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Table 2 List of 34 SSRs evaluated in 74 isolates of C. purpurea and three related species (C. pusilla, C. paspali, and C. fusiformis)

From: Simple sequence repeat markers that identify Claviceps species and strains

Primer

Primer sequence

SSR motif

Allele range (bp)

A

H

Alleles/isolate

Alleles for four species

C. humidiphila

C. pusilla

C. paspali

C. fusiformis

Cpur2a,b

F: GCTGGCTTCGTGTTCACAG

(AAAC)4

443–466

7

1.56

1

 

191, 236

138, 240

240

R: GGAAACCTCGTTGCTGACC

         

Cpur6a

F: GACTGGCATCCGCATTTCC

(ATGT)6

317–375

7

1.34

2

 

101, 243

103, 245, 442

NA

R: GTCGCGCGTGAATCTTGAG

        

Cpur7

F: TCAACGCACAGAGCAATCC

(AGC)5

371–395

9

1.67

1

351

243, 386

156, 427

432

R: CTGCACAAGCACTGGAAGG

         

Cpur8b

F: TTCTCCCGCCGTATAACCG

(GGT)8

302–317

7

1.62

1

295

97, 203

97, 136

127

R: GTTCGCGATCTGACGTTCC

         

Cpur12

F: CGGAGCAAATGTTCGTCCC

(GAT)4

413–433

4

1.15

1

419

102,125

107, 247, 364, 371

231, 378

R: AGTACATCGGCCTGGAACC

        

Cpur14

F: GCGCCTGGCATAATAGTGG

(ACAT)6

461–481

7

0.69

1

425

203, 244

135, 185

407, 432

R: TCGAAGTCGAGAGGAACCG

         

Cpur20

F: GACACCCATTGGCAACCAG

(ACC)4

318–321

2

0.42

1

 

159, 441

203, 353, 502

344

R: TCAGAGGCGCAGTATCGAC

        

Cpur23a

F: TGCCTTGCCTTCTTTCAGC

(ACAT)5

350–365

5

1.08

2

601

123, 166, 211, 378

151, 228, 341

246, 412, 477

R: GGCAACTTGGCAGAAGACC

      

Cpur24

F: CCGATTGAGCAACAGCTCG

(AAG)7

404–438

7

0.75

1

409

204, 220, 241, 368

102, 210

190, 270, 289, 354

R: CTGAGCGGCAAAGTCATCC

       

Cpur26

F: GGTCGTCTATGGCGTGGAG

(GGGAT)4

411–426

4

0.81

1

 

164, 496

92, 301, 421

84, 204, 251

R: CTCCGAATCAATCCCGTGC

       

Cpur30a,b

F: CCACCGGGCATTGTTGAAG

(ACATT)4

225–305

6

1.03

2

265

160

166, 247, 396, 417

160, 321, 506

R: CATGTCTCAAGGCGGCAAG

       

Cpur31b

F: ACTCCCGCTCAATAAGCCTC

(CTT)4

233–245

7

1.25

2

103, 163

295

233

203

R: CAGAATATGCAAAGGGTGCG

         

Cpur32a,b

F: AACGCAGCGCATGAAAGAC

(AAC)5

154–182, 393–405

6

1.39

2

 

112, 396

176

145, 159, 176, 483

R: TCGTGGAGTCCGTGAATGG

       

Cpur34a,b

F: TGGTCTCGCGGTATTAGGC

(GCT)5

285–294

4

1.07

1

 

251

123, 471

NA

R: TCTACCTTTCCGAGCCAGC

         

Cpur35b

F: CATCGCAATGCCGTCCTAC

(CGG)4

369–390

5

0.97

2

 

112, 157, 163

163

154, 176

R: GAACAGCCTACAGCATCGC

        

Cpur40a

F: CCACCACAGTTGCTCTTGC

(AGC)5

411–417

4

1.08

1

421

136, 171

129, 233

233

R: ACGACATGACCAGCTACCG

         

Cpur41

F: ACTTGACGGCTGGGTATGG

(AC)9

431–454

5

1.22

1

 

113, 450

220, 254, 379, 500

89, 112, 376, 450

R: GCTGTTTCCAAGACGGCAG

        

Cpur43

F: TGAGTCGTGACCCAACCAG

(AAGAC)4

250–280

5

1.35

1

 

576

122, 364, 479

150

R: TCACCCGTAAGTGTGCTCC

        

Cpur48a

F: TCCATCCGACAACGAGCTG

(CGT)7

431–442

4

0.44

2

 

210, 267, 336

252, 358, 510

101, 266, 478, 498

R: GGTATGCCGGAGGGTATGG

      

Cpur50a

F: TTCCCTCGGTGACGAATCC

(CGG)6

321–330

4

1.58

1

 

147, 238

110, 231

229

R: TCTCGGCCCTCCATCAAAG

         

Cpur52a

F: CTCGCCATAGCAAACAGCG

(CTT)4

433-445

4

1.06

1

 

154

154, 193

127, 154

R: CAGTACGCAGATTTGGCGG

         

Cpur53a

F: CGATGGCCAAACTCTACGG

(CT)6

469–479

5

1.12

1

 

238

166, 471

103, 107, 471

R: AGACACCCTGTTTGAGCCC

        

Cpur55a

F: TTCCAAGCCTGTCGTCCTG

(CCT)6

472–475

3

0.71

1

469

161, 294

399

197, 441, 472

R: GACCTGTTTGCCGACATCC

        

Cpur56a

F: CAAAGCAGCCCGTCACTTC

(ATC)8

340–401

15

1.85

2

407–413

361, 375

229, 305

115, 288, 375

R: CGCGCATTTCTGGTAGAGC

        

Cpur58a

F: AGGTTGGACTTGGTAGGCG

(CGT)4

437–458

6

1.11

2

446, 449

203, 254, 290

106, 205, 319

109, 207

R: GCTTCAGTACAGCATGGGC

       

Cpur61

F: ACGGAAAGGATGGAAGCCC

(GAGT)5

136, 447–465

6

0.72

1

 

NA

90

90

R: CATGCCAATCCCGCAGAAC

        

Cpur68a

F: TTGTTAACGTCGCGAAGGC

(CGT)4

97, 255–263

3

0.50

1

 

252, 322

98, 146, 175, 240

139, 150, 366, 431

R: AAGTTGGCGTTGAATGGGC

      

Cpur69

F: ATTCCTCGCCCTCTTTGGG

(GGT)8

104, 427–436

7

0.72

3

98, 325

98, 141, 261, 468

159, 176, 325

103, 207, 408

R: CGTCAACTTCGCCGATTCC

     

Cpur72

F: AGTCGTGGGAGATTGGAGC

(AAG)4

275

2

0.34

1

278

485

252, 275

222, 275

R: TCCTGTACTTGCCGAACCG

         

Cpur145

F: CTGTCGCGTGCTTTCGTAG

(GAT)5

231–241

5

1.03

2

247

111, 200, 237

237

130, 237

R: CAGCGCGTCTATTATGCGG

        

Cpur156a

F: TGGCTACGGTCCTGGTTTC

(AAAGC)4

360–475

8

1.75

1

 

105, 120, 154, 522

134

107, 135, 259

R: CCCTGCATAGAGGGTACAGC

       

Cpur157

F: GCCGTGAAGTGACGAATGC

(AAG)5

372–405

11

1.66

2

534

253, 399

249, 327

207, 248, 381, 396

R: AGTGTCAAGTGGGCGGTAG

        

Cpur177a

F: CCCTCACGGTACGAGATCC

(CCG)6

465–475

3

0.95

1

 

100, 227, 312, 475

261, 317, 475

160, 317

R: CTGCCCATCATCAAAGCCC

       

Cpur192a

F: CGCTTTGGACCGCATGTAG

(TATG)4

101–110, 290–305

7

1.04

2

 

261, 269, 290, 441

105, 343

105, 343

R: AGTACCTGGGCAAAGTCCG

       

Ave.

       

5.8

1.09

1.4

  1. SSR primer sequences, forward (F) and reverse (R), SSR motif, allele size range (bp), alleles per primer pair (A), Shannon-Weiner index coefficient for each primer pair (H), and number of alleles per isolate are listed
  2. Unique alleles for each of the four species, C. humidiphila, C. pusilla, C. paspali and C. fusiformis, are also recorded. A blank indicates absence of unique alleles for that species while NA refers to no amplification
  3. aPrimers that were polymorphic in C. humidiphila
  4. bPrimers that distinguished isolates of CA Group 3 from those of CA Group 4
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Fungal Biology and Biotechnology

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