The item contains transcriptome assemblies of Leontynka spp. and corresponding predicted proteomes used in the study as well as phylogenetic trees and source datasets.

The item contains transcriptome assemblies of Leontynka spp. and corresponding predicted proteomes used in the study as well as phylogenetic trees and source datasets.

Additional file 2: Table S1 SSU rRNA of prokaryotes identified in Leontynka metatranscriptomes using PhyloFlash. Table S2 Bacterial contaminants identified in Leontynka metatranscriptomes. Table S3 Proteins from Chlamydomonas reinhardtii used to test the automatic prediction tools. Table S4 Accuracy of selected predictors as tested on mitochondrial proteome of C. reinhardtii. Table S5 Accuracy of selected predictors as tested on plastid proteome of C. reinhardtii. Table S6 Accuracy of selected predictors as tested on proteins that were experimentally localized in the mitochondrion of C. reinhardtii. Table S7 Accuracy of selected predictors as tested on proteins that were experimentally localized in the plastid of C. reinhardtii. Table S8 Functional annotations, amino acid sequences, and predicted localization of Leontynka pallida proteins investigated in this study. Table S9 Functional annotation, amino acid sequences, and predicted localization of Leontynka elongata proteins investigated in this study. Table S10 Functional annotation, amino acid sequences, and predicted localization of C. reinhardtii proteins investigated in this study. Table S11 Functional annotation, amino acid sequences, and predicted localization of Polytomella parva proteins investigated in this study. Table S12 General features of cells used to define position of mitochondria. Table S13 Source data for Supporting Figure S14. Measurements are listed in % and px. Table S14 Functional annotation, predicted localization, and presence of F-cluster in FeFe hydrogenases. Table S15 Functional annotation, amino acid sequences, and predicted localization of PFO, FeFe hydrogenase, its maturases, and PFO in Chlamydomonadales. Table S16 Source data for Additional file 1: Figs. S3 and S4, and manual examination of typical features of plastid transit peptides or mitochondrial transit peptides in selected proteins. Table S17 Functional annotation, amino acid sequences, and predicted localization of Chlamydomonadales strain NrCl902 investigated in this study.

Additional file 2: Table S1 SSU rRNA of prokaryotes identified in Leontynka metatranscriptomes using PhyloFlash. Table S2 Bacterial contaminants identified in Leontynka metatranscriptomes. Table S3 Proteins from Chlamydomonas reinhardtii used to test the automatic prediction tools. Table S4 Accuracy of selected predictors as tested on mitochondrial proteome of C. reinhardtii. Table S5 Accuracy of selected predictors as tested on plastid proteome of C. reinhardtii. Table S6 Accuracy of selected predictors as tested on proteins that were experimentally localized in the mitochondrion of C. reinhardtii. Table S7 Accuracy of selected predictors as tested on proteins that were experimentally localized in the plastid of C. reinhardtii. Table S8 Functional annotations, amino acid sequences, and predicted localization of Leontynka pallida proteins investigated in this study. Table S9 Functional annotation, amino acid sequences, and predicted localization of Leontynka elongata proteins investigated in this study. Table S10 Functional annotation, amino acid sequences, and predicted localization of C. reinhardtii proteins investigated in this study. Table S11 Functional annotation, amino acid sequences, and predicted localization of Polytomella parva proteins investigated in this study. Table S12 General features of cells used to define position of mitochondria. Table S13 Source data for Supporting Figure S14. Measurements are listed in % and px. Table S14 Functional annotation, predicted localization, and presence of F-cluster in FeFe hydrogenases. Table S15 Functional annotation, amino acid sequences, and predicted localization of PFO, FeFe hydrogenase, its maturases, and PFO in Chlamydomonadales. Table S16 Source data for Additional file 1: Figs. S3 and S4, and manual examination of typical features of plastid transit peptides or mitochondrial transit peptides in selected proteins. Table S17 Functional annotation, amino acid sequences, and predicted localization of Chlamydomonadales strain NrCl902 investigated in this study.

Additional file 3: Table S1. Nuclear transcripts from Leontynka pallida specifically discussed in the paper. Table S2. Comparison of GC content, number of imperfect palindromes, and potential quadruplex-forming sequences in selected organellar genomes. Table S3. Strong codon usage bias in the mitochondrial genome of Leontynka pallida. Table S4. Relative frequency of amino acids with GC-rich codons (G, A, R, P) in proteins encoded by different mitogenomes. Table S5. Relative frequency of codons in plastid genes of Leontynka pallida. Table S6. Relative frequency of amino acids in proteins encoded by the plastome of Leontynka pallida. Table S7. The most abundant imperfect palindrome in the Leontynka pallida plastome that is missing in the exons.

Additional file 3: Table S1. Nuclear transcripts from Leontynka pallida specifically discussed in the paper. Table S2. Comparison of GC content, number of imperfect palindromes, and potential quadruplex-forming sequences in selected organellar genomes. Table S3. Strong codon usage bias in the mitochondrial genome of Leontynka pallida. Table S4. Relative frequency of amino acids with GC-rich codons (G, A, R, P) in proteins encoded by different mitogenomes. Table S5. Relative frequency of codons in plastid genes of Leontynka pallida. Table S6. Relative frequency of amino acids in proteins encoded by the plastome of Leontynka pallida. Table S7. The most abundant imperfect palindrome in the Leontynka pallida plastome that is missing in the exons.