Table 1.

Statistics for A. thaliana and Soybean PGs Constructed Using the DN, MTP, and IA Approaches

	A. thaliana			Soybean
	De Novo	Map-to-Pan	Iterative Assembly	De Novo	Map-to-pan	Iterative Assembly
Total pan-genes	31,860	27,958	28,254	70,898	52,058	52,287
Reference pan-genes	27,295 (85.7%)	27,295 (97.6%)	27,295 (96.6%)	51,769 (73.02%)	51,769 (99.44%)	51,769 (99%)
Nonreference pan-genes	4,565 (14.3%)	663 (2.4%)	959 (3.4%)	19,129 (26.98%)	289 (0.56%)	518 (1%)
Core pan-genes	23,426 (73.5%)	25,657 (91.8%)	25,622 (90.7%)	38,618 (54.47%)	51,027 (98.02%)	51,086 (97.7%)
Shell pan-genes	6,651 (20.9%)	2,041 (7.3%)	2,283 (8.1%)	24,197 (34.13%)	953 (1.83%)	1,106 (2.1%)
Singletons	1,783 (5.6%)	260 (0.9%)	345 (1.2%)	8,083 (11.4%)	77 (0.15%)	95 (0.18%)