Table 1.

A. Genome assembly and annotation statistics for raccoon dog (Nyctereutes procyonoides) and comparison with related species. B. Repeat statistics: De novo and homology based repeat annotations as reported by RepeatMasker and RepeatModeler; Families of repeats included here are long interspersed nuclear elements (LINEs), short interspersed nuclear elements (SINEs), long tandem repeats (LTR), DNA repeats (DNA), unclassified (unknown) repeat families, small RNA repeats (SmRNA), and others (consisting of small, but classified repeat groups). The total is the total percentage of base pairs made up of repeats in each genome assembly, respectively. C. Number and percentage of functional annotated predicted protein-coding genes.

	Nyctereutes procyonoides	Vulpes vulpes	Canis lupus familiaris
A. GENOME STATISTICS
Total sequence length	2,387,080,371	2,406,519,287	2,410,976,875
No. of contigs	877	122,687	27,144
contigs >50,000 bp	233	13,920	10,416
No. of scaffolds	810	24,706	3,268
scaffolds >50,000 bp	179	492	301
Scaffold N50	53,959,811	12,607,163	63,241,923
Scaffold L50	17	54	15
GC content (%)	41.28	41.06	41.31
BUSCO
Genome
Complete	92.9% (S:91.5%; D: 1.4%)	92.3% (S:91.1%; D: 1.2%)	93.0% (S:91.6%; D: 1.4%)
Fragmented	3.9%	4.1%	3.6%
Missing	3.2%	3.6%	3.4%
Annotation
Complete	98.9%(S:38%; D:60.9%)	97.9% (S:57.4%; D:40.5%)	98.2%(S:41.7%; D: 56.5%)
Fragmented	0.8%	1.7%	1.4%
Missing	0.3%	0.4%	0.4%
B. REPEATS
LINE	1,631,835	1,398,679	857,579
SINE	1,252,244	1,651,461	1,503,465
LTR	392,967	423,087	302,932
DNA	294,798	388,850	321,141
Unclassified	15,049	5,253	14,466
SmRNA	1,002,088	44,426	1,110,467
Others	954,227	1,007,275	1,038,344
Total (%)	34.04	39.67	42.13
C. FUNCTIONAL ANNOTATION
InterproScan	78,944 (99.41%)	37,861 (99.89%)	56,849 (99.60%)
GO	61,756 (77.77%)	29,799 (78.62%)	44,539 (78.03%)
Reactome	31,180 (39.26%)	14,809 (39.07%)	21,160 (37.07%)
SwissProt	77,152 (97.16%)	37,616 (99.25%)	56,818 (99.54%)