EXAMINING THE 26 IRIDOVIRUS CORE GENES FOR ALTERNATIVES TO THE MAJOR CAPSID PROTEIN FOR PHYLOGENETIC RECONSTRUCTION IN RANAVIRUSES: AN ONGOING SAGA
Abstract
Ranaviruses are globally emerging pathogens of ectothermic vertebrates. They are a member of the family Iridoviridae and, as such, have 26 core genes. Traditionally, one or a few genes have been used for phylogenetic inference or placing new isolates into species groupings. The most commonly used gene for this has been the major capsid protein, open reading frame (ORF) 90R in Frog Virus 3 (FV3), the type virus for the Ranaviruses. In this study, sequence data from 17 fully sequenced Ranavirus isolates, that included strains from each species of Ranavirus obtained from GenBank, was used to investigate the phylogenetic relationships reconstructed using each core gene. Sequence data was aligned using multiple alignment using fast Fournier transform, then imported in to Molecular Evolution and Genetic Analysis (MEGA version 6). Sequence data was tested for the best nucleotide substitution model in MEGA and a neighbor-joining tree (with 1000 bootstraps) using the best fit model was created for each of the 26 core genes. Trees were then exported into FigTree (version 1.4.2) and rootless trees were created for visualization. For large scale differentiation, using the major capsid protein gene creates a tree similar to the whole genome tree. Other comparable genes are ORF 19R (a serine-theonine protein kinase), ORF 81R (a transcription elongation factor TFIIS), ORF 88R (Erv I/Alr Family protein) and ORF 91R (an immediate early protein ICP-46). The poorest candidate for phylogenetic reconstruction, due to high homology, was ORF 1R (a putative replication factor or DNA binding-packing protein). In the future, we hope to test each core ORF for phylogenetic signal and use this data to create trees that capture both large and smaller scale variation.
Acknowledgements
GSC Department of Natural Sciences
Recommended Citation
Davis*, Ami J.; Fuller*, Riley B.; Garner*, Abigale R.; Mileham*, Amanda M.; Serna*, Justin D.; Brue*, Dana E.; Harding*, Cori M.; Dodgen*, C. Delilah; Culpepper*, Whitney; Piatt*, Bridget; Rosario, Sarah E.; and Duffus, Amanda L.J.
(2020)
"EXAMINING THE 26 IRIDOVIRUS CORE GENES FOR ALTERNATIVES TO THE MAJOR CAPSID PROTEIN FOR PHYLOGENETIC RECONSTRUCTION IN RANAVIRUSES: AN ONGOING SAGA,"
Georgia Journal of Science, Vol. 78, No. 1, Article 45.
Available at:
https://digitalcommons.gaacademy.org/gjs/vol78/iss1/45