 NA+ NA+ EF216645 No SSR 58°C/1.0 mM* EF216671 No SSR 58°C/1.0 mM* EF216662 No SSR 58°C/1.7 mM* EF216651 (aag)4 58°C/1.7 mM* EF216625 (acg)4 58°C/1.0 mM*
P. cambivora SCRP67 NS++ 58°C/1.0 mM* NA+ NS++ 58°C/1.0 mM* EF216673 (agc)8 58°C/1.0 mM* EF216663 (agg)4 (aag)4 (agg)4 58°C/1.7 mM* NS++ 58°C/1.7 mM* EF216626 (acg)4 58°C/1.0 mM*
P. cinnamomi SCRP115 NA+ NA+ NA+ NA+ NA+ NS++ 58°C/ 1.7 mM* NA+
P. citricola SCRP130 NA+ NA+ EF216644 No SSR 58°C/1.0 mM* NA+ NA+ NA+ EF216630 No SSR 58°C/1.0 mM*
P. europaea SCRP622 NS++ 58°C/1.0 mM* NA+ EF216643 No SSR 58°C/1.0 mM* NA+ EF216661 (agg)4 (aag)7 (agg)5 58°C/1.7 mM* EF216655 (aag)4 58°C/1.7 mM* NA+
P. fragariae var. rubi SCRP333 NS++ 58°C/1.0 mM* NS++ 58°C/1 mM** EF216634 No SSR 58°C/1.0 mM* EF216672 (agc)7 58°C/1.0 mM* EF216657 (aag)4 (agg)4 58°C/1.7 mM* EF216647 (aag)4 58°C/1.7 mM* NS++ 58°C/1.0 mM*
P. ilicis SCRP377 NS++ 58°C/1.0 mM* EF216646 (agc)4 (agc)4 58°C/1.0 mM* EF216635 (agc)4 (accat)5 58°C/1.0 mM* EF216664 (actg)3 (agc)6 58°C/1.0 mM* NS++ 58°C/1.7 mM* EF216648 No SSR 58°C/1.7 mM* NS++ 58°C/1.0 mM*
P. infestans sc 03.26.3.3 NS++ 58°C/ 1.0 mM* NA+ NA+ NA+ NS++ 58°C/1.7 mM* NA+ NA+
P. inundata SCRP644 EF216633 No SSR 58°C/ 1.0 mM* NA+ NA+ NA+ NA+ EF216654 No SSR 58°C/1.7 mM* EF216629 No SSR 58°C/1.0 mM*
P. lateralis SCRP390 EF216631 No SSR 58°C/1.0 mM* NA+ EF216642 (aac)5 (agc)5 58°C/1.7 mM* EF216669 (agc)5 (aac)6 58°C/1.0 mM* EF216660 (agg)4 58°C/1.7 mM* NA+ EF216628 (agg)8 (agc)4 58°C/1.0 mM*
P. nemorosa SCRP910 NS++ 58°C/1.0 mM* NA+ EF216639 (agc)4 (accat)4 58°C/1.0 mM* EF216668 (actg)3 (agc)6 58°C/1.7 mM* NS++ 58°C/1.7 mM* EF216653 (agg)9 58°C/1.7 mM* NA+
P. pseudosyringae SCRP674 EF216632 No SSR 58°C/1.0 mM* NA+ EF216641 (accat)4 58°C/1.0 mM* EF216667 No SSR 58°C/1.0 mM* NA+ EF216652 No SSR 58°C/1.7 mM* NA+
P. psychrophila SCRP630 NS++ 58°C/1.0 mM* NA+ EF216640 (accat)4 58°C/1.0 mM* EF216666 (actg)3 (agc)6 58°C/1.0 mM* NA+ NS++ 58°C/1.7 mM* NS++ 58°C/1.0 mM*
P. quercina SCRP541 NS++ 58°C/1.0 mM* NA+ EF216638 No SSR 58°C/1.0 mM* EF216674 No SSR 58°C/1.0 mM* NA+ EF216651 (aag)8 (aag)4 58°C/1.7 mM* NA+
P. ramorum SCRP911 NS++ 58°C/1 mM* NA+ EF216637 (agc)4 (agc)10 (agc)4 58°C/1.0 mM* EF216665 (agc)24 58°C/1.0 mM* EF216659 (aagcc)4 (agg)9 (aag)7 58°C/1.7 mM* EF216650 (aag)10 58°C/1.7 mM* EF216627 (atc)4 (agg)8 58°C/1.0 mM*
P. sojae SCRP555 NA+ NA+ EF216636 (agc)5 58°C/1.0 mM* EF216670 (agc)10 (agcg)5 58°C/1.0 mM* EF216658 (agg)5 (aag)6 (agg)4 58°C/1.7 mM* EF216649 (acg)4 (aag)4 58°C/1.7 mM* NA+
  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 R1F was replaced by primer R2F for P. cambivora, P. inundata, P. nemorosa, P. ilicis and P. fragaria.
  3. (2) = Primer R9R was replaced by primer R8R for 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.