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Comparative genomic analysis of three white spot syndrome virus isolates of different virulence

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Abstract

Three white spot syndrome virus (WSSV) isolates of different virulence were identified in our previous study, the high-virulent strain WSSV-CN01, the moderate-virulent strain WSSV-CN02 and the low-virulent strain WSSV-CN03. In this study, the genomes of these three WSSV isolates were sequenced, annotated and compared. The genome sizes for WSSV-CN01, WSSV-CN02, and WSSV-CN03 are 309,286, 294,261, and 284,148 bp, bearing 177, 164, and 154 putative protein-coding genes, respectively. The genomic variations including insertions, deletions, and substitutions were investigated. Thirty four genes show >20% variation in their sequences in WSSV-CN02 or WSSV-CN03, in comparison with WSSV-CN01, including six envelope protein genes (wsv237/vp41A, wsv238/vp52A, wsv338/vp62, wsv339/vp39, wsv077/vp36A, and wsv242/vp41B), and two immediate-early genes (wsv108 and wsv178). The genomic variations among WSSV isolates of different virulence, especially those in the coding regions, certainly provide new insight into the understanding of the molecular basis of WSSV pathogenesis.

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Acknowledgements

We thank Dr. Xiaofeng Shi for assistance in phylogenetic analysis, Dr. Mingliang Chen and Zhenping Zhong for proof-reading of the manuscript. This work was supported by the National Basic Research Program of China (973 Program, Grant Number 2012CB114401), the Natural Science Foundation of China (Grant Numbers 41376173 and 41276176), the China Agriculture Research System (Grant Number CARS-47), and the Fujian Marine Hi-tech Industry Program (Grant Number 2014-05).

Author contributions

FL and FY conceived and designed the experiments; MG performed the RT-PCR and Western blotting experiment; FL, MG, and FY participated in analyzing and interpretation of the genomic sequencing data; LX performed the virus purification, DNA extraction experiment, and PCR confirmation of the genomic variation. FL, MG, and FY drafted the manuscript. All authors read and approved the final manuscript. FL and MG contributed equally to this work.

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    Authors and Affiliations

    1. Key Laboratory of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen, 361005, China

      Fang Li, Limei Xu & Feng Yang

    2. Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, 361005, China

      Fang Li & Feng Yang

    3. Eye Hospital of Wenzhou Medical University, The State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Public Health, Wenzhou, 325027, China

      Meiling Gao

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    1. Fang Li
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    2. Meiling Gao
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    Corresponding author

    Correspondence to Feng Yang.

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    The authors declare that they have no competing interests.

    Ethical approval

    This research did not involve Human Participants or Animals.

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    This research did not involve Human Participants therefore no informed consent is required.

    Additional information

    Edited by A. Lorena Passarelli.

    Fang Li and Meiling Gao have contributed equally to this work.

    Electronic supplementary material

    Below is the link to the electronic supplementary material.

    Supplementary Fig. 1

    Schematic diagram showing the organization of the circular genome of WSSV-CN01. Schematic diagram showing the organization of the circular genome of WSSV-CN01. Positions of the predicted protein coding genes and their transcription directions are indicated with arrows (PDF 705 kb)

    Supplementary Fig. 2

    Schematic diagram showing the organization of the circular genome of WSSV-CN02. Schematic diagram showing the organization of the circular genome of WSSV-CN02. Positions of the predicted protein coding genes and their transcription directions are indicated with arrows (PDF 666 kb)

    Supplementary Fig. 3

    Schematic diagram showing the organization of the circular genome of WSSV-CN03. Schematic diagram showing the organization of the circular genome of WSSV-CN03. Positions of the predicted protein coding genes and their transcription directions are indicated with arrows (PDF 650 kb)

    Supplementary Fig. 4

    The graphic result of the whole-genome alignment of WSSV-CN, -CN02, CN02, and CN03. The genomic sequences of WSSV-CN, -CN02, CN02, and CN03 were aligned with the “align whole genomes” function of MAUVE. Homologous blocks are shown as identically colored regions. ORFs transcribed forward (above) and reverse (below) are indicated (PDF 702 kb)

    Supplementary Table 1

    Primers used to analyze large-scaled genomic variations of different WSSV strains (PDF 12 kb)

    Supplementary Table 2

    Primers used for RT-PCR analysis (PDF 13 kb)

    Supplementary Table 3

    Comparison of protein coding genes of WSSV-CN, -CN01, -CN02 and -CN03 (PDF 168 kb)

    Supplementary Table 4

    The number of indels and SNPs in the genomes of WSSV-CN01, -CN02 and –CN03 in comparison with WSSV-CN (PDF 10 kb)

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    Li, F., Gao, M., Xu, L. et al. Comparative genomic analysis of three white spot syndrome virus isolates of different virulence. Virus Genes 53, 249–258 (2017). https://doi.org/10.1007/s11262-016-1421-z

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