LOOKING FOR LOCAL ADAPTATIONS: ARE A SUBSET OF THE IRIDOVIRUS CORE GENES SUITABLE FOR RECONSTRUCTING PHYLOGENETIC RELATIONSHIPS IN AMBYSTOMA TIGRINUM VIRUS ISOLATES FROM THE SOUTHWESTERN USA?**
Ambystoma tigrinum virus (ATV) is a species of Ranavirus, which is a member of the viral family Iridoviridae. Ranaviruses are globally emerging pathogens of amphibians, fish and reptiles. However, ATV appears to be predominantly located in the Southwestern USA where it affects amphibians. It has previously been established that ATV has local variation within the Southwestern USA using a subset of its genes, however not all of the genes used were core genes. Iridoviruses have 26 core genes that are considered to be conserved, and these genes have not all been explored as possible markers for local variation. Here we will examine the phylogeny created by five different Iridovirus core genes (ORF 10L, 25R, 38R, 58R, and 80R) and compare this to the known phylogeny that includes other loci that are not members of the core for 15 strains of ATV. This will let us determine the utility of these core genes as markers for local variation. We plan to do this by obtaining the sequences of each ORF from GenBank. The sequences will then be aligned using a MAFTT server. The aligned sequences will be imported into MEGA 6, and a nucleotide substitution model best-fit will be run. The best-fit substitution model will then be used with the aligned sequences to build maximum likelihood trees for each locus. Based on preliminary analyses, we expect that there will be little to no variation between the different strains of ATV and that we will not be able to discern local variation using these conserved genes.
Wright, Mathew M. and Duffus, Amanda L.J.
"LOOKING FOR LOCAL ADAPTATIONS: ARE A SUBSET OF THE IRIDOVIRUS CORE GENES SUITABLE FOR RECONSTRUCTING PHYLOGENETIC RELATIONSHIPS IN AMBYSTOMA TIGRINUM VIRUS ISOLATES FROM THE SOUTHWESTERN USA?**,"
Georgia Journal of Science, Vol. 78, No. 1, Article 22.
Available at: https://digitalcommons.gaacademy.org/gjs/vol78/iss1/22