[Objectives]This study was conducted to investigate the molecular characteristics,genetic structure and evolutionary mechanism of cucurbit aphid-borne yellows virus(CABYV),which is of great significance for clarifying...[Objectives]This study was conducted to investigate the molecular characteristics,genetic structure and evolutionary mechanism of cucurbit aphid-borne yellows virus(CABYV),which is of great significance for clarifying the epidemic laws of the disease in the field and formulating long-term sustainable control strategies.[Methods]120 melon leaves suspected to be infected with CABYV were randomly collected from Aksu City,Xinjiang.RT-PCR was used to detect the virus.MEGA 7.0 was used to construct a phylogenetic tree.DnaSP v5.10 was used to analyze the genetic diversity among different sequences,and RDP v.4.31 software was used to analyze possible recombination events of CABYV sequence.[Results]The detection rate of CABYV was 31.67%.A new CABYV-2 was isolated,sequenced and cloned from these positive samples.The length of the genome is 5497 bp,encoding six open reading frames.Compared with 23 CABYV strains isolated from different countries in NCBI database,CABYV-2 shared the highest homology with KR231942.1 and the lowest homology with JF939812.1.The results of evolutionary tree analysis showed that the 24 isolates were divided into two branches due to different geographical factors,including CABYV-2 and KR2319421,which were clustered together and belonged to branch 1.The results of genetic diversity and neutrality tests showed that CABYV was highly variable and the population was expanding.The results of recombination analysis showed that there were two recombinants,EU636992.1 and KR231949.1,which exacerbated the variation of CABYV.[Conclusions]The CABYV isolate from Aksu City,Xinjiang had the closest relationship with the Korean isolate KR231942.1,and the farthest relationship with the isolates from European countries.There were large genetic differences between the isolates of branch 1 and branch 2,and the recombination of CABYV in different hosts aggravated the variation of CABYV.Recombination and negative selection may be important reasons for the genetic variation of CABYV.展开更多
Cucurbit aphid-borne yellows virus(CABYV)and watermelon mosaic virus(WMV)are major plant pathogens that cause severe epidemics in cucurbit crops.While there has been an increasing interest in molecular epidemiological...Cucurbit aphid-borne yellows virus(CABYV)and watermelon mosaic virus(WMV)are major plant pathogens that cause severe epidemics in cucurbit crops.While there has been an increasing interest in molecular epidemiological studies on both viruses at regional scales,their phylodynamic analysis by using the temporal data at global scale remains unexplored.In this study,we implemented the Nextstrain phylodynamic approach to comprehensively examine the coat protein gene and full-length genome sequences of the CABYV and WMV worldwide populations.Our analyses reconstructed a robust phylogeny of CABYV and confirmed the occurrence of isolates grouped into three clusters(Asian,Mediterranean,and Recombinant).Nextstrain analysis suggested that CABYV epidemics likely originated in Southeast Asia in fourteenth century,while the Mediterranean population emerged in Spain in seventeenth century.We also found a high divergence between Asian and Mediterranean isolates,with low genetic diversity and scarce evidence of selection,as reflected by the lack of gene flow.Moreover,the hierarchical analysis of molecular variance revealed a significant differentiation between CABYV populations grouped by geographical location and plant host.Additionally,the global phylogenetic reconstruction of the WMV population confirmed a clear differentiation among isolates,which grouped into two clusters(classical and emergent),and Nextstrain analysis suggested that WMV epidemics were most probably originated in USA during the sixteenth century.The initial WMV population diverged in the eighteenth century,with the origin of the emergent population in the nineteenth century.Our analysis confirmed that WMV population has a polyphyletic origin,defining an extensive genetic diversity.Overall,this work provides insights into the CABYV and WMV origin and evolutionary dynamics,gaining an understanding of the global spread of both viral diseases.Additionally,the integration of all spatiotemporal CABYV and WMV data,along with their genome sequence data by open access(https://github.com/PiR92)and the Nextstrain approach,provides a valuable tool for compiling and sharing current knowledge of these viral diseases in cucurbit crops.展开更多
基金Supported by National Natural Science Foundation of China(31760511)Linfen Key R&D Program(2009)+1 种基金2020 National Key R&D Program-Technology Helps the Economy 2020 Key Project(2020-NK-ZL34)Fundamental Research Program of Shanxi Province(201901D211403)。
文摘[Objectives]This study was conducted to investigate the molecular characteristics,genetic structure and evolutionary mechanism of cucurbit aphid-borne yellows virus(CABYV),which is of great significance for clarifying the epidemic laws of the disease in the field and formulating long-term sustainable control strategies.[Methods]120 melon leaves suspected to be infected with CABYV were randomly collected from Aksu City,Xinjiang.RT-PCR was used to detect the virus.MEGA 7.0 was used to construct a phylogenetic tree.DnaSP v5.10 was used to analyze the genetic diversity among different sequences,and RDP v.4.31 software was used to analyze possible recombination events of CABYV sequence.[Results]The detection rate of CABYV was 31.67%.A new CABYV-2 was isolated,sequenced and cloned from these positive samples.The length of the genome is 5497 bp,encoding six open reading frames.Compared with 23 CABYV strains isolated from different countries in NCBI database,CABYV-2 shared the highest homology with KR231942.1 and the lowest homology with JF939812.1.The results of evolutionary tree analysis showed that the 24 isolates were divided into two branches due to different geographical factors,including CABYV-2 and KR2319421,which were clustered together and belonged to branch 1.The results of genetic diversity and neutrality tests showed that CABYV was highly variable and the population was expanding.The results of recombination analysis showed that there were two recombinants,EU636992.1 and KR231949.1,which exacerbated the variation of CABYV.[Conclusions]The CABYV isolate from Aksu City,Xinjiang had the closest relationship with the Korean isolate KR231942.1,and the farthest relationship with the isolates from European countries.There were large genetic differences between the isolates of branch 1 and branch 2,and the recombination of CABYV in different hosts aggravated the variation of CABYV.Recombination and negative selection may be important reasons for the genetic variation of CABYV.
基金supported by the Spanish research grants(AGL2017-89550-R)from MICINN and EU FEDER fundssupported by funding of the Ministry of Economy,Industry and Competitiveness(MINECO,Spain)within a PhD programme grant(PRE2018-083915).
文摘Cucurbit aphid-borne yellows virus(CABYV)and watermelon mosaic virus(WMV)are major plant pathogens that cause severe epidemics in cucurbit crops.While there has been an increasing interest in molecular epidemiological studies on both viruses at regional scales,their phylodynamic analysis by using the temporal data at global scale remains unexplored.In this study,we implemented the Nextstrain phylodynamic approach to comprehensively examine the coat protein gene and full-length genome sequences of the CABYV and WMV worldwide populations.Our analyses reconstructed a robust phylogeny of CABYV and confirmed the occurrence of isolates grouped into three clusters(Asian,Mediterranean,and Recombinant).Nextstrain analysis suggested that CABYV epidemics likely originated in Southeast Asia in fourteenth century,while the Mediterranean population emerged in Spain in seventeenth century.We also found a high divergence between Asian and Mediterranean isolates,with low genetic diversity and scarce evidence of selection,as reflected by the lack of gene flow.Moreover,the hierarchical analysis of molecular variance revealed a significant differentiation between CABYV populations grouped by geographical location and plant host.Additionally,the global phylogenetic reconstruction of the WMV population confirmed a clear differentiation among isolates,which grouped into two clusters(classical and emergent),and Nextstrain analysis suggested that WMV epidemics were most probably originated in USA during the sixteenth century.The initial WMV population diverged in the eighteenth century,with the origin of the emergent population in the nineteenth century.Our analysis confirmed that WMV population has a polyphyletic origin,defining an extensive genetic diversity.Overall,this work provides insights into the CABYV and WMV origin and evolutionary dynamics,gaining an understanding of the global spread of both viral diseases.Additionally,the integration of all spatiotemporal CABYV and WMV data,along with their genome sequence data by open access(https://github.com/PiR92)and the Nextstrain approach,provides a valuable tool for compiling and sharing current knowledge of these viral diseases in cucurbit crops.
