Molecular characterization of an Apple stem grooving virus isolate from kiwifruit (Actinidia chinensis) in China

Figures & data

Fig. 1 Symptoms on leaves of A. chinensis infected by ASGV. 1: chlorosis and mosaic on leaves of ASGV-Ac infected kiwifruit vines from Fujian province. 2–9: symptoms on leaves of kiwifruit vines infected by ASGV from Hubei province.

Table 1. Primers designed for RT-PCR amplification of ASGV genome.

Primer ^a	Primer sequence (5′-3′) ^b	Position (nt)	Product size (bp)
5ʹRACE-F	CGCGGATCCACAGCCTACTGATGATCAGTCGATG	-	850
5ʹRACE-R	TGTTTGCCCATCTAATACCG	798–817
1F	CTTTACGTCAATGGCTTTCACT	27–48	992
1R	AGGCCATGTAAGTACTAAGGG	998–1018
2F	GAAGCAGTCATTAACAGGAGCAC	967–989	2027
2R	CCAGCRAAVACHCCTTTATCTTC	2791–2793
3F	TGTGAAGGTTGAAGACTACGG	2928–2948	1883
3R	TGGTTGACATTGACGATAGCC	4790–4810
MC-M2	AATGGCWATCGTCAAYGTCAACC	4780–4809	1760
M4-T	GTTTTCCCAGTCACGAC(T)15	-

^aF, sense primer; R, antisense primer.

^bH is A or C or T; R is A or G; V is A or C or G; W is A or T and Y is C or T.

Table 2. Per cent sequence identity of full genome and two ORFs between the isolate ASGV-Ac and 26 ASGV isolates available in GenBank.

Host	Isolate	Accession no.	Genome %	ORF1
				Replicase		CP		ORF2 (MP)
				nt%	aa%	nt%	aa%	nt%	aa%
Kiwifruit	NZ^a	AF522459	-	-	-	96.9	98.7	93.5	96.9
Citrus	Lcd-NA-1	FJ355920	82.4	80.9	86.0	90.5	95.4	85.4	96.2
	Matsuco	LC084659	82.3	80.7	85.6	90.3	94.1	85	96.6
	Kumquat 1	AY646511	82.3	80.7	85.9	90.8	94.1	85.7	96.6
	ST	JQ765412	82.3	80.8	86.1	90.9	93.7	85.7	95.9
	FKSS2	LC143387	82.2	80.1	85.7	93.8	96.6	85.2	97.5
	Pk	JX416228	82.1	80.2	85.6	89.6	92.8	84.9	96.9
	XHC	KC588947	82.1	80.6	85.1	90.3	93.2	84.9	95.6
	MTH	KC588948	81.9	79.9	86.6	92.9	96.2	87	97.8
	ML	EU553489	81.5	79.9	85.8	91	94.5	86.3	96.2
Apple	AC	JX080201	82.3	80.5	86.0	92.2	96.6	85.8	96.2
	YTG	KJ579253	82.1	80.6	85.9	92.7	97.0	86.7	97.2
	M219-3	KX668488	82.0	80.5	86.5	90.8	95.8	85.6	96.2
	P-209	D14995	81.7	80.3	86.5	90.3	96.2	85.8	95.3
	p12	HE978837	81.9	80.1	83.3	92	96.6	84.9	94.7
	M220	KX686111	81.8	80.2	86.6	90.3	94.9	86.1	95.6
	HPKu-2	LT160740	81.7	80.1	85.5	90.8	95.8	85.3	95.9
	CHN	JQ308181	81.5	79.8	85.0	91.5	95.8	84.1	93.8
	T47	KF434636	81.4	80.1	86.6	90.9	96.2	85.7	94.1
Pear	Js2	KU198289	82.0	80	86.3	93.3	97.9	85.5	97.8
	HH	JN701424	81.4	79.5	85.1	91.7	96.6	83.3	95.6
	HB	KU605672	81.3	79.7	84.9	89.9	95.4	85.3	96.6
	SK	AY596172	80.5	78.4	84.4	92.6	95.4	84.6	93.1
	kfp	KR106996	79.5	77.3	83.7	92	94.9	84	97.2
Lily	L	D16681	81.6	79.6	84.6	93.1	97.0	84.3	96.6
	Li-23	AB004063	81.5	79.4	84.3	93.4	97.0	84.5	96.6

^a The partial genomic sequence of 2759 nt of ASGV isolate (named NZ) from kiwifruit reported by Clover et al. (2003) was included in the analysis.

Fig. 2 Unrooted Neighbour-joining (NJ) phylogenetic trees basing on nucleotide sequences of genome (a) and partial coating protein gene (b) of Apple stem grooving virus (ASGV). The designations of ASGV isolates available in GenBank were followed by sequence accession numbers and original hosts of the isolates on the right. Bootstrap values (1000 replicates) greater than 60% are given at the branch nodes. The scale bar below the tree represents the number of nucleotide substitutions per site. The ASGV isolates from kiwifruit reported in New Zealand and India were included in the CP-based tree.

Clover GRG, Pearson MN, Elliott DR, Tang Z, Smales TE, Alexander BJR. 2003. Characterization of a strain of Apple stem grooving virus in Actinidia chinensis from China. Plant Pathol. 52:371–378.

 Web of Science ®Google Scholar