Introduction
Ranaviruses are nuclear cytoplasmic large DNA viruses (NCLDVs), which
are one of five genera within the family Iridoviridae (other members areChloriridovirus , Iridovirus , Lymphocystivirus andMegalocytivirus ) (Jancovich, Steckler, et al., 2015). Ranaviruses
have been found to infect a wide variety of cold-blooded vertebrates,
including amphibians, reptiles, and fish (Chinchar, 2002; Duffus et al.,
2015). Members of the genus have been isolated from at least 175 species
of ectothermic vertebrates in all continents except for Antarctica, and
they are recognized as significant pathogens causing die-offs in captive
and wild populations across the globe (Duffus et al., 2015). Ranaviruses
have become serious problems in modern aquaculture, because of their
high pathogenicity and ability to cause mortality. As pathogens of
wildlife, there are many evidences that ranaviruses can cause population
declines in wild animal (Blaustein et al., 2012; Daszak et al., 1999;
Price et al., 2014). Furthermore, outbreaks of ranaviruses could result
in population extinction (Earl et al., 2014; Miller et al., 2011).
Therefore, ranaviruses are known to be emerging pathogens that have
potential risk to cause economic losses and serious damages to the
ecological environment.
There are six species of ranaviruses recognized by the International
Committee on Taxonomy of Viruses (ICTV,
https://talk.ictvonline.org/taxonomy/) through 2018. These species
include Ambystoma tigrinum virus (ATV), Common midwife toad
virus (CMTV), Epizootic haematopoietic necrosis virus (EHNV),Frog virus 3 (FV3), Santee-cooper ranavirus (SCRV),Singapore grouper iridovirus (SGIV). Among them, the CMTV and
SGIV were newly recognized as ranaviruses in the 10th report. However,
the taxonomy of SGIV and Grouper iridovirus (GIV) have long been
controversial, because whole genome dot plot analyses indicated that the
genomes of GIV and SGIV possess few regions of collinearity with other
ranaviruses (Jancovich, Qin, et al., 2015). Traditionally, virus
taxonomy was characterized by morphological features (by electron
microscopy), physicochemical properties (by varying pH and temperature,
adding lipid solvents and detergents, etc) and antigenic properties (by
many different serologic methods) (Murphy et al., 2012). With the
development of sequencing technology, more and more viral genomes have
been successfully sequenced. These viral genomes and a number of virus
classification tools based on viral genomes (such as CVTree3(Zuo et al.,
2015), Java Dot Plot Alignments(Brodie et al., 2004) and pairwise
sequence comparison (Bao et al., 2014)) have been widely applied to
virus taxonomy (Eaton et al., 2007; Gao et al., 2007; Radoshitzky et
al., 2015).
Members of the family Iridoviridae have linear dsDNA genomes that range
from 140 to 303 kbp in size and encode 92 to211 putative viral genes
(Jancovich, Steckler, et al., 2015). With the growing number of
sequenced ranavirus genomes, there are more than 30 genome sequences of
ranaviruses deposited in National Center of Biotechnology Information
(detailed information of isolates were summarized in Table S1). However,
little is currently known about their genomic molecular biology and
evolutionary taxonomy. Despite many recent advances in viral genomic
sequencing, there is much more to learn about the relationship of
ranavirues within the genus itself. In order to gain a greater
understanding of evolutionary taxonomy within ranaviruses, we will
identify core genes of ranaviruses, construct phylogenetic tree and
perform dot plot analysis explore the relationship links between
ranaviruses.