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Table 1 Summary of sequence comparison in the entire region of sd1 gene among Oryza species using Nipponbare as a reference

From: Comparative Analysis of Rice Genome Sequence to Understand the Molecular Basis of Genome Evolution

Species/subspecies variety/accession genome

Origin

Entire region (bp)

Intron (bp)

Exon (bp)

Peptide (a. a.)

Total

SNPs

Indel

Total

SNPs

Indel

Total

Matching (%)

O. sativa ssp. japonica

Nipponbare

AA

Japan

2,743

1,573

1,170

389

Khau Mac Kho

AA

Vietnam

2,744

1,574

0

1

1,170

0

0

389

100

O. sativa ssp. Indica

Kasalath

AA

India

2,717

1,547

8

30 (7)

1,170

2 (2)

0

389

99.5

Shuusoushu

AA

China

2,719

1,549

8

28 (6)

1,170

3 (2)

0

389

99.5

93-11

AA

China

2,720

1,550

13

27 (5)

1,170

4 (3)

0

341a

99.2

O. rufipogon

W0106

AA

India

2,740

1,570

7

5 (3)

1,170

2 (2)

0

389

99.5

W0574

AA

Malaysia

2,720

1,550

8

29 (7)

1,170

2 (2)

0

389

99.5

W1943

AA

China

2,744

1,574

8

1

1,170

2 (2)

0

389

99.5

O. glaberrima

IRGC104038

AA

Senegal

2,683

1,513

10

64 (4)

1,170

6 (2)

0

389

99.5

O. barthii

W1588

AA

Cameroon

2,682

1,512

10

65 (5)

1,170

6 (2)

0

389

99.5

O. glumaepatura

IRGC105688

AA

Brazil

2,681

1,511

26

72 (8)

1,170

8 (3)

0

389

99.2

O. meridionalis

W1625

AA

Australia

2,793

1,605

116

188 (26)

1,185

13 (5)

15 (1)

394

97.7

O. longistaminata

W1413

AA

Sierra Leone

2,752

1,567

65

88 (18)

1,188

7 (2)

18 (1)

395

98.0

O. punctata

IRGC105690

BB

Bangladesh

2,466

1,290

145

695 (47)

1,176

51 (17)

26 (5)

391

94.4

O. minuta

IRGC101141

BBCC

Philippines

2,987

1,802

255

555 (51)

1,185

55 (23)

29 (5)

394

92.4

O. officinalis

IRGC100896

CC

Thailand

2,831

1,634

199

667 (46)

1,197

52 (21)

33 (4)

398

92.7

O. alta

IRGC105143

CCDD

S. America

2,546

1,322

153

691 (49)

1,224

63 (27)

62 (6)

407

89.2

O. brachyantha

IRGC101232

FF

Africa

2,787

1,590

456

577 (60)

1,197

100 (35)

39 (5)

398

88.5

O. granulata

IRGC102118

GG

Thailand

2,464

1,294

292

671 (54)

1,170

103 (41)

42 (4)

389

88.0

  1. Numbers of indels and SNPs in parentheses represent the total sites of insertion/deletion and non-synonymous substitutions, respectively
  2. a93-11 contains a non-synonymous SNP creating a stop codon within the exon 3 region