Figure S15: alignment and tree-file: Phylogenetic analyses of Rab and TBC proteins in Anaeramoeba

Phylogenetic analyses of Rab proteins of subfamilies containing endocytic Rabs a, Rabs 2, 4, and 14 b, and Rabs 1, 8, and 18 c,. d, Phylogenetic analysis of TBC proteins. For membrane-trafficking proteins, Anaeramoeba datasets were searched by BLAST using queries from previous studies (Elias et al. 2012; Gabernet-Castello et al. 2013; Klinger, Klute, and Dacks 2013). Identified Rab and TBC proteins were subjected to orthologous clustering by OrthoFinder v2.0.0 (Emms and Kelly 2019) including proteins from human, cnidarian Nematostella vectensis, and heterolobosean Naegleria gruberi. Phylogenetic analyses for selected Rab sub-families and TBC proteins were conducted. Sequences were aligned by MAFFT v7.458 (Katoh and Standley 2013) under L-INS-i strategy, and poorly aligned positions were removed by trimAl v1.4.rev15 (Capella-Gutierrez, Silla-Martinez, and Gabaldon 2009) using -gt 0.8. Maximum-likelihood trees were inferred by IQ-TREE v1.6.8 (Nguyen et al. 2015) using the posterior mean site frequency method (H.-C. Wang et al. 2018) and the LG+C20+F+G model, with the guide tree inferred under the LG+F+G model. Branch supports were obtained by the ultrafast bootstrap approximation with 1,000 replicates.