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

Rice

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

		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
Entire genic region	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
Exons	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
Synonymous	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
Non-synonymous	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
Introns	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

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