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

[1]	ARANCIBIA R, VALVERDE R, CAN F. Properties of a cryptic virus from pepper (Capsicum annuum)[J]. Plant Pathology, 1995, 44: 164-168.
[2]	SABANADZOVIC S, VALVERDE R A. Properties and detection of two cryptoviruses from pepper (Capsicum annuum)[J]. Virus Genes, 2011, 43(2): 307-312.
[3]	SARITHA R K, JAIN P, BARANWAL V K, et al. First record of Pepper cryptic virus 2 in chilli (Capsicum annuum) in India[J]. Virusdisease, 2016, 27(3): 327-328.
[4]	MARTÍNEZ R T, DE ALMEIDA M M S, RODRIGUEZ R, et al. Identification and genome analysis of tomato chlorotic spot virus and dsRNA viruses from coinfected vegetables in the Dominican Republic by high-throughput sequencing[J]. Virology Journal, 2018, 15(1): 24.
[5]	GUY P L, GERARD P J. White clover cryptic virus-1 in New Zealand and eastern Australia[J]. Annals of Applied Biology, 2016, 168(2): 225-231.
[6]	SUN M, JING C C, WU G T, et al. First report of pepper cryptic virus 2 infecting pepper in China[J]. Journal of Plant Pathology, 2017, 99(1): 298.
[7]	王少立, 谭玮萍, 杨园园, 等. 山东省辣椒主要病毒种类的分子检测与鉴定[J]. 中国农业科学, 2017, 50(14): 2728-2738.
	WANG S L, TAN W P, YANG Y Y, et al. Molecular detection and identification of main viruses on pepper in Shandong Province[J]. Scientia Agricultura Sinica, 2017, 50(14): 2728-2738. (in Chinese with English abstract)
[8]	申冕, 崔百明, 刘贞, 等. 新疆辣椒中BPEV和PCV2的鉴定与分析[J]. 植物病理学报, 2020, 50(1): 20-27.
	SHEN M, CUI B M, LIU Z, et al. Identification and analysis of BPEV and PCV2 from pepper in Xinjiang[J]. Acta Phytopathologica Sinica, 2020, 50(1): 20-27. (in Chinese with English abstract)
[9]	NIBERT M L, GHABRIAL S A, MAISS E, et al. Taxonomic reorganization of family Partitiviridae and other recent progress in partitivirus research[J]. Virus Research, 2014, 188: 128-141.
[10]	MARTIN R R, TZANETAKIS I E, SWEENEY M, et al. A virus associated with blueberry fruit drop disease[J]. Acta Horticulturae, 2006(715): 497-502.
[11]	SABANADZOVIC S, VALVERDE R A, BROWN J K, et al. Southern tomato virus: the link between the families Totiviridae and Partitiviridae[J]. Virus Research, 2009, 140(1/2): 130-137.
[12]	ROSE H, MAISS E. Plant and protozoal partitiviruses (Partitiviridae)[M]// Encyclopedia of Virology. Amsterdam: Elsevier, 2021: 632-641.
[13]	CHEN L S, HAN R, WANG H T. Development of vegetable industry in summer in cool areas in Qinghai plateau[J]. Agricultural Science & Technology, 2015, 16(4): 782-784, 792.
[14]	李全辉, 韩睿, 李志成, 等. 青海线辣椒生产状况及发展对策[J]. 中国园艺文摘, 2018, 34(6): 60-61, 124.
	LI Q H, HAN R, LI Z C, et al. Production status and development countermeasures of chili pepper in Qinghai Province[J]. Chinese Horticulture Abstracts, 2018, 34(6): 60-61, 124. (in Chinese with English abstract)
[15]	刘勇, 李凡, 李月月, 等. 侵染我国主要蔬菜作物的病毒种类、分布与发生趋势[J]. 中国农业科学, 2019, 52(2): 239-261.
	LIU Y, LI F, LI Y Y, et al. Identification, distribution and occurrence of viruses in the main vegetables of China[J]. Scientia Agricultura Sinica, 2019, 52(2): 239-261. (in Chinese with English abstract)
[16]	吴淑华, 涂丽琴, 咸文荣, 等. 青海辣椒上番茄斑萎病毒检测及鉴定[J]. 园艺学报, 2020, 47(7): 1391-1400.
	WU S H, TU L Q, XIAN W R, et al. Detection and identification of tomato spotted wilt Tospovirus on pepper from Qinghai Province[J]. Acta Horticulturae Sinica, 2020, 47(7): 1391-1400. (in Chinese with English abstract)
[17]	李廷芳, 吴淑华, 赵文浩, 等. 青海海东设施辣椒轻斑驳病毒的分子检测[J]. 江苏农业学报, 2017, 33(4): 958-960.
	LI T F, WU S H, ZHAO W H, et al. Molecular detection of mild mottle virus isolated from pepper in Haidong, Qinghai Province[J]. Jiangsu Journal of Agricultural Sciences, 2017, 33(4): 958-960. (in Chinese)
[18]	孙国胜, 马志虎, 戴忠良, 等. 3种方法提取辣椒根总RNA的效果比较[J]. 中国瓜菜, 2016, 29(1): 8-10.
	SUN G S, MA Z H, DAI Z L, et al. Comparison of three methods on total RNA extraction from the root of Capsicum annuum L[J]. China Cucurbits and Vegetables, 2016, 29(1): 8-10. (in Chinese with English abstract)
[19]	GREEN S K, KIM J S. Characteristics and control of viruses infecting peppers: A literature review[M]// Technical Bulletin Shanhua, Taiwan: Asian Vegetable Research and Development Center, 1991, 18: 60.
[20]	VAINIO E J, CHIBA S, GHABRIAL S A, et al. ICTV virus taxonomy profile: Partitiviridae[J]. The Journal of General Virology, 2018, 99(1): 17-18.
[21]	BOCCARDO G, LISA V, LUISONI E, et al. Cryptic plant viruses[J]. Advances in Virus Research, 1987, 32: 171-214.
[22]	TOMAŠECHOVÁ J, HANČINSKý R, PREDAJÝA L, et al. High-throughput sequencing reveals bell pepper Endornavirus infection in pepper (Capsicum annum) in Slovakia and enables its further molecular characterization[J]. Plants (Basel), 2019, 9(1): E41.

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

RichHTML

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

Figures/Tables 7

References 22

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	CHAI Guanqun, ZHOU Wei, LIANG Hong, FAN Feifei, ZHU Dayan, FAN Chengwu. Effect of foliar spraying of zinc fertilizer and citric acid on yield, quality and Cd absorption and transport ation of pepper [J]. Acta Agriculturae Zhejiangensis, 2023, 35(5): 1069-1079.
[2]	ZHU Li, XUE Xinru, LIANG Zongxu, XU Linyu, YU Guofeng, TANG Yi, LI Huanxiu. Correlation between capsaicin content and agronomic traits in pepper (Capsicum annuum L.) germplasm resources [J]. Acta Agriculturae Zhejiangensis, 2023, 35(4): 862-872.
[3]	DING Dongxia, LI Nenghui, LI Jing, TANG Chaonan, WANG Cheng, NIU Tianhang, YANG Yan, YANG Haitao, XIE Jianming. Effects of exogenous melatonin on chlorophyll fluorescence and antioxidant system of pepper (Capsicum annuum L.) under low temperature and low light stress [J]. Acta Agriculturae Zhejiangensis, 2022, 34(9): 1935-1944.
[4]	ZHANG Ting, LIU Huiqin, GUO Qinwei, LI Chaosen, ZHANG Xinhui, XIANG Xiaomin, ZHAO Dongfeng, WAN Hongjian. Principal component analysis and cluster analysis for evaluating free amino acids of 16 pepper materials [J]. Acta Agriculturae Zhejiangensis, 2021, 33(4): 640-650.
[5]	GOU Bingdiao, DUAN Panpan, YANG Nan, ZHAO Shufang, WANG Yongfu, ZHANG Gaoyuan, WEI Bingqiang. Heterosis analysis of photosynthetic parameters of pepper seedling responding to low temperature and low light stress [J]. Acta Agriculturae Zhejiangensis, 2021, 33(3): 429-436.
[6]	MAO Qi, YANG Youxin, FAN Feijun, WAN Hongjian, ZHOU Guozhi, YAO Zhuping, RUAN Meiying, WANG Rongqing, YE Qingjing, LI Zhimiao, CHEN Shuangchen, CHENG Yuan. Effect of different light-emitting diode (LED) light treatments on postharvest quality of chili pepper (Capsicum annum L.) [J]. Acta Agriculturae Zhejiangensis, 2021, 33(11): 2059-2067.
[7]	MENG Yan, LIU Li, LI Yi, CHEN Laisheng, DU Zhongping, HAN Rui. Effect of acid and alkali pretreatment on anaerobic co-digestion characteristics of pepper straw and sheep manure [J]. Acta Agriculturae Zhejiangensis, 2021, 33(10): 1913-1920.
[8]	CHEN De, ZHAO Shouping, YE Xuezhu, ZHANG Qi, XIAO Wendan, RUAN Yifei, WU Shaofu. Effects of soil amendments on Cd uptake and accumulation in red pepper [J]. Acta Agriculturae Zhejiangensis, 2021, 33(10): 1921-1930.
[9]	LIU Kai, FENG Xiaoyu, MA Hengjia, XIE Nan. Complete sequence and gene organization of mitochondrial genome of Megalobrama terminalis from Qiantang River [J]. , 2020, 32(9): 1591-1608.
[10]	NI Zheng, CHEN Liu, HUA Jionggang, YE Weicheng, YUN Tao, ZHU Yinchu, ZHANG Cun. Detection of leukaemia virus antigen and analysis of GP85 gene sequence in local chicken breeds in Zhejiang Province [J]. , 2020, 32(8): 1357-1362.
[11]	NIU Bo, LI Lina, PANG Guangchang, LU Dingqiang. Construction of plant root tip mesenchymal sensors and their effects on urea sensing dynamics [J]. , 2020, 32(8): 1466-1474.
[12]	WANG Weike, SONG Jiling, LU Na, YUAN Weidong, YAN Jing, CHEN Guanping. Cloning and expression of the PpFBD1 involved in primordium formation of Pleurotus pulmonarius [J]. , 2020, 32(1): 93-97.
[13]	DEXI Cuomu, WANG Yin, YANG Zexiao, YAO Xueping, LUO Yan, LIAO Changyu, ZHANG Pengfei, JIANG Dike, XIANG Mingyuan, JIANG Ruijiao, SONG Yong. Epidemiological investigation of porcine epidemic diarrhea virus and sequence analysis of ORF3 and S1 genes in Sichuan from 2016 to 2018 [J]. , 2019, 31(9): 1423-1428.
[14]	YI Keke, YIN Wenqi, ZHOU Yuancheng, JIANG Jinzhen, ZHANG Baiyu, LI Zhongyin, YAN Qigui. Isolation and identification of 4 strains of porcine pseudorabies virus and analysis of main virulence genes [J]. , 2019, 31(9): 1429-1436.
[15]	LIU Jialin, LIU Shili, JIANG Wenping, CHENG Shun, CHI Meili, ZHENG Jianbo, JIA Yongyi, ZHAO Jinliang, YIN Shaowu, GU Zhimin. Cloning and bioinformatics analysis of GH gene and its flanking region in Odontobutis potamophila [J]. , 2019, 31(9): 1461-1470.