Four virophage major capsid proteins, Mavirus GI:326439166; Sputnik virophage GI:193245560, Organic Lake virophage GI:322510455, and Yellowstone Lake virophage 7 GI:701905716, were used as queries for translating blast searches (Tblastn [29 (
link)]) against whole-genome shotgun contigs from the metagenomes available at the NCBI (taxid:408169). The hits from the four searches were combined, translated using GeneMark [30 (
link)] and searched against the NCBI nr database using Blastp [29 (
link)].
Similarly, four mimiviridae major capsid proteins, Acanthamoeba polyphaga mimivirus GI:311977828, Cafeteria roenbergensis virus BV-PW1 GI:310831332, Acanthamoeba polyphaga mimivirus GI:311977809, and Organic Lake phycodnavirus 1 GI:322510624, were used as queries for Tblastn searches against the AS, BR, FWS, Gut, and WW metagenomes.
Protein sequences were aligned using MUSCLE [31 (
link)], and gapped columns (more than 30% of gaps) and columns with low information content were removed from the alignment [32 (
link)]. A preliminary tree was constructed using the FastTree program with default parameters (JTT evolutionary model, discrete gamma model with 20 rate categories) [33 (
link)]. The best-fit substitution model was identified using ProtTest [34 (
link)]. The final maximum likelihood tree was calculated using TreeFinder [35 (
link)], with the substitution model found to be the best for a given alignment. The following substitution models were identified by ProtTest as the best fit for individual genes for which phylogenetic analysis is reported: MCP - RtREV + G + F; ATPase - LG + G + F; protease - LG + G + F; pPolB - LG + G + F. The bootstrap values represent Expected-Likelihood Weights (ELW) of 1,000 local rearrangements.
Inverted repeats were identified using Censor software [36 (
link)].
Yutin N., Kapitonov V.V, & Koonin E.V. (2015). A new family of hybrid virophages from an animal gut metagenome. Biology Direct, 10, 19.