Running title: Genomic analysis of Ranavirus
Wenjie Zhang12 ¶,
Congwei Gu23 ¶, Jindong
Chen1, Mingde Zhao2, Lu
Fu2, Jianhong Han2, Manli
He2, Qihai Xiao2, Wudian
Xiao2, Lvqin He2, Zhimin
Zhang1*, Zehui Yu2*
1 School of Basic Medical Sciences, Zunyi Medical
University, Zunyi, Guizhou, P. R. China.
2 Laboratory Animal Center, Southwest Medical
University, Luzhou, Sichuan, P. R. China;
3 College of Veterinary Medicine, Sichuan Agricultural
University, Chengdu, Sichuan, P. R. China;
¶Authors contributed equally to the study.
* Corresponding author
Zehui Yu, Tel.: +86-0830-3162122, E-mail address:
yuzehui_swmu@outlook.com,
Zhimin Zhang, Tel.: +86-0851-28642712, E-mail address: 277351099@qq.com.
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.
Keyword: Ranavirus, core genes, dot plot analysis, phylogenetics.