Table 1.

Target species, data types, and assembly statistics

Family	Species	ID	Data type	Size (Mb)	Het. (%)	Scaff. count	Scaff.N50 (Mb)	BUSCO (%)
Bovichtidae	Cottoperca gobio (Cottoperca trigloides)	fCotGob3	PB, 10X, BN, HiC	609	0.31	322	25.156	93.4
	Bovichtus diacanthus	fBovDia2	10XG	641	0.49	12,443	7.334	92.7
	Bovichtus variegatus	fBovVar2	10XG	657	0.58	11,172	14.072	92.8
Nototheniidae	Trematomus bernacchii	fTreBer1	PB, 10XG	867	0.48	864	8.748	97.5
	Gobionotothen gibberifrons	fGobGib1	10XG	784	0.57	46,943	0.848	80.7
	Lepidonotothen larseni (Nototheniops larseni)	fLepLar1	HiSeqX	839	0.69	841,998	0.004	43.9
	Lepidonotothen nudifrons (Nototheniops nudifrons)	fLepNud1	10XG	728	0.34	29,926	1.385	88.1
	Lepidonotothen squamifrons	fLepSqu1	HiSeqX	758	0.48	478,411	0.009	63.6
	Notothenia rossii	fNotRos1	10XG	988	0.76	50,621	1.691	85.2
	Trematomus hansoni	fTreHan1	HiSeqX	708	0.44	178,347	0.047	68.8
	Trematomus loennbergii	fTreLoe1	10XG	801	0.63	48,076	1.316	84.3
	Trematomus scotti	fTreSco1	HiSeqX	832	0.62	696,803	0.004	47.3
Harpagiferidae	Harpagifer antarcticus	fHarAnt1	PB, 10XG, BN	941	0.48	1541	4.997	94.1
Artedidraconidae	Histiodraco velifer	fHisVel1	10XG	831	0.33	62,325	0.059	82.4
	Dolloidraco longedorsalis	fDolLon1	HiSeqX	846	0.49	492,743	0.037	58.8
Bathydraconidae	Gymnodraco acuticeps	fGymAcu1	PB, 10XG	997	0.54	2618	1.921	93.5
	Akarotaxis nudiceps	fAkaNud1	10XG	844	1.07	83,165	0.067	75.2
	Bathydraco marri	fBatMar1	HiSeqX	890	0.53	688,793	0.005	52.6
	Vomeridens infuscipinnis	fVomInf1	HiSeqX	833	0.38	507,682	0.008	68.6
Channichthyidae	Pseudochaenichthys georgianus	fPseGeo1	PB, 10XG, HiC	1,026	0.24	1563	42.832	94.1
	Chaenodraco wilsoni	fChaWil1	10XG	956	1.00	61,567	0.943	80.0
	Chionobathyscus dewitti	fChiDew1	HiSeqX	900	0.4	555,224	0.006	64.5
	Cryodraco antarcticus (Pagetodes antarcticus)	fCryAnt1	10XG	944	0.6	46,843	0.809	82.5
	Pagetopsis macropterus	fPagMac1	10XG	958	0.6	58,353	0.485	80.5

Data types used to generate assemblies: PB: PacBio CLR, 10XG: 10X Genomics linked reads, BN: Bionano, HiSeqX: Illumina Hi-Seq, HiC: Hi-C from ARIMA (C. gobio), Dovetail (P. georgianus). Gene completeness was calculated with BUSCO v.5, and heterozygosity (Het.) estimated with GenomeScope (kmer = 31). Names in parentheses are recent nomenclature revisions³. Scaff = scaffold. Additional information regarding samples and assembly quality for all species is provided in Supplementary Data 1 and 2.