Identification and complete genome sequence cloning of the chili veinal mottle virus in Qinghai Province of China

doi:10.3969/j.issn.1004-1524.20240564

Acta Agriculturae Zhejiangensis ›› 2025, Vol. 37 ›› Issue (3): 612-620.DOI: 10.3969/j.issn.1004-1524.20240564

• Plant Protection • Previous Articles Next Articles

Identification and complete genome sequence cloning of the chili veinal mottle virus in Qinghai Province of China

WEN Xiaoxiong¹^,²(), SHU Qin¹^,², BAO Mengnan¹^,², YAN Jiahui¹^,²^,^*()

1. Institute of Plant Protection, Academy of Agricultural and Forestry Sciences, Qinghai University,Xining 810016, China
2. Key Laboratory of Integrated Pest Management in Agriculture of Qinghai Province, Xining 810016, China

Received:2024-06-28 Online:2025-03-25 Published:2025-04-02

Abstract

Abstract:

To assess the occurrence of viral diseases in chili peppers in Xunhua County, Haidong City, Qinghai Province, and to investigate the factors contributing to symptoms such as leaf curling and stunting, this study collected suspected viral samples from chili cultivation areas in September 2023. Utilizing reverse transcription-polymerase chain reaction (RT-PCR) for detection, results indicated that 8 out of 19 symptomatic chili samples were confirmed to be infected with Chilli veinal mottle virus(ChiVMV), yielding a detection rate of 42%. The complete RNA genome of the virus was determined to be 9 754 nt in length. Genomic sequencing and analysis revealed a significant recombination event in the Qinghai isolate, leading to sequence variations in certain genomic regions when compared to other ChiVMV isolates. The nucleotide sequence identity of the Qinghai isolate ranged from 84% to 100% compared to isolates from Hefei, Ningbo, Kunming, Luzhou, and Suzhou in China, as well as those from India and Pakistan. This study represents the first detection of ChiVMV in chili peppers in Xunhua County, Qinghai Province, and provides the complete genomic sequence of the virus. These findings contribute valuable insights and empirical data for the development of resistant cultivars and the management of related viral diseases, thereby enhancing our understanding of viral genetic variation and its epidemiological dynamics across different regions.

Key words: complete genome, ChiVMV, RT-PCR

CLC Number:

WEN Xiaoxiong, SHU Qin, BAO Mengnan, YAN Jiahui. Identification and complete genome sequence cloning of the chili veinal mottle virus in Qinghai Province of China[J]. Acta Agriculturae Zhejiangensis, 2025, 37(3): 612-620.

Figures/Tables 8

References 34

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引物名称 Primer name	引物序列 Primer sequences (5'→3')	退火温度 Tm/℃	长度 Length/bp
ChiVMV-F	TGACTATGATGTCACAGATGA	57.5	795
ChiVMV-R	AACGCCAACTATTGAACAGCTT	58.0
1F	TCATAAAATTTTCTTGAAATTCAGTCATCAG	55.0	1 451
1R	CTTGTTCCTAAAAAGATGTAAGGAACCT	57.0
2F	ATCATGAAGCAACGGGTAAAGT	57.5	2 500
2R	CCTTGACATATTGAATGAACTCTACCTC	58.0
3F	GGAGAAGATAGCATTAGTTCCAGTACCACT	61.0	2 500
3R	TAGTACATTGATTGTATTCACGCACTGACAT	60.0
4F	GAACCATGGCACTTTTTGAGCTTCC	61.0	2 500
4R	GCCATTCCAAAGTCTCAACCTTTGC	61.5
5F	CTTTCTCCGAACTTGGTTTGTCGTATGATTTC	61.0	1 553
5R	ATAACATATATAAAGTAGTATGAAACCGAGCGTGC	60.0

引物名称 Primer name	引物序列 Primer sequences (5'→3')	退火温度 Tm/℃	长度 Length/bp
ChiVMV-F	TGACTATGATGTCACAGATGA	57.5	795
ChiVMV-R	AACGCCAACTATTGAACAGCTT	58.0
1F	TCATAAAATTTTCTTGAAATTCAGTCATCAG	55.0	1 451
1R	CTTGTTCCTAAAAAGATGTAAGGAACCT	57.0
2F	ATCATGAAGCAACGGGTAAAGT	57.5	2 500
2R	CCTTGACATATTGAATGAACTCTACCTC	58.0
3F	GGAGAAGATAGCATTAGTTCCAGTACCACT	61.0	2 500
3R	TAGTACATTGATTGTATTCACGCACTGACAT	60.0
4F	GAACCATGGCACTTTTTGAGCTTCC	61.0	2 500
4R	GCCATTCCAAAGTCTCAACCTTTGC	61.5
5F	CTTTCTCCGAACTTGGTTTGTCGTATGATTTC	61.0	1 553
5R	ATAACATATATAAAGTAGTATGAAACCGAGCGTGC	60.0

登录号 Accession no.	分离物 Isolate	寄主 Host	地区 Country	核苷酸相似度 Nucleotide Similiarity/%
KX650863	Dzh-Qyg	Nicotiana tabacum	China: Hefei	99.97
ON168942	ChiVMV-D	Capsicum annuum	China: Ningbo	93.34
MK405594	SiChuan Luzhou	Nicotiana tabacum	China: Luzhou	93.19
OP589298	GZ	Tobacco	China: Guiyang	93.11
MT787292	ChiVMV-Dh	Chilli pepper	China: Kunming	92.23
PP582383	AH	Capsicum	China: Suzhou	87.36
OP404087	YunN	Capsicum annuum	China: Ningbo	85.75
ON838424	-	Chilli	China: Ningbo	85.64
MN207122	ChiVMV-PK	Capsicum annuum	Pakistan	86.12
MN508960	ChiVMV-Uravakonda	Hot pepper	India: Uravakonda, Andhra pradesh	84.41
OR347840	To	Tomato	India: Karnataka	84.29

登录号 Accession no.	分离物 Isolate	寄主 Host	地区 Country	核苷酸相似度 Nucleotide Similiarity/%
KX650863	Dzh-Qyg	Nicotiana tabacum	China: Hefei	99.97
ON168942	ChiVMV-D	Capsicum annuum	China: Ningbo	93.34
MK405594	SiChuan Luzhou	Nicotiana tabacum	China: Luzhou	93.19
OP589298	GZ	Tobacco	China: Guiyang	93.11
MT787292	ChiVMV-Dh	Chilli pepper	China: Kunming	92.23
PP582383	AH	Capsicum	China: Suzhou	87.36
OP404087	YunN	Capsicum annuum	China: Ningbo	85.75
ON838424	-	Chilli	China: Ningbo	85.64
MN207122	ChiVMV-PK	Capsicum annuum	Pakistan	86.12
MN508960	ChiVMV-Uravakonda	Hot pepper	India: Uravakonda, Andhra pradesh	84.41
OR347840	To	Tomato	India: Karnataka	84.29

Identification and complete genome sequence cloning of the chili veinal mottle virus in Qinghai Province of China

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