Table 1 The summary of genome assemblies.

Genome	Method	Seq Num	N50 (Mb)	Max Len (Mb)	Total Len (Mb)
R498	CANU	811	1.31	5.43	402.5
	CANU + HERA	206	13.24	25.88	399.2
	BioNano map	453	1.22	5.78	406.1
	BioNano + CANU^a	105	5.67	18.25	388.9
	BioNano + HERA^a	32	17.51	32.2	390.2
	BioNano + HERA + GF	89	14.42	30.03	391.1
	On Chromosome	73	14.42	30.03	390.5
	R498_HERA1^b	40	15.38	30.03	391.6
B73	RefGen_v4 (PBcR)	2,790	1.28	7.26	2106.3
	PBcR + HERA	416	31.53	121.28	2118.2
	BioNano map	1271	2.51	12.45	2079.7
	BioNano + PBcR^a	319	10.2	45.88	2060.3
	BioNano + HERA^a	68	107.5	194.6	2110
	BioNano + HERA + GF	130	61.2	142.5	2105.8
	B73_HERA1^c	86	61.2	142.5	2103.9
HX1	HX1_FALCON	2,710	8.33	38.18	2873.2
	FALCON + HERA	850	32.53	109.81	2840.3
	BioNano map	2,487	1.68	11.41	2890.7
	BioNano + FALCON^a	325	24.05	83.66	2724.4
	BioNano + HERA + GF	1,518	54.41	109.81	2871.3
	HX1_HERA1^c	815	54.41	109.81	2841.7
Pinku1	CANU	839	1.1	10.83	452.1
	PBcR	6,033	0.45	2.11	587.7
	PBcR + HERA	48	22.24	43.19	453.4
	BioNano map	374	1.71	6.85	461.3
	BioNano + PBcR^a	550	5.43	15.04	451.9
	BioNano + HERA^a	22	51.77	61.99	453.7
	BioNano + HERA + GF	30	27.85	49.83	453.2
	Pinku1_HERA1^c	20	51.77	62.08	453.5

Seq Num the total number of contigs or scaffolds, BioNano maps do not have sequences, +GF with gap filling, On Chromosome the HERA contigs anchored on nuclear genome chromosomes
^aHybrid scaffolds included unfilled gaps
^bWith gap filling after anchoring on chromosomes
^cOnly the contigs anchored on chromosomes were included here (no gap filling after anchoring on chromosomes). The unanchored sequences may include contaminations from other species. The sequences on chromosomes were corrected using Illumina short reads, which changed the sequence length

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