Differential Evolution of Antiretroviral Restriction Factors in Pteropid Bats as Revealed by APOBEC3 Gene Complexity

Hayward, Joshua A; Tachedjian, Mary; Cui, Jie; Cheng, Adam Z; Johnson, Adam; Baker, Michelle L; Harris, Reuben S; Wang, Lin-Fa; Tachedjian, Gilda

The impact of cytosine deamination on the genomes of ancient bat retroviruses was assessed by hypermutation analysis (Lee et al. 2008) . The genomes of all ERVs used in the analysis were extracted from the P. vampyrus genome. Multiple outgroups were tested to confirm that the position of the ancestral node remained consistent. For the betaretroviruses, we . The most closely related betaretrovirus and gammaretrovirus to our ERV groups were JSRV and MMLV, respectively, and were employed as outgroups for the phylogenies. Sequence alignments and phylogenies were conducted as described for the APOBEC3 phylogenetic analysis, and the best-fit model of nucleotide substitution was found to be T92 þ G for both groups of retroviruses. Ancestral sequences were computationally extrapolated using the MEGA6 program (Tamura et al. 2013) using the mutations accumulated in each ERV since integration by estimating the ancestral state of each node in the maximum likelihood phylogenetic tree. The state is chosen to be the one that maximizes the probability of the given sequence data. Mutational biases were then evaluated by analyzing an alignment of the ancestral sequence and the ERVs (supplementary data S2 and S3, Supplementary Material online) using the online Hypermut tool (http://www.hiv. lanl.gov/content/sequence/HYPERMUT/hypermut.html; last accessed April 3, 2018) (Rose and Korber 2000) with context enforced on the ancestral reference sequence. The Hypermut tool incorporates Fisher's exact test to determine statistical significance.