Table 5.

Nonsynonymous and synonymous substitution ratios of Turnip mosaic virus gene/region and subpopulation of China and Japan

Gene/region	China			Japan
	Whole country	Mainland	Taiwan	Whole country	Kyushu	Honshu & Hokkaido
Codeml method
P1 [nt 1–321 (nt 1–627)]	0.034 (0.042)	0.033 (0.041)	0.200 (0.219)	0.025 (0.063)	0.023 (0.061)	0.059 (0.101)
6K2 [nt 385–543]	0.027	0.029	0.058	0.024	0.021	0.019
VPg [nt 544–1119]	0.045	0.042	0.143	0.040	0.044	0.049
NIa‐Pro [nt 1120– 1848]	0.009	0.008	0.041	0.005	0.005	0.011
CP [nt 1849–2673]	0.052	0.046	0.112	0.040	0.042	0.041
Concat [nt 1–2673 (nt 1–2979)]	0.051 (0.058)	0.049 (0.055)	0.113 (0.123)	0.044 (0.053)	0.044 (0.053)	0.047 (0.063)
PBL method
P1 [nt 1–321 (nt 1–627)]	0.095 (0.133)	0.090 (0.130)	0.296 (0.295)	0.096 (0.136)	0.094 (0.133)	0.111 (0.181)
6K2 [nt 385–543]	0.096	0.098	0.067	0.067	0.059	0.091
VPg [nt 544–1119]	0.073	0.069	0.173	0.070	0.072	0.084
NIa‐Pro [nt 1120– 1848]	0.017	0.016	0.047	0.017	0.017	0.018
CP [nt 1849–2673]	0.062	0.054	0.134	0.045	0.047	0.049
Concat [nt 1–2673 (nt 1–2979)]	0.069 (0.079)	0.065 (0.076)	0.128 (0.143)	0.060 (0.071)	0.060 (0.072)	0.064 (0.083)

Nonsynonymous (d_n) and synonymous (d_s) substitution (d_n/d_s) ratios were calculated from Turnip mosaic virus gene/region and subpopulations using codeml method of paml package version 3.14 (Yang 1997) and Pamilo–Bianchi–Li (PBL) method of mega version 3.1 (Kumar et al. 2004). The d_n/d_s ratios were estimated from the concats of 2673 nts long, on the other hand, those from the concats of 2979 nts long are shown in parenthesis (see Materials and methods). An isolate from Hokkaido was not included in the analysis because it had interlineage recombination site in the genome (interlineage recombinant).