Eukaryote-to-eukaryote gene transfer pervades the genome evolution of Rhizaria

Eukaryote-to-eukaryote gene transfer pervades the genome evolution of Rhizaria | bioRxiv Skip to main content Home About Submit ALERTS / RSS Search for this keyword Advanced Search New Results Eukaryote-to-eukaryote gene transfer pervades the genome evolution of Rhizaria View ORCID Profile Jolien J.E. van Hooff , View ORCID Profile Laura Eme doi: https://doi.org/10.1101/2023.01.27.525846 Jolien J.E. van Hooff 1 Unité d’Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay , AgroParisTech Gif-sur-Yvette, France Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Jolien J.E. van Hooff For correspondence: laura.eme{at}universite-paris-saclay.fr jolien.vanhooff{at}wur.nl Laura Eme 1 Unité d’Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay , AgroParisTech Gif-sur-Yvette, France 2 Department of Cell and Molecular Biology, University of Rhode Island , Kingston, Rhode Island, USA Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Laura Eme For correspondence: laura.eme{at}universite-paris-saclay.fr jolien.vanhooff{at}wur.nl Abstract Full Text Info/History Metrics Supplementary material Data/Code Preview PDF Abstract Lateral gene transfer (LGT) has contributed to the genetic makeup of various eukaryotic lineages, yet its prevalence and long-term significance remain poorly understood, particularly for transfers between eukaryotes. Here, we investigate LGT across 29 species of Rhizaria, an ancient and ecologically diverse clade of predominantly free-living, single-celled phagotrophs. Using phylogenetic analyses of over 40,000 gene families complemented by machine learning-based prediction, we estimate that 8–20% of protein-coding genes in contemporary rhizarian genomes were acquired through LGT at various points during their billion-year history, with ~2,000 transfer events shared between at least two species across the rhizarian tree of life. Gene duplications outnumber LGTs across most lineages, yet LGT-derived genes themselves duplicate more frequently than vertically inherited ones, amplifying the genomic impact of each transfer event. Notably, transfers from other eukaryotes outnumber those from prokaryotes and show distinct signatures: prokaryote-derived LGTs are enriched among extracellular proteins, whereas eukaryote-derived LGTs are overrepresented in nuclear and informational processes. Prokaryote-derived LGT genes progressively acquire introns over evolutionary time, confirming their genomic integration and long-term retention. Our findings establish LGT as a pervasive force in rhizarian genome evolution and highlight eukaryote-to-eukaryote transfer as a substantial but often overlooked component of eukaryotic genetic innovation. Competing Interest Statement The authors have declared no competing interest. Footnotes Correction of figure order. In the previous version, Figure 4 was incorrectly presented as Figure 1. https://figshare.com/projects/Lateral_gene_transfers_LGTs_in_Rhizaria/158240 https://github.com/jolienvanhooff/lgtcallrhizaria Funder Information Declared European Council Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license . Back to top Previous Next Posted July 02, 2026. 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Share Eukaryote-to-eukaryote gene transfer pervades the genome evolution of Rhizaria Jolien J.E. van Hooff , Laura Eme bioRxiv 2023.01.27.525846; doi: https://doi.org/10.1101/2023.01.27.525846 Share This Article: Copy Citation Tools Eukaryote-to-eukaryote gene transfer pervades the genome evolution of Rhizaria Jolien J.E. van Hooff , Laura Eme bioRxiv 2023.01.27.525846; doi: https://doi.org/10.1101/2023.01.27.525846 Citation Manager Formats BibTeX Bookends EasyBib EndNote (tagged) EndNote 8 (xml) Medlars Mendeley Papers RefWorks Tagged Ref Manager RIS Zotero Tweet Widget Facebook Like Google Plus One Subject Area Evolutionary Biology Subject Areas All Articles Animal Behavior and Cognition (8003) Biochemistry (18709) Bioengineering (14841) Bioinformatics (44364) Biophysics (22561) Cancer Biology (19682) Cell Biology (26845) Clinical Trials (138) Developmental Biology (13943) Ecology (20970) Epidemiology (2067) Evolutionary Biology (25415) Genetics (16151) Genomics (23478) Immunology (18681) Microbiology (42421) Molecular Biology (18022) Neuroscience (93355) Paleontology (699) Pathology (2977) Pharmacology and Toxicology (5086) Physiology (8105) Plant Biology (15969) Scientific Communication and Education (2094) Synthetic Biology (4549) Systems Biology (10219) Zoology (2384)

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