Table 7

Success of PCR amplification and intron length variation for COSII nuclear loci in Asclepias and across Apocynaceae

Number of Individuals PCR successful/PCR attempted

Approximate Product Size (bp)#


Arabidopsis Ortholog

tair Annotation

Primer Set

Introns spanned*

Coding Sequence (bp)

As1

M2

B3

Ap4

Al5

As

M

B

Ap

Al


At1g24360

3-oxoacyl-(acyl-carrier protein) reductase, chloroplast

At1g24360a

360, 441, 487

234

15/20

1/2

1/2

2/2

1/1

1400-1500

1500

1000

300, 1000

1000

At1g24360b

582, 615

117

14/16

2/2

2/2

2/2

1/1

500-700

500

500

500

700, 1500

At1g24360c

750

117

16/16

2/2

2/2

2/2

1/1

200

200

200, 1500

200

200, 700


At1g44760

universal stress protein (USP) family protein

At1g44760a

369, 491

334

1/16

1/2

1/2

2/2

1/1

1300

1200

1200

1100

700


At1g55880

pyridoxal-5'-phosphate-dependent enzyme

At1g55880a

1043

394

13/16

2/2

2/2

2/2

1/1

1200

900

700 - 800

700

300, 700


At1g77370

glutaredoxin, putative

At1g77370a

164, 238

172

16/20

2/2

2/2

0/2

0/1

1400-1500

1100

1100 -1200

n/a

n/a


At2g03120

homologous to Signal Peptide Peptidases (SPP)

At2g03120a

156

210

19/19

2/2

2/2

2/2

1/1

300-400

300

300

300

300


At2g06530

VPS2.1 (vesicle-mediated transport)

At2g06530a

276

145

20/20

2/2

2/2

2/2

1/1

400-650

400

700 -

(600, 1000)

600 -

(800,1000)

400, 1200


At2g21960

unknown protein

At2g21960a

503, 592, 722

366

7/16

2/2

2/2

2/2

1/1

1500

1500

1700

1600 - 1700

1100

At2g21960b

813

84

12/16

2/2

2/2

2/2

1/1

200-300

200

150

150

150


At2g30200

[acyl-carrier-protein] S-malonyltransferase

At2g30200a

377, 444

185

12/16

2/2

2/2

2/2

1/1

1400

1000

1200

900

1200, >>1500

At2g30200b

587, 636, 774

392

13/20

2/2

2/2

2/2

1/1

700-1500

1200

1200

1200

1200

At2g30200c

855

160

16/16

0/2

2/2

2/2

1/1

300

n/a

300

300

300


At2g34620

mitochondrial transcription termination factor-related

At2g34620a

596

254

19/19

2/2

2/2

2/2

2/2

300

300

300

300 - 1000

300

At2g34620F/

596

531

15/16

2/2

2/2

2/2

0/2

600

600

600

600

n/a

At2g34620aR


At2g47390

serine-type endopeptidase

At2g47390a

1718

401

20/20

2/2

2/2

2/2

0/2

500-600

500

500

500

n/a

At2g47390b

2177, 2243, 2304, 2454, 2592

506

1/16

0/2

0/2

0/2

0/2

1500

n/a

n/a

n/a

n/a


At4g13430

methylthioalkylmalate isomerase

At4g13430a

510, 579, 696

275

14/16

2/2

2/2

2/2

1/1

700-1000

900, 1200

1200

1200

1200

At4g13430b

771, 849, 945, 995, 1050

391

16/20

0/2

2/2

0/2

1/1

1300-1500

n/a

>1500

n/a

1500

At4g13430c

1182, 1230

278

15/16

2/2

2/2

2/2

1/1

(500, 800)-1000

800

900 - >1500

800

500, 900, 1200


At4g26750

hydroxyproline-rich glycoprotein family protein

At4g26750a

305, 381

241

1/16

2/2

2/2

2/2

0/1

1500

>1500

1500

1000

n/a


At5g13420

putative transaldolase

At5g13420a

348, 398

295

12/16

2/2

2/2

2/2

0/1

1300

1100

1000

700

n/a

At5g13420b

699, 888

338

20/20

2/2

2/2

2/2

1/1

800-900

1200

1200

500, 1200

1500


At5g23540

26S proteasome regulatory subunit

At5g23540a

308, 390, 567

436

0/16

2/2

2/2

1/2

0/1

n/a

>>1500

300, 700, >>1500

500, 700

n/a

At5g23540aF At5g23540bR

308, 390

231

7/16

2/2

2/2

1/2

1/1

1400

>>1500

700 - 900, >>1500

700

1200


At5g49970

bifunctional pyridoxine (pyridoxamine) 5'-phosphate oxidase (PPOX)

At5g49970a

507

193

20/20

2/2

2/2

2/2

2/2

300

300

300

300

300

At5g49970b

613, 780

226

16/16

2/2

2/2

2/2

1/2

500-900

800

800

700

1000

At5g49970aFAt5g49970bR

507, 613, 780

398

15/16

n/a

n/a

n/a

n/a

1000-1500

n/a

n/a

n/a

n/a


*Intron numbers represent the starting position of the intron in Arabidopsis.

1Asclepiadinae Samples include 4 genera: Asclepias (17), Gomphocarpus, Calotropis, and Pergularia.

2Marsdenieae

3Baisseeae

4Apocyneae

5Alyxieae

#Two numbers separated by a comma indicate multiple PCR products. A range of numbers indicates size variation among individuals.

Straub et al. BMC Genomics 2011 12:211   doi:10.1186/1471-2164-12-211

Open Data