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

Table 7 Summary of pan-genomic studies

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]

All numbers are estimates in this table.
¹Only studies including more than five strains are shown.
²Pan-genome growth behaviors as described by the authors. * Estimated from figures, but not explicitly stated in the paper.
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.

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