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Genomic analysis of Ranavirus and exploring alternative genes for phylogenetics
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  • Wenjie Zhang,
  • Congwei Gu,
  • Jindong Chen,
  • Mingde Zhao,
  • Lu Fu,
  • Jianhong Han,
  • Manli He,
  • Qihai Xiao,
  • Wudian Xiao,
  • Lvqin He,
  • Zhimin Zhang,
  • Zehui Yu
Wenjie Zhang
Zunyi Medical University
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Congwei Gu
Southwest Medical University
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Jindong Chen
Zunyi Medical University
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Mingde Zhao
Southwest Medical University
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Lu Fu
Southwest Medical University
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Jianhong Han
Southwest Medical University
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Manli He
Southwest Medical University
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Qihai Xiao
Southwest Medical University
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Wudian Xiao
Southwest Medical University
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Lvqin He
Southwest Medical University
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Zhimin Zhang
Zunyi Medical University
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Abstract

Ranaviruses can infect both captive and wild cold-blooded vertebrates, leading to significant economic and environmental losses. With the cases of ranavirus infection increasing, many ranavirus genomic sequences were published, but little is known about ranavirus taxonomy on a whole genome level. In this study, 44 ranaviruses core genes were identified in 32 ranaviruses genome suquences by using PanX. The Neighbor joining phylogenetic trees (NJ-tree) based on 44 ranaviruses core genes and 24 iridoviridae core genes and composition vector phylogenetic tree (CV-Tree) based on whole genome were constructed. The three of phylogenetic trees showed that 32 ranavirus isolates can be divided to 4 different subspecies including GIV-like, EHNV-like, FV3-like and CMTV-like, and subspecies taxonomic position of three phylogenetic trees were consistent. However, the phylogenetic position of ToRV could not be determined if it belongs to FV3-like or CMTV-like group. Subsequently, we carried out dot plot analysis and confirmed that ToRV should belong to CMTV-like group. Based on dot plot analysis and phylogenetic trees, taxonomic classification of ranaviruses were confirmed. Finally, 4 genes which are suitable for the construction of phylogenetic tree were selected from ranavirus core genes by recombination analysis, substitution saturation analysis and single-gene phylogenetic analysis. Phylogenetic tree based on concatenated sequences of the 4 selected genes showed that classification of subspecies was identical with 3 of the phylogenetic trees. Conclusion: our results confirmed taxonomic identification of ranaviruses, the 4 selected genes used in phylogenic analysis will make taxonomic identification more convenient and accurate.

Peer review status:ACCEPTED

17 Apr 2020Submitted to Transboundary and Emerging Diseases
18 Apr 2020Submission Checks Completed
18 Apr 2020Assigned to Editor
19 Apr 2020Reviewer(s) Assigned
21 Jul 2020Review(s) Completed, Editorial Evaluation Pending
21 Jul 2020Editorial Decision: Revise Minor
11 Aug 20201st Revision Received
11 Aug 2020Assigned to Editor
11 Aug 2020Submission Checks Completed
12 Aug 2020Reviewer(s) Assigned
31 Aug 2020Review(s) Completed, Editorial Evaluation Pending
02 Sep 2020Editorial Decision: Revise Minor
12 Sep 20202nd Revision Received
13 Sep 2020Submission Checks Completed
13 Sep 2020Assigned to Editor
19 Sep 2020Reviewer(s) Assigned
21 Sep 2020Review(s) Completed, Editorial Evaluation Pending
25 Sep 2020Editorial Decision: Accept