Research graph
References from Comparative analysis of mitochondrial proteomes across the tree of life. Local targets link to admitted publications; unresolved targets remain external evidence.
Unresolved reference
External reference
On the origin of mitosing cells
10.1016/0022-5193(67)90079-3 · 1967 · External reference
Five-kingdom classification and the origin and evolution of cells
1974 · External reference
The Origin and Diversification of Mitochondria
10.1016/j.cub.2017.09.015 · 2017 · External reference
On the age of eukaryotes: evaluating evidence from fossils and molecular clocks
10.1101/cshperspect.a016139 · 2014 · External reference
Integrated genomic and fossil evidence illuminates life’s early evolution and eukaryote origin
10.1038/s41559-018-0644-x · 2018 · External reference
The emerging view on the origin and early evolution of eukaryotic cells
10.1038/s41586-024-07677-6 · 2024 · External reference
Reconstructing the last common ancestor of all eukaryotes
10.1371/journal.pbio.3002917 · 2024 · External reference
The genome sequence of Rickettsia prowazekii and the origin of mitochondria
10.1038/24094 · 1998 · External reference
Multiple approaches of cellular metabolism define the bacterial ancestry of mitochondria
10.1126/sciadv.adh0066 · 2023 · External reference
The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome
10.1186/s12915-020-0741-6 · 2020 · External reference
A gene-rich mitochondrion with a unique ancestral protein transport system
10.1016/j.cub.2024.07.017 · 2024 · External reference
Strikingly bacteria-like and gene-rich mitochondrial genomes throughout jakobid protists
10.1093/gbe/evt008 · 2013 · External reference
ATP synthase evolution on a cross-braced dated tree of life
10.1038/s41467-023-42924-w · 2023 · External reference
Massive protein import into the early-evolutionary-stage photosynthetic organelle of the amoeba Paulinella chromatophora
10.1016/j.cub.2017.08.010 · 2017 · External reference
A mitochondrial protein compendium elucidates complex I disease biology
10.1016/j.cell.2008.06.016 · 2008 · External reference
Definition of a high-confidence mitochondrial proteome at quantitative scale
10.1016/j.celrep.2017.06.014 · 2017 · External reference
Detecting sequence signals in targeting peptides using deep learning
10.26508/lsa.201900429 · 2019 · External reference
MitoFates: improved prediction of mitochondrial targeting sequences and their cleavage sites
10.1074/mcp.m114.043083 · 2015 · External reference
A eukaryote without a mitochondrial organelle
10.1016/j.cub.2016.03.053 · 2016 · External reference
Is the mitochondrion a good malaria drug target?
10.1016/j.pt.2016.10.002 · 2017 · External reference
Atovaquone and azithromycin for the treatment of babesiosis
10.1056/nejm200011163432004 · 2000 · External reference
Site of action of the antimalarial hydroxynaphthoquinone, 2- [trans-4-(4′-chlorophenyl) cyclohexyl]-3-hydroxy-1,4-naphthoquinone (566C80)
10.1016/0006-2952(92)90213-3 · 1992 · External reference
MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations
10.1093/nar/gkaa1011 · 2021 · External reference
10.1016/j.cell.2026.08.027 · 2026 · Admitted local publication
10.1016/j.cell.2026.08.056 · 2026 · Admitted local publication
Mitochondrial proteome of the apicomplexan Babesia divergens
2026 · External reference
A high-confidence inventory of the proteins in the mitochondrion-related organelle of Giardia
2026 · External reference
10.1016/j.molcel.2026.08.032 · 2026 · Admitted local publication
Benchmarking Orthogroup Inference Accuracy: Revisiting Orthobench
10.1093/gbe/evaa211 · 2020 · External reference
Systematic errors in orthology inference and their effects on evolutionary analyses
10.1016/j.isci.2021.102110 · 2021 · External reference
OrthoFinder: phylogenetic orthology inference for comparative genomics
10.1186/s13059-019-1832-y · 2019 · External reference
The Quest for Orthologs orthology benchmark service in 2022
10.1093/nar/gkac330 · 2022 · External reference
New developments for the Quest for Orthologs benchmark service
10.1093/nargab/lqae167 · 2024 · External reference
Orthology prediction methods: a quality assessment using curated protein families
10.1002/bies.201100062 · 2011 · External reference
Fast and accurate protein structure search with Foldseek
10.1038/s41587-023-01773-0 · 2024 · External reference
PLMSearch: Protein language model powers accurate and fast sequence search for remote homology
10.1038/s41467-024-46808-5 · 2024 · External reference
Twilight zone of protein sequence alignments
10.1093/protein/12.2.85 · 1999 · External reference
Exploring the protein universe with distant similarity detection methods
10.1002/pro.70397 · 2026 · External reference
Metabolism of nitro drugs metronidazole and nitazoxanide in Giardia lamblia: characterization of a novel nitroreductase (GlNR2)
10.1093/jac/dkt106 · 2013 · External reference
The essential genome of Plasmodium knowlesi reveals determinants of antimalarial susceptibility
10.1126/science.adq6241 · 2025 · External reference
Type-II NADH Dehydrogenase (NDH-2): a promising therapeutic target for antitubercular and antibacterial drug discovery
10.1080/14728222.2017.1327577 · 2017 · External reference
Alternative NADH dehydrogenase: A complex I backup, a drug target, and a tool for mitochondrial gene therapy
10.1016/j.bbabio.2024.149529 · 2025 · External reference
Mitochondrial type II NADH dehydrogenase of Plasmodium falciparum (PfNDH2) is dispensable in the asexual blood stages
10.1371/journal.pone.0214023 · 2019 · External reference
Type II NADH dehydrogenase of the respiratory chain of Plasmodium falciparum and its inhibitors
10.1016/j.bmcl.2008.11.071 · 2009 · External reference
Biochemical characterization and essentiality of Plasmodium fumarate hydratase
10.1074/jbc.m117.816298 · 2018 · External reference
Characterisation of the fumarate hydratase repertoire in Trypanosoma cruzi
10.1016/j.ijbiomac.2017.03.099 · 2017 · External reference
Crystal structure of an Fe-S cluster-containing fumarate hydratase enzyme from Leishmania major reveals a unique protein fold
10.1073/pnas.1605031113 · 2016 · External reference
DeepLoc 2.0: multi-label subcellular localization prediction using protein language models
10.1093/nar/gkac278 · 2022 · External reference
Biochemistry and evolution of anaerobic energy metabolism in eukaryotes
10.1128/mmbr.05024-11 · 2012 · External reference
Extreme mitochondrial reduction in a novel group of free-living metamonads
10.1038/s41467-024-50991-w · 2024 · External reference
A unique flavoenzyme operates in ubiquinone biosynthesis in photosynthesis-related eukaryotes
10.1126/sciadv.abl3594 · 2021 · External reference
Recurrent evolutionary switches of mitochondrial cytochrome c maturation systems in Archaeplastida
10.1038/s41467-024-45813-y · 2024 · External reference
Update of the sideroflexin (SLC56) gene family
10.1186/s40246-025-00779-w · 2025 · External reference
Dealing with incongruence in phylogenomic analyses
10.1098/rstb.2008.0144 · 2008 · External reference
A matter of phylogenetic scale: Distinguishing incomplete lineage sorting from lateral gene transfer as the cause of gene tree discord in recent versus deep diversification histories
10.1002/ajb2.1064 · 2018 · External reference
Mitochondrial energy generation disorders: genes, mechanisms, and clues to pathology
10.1074/jbc.r117.809194 · 2019 · External reference
Timing the origin of eukaryotic cellular complexity with ancient duplications
10.1038/s41559-020-01320-z · 2021 · External reference
A protein interactome for the last eukaryotic common ancestor illuminates the biochemical basis of modern genetic diseases
10.1016/j.xgen.2026.101254 · 2026 · External reference
Gene ancestries reveal diverse microbial associations during eukaryogenesis
10.1038/s41586-026-10639-9 · 2026 · External reference
Reconstruction of the proto-mitochondrial metabolism
10.1126/science.1085463 · 2003 · External reference
From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism
10.1371/journal.pcbi.0030219 · 2007 · External reference
Phylogenomic reconstruction indicates mitochondrial ancestor was an energy parasite
2014 · External reference
ATAD3A oligomerization causes neurodegeneration by coupling mitochondrial fragmentation and bioenergetics defects
10.1038/s41467-019-09291-x · 2019 · External reference
Novel ATAD3A recessive mutation associated to fatal cerebellar hypoplasia with multiorgan involvement and mitochondrial structural abnormalities
10.1016/j.ymgme.2019.10.012 · 2019 · External reference
Fatal perinatal mitochondrial cardiac failure caused by recurrent de novo duplications in the ATAD3 locus
10.1016/j.medj.2020.06.004 · 2021 · External reference
Recurrent DE Novo NAHR reciprocal duplications in the ATAD3 gene cluster cause a neurogenetic trait with perturbed cholesterol and mitochondrial metabolism
10.1016/j.ajhg.2020.01.007 · 2020 · External reference
mTERF18 and ATAD3 are required for mitochondrial nucleoid structure and their disruption confers heat tolerance in Arabidopsis thaliana
10.1111/nph.17717 · 2021 · External reference
ATAD3 proteins: Unique mitochondrial proteins essential for life in diverse eukaryotic lineages
10.1093/pcp/pcad122 · 2024 · External reference
Eukaryogenesis and oxygen in Earth history
10.1038/s41559-022-01733-y · 2022 · External reference
The hydrogen hypothesis for the first eukaryote
10.1038/32096 · 1998 · External reference
BacDive in 2025: the core database for prokaryotic strain data
10.1093/nar/gkae959 · 2025 · External reference
Genomes OnLine Database (GOLD) v.10: New features and updates
10.1093/nar/gkae1000 · 2025 · External reference
Diversity and origins of anaerobic metabolism in mitochondria and related organelles
10.1098/rstb.2014.0326 · 2015 · External reference
Chlamydial contribution to anaerobic metabolism during eukaryotic evolution
10.1126/sciadv.abb7258 · 2020 · External reference
Unresolved reference
2020 · External reference
Hydrogenosome, a cytoplasmic organelle of the anaerobic flagellate Tritrichomonas foetus, and its role in pyruvate metabolism
10.1016/s0021-9258(19)43249-3 · 1973 · External reference
A hydrogenosomal [Fe]-hydrogenase from the anaerobic chytrid neocallimastix sp. L2
10.1016/s0378-1119(02)00388-8 · 2002 · External reference
A hydrogenosome with a genome
10.1038/25023 · 1998 · External reference
Evidence for a hydrogenosomal-type anaerobic ATP generation pathway in Acanthamoeba castellanii
10.1371/journal.pone.0069532 · 2013 · External reference
Fe-hydrogenase maturases in the hydrogenosomes of Trichomonas vaginalis
10.1128/ec.5.3.579-586.2006 · 2006 · External reference
Fumarate hydratase isoforms of Leishmania major: subcellular localization, structural and kinetic properties
10.1016/j.ijbiomac.2012.04.025 · 2012 · External reference
Phylogenomic insights into the origin of primary plastids
10.1093/sysbio/syab036 · 2021 · External reference
Dated gene duplications elucidate the evolutionary assembly of eukaryotes
10.1038/s41586-025-09808-z · 2025 · External reference
A novel eukaryotic denitrification pathway in Foraminifera
10.1016/j.cub.2018.06.027 · 2018 · External reference
Compositional complexity of the mitochondrial proteome of a unicellular eukaryote (Acanthamoeba castellanii, supergroup Amoebozoa) rivals that of animals, fungi, and plants
10.1016/j.jprot.2014.07.005 · 2014 · External reference
Late acquisition of mitochondria by a host with chimaeric prokaryotic ancestry
10.1038/nature16941 · 2016 · External reference
Gene Duplications Trace Mitochondria to the Onset of Eukaryote Complexity
10.1093/gbe/evab055 · 2021 · External reference
Mosaic nature of the mitochondrial proteome: Implications for the origin and evolution of mitochondria
10.1073/pnas.1421379112 · 2015 · External reference
A yeast-based drug discovery platform to identify Plasmodium falciparum type II NADH dehydrogenase inhibitors
10.1128/aac.02470-20 · 2021 · External reference
Functional characterization and target validation of alternative complex I of Plasmodium falciparum mitochondria
10.1128/aac.50.5.1841-1851.2006 · 2006 · External reference
Leishmania type II dehydrogenase is essential for parasite viability irrespective of the presence of an active complex I
10.1073/pnas.2103803118 · 2021 · External reference
Biochemical similarities and differences between the catalytic [4Fe-4S] cluster containing fumarases FumA and FumB from Escherichia coli
10.1371/journal.pone.0055549 · 2013 · External reference
Two biochemically distinct classes of fumarase in Escherichia coli
10.1016/0167-4838(88)90050-7 · 1988 · External reference
Reconstitution of the mitochondrial calcium uniporter in yeast
10.1073/pnas.1400514111 · 2014 · External reference
Newly born peroxisomes are a hybrid of mitochondrial and ER-derived pre-peroxisomes
10.1038/nature21375 · 2017 · External reference
The evolutionary origin of peroxisomes: an ER-peroxisome connection
10.1093/molbev/msj103 · 2006 · External reference
Origin and evolution of metabolic sub-cellular compartmentalization in eukaryotes
10.1016/j.biochi.2015.03.021 · 2015 · External reference
Evolutionary considerations on the origin of peroxisomes from the endoplasmic reticulum, and their relationships with mitochondria
10.1007/s00018-014-1640-1 · 2014 · External reference
Reconsidering ideas regarding the evolution of peroxisomes: the case for a mitochondrial connection
10.1007/s00018-013-1507-x · 2014 · External reference
The Syntrophy hypothesis for the origin of eukaryotes revisited
10.1038/s41564-020-0710-4 · 2020 · External reference
Mitochondrial evolution
10.1126/science.283.5407.1476 · 1999 · External reference
Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes
10.1038/s41586-023-06186-2 · 2023 · External reference
Expanded diversity of Asgard archaea and their relationships with eukaryotes
10.1038/s41586-021-03494-3 · 2021 · External reference
Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor
10.1038/s41586-026-10128-z · 2026 · External reference
Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes
10.1073/pnas.86.17.6661 · 1989 · External reference
Oxygen reductases in alphaproteobacterial genomes: Physiological evolution from low to high oxygen environments
10.3389/fmicb.2019.00499 · 2019 · External reference
Alpha proteobacterial ancestry of the [Fe-Fe]-hydrogenases in anaerobic eukaryotes
10.1186/s13062-016-0136-3 · 2016 · External reference
Analysis of 1,000+ type-strain genomes substantially improves taxonomic classification of Alphaproteobacteria
10.3389/fmicb.2020.00468 · 2020 · External reference
New Alphaproteobacteria thrive in the depths of the ocean with oxygen gradient
10.3390/microorganisms10020455 · 2022 · External reference
Protist genomics: key to understanding eukaryotic evolution
10.1016/j.tig.2025.05.004 · 2025 · External reference
How many species are there on Earth and in the ocean?
10.1371/journal.pbio.1001127 · 2011 · External reference
Acanthamoeba castellanii genome reannotation and multi-omic encystation profiling reveals cyst wall proteins and carbohydrate-active enzymes
2026 · External reference
MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes
10.1111/j.1365-313x.2004.02016.x · 2004 · External reference
Structures of Tetrahymena’s respiratory chain reveal the diversity of eukaryotic core metabolism
10.1126/science.abn7747 · 2022 · External reference
A ferredoxin bridge connects the two arms of plant mitochondrial complex I
10.1093/plcell/koab092 · 2021 · External reference
Cryo-EM structure of the NDH-PSI-LHCI supercomplex from Spinacia oleracea
10.1038/s41594-024-01478-1 · 2025 · External reference
Supramolecular assembly of chloroplast NADH dehydrogenase-like complex with photosystem I from Arabidopsis thaliana
10.1016/j.molp.2022.01.020 · 2022 · External reference
Structure of the human ATP synthase
10.1016/j.molcel.2023.04.029 · 2023 · External reference
High-resolution cryo-EM analysis of the yeast ATP synthase in a lipid membrane
10.1126/science.aas9699 · 2018 · External reference
An ancestral interaction module promotes oligomerization in divergent mitochondrial ATP synthases
10.1038/s41467-022-33588-z · 2022 · External reference
ATP synthase hexamer assemblies shape cristae of Toxoplasma mitochondria
10.1038/s41467-020-20381-z · 2021 · External reference
Structure, mechanism, and regulation of the chloroplast ATP synthase
10.1126/science.aat4318 · 2018 · External reference
Evolutionary shift toward protein-based architecture in trypanosomal mitochondrial ribosomes
10.1126/science.aau7735 · 2018 · External reference
The structure of the yeast mitochondrial ribosome
10.1126/science.aal2415 · 2017 · External reference
Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM
10.1038/s41586-018-0373-y · 2018 · External reference
Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor
10.1038/s41477-018-0129-6 · 2018 · External reference
Small is big in Arabidopsis mitochondrial ribosome
10.1038/s41477-018-0339-y · 2019 · External reference
Structure of the human 80S ribosome
10.1038/nature14427 · 2015 · External reference
The structure of the eukaryotic ribosome at 3.0 Å resolution
10.1126/science.1212642 · 2011 · External reference
High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome
10.1038/nature11872 · 2013 · External reference
Structure of the actively translating plant 80S ribosome at 2.2 Å resolution
10.1038/s41477-023-01407-y · 2023 · External reference
Cryo-EM structure of the ancient eukaryotic ribosome from the human parasite Giardia lamblia
10.1093/nar/gkac046 · 2022 · External reference
Regulatory dynamics of the higher-plant PSI-LHCI supercomplex during state transitions
10.1016/j.molp.2023.11.002 · 2023 · External reference
Structure of spinach photosystem II–LHCII supercomplex at 3.2 Å resolution
10.1038/nature18020 · 2016 · External reference
10.1093/nar/gkae909
10.1093/nar/gkae909 · External reference
Toward understanding the origin and evolution of cellular organisms
10.1002/pro.3715 · 2019 · External reference
KEGG: kyoto encyclopedia of genes and genomes
10.1093/nar/28.1.27 · 2000 · External reference
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
10.1038/75556 · 2000 · External reference
The Gene Ontology knowledgebase in 2023
10.1093/genetics/iyad031 · 2023 · External reference
Basic local alignment search tool
10.1016/s0022-2836(05)80360-2 · 1990 · External reference
Sensitive protein alignments at tree-of-life scale using DIAMOND
10.1038/s41592-021-01101-x · 2021 · External reference
Muscle5: High-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny
10.1038/s41467-022-34630-w · 2022 · External reference
MAFFT multiple sequence alignment software version 7: improvements in performance and usability
10.1093/molbev/mst010 · 2013 · External reference
FAMSA: Fast and accurate multiple sequence alignment of huge protein families
10.1038/srep33964 · 2016 · External reference
ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference
10.1371/journal.pbio.3001007 · 2020 · External reference
HMMER web server: interactive sequence similarity searching
10.1093/nar/gkr367 · 2011 · External reference
HH-suite3 for fast remote homology detection and deep protein annotation
10.1186/s12859-019-3019-7 · 2019 · External reference
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
10.1038/nbt.3988 · 2017 · External reference
CD-HIT: accelerated for clustering the next-generation sequencing data
10.1093/bioinformatics/bts565 · 2012 · External reference
IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era
10.1093/molbev/msaa015 · 2020 · External reference
ModelFinder: fast model selection for accurate phylogenetic estimates
10.1038/nmeth.4285 · 2017 · External reference
UFBoot2: Improving the ultrafast bootstrap approximation
10.1093/molbev/msx281 · 2018 · External reference
Phylogenetic rooting using minimal ancestor deviation
10.1038/s41559-017-0193 · 2017 · External reference
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2024 · External reference
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10.1093/bioinformatics/btl529 · 2007 · External reference
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
10.1093/bioinformatics/btv351 · 2015 · External reference
eggNOG 6.0: enabling comparative genomics across 12 535 organisms
10.1093/nar/gkac1022 · 2023 · External reference
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs
10.1093/nar/gks1116 · 2013 · External reference
AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences
10.1093/nar/gkad1011 · 2024 · External reference
Highly accurate protein structure prediction with AlphaFold
10.1038/s41586-021-03819-2 · 2021 · External reference
ColabFold: making protein folding accessible to all
10.1038/s41592-022-01488-1 · 2022 · External reference
Pfam: the protein families database
10.1093/nar/gkt1223 · 2014 · External reference
Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
10.1006/jmbi.2000.4315 · 2001 · External reference
Improved tools for biological sequence comparison
10.1073/pnas.85.8.2444 · 1988 · External reference
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10.1093/nargab/lqad088 · 2023 · External reference
Unresolved reference
2023 · External reference
Welcome to the tidyverse
10.21105/joss.01686 · 2019 · External reference
Ggplot2
10.1002/wics.147 · 2011 · External reference
ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R
10.1093/bioinformatics/bty633 · 2019 · External reference
Efficient comparative phylogenetics on large trees
10.1093/bioinformatics/btx701 · 2018 · External reference
phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things)
10.7717/peerj.16505 · 2024 · External reference
Unresolved reference
External reference
UpSet: Visualization of intersecting sets
10.1109/tvcg.2014.2346248 · 2014 · External reference
Biostrings: Efficient manipulation of biological strings
2025 · External reference
A new view of the tree of life
10.1038/nmicrobiol.2016.48 · 2016 · External reference
Efficient exploration of the space of reconciled gene trees
10.1093/sysbio/syt054 · 2013 · External reference
