Table 1 Statistics for assembly of cp and nR sequences from 30 Oryza species.

From: Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species

 

Species

Genome size (Mbp)

WGS reads for cp assembly

Complete sequence (bp)

Estimated copy numberb

Amount (Mbp)

Coverage (x)

     

Genome

Cp

Cp

45Sa

5Sa

45S

5S

1

O. sativa J. NP

430

860 (SRR1178954c)

2.0`

99

134,551 (KM088016c)

7,928 (KM036282c)

324 (KM036298c)

390

593

2

O. sativa J. Yukara

430

303 (SRR1182447)

0.7

227

134,551 (KM088017)

7,929 (KM036283)

324 (KM036299)

186

458

3

O. sativa JxI. M23

460

303 (SRR1182807)

0.7

147

134,551 (KM103382)

8,160 (KM036287)

322 (KM036303)

131

971

4

O. sativa IxJ. Tongil

460

253 (SRR1182443)

0.5

69

134,502 (KM103369)

8,160 (KM036286)

322 (KM036302)

255

1,593

5

O. sativa I. IR8

460

327 (SRR921498)

0.7

251

134,502 (KM103367)

8,166 (KM036284)

322 (KM036300)

140

746

6

O. sativa I. TN1

460

303 (SRR921505)

0.7

206

134,502 (KM103368)

8,164 (KM036285)

322 (KM036301)

210

894

7

O. rufipogon (W1943)36

439

500 (ERX096841)

1.1

128

134,510 (KM103372)

8,004 (KM117266)

303 (KM036304)

275

495

8

O. rufipogon (AC11-1008369)37

38034

1,442 (SRX480817)

3.8

245

134,586 (Dataset S1)

6,090d (Dataset S2)

322 (Dataset S3)

793

2,718

9

O. rufipogon (AC01-1002323)37

38034

712 (SRX480820)

1.9

685

134,572 (Dataset S1)

5,816d (Dataset S2)

499 (Dataset S3)

310

354

10

O. nivara (IRGC88812)30

39535

571 (SRX809784)

1.5

203

134,483 (Dataset S1)

5,823d (Dataset S2)

322 (Dataset S3)

439

5,561

11

O. nivara (IRGC100897)

448

775 (SRR1264534)

1.4

112

134,516 (KM088022)

7,904 (KM036288)

322 (KM036305)

441

1,129

12

O. barthii (WAB0028976)

411

159 (SRX502175)

0.4

91

134,585 (KM103378)

7,835 (KM117256)

325 (KM117247)

667

4,418

13

O. barthii (WAB0028903)

411

437 (SRX502171)

1.1

257

134,678 (KM103379)

7,845 (KM117257)

325 (KM117248)

748

2,380

14

O. barthii (WAB0028952)

411

441 (SRX502173)

1.1

319

134,678 (KM103380)

7,845 (KM117258)

325 (KM117249)

771

1,291

15

O. barthii (WAB0028987)

411

163 (SRX502178)

0.4

97

134,613 (KM103381)

7,836 (KM117252)

325 (KM117250)

368

1,989

16

O. barthii (IRGC101252)30

37635

1,113 (SRX809864)

3.0

1,277

134,598 (Dataset S1)

5,888d (Dataset S2)

325 (Dataset S3)

3,769

5,984

17

O. barthii (IRGC100934)

411

343 (SRX502164)

0.8

113

134,598 (KM103371)

7,836 (KM117253)

325 (KM117251)

630

4,414

18

O. barthii (W1588)

411

375 (SRR1264535)

0.9

60

134,590 (KM088023)

7,836 (KM036290)

325 (KM036307)

617

6,045

19

O. glaberrima (IRGC104574)

357

330 (SRX502311)

0.9

343

134,586 (KM103377)

7,836 (KM117254)

325 (KM117246)

198

1,820

20

O. glaberrima (IRGC96717)

357

188 (SRR1181643)

0.5

50

134,598 (KM088021)

7,836 (KM036289)

325 (KM036306)

455

3,670

21

O. glaberrima (IRGC103486)30

37035

647 (SRX809780)

1.7

218

134,614 (Dataset S1)

5,899d (Dataset S2)

325 (Dataset S3)

773

6,447

22

O. glaberrima (IRGC103937)

357

268 (SRX502309)

0.8

257

134,598 (KM103370)

7,836 (KM117255)

325 (KM117245)

358

2,374

23

O. glumaepatula (W1187)

400

1,536 (SRR1997915)

3.9

1,338

134,606 (KR364802)

6,427d (KR364804)

440 (KR364807)

1,461

528

24

O. glumaepatula (IRGC88793)30

36635

397 (SRX809892)

1.1

91

134,296 (Dataset S1)

5,841d (Dataset S2)

440 (Dataset S3)

554

278

25

O. glumaepatula (W2201)

400

1,728 (SRR1997912)

4.3

1,446

134,575 (KR364803)

5,830d (KR364805)

440 (KR364806)

2,292

1,107

26

O. glumaepatula (GEN1233)

464

253 (SRR1264537)

0.5

78

134,575 (KM103374)

8,074 (KM036292)

460 (KM036309)

598

191

27

O. meridionalis (IRGC105298)30

38835

760 (SRX809898)

2.0

270

134,555 (Dataset S1)

5,839d (Dataset S2)

499 (Dataset S3)

1,367

731

28

O. meridionalis (W2112)

435

1,000 (SRR1264536)

2.3

109

134,556 (KM103373)

8,190 (KM036291)

499 (KM036308)

461

2,525

29

O. longistaminata (IRGC110404)

352

563 (SRR1264538)

1.6

187

134,558 (KM088024)

7,844 (KM036293)

302 (KM036310)

200

69

30

O. punctata (IRGC105690)

423

250 (SRR1264539)

0.6

60

134,604 (KM103375)

7,745 (KM036294)

326 (KM036311)

307

1,317

  1. a The lengths of the most redundant and longest representative nR units are given for each species. The 45S transcription units were 5,769–5,783 bp long for Oryza species. We cannot rule out the presence of other nR units in each species because there is some variance in the length of the IGS.
  2. bCopy numbers of 45S and 5S are based on the average depth of raw reads mapping to each sequence and were calculated based on the 1x haploid genome equivalent of raw reads.
  3. cSRA and accession numbers of reads and assembled sequences deposited in GenBank.
  4. dLength of 45S transcription units.
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