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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.