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EXPLORING ALTERNATE GENES FOR RANAVIRUS PHYLOGENETICS

Abstract

Ranaviruses, from the family Iridovididae, are a group of viruses that are infectious in amphibians, reptiles, and fish. Outbreaks of ranaviral disease have caused economic losses in aquaculture. In amphibians, they have been associated with local population extinctions and declines. Traditionally, the sequence of the major capsid protein (MCP) has been used to examine the phylogenetic relationships between different isolates and species of ranaviruses. However, the MCP is highly conserved and, when used for phylogenetic inferences, may not be representative of the evolutionary history of the specific isolate/strain being examined. Here we take two different genes from GenBank whole genome sequences, an ATPase-like protein and a myristilated membrane protein, and use them to build phylogenetic trees, which we will then compare to a tree that we have built using the MCP of the same ranavirus isolates and species. We will first align the sequences using MAFTT, then they will be imported into MEGA for further analysis. The aligned sequences will be analyzed for the best fit nucleotide substitution model and the best fit model will be used to build neighbor joining and maximum likelihood phylogenetic trees. The trees will be compared to previously published work and the constructed MCP tree. We anticipate that the trees will be similar to those that have previously been published using whole genomes, but we believe that the tree constructed with the myristilated membrane protein sequence will be the most divergent.

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