Sequence analysis and detection of grapevine geminivirus A

doi:10.6048/j.issn.1001-4330.2025.04.012

Abstract

Abstract:

【Objective】 This project aims to determine the field infection status of Grapevine Geminivirus A in Turpan City,Xinjiang.【Methods】 71 suspected grape virus samples were collected and detected and according to the results of high-throughput sequencing, the existence of grapevine geminivirus A in the sample was verified, and the whole gene sequence of GGVA was determined. The whole gene sequence of grapevine geminivirus A was used as the target to design specific primers for the detection of suspected grape virus samples. 【Results】 The whole genome sequence of GGVA was determined, and GGVA-QKT isolates were obtained, with nucleotide identity of 94.3%-99.3%, and published isolates were highly homologous, among which, they were closely related to two GGVA isolates from Israel (KX618694.1) and (NC_031340.1). 【Conclusion】 71 different parts of the grape samples were Grapevine geminivirus A, 71 grape samples from different regions were infected with Grapevine geminivirus A. among them, Shanshan County,Xinjiang had the highest detection rate 30.55%, while Tokson County,Xinjiang had the lowest detection rate 9.10%. The virus was very common in the grape growing area of Turpan County,Xinjiang. In this study, the field infection status of Grapevine geminivirus A in Turpan City is detected.

Key words: grape virus; DNA virus; sequence analysis; detection

摘要：

【目的】研究新疆吐鲁番市葡萄双生病毒A(Grapevine geminivirus A)的田间侵染状况,检测采集71份疑似葡萄病毒样本,为明确葡萄双生病毒A的发生、分布及其分子检测提供理论指导。【方法】依据高通量测序结果,验证样本中葡萄双生病毒A,测定GGVA的全基因序列,以葡萄双生病毒A的全基因序列为靶标设计特异性引物进行疑似葡萄病毒样本的检测。【结果】测定GGVA的全基因组序列,获得GGVA-QKT分离株,其核苷酸同源性为94.3%~99.3%,与已公布的分离株具有高度同源性,其中与来自以色列(KX618694.1)、(NC_031340.1)的2个GGVA分离株亲缘关系最近。【结论】71份不同葡萄样本均有感染双生病毒A,其中,新疆鄯善县检出率最高,检出率为30.55%,新疆托克逊县检出率最低,检出率为9.10%。该病毒在新疆吐鲁番市葡萄种植区普遍发生。

关键词: 葡萄病毒, DNA病毒, 序列分析, 检测

CLC Number:

WANG Shu, LIU Baojun, ZHANG Liya, SHAN Jiaqi, LI Kemei, BAI Jianyu. Sequence analysis and detection of grapevine geminivirus A[J]. Xinjiang Agricultural Sciences, 2025, 62(4): 887-893.

王澍, 刘保军, 张李娅, 单佳祁, 李克梅, 白剑宇. 葡萄双生病毒A的序列分析及检测[J]. 新疆农业科学, 2025, 62(4): 887-893.

Figures/Tables 7

References 23

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采样地点 Sampling spots		采集时间 Sampling time	品种 Variety	编号 Number	样本数 Samples
鄯善县 Shanshan county	七克台镇	2022.6.25	无核白	QKT-1-13	36
	辟展镇	2022.6.25	无核白	PZZ-1-5
	东巴扎回民乡	2022.6.25	无核白	DBZHMX-1-6
	鲁克沁镇	2022.6.25	无核白	LKQX-1-5
	连木沁镇	2022.6.25	无核白	LMQX-1-7
吐鲁番市高昌区 Gaochang oistrict turpan city	七泉湖镇	2022.6.26	无核白	QQHZ-1-8	24
	艾丁湖镇	2022.6.26	无核白	ADHZ-1-5
	胜金乡	2022.6.26	无核白	SJX-1-11
托克逊县 Tokson county	夏镇	2022.6.27	无核白	XZ-1-11	11
总计Total		-	-	-	71

采样地点 Sampling spots		采集时间 Sampling time	品种 Variety	编号 Number	样本数 Samples
鄯善县 Shanshan county	七克台镇	2022.6.25	无核白	QKT-1-13	36
	辟展镇	2022.6.25	无核白	PZZ-1-5
	东巴扎回民乡	2022.6.25	无核白	DBZHMX-1-6
	鲁克沁镇	2022.6.25	无核白	LKQX-1-5
	连木沁镇	2022.6.25	无核白	LMQX-1-7
吐鲁番市高昌区 Gaochang oistrict turpan city	七泉湖镇	2022.6.26	无核白	QQHZ-1-8	24
	艾丁湖镇	2022.6.26	无核白	ADHZ-1-5
	胜金乡	2022.6.26	无核白	SJX-1-11
托克逊县 Tokson county	夏镇	2022.6.27	无核白	XZ-1-11	11
总计Total		-	-	-	71

引物名称 Primer name	引物序列(5’— 3’) Primer sequence (5 '- 3')	退火温度 Annealing temperature	扩增产物 Amplified product
F¹ R¹	GCTCCCTGTCACTATCTAGG GGTATGACGTTGACTAGCAC	55	582
F^2* R^2*	ACCATGTCTGAGGGTAAGGC GGAGTCAATTGGAACGTGCG	55	329
F³ R³	AGCTCAAGCATTCGATGACC GGAGTCACTTACATCGCAGC	55	671
F⁴ R⁴	GTCCCAACTCTGTATGATCG TAGAGGGAGATTCAAGGACG	55	607
F⁵ R⁵	GGAAGATTGAGGGCATTGTC GAGAATTTCAGATCGACGGC	55	597
F⁶ R⁶	CTCAGCATAAGCGTCGTTAG GTAAGCCATCTTCGTTCAGG	55	404
F⁷ R⁷	TGATGGGATTCTGCTGAGAC AGAGGCGATCCATAAACACC	55	596

引物名称 Primer name	引物序列(5’— 3’) Primer sequence (5 '- 3')	退火温度 Annealing temperature	扩增产物 Amplified product
F¹ R¹	GCTCCCTGTCACTATCTAGG GGTATGACGTTGACTAGCAC	55	582
F^2* R^2*	ACCATGTCTGAGGGTAAGGC GGAGTCAATTGGAACGTGCG	55	329
F³ R³	AGCTCAAGCATTCGATGACC GGAGTCACTTACATCGCAGC	55	671
F⁴ R⁴	GTCCCAACTCTGTATGATCG TAGAGGGAGATTCAAGGACG	55	607
F⁵ R⁵	GGAAGATTGAGGGCATTGTC GAGAATTTCAGATCGACGGC	55	597
F⁶ R⁶	CTCAGCATAAGCGTCGTTAG GTAAGCCATCTTCGTTCAGG	55	404
F⁷ R⁷	TGATGGGATTCTGCTGAGAC AGAGGCGATCCATAAACACC	55	596

属 Genus	种 Species	重叠数 Number of contigs	病毒读取数 Number of reads form virus
Foveavirus	Grapevine rupestris stem pitting-associated virus	27	19 319
Maculavirus	Grapevine fleck virus	27	5 196
Trichovirus	Grapevine Pinot gris virus	1	2 408
Trichovirus	Grapevine berry inner necrosis virus	32	66 105
Not classified	not classified	4	3 588
Maldovirus	Grapevine geminivirus A	1	1 473