ArticleProceedings of the National Academy of Sciences of the United States of America2015
Endosymbiotic gene transfer from prokaryotic pangenomes: Inherited chimerism in eukaryotes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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72 citing papers in PubMed, 132 citations in OpenAlex.
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- Integrated Symbiotic Pleiotropy: Long Non-Coding RNAs and Disordered Proteins Interweaving the Functional Layers of the Eukaryotic Cell.International journal of molecular sciences · 2026Review
- What impact do new homologs have on detecting interdomain horizontal gene transfer in eukaryotes? A reassessment of Katz (2015).Biology open · 2026Article
- Multi-scale ecological drivers shape the genome flexibility of soil-dwellingISME communications · 2026Article
- Tracing the evolutionary pathway: on the origin of mitochondria and eukaryogenesis.The FEBS journal · 2025Article
- A Perspective on the Role of Mitochondrial Biomolecular Condensates (mtBCs) in Neurodegenerative Diseases and Evolutionary Links to Bacterial BCs.International journal of molecular sciences · 2025Review
- Mosaic evolution of eukaryotic carbon metabolism.Nature ecology & evolution · 2025Article
- Comparative analysis of chloroplast genomes in three Araceae species: genomic difference, genetic distance and species morphology association.Frontiers in genetics · 2025Article
- Plant terrestrialization: an environmental pull on the evolution of multi-sourced streptophyte phenolics.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- Evolution of plant metabolism: the state-of-the-art.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- Reconstructing the last common ancestor of all eukaryotes.PLoS biology · 2024Review
- Evolutionary assembly of the plant terrestrialization toolkit from protein domains.Proceedings. Biological sciences · 2024Article
- Apomixis and the paradox of sex in plants.Annals of botany · 2024Review
- Horizontal gene transfer in eukaryotes: aligning theory with data.Nature reviews. Genetics · 2024Review
- Codon usage bias and phylogenetic analysis of chloroplast genome in 36 gracilariaceae species.Functional & integrative genomics · 2024Article
- Plastid ancestors lacked a complete Entner-Doudoroff pathway, limiting plants to glycolysis and the pentose phosphate pathway.Nature communications · 2024Article
- Origin of minicircular mitochondrial genomes in red algae.Nature communications · 2023Article
- The persistent homology of mitochondrial ATP synthases.iScience · 2023Article
- Loss of plastidComputational and structural biotechnology journal · 2023Article
- hgtseq: A Standard Pipeline to Study Horizontal Gene Transfer.International journal of molecular sciences · 2022Article
12 more citing papers are in PubMed but not listed here.
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6 authors at 2 institutions in 2 countries.
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Abstract
Endosymbiotic theory in eukaryotic-cell evolution rests upon a foundation of three cornerstone partners--the plastid (a cyanobacterium), the mitochondrion (a proteobacterium), and its host (an archaeon)--and carries a corollary that, over time, the majority of genes once present in the organelle genomes were relinquished to the chromosomes of the host (endosymbiotic gene transfer). However, notwithstanding eukaryote-specific gene inventions, single-gene phylogenies have never traced eukaryotic genes to three single prokaryotic sources, an issue that hinges crucially upon factors influencing phylogenetic inference. In the age of genomes, single-gene trees, once used to test the predictions of endosymbiotic theory, now spawn new theories that stand to eventually replace endosymbiotic theory with descriptive, gene tree-based variants featuring supernumerary symbionts: prokaryotic partners distinct from the cornerstone trio and whose existence is inferred solely from single-gene trees. We reason that the endosymbiotic ancestors of mitochondria and chloroplasts brought into the eukaryotic--and plant and algal--lineage a genome-sized sample of genes from the proteobacterial and cyanobacterial pangenomes of their respective day and that, even if molecular phylogeny were artifact-free, sampling prokaryotic pangenomes through endosymbiotic gene transfer would lead to inherited chimerism. Recombination in prokaryotes (transduction, conjugation, transformation) differs from recombination in eukaryotes (sex). Prokaryotic recombination leads to pangenomes, and eukaryotic recombination leads to vertical inheritance. Viewed from the perspective of endosymbiotic theory, the critical transition at the eukaryote origin that allowed escape from Muller's ratchet--the origin of eukaryotic recombination, or sex--might have required surprisingly little evolutionary innovation.
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