Genomic analysis of Ranavirus and exploring alternative genes for phylogenetics

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 sequences by using PanX. The neighbour-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

Genomic analysis of Poxviridae and exploring qualified gene sequences for phylogenetics

“…3 and Table S4). Such recombination events could severely decrease the accuracy of phylogenetic trees [12] , [13] . However, further algorithmic research is still needed to determine the influence of recombination events on the construction of phylogenetic trees based on amino acid sequences.…”

“…The sequences that had experienced severe substitution saturation [11] or recombination [12] , [13] were not suitable for phylogenetic analysis [11] , [12] , [13] . In order to explore qualified genes from core genes, recombination analysis and substitution saturation analysis of Poxvirus core genes were performed using Recombination Detection Program (RDP) BETA4.67 [13] and DAMBE v5.3.19 [11] .…”

“…In the “Seq.analysis” drop-down list, the “Measure Substitution Saturation > Test by Xia et al” option was chosen to perform substitution saturation analysis. The detailed steps have been outlined in our previous research paper [12] . The NJ-Trees and ML-Trees based on single core gene were constructed using MEGA-X [10] (detailed parameter settings are shown in Table 2 ).…”

Environmental DNA‐derived pathogen gene sequences can expand surveillance when pathogen titers are decoupled in eDNA and hosts

“…Though we maintained ample coverage for whole gene assembly, we did not have sufficiently high coverage for variant discovery in all targeted genes and exclusively included the MCP in our fine‐scale analysis. Variant discovery of all genes may have improved the resolution of our analysis because the MCP gene is highly conserved and may not be able to distinguish between variants (Chinchar et al, 2009; Yu et al, 2020).…”

Detection of Frog virus 3 via the system integrating RPA-CRISPR/Cas12a-SPM with deep learning

“…Ranaviruses, including the type species frog virus 3 (FV3), are double-stranded DNA (dsDNA) viruses within the family Iridoviridae (Jancovich et al 2010; Robert and Gregory 2012). Diseases caused by ranaviruses are a major concern for biodiversity and aquaculture (Chen and Robert 2011; Price et al 2014; Whittington et al 2010; Youker-Smith et al 2018; Yu et al 2021). FV3 infections induce hematopoietic necrosis in the bone marrow, lesions in the skin and hematopoietic tissue, and necrosis of lymphoid tissue and mucosal epithelium, which results in the death of the host within a few days to several weeks (Forzan et al 2017a; Morrison et al 2014).…”