Assessing the Extent of Substitution Rate Variation of Retrotransposon Long Terminal Repeat Sequences in Oryza sativa and Oryza glaberrima

Rice

Table 4 Kimura 2p Nucleotide Distances of Complete Retrotransposons

No	Element family	Kdx	Kdx (G)	Kdx(S)	MY (G)	MY (S)
1		0.0332
2	Copia_Ecgs	0.0241	0.0629	0.0331	1.5725	0.8275
8		0.0232
9	SZ-50	0.0271	0.0382	0.0528	0.9550	1.3200
10		0.0336
11	RIRE 2	0.0196	0.0341	0.0318	0.8525	0.7950
16		0.0288
17	BAJIE	0.0492	0.0507	0.0401	1.2675	1.0025
21		0.0442
22	RIRE10	0.0203	0.0533	0.0403	1.3325	1.0075
23		0.0281
24	RIRE10	0.0200	0.022	0.0261	0.5500	0.6525
25		0.0328
26	Gypsy/T	0.0258	0.0452	0.0443	1.1300	1.1075
31		0.0348
32	BAJIE	0.0342	0.0475	0.0572	1.1875	1.4300
42		0.0216
43	^aGYPSY1	0.0359	0.0468	0.0452	1.1700	1.1300
64		0.0108
65	RIRE10	0.0162	0.0217	0.0199	0.5425	0.4975
66		0.0552
67	Copia_Ecgs	0.0373	0.0346	0.0464	0.8650	1.1600
69		0.0103
70	Copia/L	0.0186	0.0144	0.0102	0.3600	0.2550
71		0.0225
72	Copia/I	0.0219	0.0355	0.0358	0.8875	0.8950
73		0.0482
74	BAJIE	0.0312	0.0341	0.0482	0.8525	1.2050

No LTRs as described in Supplementary Table 1; Element family retrotransposon classification; Kdx K2p nucleotide distance calculated between orthologous LTRs in O. sativa and O. glaberrima; Kdx (G) Kimura 2p nucleotide distance calculated between the LTRs of the complete retrotransposon in O. glaberrima; Kdx (S) Kimura2p nucleotide distance calculated between the LTRs of the complete retrotransposon in O. sativa; MY (G) insertion time estimate in million years in O. glaberrima: substitution rate of 2 × 10⁻⁸ mutations per synonymous site per year is used (Vitte et al. 2004); MY (S) insertion time estimate in million years in O. sativa: substitution rate of 2 × 10⁻⁸ mutations per synonymous site per year is used (Vitte et al. 2004)
^aDoes not have TSDs