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Table 7 Summary of pan-genomic studies

From: Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification

Species No. Genomes1 Pan genome2 No. core genes No. pan genes Avg. no. genes % Core genes Blast cutoff3 Ref
Escherichia coli &Shigella 20 Open 1976 > 17838 4700 42% 80/80 [33]
Escherichia coli 17 Open 2200 > 13000 5020 44% 0.8 BSR [32]
Escherichia coli 32 Open 1563 > 9433 4537 34% 50/50 [31]
Haemophilus influenzae 13 Finite 1461 4425-6052 1970 74% 70/70 [25]
Listeria monocytogenes 26 Open 2350-2450 > 4000 2978 80% 0.5 SSR This study
Neisseria meningitides 7 Open 1333 > 3290 1963 68% 50/50 [30]
Streptococcus agalactiae 8 Open 1806 > 2750 2245 80% 50/50 [24]
Streptococcus agalactiae 8 *Open 1472 *> 2800 2198 67% 1e-5 E-value [29]
Streptococcus pneumoniae 17 Finite 1380 5100 2438 57% 70/70 [28]
Streptococcus pyrogenes 11 *Closed 1376 *2500 1878 73% 1e-5 E-value [29]
  1. All numbers are estimates in this table.
  2. 1Only studies including more than five strains are shown.
  3. 2Pan-genome growth behaviors as described by the authors. * Estimated from figures, but not explicitly stated in the paper.
  4. 3Cutoff values and methods for defining core and pan genes vary widely across the different studies. This column only gives a rough summary of the similarity cutoff. Cutoffs of the form I/L indicate a minimum BLAST hit of I% similarity over L% of the protein length. BSR is Blast Score Ratio [32]. SSR is the similarity score ratio used in this study, similar to BSR.