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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.
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