Cloning and identification of Pepper cryptic virus 2 in Qinghai Province, China

doi:10.3969/j.issn.1004-1524.2023.06.14

Acta Agriculturae Zhejiangensis ›› 2023, Vol. 35 ›› Issue (6): 1368-1374.DOI: 10.3969/j.issn.1004-1524.2023.06.14

• Plant Protection • Previous Articles Next Articles

Cloning and identification of Pepper cryptic virus 2 in Qinghai Province, China

LUO Hailin(), YUAN Lei, YAN Jiahui^*(), GUO Qingyun

Key Laboratory of Agricultural Integrated Pest Management of Qinghai Province, Scientific Observing and Experimental Station of Crop Pest in Xining, Ministry of Agriculture and Rural Affairs, Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China

Received:2022-05-12 Online:2023-06-25 Published:2023-07-04

Abstract

Abstract:

Pepper cryptic virus 2 is one of the new viruses in pepper. It often infects with other viruses, seriously reducing the yield and quality of pepper. In 2021, suspected pepper’s leaf samples were collected from Haidong, Qinghai. Two dsRNA complete gene sequences of PCV2 were obtained by using RT-PCR and gene cloning. The two-length sequence of Qinghai isolates were 1 579 bp and 1 435 bp. The nucleotide sequence identities against other Pepper cryptic virus 2 isolates were over 95%. Phylogenetic analysis showed that PCV2 Qinghai isolate clustered with Chiltepin53 in a sub-clade. All these results showed that the virus infected pepper was an isolate of PCV2. Analyzing the nucleotide sequence of PCV2-QH and PCV2-XJ, the results showed that there were multiple differences. This is the first report of PCV2 infecting pepper in Qinghai.

Key words: pepper, Pepper cryptic virus 2, complete gene sequence, sequence analysis

CLC Number:

S436.418

LUO Hailin, YUAN Lei, YAN Jiahui, GUO Qingyun. Cloning and identification of Pepper cryptic virus 2 in Qinghai Province, China[J]. Acta Agriculturae Zhejiangensis, 2023, 35(6): 1368-1374.

Figures/Tables 7

References 22

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基因/片段 Gene/Segment	退火温度 Tm/℃	目的片段长度 Length/bp	引物名称 Primer name	引物序列 Primer sequence(5'→3')
PVC2	59.0	375	PCV2F	TCATCCGTCCAGCTAACGTA
			PCV2R	CGTCTCTTTTCTGAGCGGTA
RNA1	57.8	1 579	PCV2_RNA1-F	CAGTATCGAGAGATCACTGTGAC
			PCV2_RNA1-R	GGTTAGTGCCTTATGCCCA
RNA2	58.3	1 435	PCV2_RNA2-F	AGAATTTTCTGATCACAGTATCAAGAGATCACTG
			PCV2_RNA2-R	GACAAGGGGTACTAACCTCTTG

基因/片段 Gene/Segment	退火温度 Tm/℃	目的片段长度 Length/bp	引物名称 Primer name	引物序列 Primer sequence(5'→3')
PVC2	59.0	375	PCV2F	TCATCCGTCCAGCTAACGTA
			PCV2R	CGTCTCTTTTCTGAGCGGTA
RNA1	57.8	1 579	PCV2_RNA1-F	CAGTATCGAGAGATCACTGTGAC
			PCV2_RNA1-R	GGTTAGTGCCTTATGCCCA
RNA2	58.3	1 435	PCV2_RNA2-F	AGAATTTTCTGATCACAGTATCAAGAGATCACTG
			PCV2_RNA2-R	GACAAGGGGTACTAACCTCTTG

国家 Country	寄主 Host	分离物 Isolate	RNA1登录号 Accession No.	核苷酸序列一致性 Nucleotide Similarities/%	氨基酸序列一致性 Amion acids Similarities/%	RNA 2登录号 Accession No.	核苷酸序列一致性 Nucleotide Similarities/%	氨基酸序列一致性 Amion acids Similarities/%
中国China	Capsicum annuum	PCV2-XJ	MT328005.1	99	99.21	MT328056.1	99	99.64
多米尼加共和国	Capsicum annuum	DR	KX525268.1	99	99.02	KX525269.1	99	99.50
Dominican Republic
韩国Korea	Capsicum annuum	SC10-2	KY923703.1	99	98.89	KY923704.1	99	99.50
韩国Korea	Ixais dentate NAKAI	YY	LC195294.1	99	98.36	LC195295.1	99	99.21
土耳其Turkey	Capsicum annuum	Tur	LC325817.1	99	96.00	LC325818	99	97.99
斯洛伐克	Capsicum annuum	N65	MN723540.1	99	95.96	MN723541.1	99	97.92
Slovakia
美国USA	Capsicum annuum	HW-01	JN117278.1	99	95.94	JN117279.1	99	97.92
中国China	Capsicum annuum	PCV2-CQ	KX905077.1	78	98.92	KX905078.1	99	99.50
美国USA	Capsicum annuum	Ember	MG542626.1	65	99.11	MG542618.1	83	99.83

国家 Country	寄主 Host	分离物 Isolate	RNA1登录号 Accession No.	核苷酸序列一致性 Nucleotide Similarities/%	氨基酸序列一致性 Amion acids Similarities/%	RNA 2登录号 Accession No.	核苷酸序列一致性 Nucleotide Similarities/%	氨基酸序列一致性 Amion acids Similarities/%
中国China	Capsicum annuum	PCV2-XJ	MT328005.1	99	99.21	MT328056.1	99	99.64
多米尼加共和国	Capsicum annuum	DR	KX525268.1	99	99.02	KX525269.1	99	99.50
Dominican Republic
韩国Korea	Capsicum annuum	SC10-2	KY923703.1	99	98.89	KY923704.1	99	99.50
韩国Korea	Ixais dentate NAKAI	YY	LC195294.1	99	98.36	LC195295.1	99	99.21
土耳其Turkey	Capsicum annuum	Tur	LC325817.1	99	96.00	LC325818	99	97.99
斯洛伐克	Capsicum annuum	N65	MN723540.1	99	95.96	MN723541.1	99	97.92
Slovakia
美国USA	Capsicum annuum	HW-01	JN117278.1	99	95.94	JN117279.1	99	97.92
中国China	Capsicum annuum	PCV2-CQ	KX905077.1	78	98.92	KX905078.1	99	99.50
美国USA	Capsicum annuum	Ember	MG542626.1	65	99.11	MG542618.1	83	99.83

片段 Segments	序列位点 Sequence position	PCV2-QH	PCV2-XJ	蛋白/非编码区 Protein/Untranslated region	突变 Mutation
dsRNA1	247	C	T	RNA依赖的RNA聚合酶 RNA dependent RNA polymerase(RdRp)	非同义替换 Nonsynonymous substitution
	478	C	T	RNA依赖的RNA聚合酶 RNA dependent RNA polymerase(RdRp)	非同义替换 Nonsynonymous substitution
	679	A	G	RNA依赖的RNA聚合酶 RNA dependent RNA polymerase(RdRp)	非同义替换 Nonsynonymous substitution
	1 039	G	T	RNA依赖的RNA聚合酶 RNA dependent RNA polymerase(RdRp)	非同义替换 Nonsynonymous substitution
	1 055	G	T	RNA依赖的RNA聚合酶 RNA dependent RNA polymerase(RdRp)	非同义替换 Nonsynonymous substitution
	1 060	G	T	RNA依赖的RNA聚合酶 RNA dependent RNA polymerase(RdRp)	非同义替换 Nonsynonymous substitution
	1 083	G	T	RNA依赖的RNA聚合酶 RNA dependent RNA polymerase(RdRp)	同义替换 Synonymous substitution
dsRNA2	51	G	A	非编码区Non-coding region	—
	52	A	G	非编码区Non-coding region	—
	53	T	A	非编码区Non-coding region	—
	54	A	C	非编码区Non-coding region	—
	55	C	G	非编码区Non-coding region	—
	450	C	T	外壳蛋白Coat protein(CP)	同义替换Synonymous substitution
	1 431	A	T	非编码区Non-coding region	—
	1 433	T	A	非编码区Non-coding region	—
	1 435	C	T	非编码区Non-coding region	—
	1 436	G	T	非编码区Non-coding region	—
	1 437	C	T	非编码区Non-coding region	—

Cloning and identification of Pepper cryptic virus 2 in Qinghai Province, China

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