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Table 1 Evolution of gene regulation by duplication or by convergent evolution

From: Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli

Type of shared regulation Interactions (n) Percentage
All three types of shared regulation, combined 425 14.2%
   Evolved by duplication 145 4.8%
   Unclear 94 3.1%
   Convergent evolution 186 6.2%
Interactions that are not shared with paralogs 2,570 85.8%
All of RegulonDB (with autoregulation removed) 2,995 100.0%
Type 1: paralogous TFs regulate the same genes 212 7.1%
   Evolved by duplication 84 2.8%
   Unclear 64 2.1%
Relative ages are unclear, and TFs bind the same site 62 2.1%
Duplication of TFs is recent, but TFs bind different sites 2 0.1%
   Convergent evolution 64 2.1%
   Duplication of TFs is old, and TFs bind different sites 26 0.9%
   Duplication of TFs is old, but TFs bind the same site 28 0.9%
   Duplication of TFs is old, and sites are not known 10 0.3%
Type 2: paralogous genes are regulated by the same TF 290 9.7%
   Evolved by duplication 76 2.5%
   Unclear 26 0.9%
   Convergent evolution 188 6.3%
Differences in operon structure 166 5.5%
Operons are consistent, but acquired after duplication 22 0.7%
Type 3: paralogous TFs regulate paralogous genes 54 1.8%
   Evolved by duplication (similar ages) 8 0.3%
   Convergent evolution 46 1.5%
Complex HGT of regulated genes after TF duplication 16 0.5%
TF duplication precedes that of regulated genes 30 1.0%
  1. For each case of shared regulation between paralogs, we examined the evolutionary histories of the duplicated genes to determine whether the regulation was likely to be conserved from the common ancestor. If so, then the regulatory similarity probably evolved by duplication; if not, then the similarity results from convergent evolution. For cases where two paralogous transcription factors (TFs) regulate the same operon, we also considered whether the TFs bind to the same site. For cases where two paralogous genes are regulated by the same TF, we also considered whether the first genes in the operons were homologous, as would be expected for evolution by duplication. The results are tabulated here (see Additional data file 5 for individual interactions). Because some regulatory interactions are shared with paralogs in more than one way, the totals are smaller than the sums over the types.