ArticleNucleic acids research2012
Joint scaling laws in functional and evolutionary categories in prokaryotic genomes.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 28 citations in OpenAlex.
- Scaling laws of bacterial and archaeal plasmids.Nature communications · 2025Article
- Taxonomic classification method for metagenomics based on core protein families with Core-Kaiju.Nucleic acids research · 2020Article
- Article
- Covariations in ecological scaling laws fostered by community dynamics.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Family-specific scaling laws in bacterial genomes.Nucleic acids research · 2017Article
- A census of α-helical membrane proteins in double-stranded DNA viruses infecting bacteria and archaea.BMC bioinformatics · 2015Article
- Horizontal transfer beyond genes.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Cross-species gene-family fluctuations reveal the dynamics of horizontal transfers.Nucleic acids research · 2014Article
- Carl Woese's vision of cellular evolution and the domains of life.RNA biology · 2014Review
- Increments and duplication events of enzymes and transcription factors influence metabolic and regulatory diversity in prokaryotes.PloS one · 2013Article
- Large-scale dynamics of horizontal transfers.Mobile genetic elements · 2012Article
- Are there laws of genome evolution?PLoS computational biology · 2011Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We propose and study a class-expansion/innovation/loss model of genome evolution taking into account biological roles of genes and their constituent domains. In our model, numbers of genes in different functional categories are coupled to each other. For example, an increase in the number of metabolic enzymes in a genome is usually accompanied by addition of new transcription factors regulating these enzymes. Such coupling can be thought of as a proportional 'recipe' for genome composition of the type 'a spoonful of sugar for each egg yolk'. The model jointly reproduces two known empirical laws: the distribution of family sizes and the non-linear scaling of the number of genes in certain functional categories (e.g. transcription factors) with genome size. In addition, it allows us to derive a novel relation between the exponents characterizing these two scaling laws, establishing a direct quantitative connection between evolutionary and functional categories. It predicts that functional categories that grow faster-than-linearly with genome size to be characterized by flatter-than-average family size distributions. This relation is confirmed by our bioinformatics analysis of prokaryotic genomes. This proves that the joint quantitative trends of functional and evolutionary classes can be understood in terms of evolutionary growth with proportional recipes.
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