Table 1. List of samples used in this study.

Clade	Species	Voucher	Accessiona	Noteb
Aplanulata	Boreohydra simplex	Borehydra20100904.3	KT809334	Long-range PCR
	Ectopleura larynx		JN700938
	Ectopleura larynx *		LN901195	RNA-seq; SRR923510
	Euphysa aurata	GR10-145.2	KT809330	Long-range PCR
	Hydra oligactis		NC_010214
	Hydra magnipapillata		NC_011220–NC_011221
	Hydra vulgaris		HM369413–HM369414
	Plotocnide borealis	RU087.1	KT809334	Long-range PCR
Capitata	Cladonema pacificum		KT809323	DNA-seq; unpublished raw reads
	Millepora platyphylla		JN700943	Old Millepora EK-2011
	Pennaria disticha		JN700950
	Sarsia tubulosa	RU053	KT809333	Long-range PCR
Filifera IV	Catablema vesicarium	RU006	KT809324	Long-range PCR
III	Clava multicornis		NC_016465
I	Eudendrium capillare	PS101	KT809336	Long-range PCR
IV	Halitholus cirratus	GR10-115	KT809337	Long-range PCR
III	Hydractinia polyclina		LN901196	RNA-seq; SRR923509
III	Hydractinia symbiolongicarpus		LN901197	RNA-seq; SRR1174275 & SRR1174698
IV	Leuckartiara octona	PS487	KT809325	Long-range PCR
IV	Nemopsis bachei		JN700947
III	Podocoryna carnea		LN901210	RNA-seq; SRR1796518
II	Proboscidactyla flavicirrata	PS139	KT809319, KT809329	Long-range PCR
IV	Rathkea octopunctata	RU008	HT809320	Long-range PCR
Leptothecata	Laomedea flexuosa		NC_016463
	Melicertum octocostatum	RU082	KT809321	Long-range PCR
	Mitrocomella polydiademata	RU060	KT809332	Long-range PCR
	Ptychogena lactea	GR10-152.1	KT809322	Long-range PCR
	Tiaropsis multicirrata	GR10-053.1	KT809326	Long-range PCR
Siphonophorae	Nanomia bijuga		LN901198–LN901208	RNA-seq; SRR871527
	Physalia physalis		LN901209	RNA-seq; SRR871528
	Physalia physalis	Angel	KT809328	RNA-seq; unpublished raw reads
	Rhizophysa eysenhardti	DLSI230	KT809335	Long-range PCR
Trachylina	Craspedacusta sowerbyi		NC_018537
	Craspedacusta sowerbyi		LN901194	RNA-seq; SRR923472
	Cubaia aphrodite		NC_016467
	Geryonia proboscidalis	BCS32a	KT809331	Long-range PCR
	Liriope tetraphylla		KT809327	DNA-seq; unpublished raw reads
Discomedusae	Aurelia aurita		NC_008446	Shao et al. (2006)
	Aurelia aurita		HQ694729	Park et al. (2012)
	Cassiopea andromeda		JN700934
	Cassiopea frondosa		NC_016466
	Catostylus mosaicus		JN700940
	Chrysaora quinquecirrha		HQ694730
	Chrysaora sp. EK-2011		JN700941
	Cyanea capillata		JN700937
	Rhizostoma pulmo		JN700987–JN700988
	Pelagia noctiluca		JN700949
Coronatae	Linuche unguiculata		JN700939
Staurozoa	Craterolophus convolvulus		JN700975–JN700976
	Haliclystus sanjuanensis		JN700944
	Lucernaria janetae		JN700946
Cubozoa	Alatina moseri		JN642330–JN642344
	Carukia barnesi		JN700959–JN700962
	Carybdea xaymacana		JN700977–JN700983
	Chironex fleckeri		JN700963–JN700968
	Chiropsalmus quadrumanus		JN700969–JN700974

Notes.

^*Not included in phylogenetic analyses.

^aAccession name correspond to KT for Genbank and LN for the European Nucleotide Archive (ENA).

^bSRR codes are GenBank Archive numbers of the DNA-seq and RNA-seq runs used in this study.