Table 1.

Phased block statistics

Species	Assembler	Input data	Total (Mbp)	Bubble total (Mbp)	Bubble-total / genome-size	Scaffold NG50 (kbp)	Scaffold LG50 (#)	Contig NG50 (kbp)	Contig LG50 (#)	% gaps	BUSCO duplicate complete (%)	% exact-match MP15k pairs
P. polytes	Platanus-allee	PE + 4 MP	442	393	0.818	404	344	102	1,282	2.80	79.03	35.83
		PE + 4 MP + PacBio(20 × )	473	456	0.950	3,225	51	161	868	2.79	89.15	33.82
		PE + 4 MP + 10X	449	407	0.848	698	207	113	1,214	2.60	83.25	35.61
		PE + 4 MP + PacBio(20 × ) + 10X	476	460	0.959	2,392	65	143	987	2.71	88.94	33.57
	FALCON-Unzip	PacBio(99 × )	481	404	0.843	413	352	413	352	0.00	70.68	31.10
	FALCON-Unzip, Pilon, PH	PacBio(99×) + PE	471	422	0.880	421	353	421	353	0.00	77.48	34.60
	Supernova	10X	313	122	0.253	79	789	31	2,362	1.92	24.32	29.98
B. japonicum	Platanus-allee	PE + 3 MP	720	686	0.880	1,090	194	47	4,406	3.79	86.30
		PE + 3 MP + PacBio(20 × )	739	715	0.916	1,514	142	48	4,300	4.40	87.53
		PE + 3 MP + 10X	732	694	0.889	1,155	172	33	6,271	3.94	84.15
		PE + 3 MP + PacBio(20 × ) + 10X	750	720	0.923	1,516	140	34	6,124	4.53	85.28
	FALCON-Unzip	PacBio(156×)	918	378	0.484	172	1,179	172	1,179	0.00	74.34
	FALCON-Unzip, Pilon, PH	PE + PacBio(156 × )	978	852	1.092	1,075	162	1,075	162	0.00	80.98
	Supernova	10X	697	177	0.227	18	8,779	11	17,306	2.98	41.41
C. elegans	Platanus-allee	PE + 3 MP	195	179	0.897	470	112	43	1,242	4.89	77.09
		PE + 3 MP + PacBio(20 × )	205	198	0.988	902	64	60	992	4.95	86.05
	FALCON-Unzip	PacBio(192 × )	243	224	1.121	511	105	511	105	0.00	82.28
	FALCON-Unzip, Pilon, PH	PacBio(192 × ) + PE	232	222	1.109	512	105	512	105	0.00	82.49
H. sapiens	Platanus-allee	PE + 4 MP	3,898	2,018	0.325	4	194,055	2	454,273	6.25	6.35
		PE + 4 MP + PacBio(x20)	5,684	5,406	0.872	306	5,294	19	78,213	6.72	59.71
		PE + 4 MP + 10X	4,918	4,025	0.649	59	23,612	13	118,218	2.64	39.15
		PE + 4 MP + PacBio(20 × ) + 10X	5,673	5,460	0.881	658	2,584	23	71,898	3.53	68.33
	FALCON-Unzip	PacBio(77 × )	4,721	3,691	0.595	109	13,508	109	13,508	0.00	30.36
	FALCON-Unzip, Pilon, PH	PacBio(77×) + PE	4,851	3,783	0.610	124	11,817	124	11,817	0.00	30.98
	Supernova	10X	5,405	5,028	0.811	2,489	675	124	13,651	1.38	72.38
	Mostovoy et al. 2016	PE + 1 MP + 10X + Bionano	5,535	5,353	0.863	3,998	423	9	184,955	8.25	75.10

Statistics were calculated for phased blocks whose length ≥ 500 bp. A bold value indicates the best one for each species. Bubbles are phased heterozygous regions. Genome sizes and heterozygosities were estimated based on the k-mer frequency information of PEs and GenomeScope²⁶. Bubble-total/genome-size, NG50s and LG50s were calculated based on the estimated diploid genome sizes (P. polytes, 480 Mbp; B. japonicum, 780 Mbp; C. elegans, 200 Mbp; H. sapiens 6.2 Gbp). Estimated heterozygosities are shown in Supplementary Table 5. BUSCO²⁷ (version 3.0.2) was used to estimate the rate of the phased single-copy genes for P. polytes, B. japonicum, C. elegans and H. sapiens with the endopterygota set (2442 orthologs), the metazoa set (978 orthologs), the nematoda set (982 orthologs) and the euarchotoglires set (6192 orthologs), respectively