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SCIENCE CHINA Life Sciences, https://doi.org/10.1007/s11427-020-1936-2

Viromes in marine ecosystems reveal remarkable invertebrate RNA virus diversity

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  • ReceivedDec 21, 2020
  • AcceptedApr 19, 2021
  • PublishedJun 17, 2021

Abstract


Funded by

the National Natural Science Foundation of China(31970176)

Collaborative Research Grant(KLMVI-OP-202002)

Institut Pasteur of Shanghai

Chinese Academy of Sciences

Guangdong Provincial Key Laboratory of Fishery Ecology and Environment(FEEL-2019-6)

and CAS Pioneer Hundred Talents Program.


Acknowledgment

This work was supported by the National Natural Science Foundation of China (31970176), Collaborative Research Grant (KLMVI-OP-202002) of CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment (FEEL-2019-6), and CAS Pioneer Hundred Talents Program.


Interest statement

The author(s) declare that they have no conflict of interest.


Supplement

SUPPORTING INFORMATION

The supporting information is available online at https://doi.org/10.1007/s11427-020-1936-2. The supporting materials are published as submitted, without typesetting or editing. The responsibility for scientific accuracy and content remains entirely with the authors.


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  • Figure 1

    The overall characterization of virus distribution. A, The distribution and diversity of virus in invertebrate transcriptomes. The top graph depicts the number of reads in each library. The colors of the bars indicate the sample collecting location: the Yellow Sea (yellow), the East China Sea (red), and the South China Sea (blue). The full name of each library is shown on top of each bar, and major host classifications are shown above the bar graph. The bottom graph depicts a summary of the classification of virus species found in this study. B, Overlap of RNA viral families in aquatic invertebrates across different seas. The number of viruses in each order or family is shown in brackets. Circles are color-coded according to the sample collecting location, i.e., the Yellow Sea (yellow), the East China Sea (red), and the South China Sea (blue).

  • Figure 2

    Phylogenetic trees of the dsRNA viruses, including the viruses identified in this study and related representative viruses. The trees were inferred using amino acid sequences of the RdRp gene and flanking conserved domain. These trees are midpoint rooted for clarity only. Viruses identified in this study are denoted with a filled colored circle based on the areas where their hosts were acquired: the Yellow Sea (yellow), the East China Sea (red), and the South China Sea (blue). Other representative, publicly available viruses are denoted with a gray circle. An asterisk indicates node SH-aLRT support >70%. The scale bar indicates the number of amino acid changes per site.

  • Figure 3

    Phylogenetic trees of the ssRNA(−) viruses, including the viruses identified in this study and related representative viruses. The trees were inferred using amino acid sequences of the RdRp gene and flanking conserved domain. These trees are midpoint rooted for clarity only. Viruses identified in this study are denoted with a filled colored circle based on the area where their hosts were acquired: the Yellow Sea (yellow), the East China Sea (red), and the South China Sea (blue). Other representative publicly available viruses are denoted with a gray circle. An asterisk indicates node SH-aLRT support >70%. The scale bar indicates the number of amino acid changes per site.

  • Figure 4

    Phylogenetic trees of the ssRNA(+) viruses, including the viruses identified in this study and related representative viruses. The trees were inferred using amino acid sequences of the RdRp gene and flanking conserved domain. These trees are midpoint rooted for clarity only. Viruses identified in this study are denoted with a filled colored circle based on the area where their hosts were acquired: the Yellow Sea (yellow), the East China Sea (red), and the South China Sea (blue). Other representative, publicly available viruses are denoted with a gray circle. An asterisk indicates node SH-aLRT support >70%. The scale bar indicates the number of amino acid changes per site.

  • Figure 5

    Genome organization of representative viruses within major viral clades. The contigs and genomes are drawn to scale as lines and boxes, respectively. The predicted regions that encode major functional proteins or domains are labeled with colored boxes. The filled colored circles indicate the area where their hosts were acquired: the Yellow Sea (yellow), the East China Sea (red), and the South China Sea (blue).

  • Figure 6

    Possible host-sharing pattern of viruses in major invertebrate habitats. A, The viral network indicating the uneven distribution of host sharing. Nodes represent the class of the host groups. Node size is proportional to the number of viruses collected and used in the analysis, whereas node color is related to the areas in which the hosts live. Edge width is proportional to the putative host-sharing frequency. B, Correlation of host-sharing frequency ratio, calculated using host-sharing frequency with the number of viruses in each type of host in different seas. Best-fit lines with 95% confidence intervals from linear regression are plotted. The filled colored circles indicate the area where their hosts were acquired: terrestrial (bluish violet), freshwater (blue green), the Yellow Sea (yellow), the East China Sea (red), and the South China Sea (blue).

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