Genetic variability and population structure of Grapevine virus A in China based on the analysis of its coat protein gene

Figures & data

Table 1.  Analyses of SSCP profiles of cloned RT-PCR products of CP genes, and genetic diversity among CP haplotypes from each of 14 GVA isolates

		SSCP analysis		Sequence analysis
		No. haplotypes^a/	Percentage of predominant	No. clones	No.	Genetic diversity (± SE) among
Sources	Isolates	No. clones tested	haplotypes^b (%)	sequenced	sub-isolates^c	haplotypes of intra-isolate^d
Henan	AE	7/23	73.9%	8	2	0.0032 ± 0.0022–0.1623 ± 0.0195
	AF	13/20	20.0%	9	2	0.0016 ± 0.0016–0.1693 ± 0.0202
	BSBD	16/18	–	10	2	0.0016 ± 0.0015–0.0936 ± 0.0133
	BSSL	11/11	–	11	1	0.0032 ± 0.0022–0.0503 ± 0.0090
	DB	13/23	43.5%	13	2	0.0016 ± 0.0014–0.1412 ± 0.0152
	DBPT	7/22	54.5%	10	1	0.0016 ± 0.0015–0.0095 ± 0.0034
	FB	10/20	35.0%	8	2	0.0016 ± 0.0015–0.1154 ± 0.0138
	FLX	3/16	68.8%	5	2	0.0016 ± 0.0015–0.1356 ± 0.0153
	HZJM	9/23	43.5%	11	1	0.0016 ± 0.0015–0.0414 ± 0.0082
	MFLT	5/23	78.3%	6	1	0.0016 ± 0.0015–0.0128 ± 0.0043
Liaoning	HBS	3/17	88.2%	5	1	0.0016 ± 0.0015–0.0554 ± 0.0092
Hubei	GFMG	4/6	50.0%	5	2	0.0063 ± 0.0031–0.1374 ± 0.0135
	HU	4/21	85.7%	6	1	0.0016 ± 0.0015–0.0144 ± 0.0048
	SFLS	8/10	30.0%	9	1	0.0016 ± 0.0015–0.0239 ± 0.0053
Notes: ^aPCR products of tested clones from each isolate showing unique SSCP band pattern was designed a haplotype.
^bA haplotype ≥ 20 % within each isolates was considered as a predominant haplotype.
^cGenetic diversities between sub-isolates ≥ 0.0780 were considered different sub-isolates.
^dNucleotide distance with stand error was evaluated according to the method of Juke & Cantor (1969) for correction of superimposed substitutions with MEGA 4.1.

Fig. 1. SSCP analyses for coat protein genes cloned from four Grapevine virus A isolates showing different population structures. Numbers above each lane refer to different clones. a and b, show simple SSCP types with predominant haplotypes from isolates HBS and AF. c and d, show complex SSCP types without predominant haplotypes from isolates BSSL and BSBD.

Fig. 2. Phylogenetic analysis of Grapevine virus A (GVA) coat protein (CP) genes. In total, 24 CP sequences representing different sub-isolates within each of 14 isolates were included in the analysis. Six CP sequences from GenBank (accession no. AF441234, AF441235, AF441236, NC003604, AF007415 and AY340581) were used as references. The tree was constructed with MEGA 4.1 using the neighbour-joining method with 1000 bootstrap replicates. Values below 50% were suppressed. The bar represents 0.02 substitutions per site.

Juke , T.H. and Cantor , C.R. 1969 . “ Evolution of protein molecules ” . In Mammalian protein metabolism , Edited by: Munro , H.N. 21 – 32 . New York : Academic Press .

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