Molecular Detection and Genetic Evolution Analysis of Yunnan Isolates of Lettuce Chlorosis Virus in Tomato

doi:10.16420/j.issn.0513-353x.2020-1087

Acta Horticulturae Sinica ›› 2022, Vol. 49 ›› Issue (1): 141-147.doi: 10.16420/j.issn.0513-353x.2020-1087

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Molecular Detection and Genetic Evolution Analysis of Yunnan Isolates of Lettuce Chlorosis Virus in Tomato

FENG Lixiao¹, HU Rong¹, BU Shan¹, ZHANG Deyong¹^,², LUO Xiangwen², LI Fan³, DING Ming⁴, ZHANG Zhuo², ZHANG Songbai¹^,²^,^*(), LIU Yong¹^,²^,^*()

¹College of Longping,Graduate School of Hunan University,Changsha 410125,China
²Plant Protection Institute,Hunan Academy of Agricultural Sciences,Changsha 410125,China
³Plant Protection College Yunnan Agricultural University,Kunming 650201,China
⁴Yunnan Academy of Agricultural Sciences,Kunming 650231,China

Received:2021-03-09 Revised:2021-08-20 Online:2022-01-25 Published:2022-01-24
Contact: ZHANG Songbai,LIU Yong E-mail:zsongb@hunaas.cn;haoasliu@hunaas.cn

Abstract

Abstract:

The 77 tomato leaves suspected to be infected by lettuce chlorosis virus（LCV）were sampled in Yunnan Province,China. The reverse transcriptional（RT）-PCR amplified near full length of minor coat protein gene（CPm）of LCV,which was sequenced by Sanger sequencing method. The genetic evolution was analyzed based on the sequences of near full length CPm genes. The results showed that the specific 1.38 kb fragment was amplified by RT-PCR,and 12.99% LCV-positive samples were detected in the 77 tomato leaf samples. The sequences of near full length CPm genes of Yunnan Province,China,shared the highest nucleotide sequence identity of 99.27%-99.78% with LCV Shandong isolate（MK370741）. Phylogenetic analysis indicated that all of LCV isolates were divided into three subclusters with region-dependent,LCV Yunnan isolates grouped into same subcluster with other LCV isolates of China,and America isolates and European isolates grouped into other two subclusters separately. Genetic evolution analysis revealed one recombinant event exiting in LCV Yunnan isolate YN58,and the highest nucleotide substitution of 25.25 occurring in pyrimidine C/T,which shown LCV had the tendency of independent evolution and expedited diffusion in China. This is the first report of LCV in Yunnan Province.

Key words: tomaoto, lettuce chlorosis virus, molecular detection, phylogenetic analysis, evolution

CLC Number:

S641.2

FENG Lixiao, HU Rong, BU Shan, ZHANG Deyong, LUO Xiangwen, LI Fan, DING Ming, ZHANG Zhuo, ZHANG Songbai, LIU Yong. Molecular Detection and Genetic Evolution Analysis of Yunnan Isolates of Lettuce Chlorosis Virus in Tomato[J]. Acta Horticulturae Sinica, 2022, 49(1): 141-147.

Figures/Tables 6

Fig. 1 The symptom of a tomato plant in field suspected to be infected by lettuce chlorosis virus A：Chlorosis symptom in a tomato plant;B：Chlorosis and browning necrosis on a tomato leaf.

Fig. 2 Electrophoresis of products of LCV-specific RT-PCR 1：Negative control（ddH2O as template）;2-13：Tomato samples;14：Positive control.

Fig. 3 Phylogenetic tree based on the near full length sequences of minor coat protein（CPm）gene of LCV isolates

Table 1 Recombinant events analysis of near full length of minor coat of protein gene（CPm）of LCV isolates

重组事件 Recombinant event	重组子 Recombinant	主要来源 Major parent	次要来源 Minor parent	算法Algorithm
重组事件 Recombinant event	重组子 Recombinant	主要来源 Major parent	次要来源 Minor parent	RDP	Geneconv	Bootscan	MaxChi	Chimaera	SiScan	Topal
1	BR （巴西Brazil）	Can1 （以色列Israel）	未知 Unknown	+	-	-	+	+	+	-
2	YN58 （云南Yunnan）	SD （山东Shandong）	未知 Unknown	-	+	+	-	+	+	+

Table 2 Maximum composite likelihood estimate of the pattern of nucleotide substitution of near full length of minor coat protein gene（CPm）of LCV isolates

核苷酸 Nucleotide	A	T	C	G
A	-	3.11	2.02	13.20
T	3.96	-	16.38	2.34
C	3.96	25.25	-	2.34
G	22.31	3.11	2.02	-

Table 3 Gene flow and genetic differentiation between near full length of minor coat protein（CPm）genes of LCV isolates

亚群Lineage	序列数量Number of sequences	Ss	h	Hd	k	Pi
Ⅰ	13	36	13	1	13.54	0.0099
Ⅱ	3	8	3	1	5.33	0.0039
Ⅲ	2	3	2	1	18.00	0.0670

References 17

[1]	Alabi O J, Gaytán B C, Rwahnih M A, Villegas C. 2020. A description of the possible etiology of the Cilantro yellow blotch disease. Plant Disease, 104 (3):630-633. doi: 10.1094/PDIS-09-19-1958-SC URL
[2]	Chen A Y S, Pavitrin A, Ng J C K. 2012. Agroinoculation of the cloned infectious cDNAs of Lettuce chlorosis virus results in systemic plant infection and production of whitefly transmissible virions. Virus Research, 169:310-315. doi: 10.1016/j.virusres.2012.08.010 URL
[3]	Chu Dong, Pan Hui-peng, Guo Dong, Tao Yun-li, Liu Bai-ming, Zhang You-jun. 2012. Ecological processes and mechanisms of invasion of the alien whitefly Bemisia tabaci biotype Q in China. Acta Entomologica Silico, 55 (12):1399-1405. (in Chinese)
	褚栋, 潘慧鹏, 国栋, 陶云荔, 刘佰明, 张友军. 2012. Q型烟粉虱在中国的入侵生态过程及机制. 昆虫学报, 55 (12):1399-1405.
[4]	Duffus J E, Liu H Y, Wisler G C, Li R H. 1996. Lettuce chlorosis virus-a new whitefly-transmitted closterovirus. European Journal of Plant Pathology, 102 (6):591-596. doi: 10.1007/BF01877027 URL
[5]	Hadad L, Luria N, Smith E, Sela N, Lachman O, Dombrovsky A. 2019. Lettuce chlorosis virus disease:a new threat to Cannabis production. Viruses, 11 (9):802. doi: 10.3390/v11090802 URL
[6]	Librado P, Rozas J. 2009. DnaSP v5:a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25:1451-1452. doi: 10.1093/bioinformatics/btp187 pmid: 19346325
[7]	Liu Yong, Li Fan, Li Yue-yue, Zhang Song-bai, Gao Xi-wu, Xie Yan, Yan Fei, Zhang An-sheng, Dai Lian-ying, Cheng Zhao-bang, Ding Ming, Niu Yan-bing, Wang Shen-ji, Che Hai-yan, Jiang Tong, Shi Xiao-bing, He Zi-fu, Wu Yun-feng, Zhang De-yong, Qing Lin, Yan Wan-rong, Yang Xue-hui, Tang Ya-fei, Zheng Hong-ying, Tang Qian-jun, Zhang Song-bai, Zhang Dong-fang, Cai Li, Tao Xiao-rong. 2019. Identification, distribution and occurrence of viruses in the main vegetables of China. Scientia Agricultura Sinica, 52 (2):239-261. (in Chinese)
	刘勇, 李凡, 李月月, 张松柏, 高希武, 谢艳, 燕飞, 张安盛, 戴良英, 程兆榜, 丁铭, 牛颜冰, 王升吉, 车海彦, 江彤, 史晓斌, 何自福, 吴云锋, 张德咏, 青玲, 严婉荣, 杨学辉, 汤亚飞, 郑红英, 唐前君, 章松柏, 章东方, 蔡丽, 陶小荣. 2019. 侵染我国主要蔬菜作物的病毒种类、分布与发生趋势. 中国农业科学, 52 (2):239-261.
[8]	Martin D, Rybicki E. 2000. RDP:detection of recombination amongst aligned sequences. Bioinformatics, 16:562-563. pmid: 10980155
[9]	McLain J, Castle S, Holmes G, Creamer R. 1998. Physiochemical characterization and field assessment of Lettuce chlorosis virus. Plant Disease, 82 (11):1248-1252. doi: 10.1094/PDIS.1998.82.11.1248 URL
[10]	Ng J C K, Chen A Y S. 2011. Acquisition of Lettuce infectious yellows virus by Bemisia tabaci perturbs the transmission of Lettuce chlorosis virus. Virus Research, 156:64-71. doi: 10.1016/j.virusres.2010.12.019 URL
[11]	Ruiz M L, Simon A, Garcia M C, Janssen D. 2014. First report of Lettuce chlorosis virus infecting bean in Spain. Plant Disease, 98 (6):857.
[12]	Tamura K, Nei M, Kumar S. 2004. Prospects for inferring very large phlogenies by using the Neighbor-joining method. Proceedings of the National Academy of Sciences of the United States of America, 101:11030-11035.
[13]	Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5:molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance,and maximum parsimony methods. Molecular Biology and Evolution, 28:2731-2739. doi: 10.1093/molbev/msr121 URL
[14]	Tian X, Tian Y, Yu Y Q, Wang X F, Li Z A, Li R H, Cao M J, Zhou C Y. 2018. Periwinkle:a new natural host of Lettuce chlorosis virus in China. Plant Disease, 102 (2):462. doi: 10.1094/PDIS-07-17-1100-PDN
[15]	Wang Yu-meng, He Ya-zhou, Liu Shu-sheng, Wang Xiao-wei. 2020. Mechanisms of plant virus transmission by the whitefly Bemisia tabaci. Chinese Science Bulletin, 65 (15):1463-1475. (in Chinese)
	王雨蒙, 何亚洲, 刘树生, 王晓伟. 2020. 烟粉虱传播植物病毒特性及机制研究进展. 科学通报, 65 (15):1463-1475.
[16]	Zhang S B, Zhang D Y, Liu Y, Luo X W, Liu M Y, Du J, Wang M C. 2017. First report of Lettuce chlorosis virus infecting tomato in China. Plant Disease, 101 (5):846.
[17]	Zhao X H, Zhu M, Wu Q, Zhang J, Xu Y, Tao X R. 2018. Complete genome sequence of a lettuce chlorosis virus isolate from China and genome recombination/rearrangement analysis. Archives of Virology, 163 (3):751-754. doi: 10.1007/s00705-017-3604-x URL

Molecular Detection and Genetic Evolution Analysis of Yunnan Isolates of Lettuce Chlorosis Virus in Tomato

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