Juan Lu, Shixing Yang, Xiaodan Zhang, Xiangming Tang, Ju Zhang, Xiaochun Wang, Hao Wang, Quan Shen and Wen Zhang. Metagenomic analysis of viral community in the Yangtze River expands known eukaryotic and prokaryotic virus diversity in freshwater[J]. Virologica Sinica, 2022, 37(1): 60-69. doi: 10.1016/j.virs.2022.01.003
Citation: Juan Lu, Shixing Yang, Xiaodan Zhang, Xiangming Tang, Ju Zhang, Xiaochun Wang, Hao Wang, Quan Shen, Wen Zhang. Metagenomic analysis of viral community in the Yangtze River expands known eukaryotic and prokaryotic virus diversity in freshwater .VIROLOGICA SINICA, 2022, 37(1) : 60-69.  http://dx.doi.org/10.1016/j.virs.2022.01.003

长江病毒宏基因组分析扩充了淡水中原核和真核生物病毒的多样性

  • 水生态系统中包含着极其丰富多样的病毒群,但目前对江河水中的病毒组成情况却知之甚少。本研究使用病毒宏基因组学方法探究了长江三角洲水域的病毒群特征,分析比较了6个采样点的病毒组。虽然各采样点病毒组在物种丰度上有细微差异,但总体上组成相似,均以有尾噬菌体目(Caudovirales)为主,并且淡水噬菌体种(Freshwater phage uvFW)也在各样本中普遍存在。位于南京的病毒群具有独特的组成特征,其中细小病毒科(Parvoviridae)的丰度较高。基于各病毒群特征基因的系统发育分析显示,有尾噬菌体目和CRESS-DNA病毒具有较高的遗传多样性。相反,微小噬菌体科(Microviridae)、细小病毒科(Parvoviridae)和核糖病毒域(Riboviria)的病毒相对保守。本研究首次揭示了大型江河生态系统中病毒群的组成结构及其多样性和保守性,有助于淡水资源的合理利用。

Metagenomic analysis of viral community in the Yangtze River expands known eukaryotic and prokaryotic virus diversity in freshwater

  • Viruses in aquatic ecosystems are characterized by extraordinary abundance and diversity. Thus far, there have been limited studies focused on viral communities in river water systems. Here, we investigated the virome of the Yangtze River Delta using viral metagenomic analysis. The compositions of viral communities from six sampling sites were analyzed and compared. By using library construction and next generation sequencing, contigs and singlet reads similar to viral sequences were classified into 17 viral families, including nine dsDNA viral families, four ssDNA viral families and four RNA viral families. Statistical analysis using Friedman test suggested that there was no significant difference among the six sampling sites (P > 0.05). The viromes in this study were all dominated by the order Caudovirales, and a group of Freshwater phage uvFW species were particularly prevalent among all the samples. The virome from Nanjing presented a unique pattern of viral community composition with a relatively high abundance of family Parvoviridae. Phylogenetic analyses based on virus hallmark genes showed that the Caudovirales order and CRESS-DNA viruses presented high genetic diversity, while viruses in the Microviridae and Parvoviridae families and the Riboviria realm were relatively conservative. Our study provides the first insight into viral community composition in large river ecosystem, revealing the diversity and stability of river water virome, contributing to the proper utilization of freshwater resource.

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    Metagenomic analysis of viral community in the Yangtze River expands known eukaryotic and prokaryotic virus diversity in freshwater

      Corresponding author: Hao Wang, wyj_ujs@163.com
      Corresponding author: Quan Shen, shenquan@ujs.edu.cn
      Corresponding author: Wen Zhang, z0216wen@yahoo.com
    • a Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
    • b Department of Clinical Laboratory, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, 223002, China
    • c Zhenjiang Center for Disease Prevention and Control, Zhenjiang, 212000, China
    • d State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China

    Abstract: Viruses in aquatic ecosystems are characterized by extraordinary abundance and diversity. Thus far, there have been limited studies focused on viral communities in river water systems. Here, we investigated the virome of the Yangtze River Delta using viral metagenomic analysis. The compositions of viral communities from six sampling sites were analyzed and compared. By using library construction and next generation sequencing, contigs and singlet reads similar to viral sequences were classified into 17 viral families, including nine dsDNA viral families, four ssDNA viral families and four RNA viral families. Statistical analysis using Friedman test suggested that there was no significant difference among the six sampling sites (P > 0.05). The viromes in this study were all dominated by the order Caudovirales, and a group of Freshwater phage uvFW species were particularly prevalent among all the samples. The virome from Nanjing presented a unique pattern of viral community composition with a relatively high abundance of family Parvoviridae. Phylogenetic analyses based on virus hallmark genes showed that the Caudovirales order and CRESS-DNA viruses presented high genetic diversity, while viruses in the Microviridae and Parvoviridae families and the Riboviria realm were relatively conservative. Our study provides the first insight into viral community composition in large river ecosystem, revealing the diversity and stability of river water virome, contributing to the proper utilization of freshwater resource.

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