Skip to main content

Table 2 Estimated nucleotide diversity within the sd1 gene region of O. sativa and its divergence with other Oryza species in comparison with Adh1 gene region

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

  No of sites S π K sat-ruf K sat-gla K sat-bar K sat-glu K sat-mer K sat-lon K sat-pun K sat-min K sat-off K sat-alt K sat-bra K sat-gra
Entire genic region sd1 2,713 19 0.0036 0.0022 0.0058 0.0058 0.0074 0.0223 0.0175 0.0772 0.0778 0.0749 0.0812 0.1635 0.1446
Adh1 2,891 7 0.0014 0.0013 0.0061 0.0019 0.0058 0.0160 0.0182 0.0752 0.0685 0.0676 0.0690 0.1655 0.1381
Exons sd1 1,170 4 0.0019 0.0012 0.0047 0.0047 0.0065 0.0109 0.0065 0.0454 0.0482 0.0454 0.0528 0.0844 0.0942
Adh1 1,140 2 0.0011 0.0008 0.0016 0.0007 0.0016 0.0042 0.0042 0.0257 0.0339 0.0348 0.0385 0.0487 0.0603
Synonymous sd1 300.6 1 0.0020 0.0014 0.0154 0.0154 0.0190 0.0326 0.0218 0.1229 0.1036 0.1036 0.1228 0.2198 0.1889
Adh1 265.4 2 0.0045 0.0035 0.0068 0.0030 0.0068 0.0183 0.0183 0.1085 0.1487 0.1534 0.1720 0.2040 0.2373
Non-synonymous sd1 869.4 3 0.0018 0.0012 0.0012 0.0012 0.0024 0.0038 0.0014 0.0214 0.0261 0.0236 0.0300 0.0396 0.0585
Adh1 874.6 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0023 0.0023 0.0023 0.0023 0.0074 0.0139
Introns sd1 1,543 15 0.0049 0.0037 0.0074 0.0074 0.0087 0.0416 0.0336 0.1300 0.1255 0.1240 0.1255 0.3001 0.2512
Adh1 1,751 5 0.0015 0.0013 0.0104 0.0030 0.0097 0.0272 0.0314 0.1246 0.1023 0.0995 0.0986 0.2938 0.2189
  1. S and π: number of substitutions (polymorphic sites) and nucleotide diversity in O. sativa (five varieties). K: nucleotide divergence calculated by Jukes and Cantor method between two species as shown in subscript; sat = O. sativa, ruf = O. rufipogon, gla = O. glaberrima, bar = O. barthii, glu = O. glumeapatula, mer = O. meridionalis, lon = O. longistamonata, pun = O. punctata, min = O. minuta, off = O. officinalis, alt = O. alta, bra = O. brachyantha, gra = O. granulata