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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