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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.