侵染广西甜瓜的新德里曲叶病毒全基因组序列测定及遗传进化分析

Whole genome sequencing and genetic evolution analysis of leaf curl New Delhi virus infecting melons in Guangxi

  • 摘要: 【目的】 明确侵染广西北海市大棚甜瓜呈现叶片卷曲、叶脉突起、植株矮化等症状的病原病毒,并对其全基因组序列进行测定及遗传进化分析,为广西甜瓜病毒病防控提供理论依据。【方法】 从北海市甜瓜大棚采集叶片呈现皱缩、叶脉突出、叶色褪绿等症状的样品,采用PCR检测、全基因组序列扩增、系统发育分析及重组分析等方法对样品进行病原病毒种类鉴定及遗传进化关系分析。【结果】 利用双生病毒简并引物(PA/PB)从甜瓜样品中扩增出约500 bp的目的片段,PCR产物经纯化后进行测序,所得序列与GenBank上已报道的新德里番茄曲叶病毒(Tomato leaf curl New Delhi virus, ToLCNDV)各分离物的相似性均在95.00%以上,表明甜瓜样品受到双生病毒科(Geminiviridae)菜豆金色黄花叶病毒属(Begomovirus)病毒侵染。分别利用背靠背引物ToLCNDV-AF/AR、ToLCNDV-BF/BR扩增ToLCNDV GXBH-TG的DNA-A和DNA-B序列,所得PCR产物分别纯化后进行序列测定及拼接,获得1条全长为2739 bp的DNA-A序列(GenBank登录号:PX021751)和1条全长为2692 bp的DNA-B序列(GenBank登录号:PX021752),其中DNA-A包含7个开放阅读框(ORF),编码7个蛋白;DNA-B包含2个ORF,编码2个蛋白,在DNA-A和DNA-B基因组上均有1个9 nt的TAATATT/AC茎环结构。核苷酸序列分析结果显示,ToLCNDV GXBH-TG的DNA-A与已登录GenBank的ToLCNDV各分离物相似性高达99.89%,DNA-B相似性达99.15%以上。系统发育分析发现,ToLCNDV GXBH-TG的DNA-A与用于分析的ToLCNDV各分离物的DNA-A处于一个大分支,其中与ToLCNDV 8066(寄主:cucumber)处于一个小分支,暗示2个分离物具有较近的亲缘关系;ToLCNDV GXBH-TG的DNA-B与来自广东省的ToLCNDV分离物STSiG(寄主:luffa)、YJSiG(寄主:luffa)、STHL(寄主:cucurbit)、STFQ(寄主:tomato)、STDG(寄主:wax gourd)和STNG(寄主:pumpkin) 处于一个小分支,暗示其较近的亲缘关系。【结论】 侵染广西北海市甜瓜呈现叶面皱缩、叶色褪绿、叶脉突起等症状的病原病毒为ToLCNDV。

     

    Abstract: 【Objective】 This study aimed to identify the viral pathogen causing leaf curling, vein clearing, and plant stunting for Cucumis melo L. in greenhouses of Beihai, Guangxi, sequence its whole genome, and conduct genetic evolution of the virus, so as to provide a theoretical basis for the prevention and control of virus diseases in Cucumis melo L. in Guangxi. 【Method】 Cucumis melo L. samples showing symptoms of leaf rugosity, vein clearing, and chlorosis were collected from greenhouses in Beihai. The identification of viruses and phylogenetic analysis of the samples were carried out by PCR detection, whole genome sequence amplification, recombination analysis, and genetic evolution relationship analysis. 【Result】 The target fragment of approximately 500 bp was amplified from the Cucumis melo L. samples by geminivirus degenerate primers (PA/PB). The purified PCR products were sequenced, and the obtained sequences showed a similarity of over 95.00% with each isolate of tomato leaf curl New Delhi virus (ToLCNDV) in GenBank, indicating that the Cucumis melo L. samples were infected by the virus of Begomovirus and Geminiviridae. The whole genome sequences of DNA-A and DNA-B of GXBH-TG were amplified using back-to-back primers ToLCNDV-AF/AR and ToLCNDV-BF/BR. The PCR products were purified, sequenced, and then assembled to obtain a DNA-A sequence with lengths of 2739 bp (GenBank accession No.:PX021751) and a DNA-B sequence with lengths of 2692 bp (GenBank accession No.:PX021752). DNA-A contained seven open reading frames (ORFs), encoding 7 proteins; DNA-B contained 2 ORFs, encoding 2 proteins. A 9 nt TAATATT/AC stem-loop structure was found in both the DNA-A and DNA-B genomes. Nucleotide sequence analysis showed that the DNA-A of ToLCNDV GXBH-TG shared a high similarity of 99.89% with the DNA-A sequences of ToLCNDV isolates deposited in GenBank; DNA-A shared a similarity above 99.15%. Phylogenetic analysis revealed that DNA-A of ToLCNDV GXBH-TG was in a large branch with that of other ToLCNDV isolates, and in a small branch with that of ToLCNDV 8066 (host: cucumber), implying a close evolutionary relationship between the two isolates; DNA-B of oLCNDV GXBH-TG was in a small branch with that of ToLCNDV isolates from Guangdong Province, STSiG (host: luffa), YJSiG (host: luffa), STHL (host: cucurbit), STFQ (host: tomato), STDG (host: wax gourd), and STNG (host: pumpkin), indicating they shared a close relationship. 【Conclusion】 ToLCNDV is identified as the virus infecting Cucumis melo L. samples from Beihai, Guangxi and causing symptoms such as leaf rugosity, chlorosis, and vein clearing.

     

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