ArticleNature communications2025
Scaling laws of bacterial and archaeal plasmids.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- The shared evolutionary capacities of plasmids and extrachromosomal DNA.Nature reviews. Genetics · 2026Review
- Comprehensive Genomic Analysis of the pO157 Plasmid in Enterohemorrhagic Escherichia coli O157:H7 Reveals Non-synonymous Variation in Virulence Factors.Current microbiology · 2026Article
- Stable inheritance of the Streptomyces linear plasmid SCP1 by dual ParABS partition systems.Nucleic acids research · 2026Article
- Large extrachromosomal replicons are widespread across bacterial lineages and show coordinated replication termination and spatial coupling with the chromosome.Nature communications · 2026Article
- Integrating theory and machine learning to reveal determinants of plasmid copy number.Nature communications · 2026Article
- Plasmids serve as vehicles and reservoirs of type VI secretion systems.ISME communications · 2026Article
- Megaplasmids associate withbioRxiv : the preprint server for biology · 2025Article
- Plasmid copy number as a modulator in bacterial pathogenesis and antibiotic resistance.npj antimicrobials and resistance · 2025Review
- The extended mobility of plasmids.Nucleic acids research · 2025Review
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
The capacity of a plasmid to express genes is constrained by its length and copy number. However, the interplay between these parameters and their constraints on plasmid evolution have remained elusive due to the absence of comprehensive quantitative analyses. Here, we present 'Pseudoalignment and Probabilistic Iterative Read Assignment' (pseuPIRA), a computational method that overcomes previous computational bottlenecks, enabling rapid and accurate determination of plasmid copy numbers at large scale. We apply pseuPIRA to all microbial genomes in the NCBI RefSeq database with linked short-read sequencing data (4644 bacterial and archaeal genomes including 12,006 plasmids). The analysis reveals three scaling laws of plasmids: first, an inverse power-law correlation between plasmid copy number and plasmid length; second, a positive linear correlation between protein-coding genes and plasmid length; and third, a positive correlation between metabolic genes per plasmid and plasmid length, particularly for large plasmids. These scaling laws imply fundamental constraints on plasmid evolution and functional organization, indicating that as plasmids increase in length, they converge toward chromosomal characteristics in copy number and functional content.
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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.