Table 2.

Exceptional mtDNA codon usage

		Hexactinellida			Demospongiae
		A.v.	I.p.	S.n.	A.q.	A.c.	G.n.	T.a.	O.c.
AA	codon
Ile	AUA	458	628	433	221	205	218	284	278
	AUU	128	69	161	95	222	207	209	160
	AUC	91	107	86	46	45	18	3	38
Arg	AGG				32	17	15	18	12
	AGA				42	35	55	49	54
	CGG	1	2	0	23	14	4	8	3
	CGA	44	56	51	25	16	21	11	21
	CGU	5	4	3	1	13	5	12	10
	CGC	4	13	4	2	4	0	0	0
Ser	AGG	3	10	7
	AGA	187	221	175
	AGU	21	16	9	65	74	79	113	68
	AGC	15	34	14	25	23	15	3	24
	UCG	0	3	3	48	37	25	17	10
	UCA	84	71	85	52	69	67	92	80
	UCU	56	41	38	49	94	106	99	100
	UCC	44	67	43	36	21	16	3	12
Trp	UGG	0	0	3	62	22	20	31	14
	UGA	72	97	76	39	68	62	58	75

For each sponge species with a published mtDNA, the number of occurrences in protein coding sequence is given of codons with exceptional usage (A.v., Aphrocallistes vastus; I.p., Iphiteon panicea; S.n., Sympagella nux; A.q. Amphimedon queenslandica; A.c., Axinella corrugata; G.n., Geodia neptuni; T.a., Tethya actinia; O.c., Oscarella carmela). The hexactinellid sponges strongly favor Ile(AUA) despite coding for a tRNA with (gau) specificity. AGR codons (in bold) are reassigned from arginine to serine in the glass sponges. The hexactinellids rarely if ever employ the Trp(UGG) codon for translation, but rather seem to use it as a signal for programmed frameshifting.