ArticleGenome biology2009
A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes.
Article in Genome biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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64 citing papers in PubMed.
- Imported, not invented, genes prevail amongProceedings of the National Academy of Sciences of the United States of America · 2026Article
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- Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins.Genome research · 2024Article
- Promoter recruitment drives the emergence of proto-genes in a long-term evolution experiment with Escherichia coli.PLoS biology · 2024Article
- Active in vivo translocation of the Methanosarcina mazei Gö1 Casposon.Nucleic acids research · 2023Article
- RAP44 phage integrase-guided 50K genomic island integration inFrontiers in veterinary science · 2022Article
- Functional characterization of prokaryotic dark matter: the road so far and what lies ahead.Current research in microbial sciences · 2022Review
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- An assessment of genome annotation coverage across the bacterial tree of life.Microbial genomics · 2020Article
- A Biological Inventory of Prophages inFrontiers in microbiology · 2020Article
- Origin of a Core Bacterial Gene via Co-option and Detoxification of a Phage Lysin.Current biology : CB · 2019Article
- Whole-Genome Comparisons Among the GenusFrontiers in microbiology · 2019Article
- Genus-wide comparison of Pseudovibrio bacterial genomes reveal diverse adaptations to different marine invertebrate hosts.PloS one · 2018Article
- How a Genetically Stable Extremophile Evolves: Modes of Genome Diversification in the Archaeon Sulfolobus acidocaldarius.Journal of bacteriology · 2017Article
- Do Viruses Exchange Genes across Superkingdoms of Life?Frontiers in microbiology · 2017Article
- A Preliminary List of Horizontally Transferred Genes in Prokaryotes Determined by Tree Reconstruction and Reconciliation.Frontiers in genetics · 2017Article
- Horizontally Acquired Genes Are Often Shared between Closely Related Bacterial Species.Frontiers in microbiology · 2017Article
- Phylogenetic Tracings of Proteome Size Support the Gradual Accretion of Protein Structural Domains and the Early Origin of Viruses from Primordial Cells.Frontiers in microbiology · 2017Article
- Probabilistic inference of lateral gene transfer events.BMC bioinformatics · 2016Article
4 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
backgroundArchaeal and bacterial genomes contain a number of genes of foreign origin that arose from recent horizontal gene transfer, but the role of integrative elements (IEs), such as viruses, plasmids, and transposable elements, in this process has not been extensively quantified. Moreover, it is not known whether IEs play an important role in the origin of ORFans (open reading frames without matches in current sequence databases), whose proportion remains stable despite the growing number of complete sequenced genomes.
resultsWe have performed a large-scale survey of potential recently acquired IEs in 119 archaeal and bacterial genomes. We developed an accurate in silico Markov model-based strategy to identify clusters of genes that show atypical sequence composition (clusters of atypical genes or CAGs) and are thus likely to be recently integrated foreign elements, including IEs. Our method identified a high number of new CAGs. Probabilistic analysis of gene content indicates that 56% of these new CAGs are likely IEs, whereas only 7% likely originated via horizontal gene transfer from distant cellular sources. Thirty-four percent of CAGs remain unassigned, what may reflect a still poor sampling of IEs associated with bacterial and archaeal diversity. Moreover, our study contributes to the issue of the origin of ORFans, because 39% of these are found inside CAGs, many of which likely represent recently acquired IEs.
conclusionsOur results strongly indicate that archaeal and bacterial genomes contain an impressive proportion of recently acquired foreign genes (including ORFans) coming from a still largely unexplored reservoir of IEs.
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