ArticleGenome biology and evolution2021
Gene Duplications Are At Least 50 Times Less Frequent than Gene Transfers in Prokaryotic Genomes.
Article in Genome biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
23 citing papers in PubMed, 46 citations in OpenAlex.
- Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages.Nature communications · 2026Article
- Imported, not invented, genes prevail amongProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Article
- SegMantX: A Novel Tool for Detecting DNA Duplications Uncovers Prevalent Duplications in Plasmids.Molecular biology and evolution · 2025Article
- De novo gene birth and the conundrum of ORFan genes in bacteria.Genome research · 2025Review
- EvANI benchmarking workflow for evolutionary distance estimation.Briefings in bioinformatics · 2025Article
- EvANI benchmarking workflow for evolutionary distance estimation.bioRxiv : the preprint server for biology · 2025Article
- SCARAP: scalable cross-species comparative genomics of prokaryotes.Bioinformatics (Oxford, England) · 2024Article
- Investigating Additive and Replacing Horizontal Gene Transfers Using Phylogenies and Whole Genomes.Genome biology and evolution · 2024Article
- Lessons from Extremophiles: Functional Adaptations and Genomic Innovations across the Eukaryotic Tree of Life.Genome biology and evolution · 2024Article
- Identification of homologs of the Chlamydia trachomatis effector CteG reveals a family of Chlamydiaceae type III secreted proteins that can be delivered into host cells.Medical microbiology and immunology · 2024Article
- Pseudogenes in plasmid genomes reveal past transitions in plasmid mobility.Nucleic acids research · 2024Article
- Multisubstrate specificity shaped the complex evolution of the aminotransferase family across the tree of life.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Illuminating the coevolution of photosynthesis and Bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Promoter recruitment drives the emergence of proto-genes in a long-term evolution experiment with Escherichia coli.PLoS biology · 2024Article
- A universal and constant rate of gene content change traces pangenome flux to LUCA.FEMS microbiology letters · 2024Article
- Parameter Estimation and Species Tree Rooting Using ALE and GeneRax.Genome biology and evolution · 2023Article
- Phylogenomic Testing of Root Hypotheses.Genome biology and evolution · 2023Article
- Article
- Early effects of gene duplication on the robustness and phenotypic variability of gene regulatory networks.BMC bioinformatics · 2022Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The contribution of gene duplications to the evolution of eukaryotic genomes is well studied. By contrast, studies of gene duplications in prokaryotes are scarce and generally limited to a handful of genes or careful analysis of a few prokaryotic lineages. Systematic broad-scale studies of prokaryotic genomes that sample available data are lacking, leaving gaps in our understanding of the contribution of gene duplications as a source of genetic novelty in the prokaryotic world. Here, we report conservative and robust estimates for the frequency of recent gene duplications within prokaryotic genomes relative to recent lateral gene transfer (LGT), as mechanisms to generate multiple copies of related sequences in the same genome. We obtain our estimates by focusing on evolutionarily recent events among 5,655 prokaryotic genomes, thereby avoiding vagaries of deep phylogenetic inference and confounding effects of ancient events and differential loss. We find that recent, genome-specific gene duplications are at least 50 times less frequent and probably 100 times less frequent than recent, genome-specific, gene acquisitions via LGT. The frequency of gene duplications varies across lineages and functional categories. The findings improve our understanding of genome evolution in prokaryotes and have far-reaching implications for evolutionary models that entail LGT to gene duplications ratio as a parameter.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.