TABLE 2.

Intraisolate genetic complexity and heterogeneity of mutant spectra in 13 field isolates of ToCV

Isolate	Origin	RNA1		RNA2
		RdRpc		Hsp70hd		CPe		CPmf
		Mutation frequencya (10−4)	Shannon entropyb	Mutation frequency (10−4)	Shannon entropy	Mutation frequency (10−4)	Shannon entropy	Mutation frequency (10−4)	Shannon entropy
AT 1/97	Málaga	9.22	0.680	3.24	0.213	1.60	0.089	3.47	0.263
AT 3/98	Almería	3.41	0.256	<1.08	0.000	2.22	0.121	6.12	0.232
AT 24/99	Málaga	3.42	0.265	4.32	0.395	<1.16	0.000	1.02	0.077
AT 80/99	Málaga	22.70	0.706	NDg	ND	ND	ND	ND	ND
AT 198/00	Málaga	13.00	0.321	2.16	0.177	1.09	0.083	3.47	0.263
AT 205/00	Murcia	4.55	0.404	3.60	0.33	1.84	0.069	<1.08	0.000
AT 230/00	Almería	1.80	0.209	5.71	0.443	3.50	0.275	2.17	0.165
AT 36/02	Murcia	2.76	0.296	4.05	0.325	3.08	0.179	2.31	0.177
AT 45/02	Málaga	0.90	0.089	4.05	0.246	5.82	0.429	5.78	0.347
AT 31/03	Almería	2.95	0.177	2.16	0.299	2.05	0.154	1.15	0.089
AT 138/03	Murcia	0.98	0.097	3.24	0.452	2.33	0.416	3.47	0.229
AT 204/04	Almería	2.76	0.296	6.07	0.477	3.50	0.263	1.15	0.089
AT 379/04	Murcia	6.08	0.432	2.16	0.177	2.33	0.177	2.31	0.177

^aMutation frequencies (substitutions per nucleotide) were calculated by scoring the mutations present in sequences of molecular clones relative to their consensus sequence. One substitution was considered to compute the maximum mutation frequencies if no mutations were scored. Repeated mutations were scored only once for each isolate and genomic region. The consensus sequence was obtained by direct sequencing of RT-PCR products.

^bShannon entropy values were calculated using the following formula: −Σ_i [(p_i × ln p_i)/ln N], in which p_i is the frequency of each sequence in the mutant spectrum and N is the total number of sequences compared (54).

^c189 molecular clones (129,886 nt) were sequenced.

^d191 molecular clones (117,767 nt) were sequenced.

^e189 molecular clones (108,297 nt) were sequenced.

^f186 molecular clones (107,322 nt) were sequenced.

^gND, not determined.