Additional file 2 of Single-cell genomics unveils a canonical origin of the diverse mitochondrial genomes of euglenozoans
Bibliographic record
Abstract
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 < 50% BS and < 75% UFB are denoted by a dash (-), whereas an asterisk (*) marks a topology that does not exist in a particular analysis. Fully supported nodes are shown as black circles. Fig. S6. Characterization of tRNAs encoded in mtDNA of EU17/18 and EU2. a-b) Sequences of trnK (a) and trnM (b) were aligned with mitochondrially encoded tRNAs of other species of Discoba. Residue shading indicates sequence conservation. c-d) Secondary structures of trnK (c) and trnM (d) as predicted by tRNAScan-SE. Double and triple bonds are depicted as dark- and light-blue circles, respectively. Anticodons are highlighted with a green background. Since all other known euglenozoans import all tRNAs into mitochondria from the nucleus [48], we built tRNA alignments with homologues from the mtDNAs of other discobans to take into account different evolutionary pressures and mutational rates in nuclei and mitochondria [52]. The identity across nine trnK and 20 trnM sequences was 38.7% and 15.8%, respectively (a-b). Predicted secondary structures resembled other tRNAs supporting their functionality (c-d). While most eukaryotes have at least some tRNA mitochondrial-encoded, the long-standing paradigm was that euglenozoans and unrelated apicomplexans (which share with euglenozoans a range of unique features [79]) import all tRNAs from the cytosol [80]. This has significant consequences, since the bacterial-type translation system has to cope solely with the eukaryotic-type tRNAs [81]. Fig. S7. Mitoribosomal RNAs of EU17/18. Sequences of rns (a) and rnl (b) genes, as predicted by MFannot, were aligned with sequences of Escherichia coli. E. coli sequences were obtained from http://rna.ucsc.edu/rnacenter/ribosome_images.html , and their predicted domains [82, 83] are shown as magenta and blue boxes below the sequences. Nucleotide identities are shown by black background with white nucleotides.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.002 | 0.013 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.003 | 0.001 |
| Bibliometrics | 0.003 | 0.005 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.003 | 0.003 |
| Open science | 0.003 | 0.002 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.812 | 0.216 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".