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IRIDOVIRUS CORE GENES AS INDICATORS OF LOCAL VARIATION: A TEST CASE WITH THE RANAVIRUS, AMBYSTOMA TIGRINUM VIRUS

Abstract

Ranaviruses are globally emerging pathogens of ectothermic vertebrates. They have been implicated in the decline and even local extirpations of several species. Ambystoma tigrunum virus (ATV) appears to be located only in the southwestern USA where it primarily affects salamander species of the family Ambystomatidae. Ranaviruses are members of the viral family Iridoviridae. As such, they have 26 core genes, only a few of which are commonly used in phylogenetic reconstruction. Here we obtained gene sequences from five ATV core genes (Open Reading Frames: 7L, 20L, 64R, 91R, and 87R) from 15 strains of ATV from GenBank which are known to have local variation from previous studies of that included non-core genes and one core gene. We exported the sequence data from GenBank and aligned it using a MAFTT server for each gene. The aligned sequences were then imported into MEGA where the best fit nucleotide substitution model was assessed for each gene. Then, using the best fit model, we built maximum-likelihood trees for each gene and visually compared them to each other, a tree build from the major capsid protein gene (ORF 90R), a tree made from the whole genome, and a known tree made from a previous study performed by others. All of the trees produced from the five core genes were highly homologous, and were not particularly phylogenetically informative. Therefore, we suggest that these core genes may not reveal smaller scale local sequence variation and that other target genes are more appropriate to study this.

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