A recent duplication revisited: phylogenetic analysis reveals an ancestral duplication highly-conserved throughout the Oryza genus and beyond

Table 3 Divergence rate of Oryza minuta copies

	dS	dN	dN/dS	K
O. punctata 1/O. minuta 1	0.000	0.007	/	0.0484
O. punctata 2/O. minuta 2	0.003	0.011	3.667	0.0525
O. officinalis 2/O. minuta 3	0.024	0.021	0.875	0.08
O. minuta 1/O. minuta 2	0.024	0.023	0.958	0.0815
O. minuta 1/O. minuta 3	0.045	0.043	0.956	0.0742
O. minuta 2/O. minuta 3	0.035	0.037	1.057	0.0873
O. punctata 1/O. punctata 2	0.021	0.033	1.571	0.0805
O. punctata 1/O. officinalis 2	0.035	0.036	1.029	0.1141
O. punctata 2/O. officinalis 2	0.035	0.035	1.000	0.079
	Ns	Nn
O. punctata 1	8	25
O. punctata 2	8.5	31.5
O. minuta 1	8	26
O. minuta 2	10	27
O. minuta 3	11	36
O. officinalis 2	8	29

Synonymous (dS), non-synonymous (dN) and intronic (K) substitution rates are indicated between the allotetraploid O. minuta combined copies (from the five genes B, D, E, H and I), and their putative orthologs in diploid progenitors (O. punctata and O. officinalis), between the homeologous copies in O. minuta, and between the diploid parental orthologous copies. Number of synonymous (Ns) and non-synonymous substitutions (Nn) are indicated for the tetraploid and its parental genomes, with Nipponbare as outgroup.

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