Additional file 2 of Single-cell genomics unveils a canonical origin of the diverse mitochondrial genomes of euglenozoans

Additional file 2: Fig. S1. BlobTools plots showing contamination of several sequenced SAGs. The bacterial contamination is shown as blue circles, while sequences with eukaryotic signal are in magenta. For comparison, BlobTools plots for SAGs EU17 and EU18 are also shown. Fig. S2. 18S rDNA phylogeny of eukaryotes. The Maximum Likelihood phylogenetic tree was estimated from an alignment containing 131 taxa and 1551 nucleotide positions under the GTR + Γ model with standard bootstrapping (BS) and ultrafast bootstrapping (UFB). Support values are shown if ≥ 50% and ≥ 75% for BS and UFB, respectively. Fully supported nodes are shown as black circles. Fig. S3. 18S rDNA phylogeny of euglenozoans. The Maximum Likelihood phylogenetic tree was estimated from an alignment containing 368 taxa and 1269 nucleotide positions under the GTR + Γ model with standard bootstrapping. Support values are shown if ≥ 50%. Fig. S4. Predicted domains in EU17/18 mtDNA-encoded ORFs. ORFs annotated by MFannot ( https://megasun.bch.umontreal.ca/cgi-bin/dev_mfa/mfannotInterface.pl ) were submitted to an InterProScan [76] search. Predicted domains are highlighted as explained in the graphical legend. Fig. S5. Concatenated mitochondrial phylogenetic analysis including atp6 from EU17/18. The alignment contained 37 taxa and 4348 amino acid positions, with EU17/18 missing 3.65% of data. The Maximum Likelihood tree was estimated under two models, LG + C20 + F + Γ (C20) and LG + F + I + G4 (LG; the best-fitting model as determined by IQ-TREE), with 1000 standard bootstraps (BS) and 1000 ultrafast bootstraps (UFB). The tree topology shown is from the C20 analysis. Support values for