ReviewNucleic acids research2008
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world.
Review in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 373 papers.
What it found
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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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
373 citing papers in PubMed, 786 citations in OpenAlex.
- A generative model for bipartite gene-sharing networks.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Replication-transcription collisions impose DNA strand-specific constraints on gene length in bacteria.PLoS genetics · 2026Article
- Gain and loss of plasmid-borne antibiotic resistance genes are associated with chromosomal resistance presence in Enterobacteriaceae.mSystems · 2026Article
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- Bacterial proteome foundation model enhances functional prediction from enzymes to ecological interactions.bioRxiv : the preprint server for biology · 2026Article
- Microbial communities and biomineralization potential within mountain permafrost of the Devaux ice cave in the Central Pyrenees.Scientific reports · 2026Article
- Article
- The pangenome: a statistical model, not a fixed biological property.Bioinformatics advances · 2026Review
- Comparative genomics links ecological dominance and genome plasticity in sediment-derivedFrontiers in microbiology · 2026Article
- Characterization of syntons across bacterial genomes using non-redundant genomic contexts.microLife · 2026Article
- Leveraging FracMinHash Containment for GenomicbioRxiv : the preprint server for biology · 2025Article
- Translational coupling of neighboring genes in prokaryotes.Journal of bacteriology · 2025Review
- The Complete Genomes ofMicroorganisms · 2025Article
- Evolutionary dynamics in the genome of ocularMicrobial genomics · 2025Article
- Evolution of gene order in prokaryotes is driven primarily by gene gain and loss.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Comprehensive profiling of integrative conjugative elements (ICEs) in Mollicutes: distinct catalysts of gene flow and genome shaping.NAR genomics and bioinformatics · 2025Article
- Pan-Genomic Insights into Rumen Microbiome-Mediated Short-Chain Fatty Acid Production and Regulation in Ruminants.Microorganisms · 2025Review
- Evolution of gene order in prokaryotes is driven primarily by gene gain and loss.bioRxiv : the preprint server for biology · 2025Article
- Low leucine levels in the blood enhance the pathogenicity of neonatal meningitis-causing Escherichia coli.Nature communications · 2025Article
- Raiding nature's genetic toolbox for UV-C resistance by functional metagenomics.Scientific reports · 2025Article
313 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
The first bacterial genome was sequenced in 1995, and the first archaeal genome in 1996. Soon after these breakthroughs, an exponential rate of genome sequencing was established, with a doubling time of approximately 20 months for bacteria and approximately 34 months for archaea. Comparative analysis of the hundreds of sequenced bacterial and dozens of archaeal genomes leads to several generalizations on the principles of genome organization and evolution. A crucial finding that enables functional characterization of the sequenced genomes and evolutionary reconstruction is that the majority of archaeal and bacterial genes have conserved orthologs in other, often, distant organisms. However, comparative genomics also shows that horizontal gene transfer (HGT) is a dominant force of prokaryotic evolution, along with the loss of genetic material resulting in genome contraction. A crucial component of the prokaryotic world is the mobilome, the enormous collection of viruses, plasmids and other selfish elements, which are in constant exchange with more stable chromosomes and serve as HGT vehicles. Thus, the prokaryotic genome space is a tightly connected, although compartmentalized, network, a novel notion that undermines the 'Tree of Life' model of evolution and requires a new conceptual framework and tools for the study of prokaryotic evolution.
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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.