Fig. 2

Mitochondria-to-nucleus gene transfer is relatively rare. Coulson plots showing the distribution of genes encoding components of small (A) and large (B) subunits of mitoribosomes, as well as electron transport chain (C) and other (D) proteins across mitochondrial and nuclear genomes of the representatives of major eukaryotic supergroups. Genes retained in the mitogenomes are depicted in purple, nucleus-encoded genes are in orange, and those lost or not detected are in white. Within each eukaryotic group, the species with identical gene distribution patterns were unified into one sector of a circle. Species with available genome and transcriptome assemblies are marked with back circles and triangles, respectively. The cladogram reflecting the phylogenetic relationships among major eukaryotic lineages is based on [9] and [10]. The bar charts at the top of the Coulson plots indicate the percentage of investigated taxa where the respective gene is encoded in mitochondrial (purple) and nuclear genome (orange) or lost/not detected. The numerical values above the bar charts correspond to the number of presumably independent mitochondrion-to-nucleus gene transfer events in the evolution of eukaryotes. Proteins predicted to possess a mitochondrial presequence by at least two out of three bioinformatic tools (MitoFates, TargetP, and TPpred3) are marked with cyan circles. The presence of a gene encoding cytochrome c heme-lyase in the nuclear genome is indicated with an asterisk over the ccmA gene charts. Coulson plots were produced with a Coulson plot generator [11]. For compact representation, some species were assigned numbers as follows: 1, Naegleria gruberi; 2, Naegleria fowleri; 3, Andalucia godoyi; 4, Reclinomonas americana; 5, Euglena gracilis; 6, Euglenozoa ‘SAG EU17/18’; 7, Diplonema papillatum; 8, Trypanosoma brucei; 9, Tsukubamonas globosa; 10, Heterolobosea sp. ‘BB2’; 11, Acrasis kona; 12, Pharyngomonas kirbyi; 13, Plasmodium falciparum; 14, Babesia microti; 15, Cyclospora cayetanensis; 16, Theileria annulata; 17, Toxoplasma gondii; 18, Phaeodactylum tricornutum; and 19, Thalassiosira pseudonana. The species abbreviations: Acar, Amphidinium carterae; Acas, Acanthamoeba castellanii; Ainv, Aphanomyces invadans; Amac, Allomyces macrogynus; Apac, Alexandrium pacificum; Aper, Acavomonas peruviana; Atwi, Ancoracysta twista; Blasto, Blastocystis sp.; Bmot, Brevimastigomonas motovehiculus; Bnat, Bigelowiella natans; Cbur, Cafeteria burkhardae; Cmar, Chattonella marina; Cmer, Cyanidioschyzon merolae; Cowc, Capsaspora owczarzaki; Cpar, Cyanophora paradoxa; Crei, Chlamydomonas reinhardtii; Ctob, Chrysochromulina tobinii; Cvel, Chromera velia; Cvie, Colponema vietnamica; Dbru, Dekkera bruxellensis; Ddis, Dictyostelium discoideum; Drot, Diphylleia rotans; Ehux, Emiliania huxleyi; Eten, Eimeria tenella; Falb, Fonticula alba; Ginc, Glaucocystis incrassata; Gsul, Galdieria sulphuraria; Gthe, Guillardia theta; Hand, Hemiselmis andersenii; Hema, Hematodinium sp.; Hmar, Hemiarma marina; Hsap, Homo sapiens; Lcau, Leucocytozoon caulleryi; Lmar, Leucocryptos marina; Maro, Marophrys sp.; MAST, marine stramenopile; Mbre, Monosiga brevicollis; Mcal, Malawimonas californiana; Mjak, Malawimonas jakobiformis; Mpol, Marchantia polymorpha; Mvir, Mesostigma viride; Noli, Nephroselmis olivacea; Nova, Nyctotherus ovalis; Nqua, Nibbleromonas quarantinus; Nsim, Nuclearia simplex; Ntab, Nicotiana tabacum; Omar, Oxyrrhis marina; Otri, Oxytricha trifallax; Pbil, Palpitomonas bilix; Pbra, Plasmodiophora brassicae; Perkma, Perkinsus marinus; Pico, Picozoa sp.; Pmar, Paracercomonas marina; Pmin, Pedinomonas minor; Ppro, Pycnococcus provasolii; Ppur, Porphyra purpurea; Pwic, Prototheca wickerhamii; Rsal, Rhodomonas salina; Scer, Saccharomyces cerevisiae; Stro, Strombidium sp.; Taur, Thraustochytrium aureum; TelT, Telonemid sp.; The, Tetrahymena thermophila; Ttra, Thecamonas trahens; Vbra, Vitrella brassicaformis; and Vver, Vermamoeba vermiformis