Molecular Identification and Sequence Analysis of Begomoviruses Infecting Impatiens balsamina

doi:10.16420/j.issn.0513-353x.2021-0221

Acta Horticulturae Sinica ›› 2022, Vol. 49 ›› Issue (5): 1136-1144.doi: 10.16420/j.issn.0513-353x.2021-0221

• Research Notes • Previous Articles Next Articles

Molecular Identification and Sequence Analysis of Begomoviruses Infecting Impatiens balsamina

ZHONG Jing, ZHAO Liling, LI Tingting, ZHANG Shuiying, CHEN Yue, DING Ming()

Key Laboratory of Agricultural Biotechnology of Yunnan Province,Key Laboratory of the Southwestern Crop Gene Resources and Germplasm Innovation,Ministry of Agriculture and Rural Affairs,Institute of Biotechnology and Germplasm Resources,Yunnan Academy of Agricultural Sciences,Kunming 650223,China

Received:2021-11-25 Revised:2022-03-28 Online:2022-05-25 Published:2022-05-25
Contact: DING Ming E-mail:mingd73@163.com

Abstract

Abstract:

An investigation about diseases in Xishuangbanna Autonomous Prefecture,Yunnan Province identified an Impatiens balsamina plant with leaf shrinking and mosaic symptoms typical of begomovirus infections. To identify the possible virus associated with the disease,the sample was collected and detected by PCR with begomovirus degenerate primers. The amplicons were cloned and sequenced,and two sequences（YN6198-28 and YN6198-31）of 2 763 bp corresponding to begomovirus DNA-A genome with six open reading frames were identified from this sample. The YN6198-28 DNA-A sequence shares the highest identity（94.90%）with Ludwigia yellow vein Vietnam virus（LuYVVNV）,which confirmed that the virus was an isolate of LuYVVNV. Recombination analysis revealed that the YN6198-28 isolate is a recombinant begomovirus derived from Ludwigia yellow vein virus and Ageratum yellow vein China virus.

Key words: Impatiens balsamina, Begomoviruses, recombination virus

CLC Number:

S681.1

ZHONG Jing, ZHAO Liling, LI Tingting, ZHANG Shuiying, CHEN Yue, DING Ming. Molecular Identification and Sequence Analysis of Begomoviruses Infecting Impatiens balsamina[J]. Acta Horticulturae Sinica, 2022, 49(5): 1136-1144.

Figures/Tables 5

References 30

[1]	Anurag K S, Avinash M, Shahid M S, Chitra N, Gaur R K. 2014. First report of a begomovirus and associated betasatellite in Rosa indica and in India. Australasian Plant Disease Notes, 9 (1):147-150.
[2]	Briddon R W, Bull S E, Mansoor S, Amin I, Markham P G. 2002. Universal primers for the PCR-mediated amplification of DNA beta-a molecule associated with some monopartite begomoviruses. Molecular Biotechnology, 20 (3):315-318. pmid: 11936260
[3]	Brown J K, Fauquet C M, Briddon R W, Zerbini M, Moriones E, NavasCastillo J, King A M Q, Adams M J, Carstens E B, Lefkowitz E J. 2012. Virus taxonomy-ninth report of the international committeeon taxonomy of viruses. London: Associated Press,Elsevier Inc:351-373.
[4]	Brown J K, Zerbini F, MNavas-Castillo J, Moriones E, Ramos-Sobrinho R, Silva J C F, Fiallo-Olivé E, Briddon R W, Hernández-Zepeda C, Idris A, Malathi V G, Martin D P, Rivera-Bustamante R, Ueda S, Varsani A. 2015. Revision of Begomovirus taxonomy based on pairwise sequence comparisons. Archives of Virology, 160 (6):1593-1619. doi: 10.1007/s00705-015-2398-y URL
[5]	Bull S E, Briddon R W, Markham P G. 2003. Universal primers for the PCR-mediated amplification of DNA 1:a satellite-like molecule associated with begomovirus-DNA β complexes. Molecular Biotechnology, 23 (1):83-86. pmid: 12611272
[6]	Castillo-Urquiza G P, Beserra J E A, Bruckner F P, Lima A T M, Varsani A, Alfenas-Zerbini P, Zerbini F M. 2008. Six novel begomoviruses infecting tomato and associated weeds in Southeastern Brazil. Archives of Virology, 153 (10):1985-1989. doi: 10.1007/s00705-008-0172-0 pmid: 18726171
[7]	Charoenvilaisiri S, Seepiban C, Phironrit N, Phuangrat B, Gajanandana O. 2019. Occurrence and distribution of begomoviruses infecting tomatoes,peppers and cucurbits in Thailand. Crop Protection, 127:104948. doi: 10.1016/j.cropro.2019.104948 URL
[8]	Cheng Yi-lin. 2001. Flora of China. Vol 47. Beijing: Science Press. (in Chinese)
	陈艺林. 2001. 中国植物志. 47卷. 北京: 科学出版社.
[9]	Choi S K, Choi G S, Kwon S J, Cho I S, Yoon J Y. 2015. First report of Cucumber mosaic virus in African Impatiens(Impatiens walleriana)in Korea. Research in Plant Disease, 21 (4):341-345.
[10]	Chong Yi-yan. 2007. Study on the Flora of Impatiens L. in the Gaoligong Mounyains Region,Yunnan[M. D. Dissertation]. Changsha: Hunan Normal University. (in Chinese)
	丛义艳. 2007. 云南高黎贡山凤仙花属(Impatiens L.)植物区系研究[硕士论文]. 长沙: 湖南师范大学.
[11]	Deepa, Sunkad G, Govindappa M R, Naik M K, Somasekhar. 2014. Management of new sunflower leaf curl virus disease caused by Begomovirus. Indian Journal of Animal Nutrition, 7 (16):2127-2131.
[12]	Doyle J J, Doyle J L. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemistry Bulletin, 19:11-15.
[13]	Elliott D R, Lebas B S M, Ochoa-Corona F M, Tang J, Alexander B J R. 2009. Investigation of Impatiens necrotic spot virus outbreaks in New Zealand. Australasian Plant Pathology, 38 (5):490-495. doi: 10.1071/AP09031 URL
[14]	Khatri S, Nahid N, Fauquet C M, Mubin M, Nawaz-UI-Rehman. 2014. A betasatellite-dependent begomovirus infects ornamental rose:characterization of begomovirus infecting rose in Pakistan. Virus Genes, 49 (1):124-131. doi: 10.1007/s11262-014-1076-6 URL
[15]	Koeda S, Kesumawti E, Tanaka Y, Hosokamv M, Doi M, KitajimaI A. 2016. Mixed infection of Begomoviruses on pepper plants at Northern Sumatra,Indonesia. Tropical Agriculture and Development, 60 (2):59-64.
[16]	Martin D P, Rybicki E P. 2000. RDP:Detection of recombination amongst aligned sequences. Bioinformatics, 16 (6):562-563. pmid: 10980155
[17]	Marwal A, Prajapat R, Sahu A, Gaur K R. 2013. First report of Begomovirus infecting two ornamental plants: Jasminum sambac and Millingtonia hortensis. Indian Phytopathology, 5 (5):240-249.
[18]	Monci F, Sánchez-Campos S, Navas-Castillo J, Moriones E. 2002. A natural recombinant between the geminiviruses Tomato yellow leaf curl sardinia virus and Tomato yellow leaf curl virus exhibits a novel pathogenic phenotype and is becoming prevalent in Spanish populations. Virology, 303 (2):317-326. doi: 10.1006/viro.2002.1633 URL
[19]	Muhizi M B, Arvind V, Patrick M D, Kuhn J H. 2014. SDT:a virus classification tool based on pairwise sequence alignment and identity calculation. PLoS ONE, 9 (9):e108277. doi: 10.1371/journal.pone.0108277 URL
[20]	Nawaz-ul-Rehman M S, Mansoor S, Briddon R W, Fauquet C M. 2009. Maintenance of an old world betasatellite by a new world helper begomovirus and possible rapid adaptation of the betasatellite. Journal of Virology, 83 (18):9347-9355. doi: 10.1128/JVI.00795-09 pmid: 19570867
[21]	Rojas M R, Hagen C, Lucas W J, Gilbertson R L. 2005. Exploiting chinks in the plant’s armor:evolution and emergence of geminiviruses. Annual Review of Phytopathology, 43:361-394. doi: 10.1146/annurev.phyto.43.040204.135939 URL
[22]	Senanayake D M J B, Jayasinghe J E A R M, Shilpi S, Wasals S K, Mandal B. 2013. A new begomovirus-betasatellite complex is associated with chilli leaf curl disease in Sri Lanka. Virus Genes, 46 (1):128-139. doi: 10.1007/s11262-012-0836-4 pmid: 23090833
[23]	Srivastava A, Kumar S, Raj S K. 2014. Association of Pedilanthus leaf curl virus with yellow mottling and leaf curl symptoms in two jasmine species grown in India. Journal of General Plant Pathology, 80 (4):370-373. doi: 10.1007/s10327-014-0517-3 URL
[24]	Stanley J. 1985. The molecular biology of Geminiviruses. Advances in Virus Research, 30:139-177. pmid: 3914211
[25]	Thierry W, Njapo-Ngangom H O, Sasithorn C, Gabi K. 2006. Nucleotide sequence of a new isolate of ribgrass mosaic tobamovirus infecting Impatiens New Guinea. Archives of Virology, 151 (4):787-791. doi: 10.1007/s00705-005-0677-8 URL
[26]	Xue Hong-yan, Tan Li-pan, Lu Guo-ming, Zhang He-qin, Xue Qin-fen. 2017. Occurrence and control methods of main diseases and insect pests of Impatiens balsamina L. Plant Doctor, 30 (12):57-59. (in Chinese)
	薛洪雁, 谭礼盘, 陆国敏, 张和芹, 薛琴芬. 2017. 凤仙花主要病虫害发生及防治方法. 植物医生, 30 (12):57-59.
[27]	Zhang Wei-zhuang. 2016. Analysis on the development status of Yunnan flower industry. Market Modernization, (17):189-190. (in Chinese)
	张维壮. 2016. 云南花卉产业发展现状分析. 商场现代化,(17):189-190.
[28]	Zhao L L, Ding M, Zhang X Y, Yin Y Y, Zhang Z K. 2017. First report of tobacco curly shoot virus(TBCSV)and its associated satellites from watermelon in China. Journal of Plant Pathology, 99 (3):761-764.
[29]	Zhao Li-ling, Shi Zhang-jie, Li Ting-ting, Zhong Jing, Ding Ming, Zhang Zhong-kai. 2020. Natural hosts and genetic diversity of Crassocephalum yellow vein virus. Journal of Plant Protection, 47 (3):647-656. (in Chinese)
	赵丽玲, 施章吉, 李婷婷, 钟静, 丁铭, 张仲凯. 2020. 野茼蒿黄脉病毒的田间寄主范围及其基因多样性特征. 植物保护学报, 47 (3):647-656.
[30]	Zhao Li-ling, Zhong Jing, Yin Yue-yan, Zhang Zhong-kai. 2017. Molecular characterization of two distinct begomoviruses from the weed Amaranthus lividus in Yunnan,China. Acta Phytopathologica Sinica, 47 (6):738-746. (in Chinese)
	赵丽玲, 钟静, 尹跃艳, 张仲凯. 2017. 云南凹头苋上分离到的2种菜豆金色花叶病毒属病毒基因组结构特征. 植物病理学报, 47 (6):738-746.

病毒 Viruses	分离物 Isolate	登录号 Accession No.	Total Nt	IR	V1		V2		C1		C2		C3		C4
病毒 Viruses	分离物 Isolate	登录号 Accession No.	Total Nt	IR	Nt	AA	Nt	AA	Nt	AA	Nt	AA	Nt	AA	Nt	AA
AlYVV	P-663	MH538342.1	73.33	65.82	80.16	92.96	73.40	46.77	73.66	72.85	76.29	60.66	73.58	67.91	72.50	46.87
AlYVV	YN598	FJ015062.1	73.62	67.03	80.00	92.46	75.00	50.00	72.55	73.40	76.54	60.66	75.55	70.89	70.10	42.70
AYVCNV	BS1	KU954377.1	79.22	75.88	73.74	80.40	84.81	69.84	83.74	87.56	80.39	71.85	80.89	76.86	88.65	76.04
AYVCNV	BS3	KU954379.1	78.51	74.50	74.41	80.40	78.01	55.55	83.83	87.01	79.65	71.11	79.50	75.37	89.00	77.08
AYVV	Thai3	MK238277.1	78.04	76.40	75.25	81.40	82.72	71.42	80.38	86.46	81.86	73.33	80.74	77.61	72.91	43.75
AYVV	YN2528-3	MN233600.1	79.36	78.71	73.07	80.90	83.24	66.66	83.47	88.12	80.63	72.59	80.64	75.37	83.84	63.54
CoLCV	Lucknow	GU440580.1	79.67	80.24	74.74	80.90	77.12	59.67	83.37	86.31	82.59	73.33	84.44	82.83	84.19	72.91
LuYVV		DQ641708.1	75.97	82.53	96.83	98.99	99.47	92.06	84.29	80.66	99.50	100.00	97.03	97.01	54.60	47.05
LuYVV	G37	AJ965539.2	75.88	87.30	97.50	96.55	98.95	92.06	81.34	77.17	98.03	98.51	96.79	95.52	73.15	47.05
LuYVVNV		DQ641699.1	94.90	86.64	97.16	99.49	99.47	93.65	94.18	94.19	98.77	97.77	95.80	97.01	92.43	86.45
LuYVVNV	YN6154	MN210349.1	94.61	80.00	97.33	100.00	98.42	92.06	94.03	95.85	99.26	97.77	97.53	98.50	96..21	93.75
SaLCV	AFSP5e	NC_038455.1	89.26	88.03	95.83	96.98	82.72	66.66	85.85	87.29	96.56	97.03	98.02	97.01	96..21	55.29
SiYVVNV		NC_009547.1	79.94	75.19	75.16	81.40	85.34	66.66	82.82	85.08	83.08	77.77	86.66	81.34	84.87	69.79
TbLCPatV	INBD	KM383746.1	80.15	75.49	73.95	80.90	77.48	58.73	85.04	89.44	85.29	77.77	86.17	83.58	84.53	69.79
ToLCMaV	MT1-5	NC_004648.1	80.02	75.30	74.74	80.40	80.20	61.90	84.94	88.12	82.35	76.29	85.18	77.61	86.94	71.87
ToLCPatV	Ballia	MK122994.1	79.42	76.19	74.74	80.40	77.48	58.73	83.62	86.11	82.10	74.07	84.19	80.59	84.53	72.91
TYLCYnV	YN2013-10	NC_021341.1	78.34	77.82	74.50	81.90	79.58	60.31	83.51	87.81	79.50	70.14	78.10	71.64	83.84	66.66
TYLCYnV	YN4265-4	MN233598.1	78.11	76.21	74.50	81.90	78.23	50.79	83.05	86.14	80.24	71.64	78.90	73.13	83.84	64.58

病毒 Viruses	分离物 Isolate	登录号 Accession No.	Total Nt	IR	V1		V2		C1		C2		C3		C4
病毒 Viruses	分离物 Isolate	登录号 Accession No.	Total Nt	IR	Nt	AA	Nt	AA	Nt	AA	Nt	AA	Nt	AA	Nt	AA
AlYVV	P-663	MH538342.1	73.33	65.82	80.16	92.96	73.40	46.77	73.66	72.85	76.29	60.66	73.58	67.91	72.50	46.87
AlYVV	YN598	FJ015062.1	73.62	67.03	80.00	92.46	75.00	50.00	72.55	73.40	76.54	60.66	75.55	70.89	70.10	42.70
AYVCNV	BS1	KU954377.1	79.22	75.88	73.74	80.40	84.81	69.84	83.74	87.56	80.39	71.85	80.89	76.86	88.65	76.04
AYVCNV	BS3	KU954379.1	78.51	74.50	74.41	80.40	78.01	55.55	83.83	87.01	79.65	71.11	79.50	75.37	89.00	77.08
AYVV	Thai3	MK238277.1	78.04	76.40	75.25	81.40	82.72	71.42	80.38	86.46	81.86	73.33	80.74	77.61	72.91	43.75
AYVV	YN2528-3	MN233600.1	79.36	78.71	73.07	80.90	83.24	66.66	83.47	88.12	80.63	72.59	80.64	75.37	83.84	63.54
CoLCV	Lucknow	GU440580.1	79.67	80.24	74.74	80.90	77.12	59.67	83.37	86.31	82.59	73.33	84.44	82.83	84.19	72.91
LuYVV		DQ641708.1	75.97	82.53	96.83	98.99	99.47	92.06	84.29	80.66	99.50	100.00	97.03	97.01	54.60	47.05
LuYVV	G37	AJ965539.2	75.88	87.30	97.50	96.55	98.95	92.06	81.34	77.17	98.03	98.51	96.79	95.52	73.15	47.05
LuYVVNV		DQ641699.1	94.90	86.64	97.16	99.49	99.47	93.65	94.18	94.19	98.77	97.77	95.80	97.01	92.43	86.45
LuYVVNV	YN6154	MN210349.1	94.61	80.00	97.33	100.00	98.42	92.06	94.03	95.85	99.26	97.77	97.53	98.50	96..21	93.75
SaLCV	AFSP5e	NC_038455.1	89.26	88.03	95.83	96.98	82.72	66.66	85.85	87.29	96.56	97.03	98.02	97.01	96..21	55.29
SiYVVNV		NC_009547.1	79.94	75.19	75.16	81.40	85.34	66.66	82.82	85.08	83.08	77.77	86.66	81.34	84.87	69.79
TbLCPatV	INBD	KM383746.1	80.15	75.49	73.95	80.90	77.48	58.73	85.04	89.44	85.29	77.77	86.17	83.58	84.53	69.79
ToLCMaV	MT1-5	NC_004648.1	80.02	75.30	74.74	80.40	80.20	61.90	84.94	88.12	82.35	76.29	85.18	77.61	86.94	71.87
ToLCPatV	Ballia	MK122994.1	79.42	76.19	74.74	80.40	77.48	58.73	83.62	86.11	82.10	74.07	84.19	80.59	84.53	72.91
TYLCYnV	YN2013-10	NC_021341.1	78.34	77.82	74.50	81.90	79.58	60.31	83.51	87.81	79.50	70.14	78.10	71.64	83.84	66.66
TYLCYnV	YN4265-4	MN233598.1	78.11	76.21	74.50	81.90	78.23	50.79	83.05	86.14	80.24	71.64	78.90	73.13	83.84	64.58

重组分离物 Recombinant isolate	主要亲本 Major parent	次要亲本 Mino parent	重组发生位置/nt Break point	重组检测 Detected of recombination events
重组分离物 Recombinant isolate	主要亲本 Major parent	次要亲本 Mino parent	重组发生位置/nt Break point	方法Method	P
LuYVVNV（MN210346）	LuYVV	AYVCNV-BS3	2 082 ~ 2 640	RDP	1.146 × 10^-38
LuYVVNV（MN210349）	LuYVV	AYVCNV-BS3	2 094 ~ 2 607	GENECONV	6.965 × 10^-18
LuYVVNV（NC_038451）	LuYVV	AYVCNV-BS3	2 094 ~ 2 576	BootScan	3.351 × 10^-27
LuYVVNV（DQ641699）	AYVCNV-BS3	LuYVV	2 094 ~ 2 578	MaxChi	5.266 × 10^-21
LuYVVNV（MN210345）	AYVCNV-BS3	LuYVV	2 094 ~ 2 607	Chimaera	1.086 × 10^-17
				SiScan	2.001 × 10^-16
				3Seq	5.476 × 10^-48

重组分离物 Recombinant isolate	主要亲本 Major parent	次要亲本 Mino parent	重组发生位置/nt Break point	重组检测 Detected of recombination events
重组分离物 Recombinant isolate	主要亲本 Major parent	次要亲本 Mino parent	重组发生位置/nt Break point	方法Method	P
LuYVVNV（MN210346）	LuYVV	AYVCNV-BS3	2 082 ~ 2 640	RDP	1.146 × 10^-38
LuYVVNV（MN210349）	LuYVV	AYVCNV-BS3	2 094 ~ 2 607	GENECONV	6.965 × 10^-18
LuYVVNV（NC_038451）	LuYVV	AYVCNV-BS3	2 094 ~ 2 576	BootScan	3.351 × 10^-27
LuYVVNV（DQ641699）	AYVCNV-BS3	LuYVV	2 094 ~ 2 578	MaxChi	5.266 × 10^-21
LuYVVNV（MN210345）	AYVCNV-BS3	LuYVV	2 094 ~ 2 607	Chimaera	1.086 × 10^-17
				SiScan	2.001 × 10^-16
				3Seq	5.476 × 10^-48

Molecular Identification and Sequence Analysis of Begomoviruses Infecting Impatiens balsamina

RichHTML

PDF

Knowledge

Abstract

Cite this article

share this article

Figures/Tables 5

References 30

Related Articles 0

Recommended Articles

Metrics

Comments