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Table 2 Genome characteristics of Escherichia coli, Buchnera, Prochlorococcus and simulations.

From: In silico experimental evolution: a tool to test evolutionary scenarios

Genome characteristics Free-living vs Endosymbionts Prochlorococcus Experimental evolution
  E. coli Buchnera   Non reduced Reduced   k = 750 k = 250  
Genome size (bp) 5.13 × 106 ±0.2 × 106 0.586 × 106 ±0.09 × 106 -89% 2.545 × 106 ±0.19 × 106 1.726 × 106 ±0.07 × 106 -32% 11,836 ±261 7,746 ±652 -35%
Coding bases (bp) 4.54 × 106 ±0.14 × 106 0.508 × 106 ±0.1 × 106 -89% 2.136 × 106 ±0.22 × 106 1.54 × 106 ±0.05 × 106 -28% 6,797 ±320 5,453 ±729 -20%
Non coding bases (bp) 5.882 × 105 ±0.74 × 105 0.774 × 105 ±0.18 × 105 -87% 4.112 × 105 ±0.26 × 105 1.849 × 105 ±0.27 × 105 -55% 5,038 ±168 2,293 ±329 -55%
% coding bases 88.6 ±1 86.5 ±4 -2% 83.2 ±2.3 89.3 ±1.2 +7% 57.4 ±1.7 70.2 ±5 +22%
Gene number 5,095 ±166 545 ±98 -89% 2,733 ±570 1,987 ±153 -27% 107 ±9 91 ±8 -15%
Average gene length (bp) 896.2 ±4.7 931 ±14.2 +4% 797 ±85.6 769.1 ±36.3 -4% 66.6 ±6.2 67.5 ±14.1 +1%
  1. Genomic data (genome size, genes) was obtained from the NCBI database. Coding and non coding bases, gene length and percentage of coding bases are computed using custom Python scripts for Escherichia coli (O157:H7 str. Sakai, 55989, E24377A, O127:H6 str. E2348/69, S88), Buchnera aphidicola (str. APS, Cinara tujafilina, Bp, Sg), non reduced Prochlorococcus (MIT9303, MIT9313), reduced Prochlorococcus (str. AS9601, MIT9211, MIT9215, MIT9301, MIT9312, MIT9515, NATL1A, NATL2A, CCMP1375, CCMP1986) and simulations with k = 750 and k = 250. For the simulated genomes the real values are irrelevant and cannot be compared with real organisms. To compare with the evolutionary scenario, we show the percentages of reduction (resp. increase) of the different structural parameters. While the reductive evolution of Buchnera has equally affected all genomic compartments, in Prochlorococcus as well as in aevol the reductive evolution mainly affected the non-coding sequences, resulting in an increase in the coding proportion and a moderate loss of genes.