TABLE 2.

Core genome and pangenome estimations of Clostridium perfringens.

Study	No. of input strains (subgroup)	Pangenome Pipeline and chosen parameters	No. of core CDSs per core threshold Present in% of genomes			No. of CDSs in the pangenome	The proportion (%) of core genome (99%) of the pangenome and the average genomeb
			100	99	95a
This study	290	Panaroo, strict	1034	1660	2059	14306	11.6, 53.2
This study	290	Roary, 95% identity, split paralogs	231	590	1078	23148	2.5, 18.9
This study	283c	Roary, 95% identity, split paralogs	696	1170	1581	16875	6.9, 37.5
This study	86 (cpe-carrying strains)	Roary, 95% identity, split paralogs	1577	1577	1797	7835	20.1, 50.7
This study	86 (cpe-carrying strains)	Panaroo, strict	1941	1941	2101	7721	25.1, 63.2
This study	63 (lineage IV strains)	Panaroo, strict	1840	1840	2090	5917	31.0, 65.4
Kiu et al., 2019	110 (human enteric isolates)	Roary, 90%, don’t split paralogs	N/A	1965	N/A	∼6300	31.2, 63.2
Kiu et al., 2017	56	Roary, 95% identity, split paralogs	1470	1470	N/A	11667	12.6, 47.3
Abdel-Glil, 2019	76	Roary, 90%, split paralogs	N/A	N/A	2057	10098	20.3, 66.1d
Feng et al., 2020	173	Roary, parameters not specified	N/A	N/A	1020	26954	3.8, 32.8d

^aTo enable comparison with previous results the core genome present in 95% of strains is given. Due to the concerns explained in the text, these should not be considered biologically relevant

^bThe average CDSs of analyzed genomes: 3120 CDSs for 290 strains, 3,071 for cpe-carrying strains, and 2814 for lineage IV strains.

^cConfounding strains BER-NE33, K473, T3381, W1319, PC5, PBD1, and PBS5 were excluded from the analysis of 283 strains.

^d95% core threshold was used instead of 99%.