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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.
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BMC Genomics

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