Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta

McNeal, Joel R; Kuehl, Jennifer V; Boore, Jeffrey L; de Pamphilis, Claude W

doi:10.1186/1471-2229-7-57

Table 5 Relative synonymous codon usage (RSCU) patterns across the plastid genomes

From: Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta

AA	Codon	N	RSCU	AA	Codon	N	RSCU
A. Ipomoea Cumulative Codon Usage
Phe	UUU	907	1.33	Ser	UCU	463	1.53
	UUC	455	0.67		UCC	291	0.96
Leu	UUA	742	1.91		UCA	344	1.14
	UUG	467	1.2		UCG	184	0.61
Tyr	UAU	649	1.6	Cys	UGU	211	1.45
	UAC	160	0.4		UGC	80	0.55
ter	UAA		0	ter	UGA		0
ter	UAG		0	Trp	UGG	407	1
Leu	CUU	523	1.35	Pro	CCU	347	1.49
	CUC	149	0.38		CCC	194	0.84
	CUA	314	0.81		CCA	257	1.11
	CUG	135	0.35		CCG	131	0.56
His	CAU	392	1.49	Arg	CGU	284	1.23
	CAC	135	0.51		CGC	107	0.46
Gln	CAA	631	1.56		CGA	315	1.37
	CAG	180	0.44		CGG	112	0.49
Ile	AUU	957	1.5	Thr	ACU	505	1.61
	AUC	389	0.61		ACC	257	0.82
	AUA	562	0.88		ACA	358	1.14
Met	AUG	511	1		ACG	132	0.42
Asn	AAU	828	1.54	Ser	AGU	377	1.25
	AAC	247	0.46		AGC	155	0.51
Lys	AAA	938	1.49	Arg	AGA	410	1.78
	AAG	317	0.51		AGG	153	0.66
Val	GUU	437	1.45	Ala	GCU	591	1.83
	GUC	148	0.49		GCC	197	0.61
	GUA	448	1.49		GCA	353	1.09
	GUG	170	0.57		GCG	152	0.47
Asp	GAU	698	1.58	Gly	GGU	508	1.3
	GAC	186	0.42		GGC	171	0.44
Glu	GAA	900	1.47		GGA	579	1.48
	GAG	326	0.53		GGG	304	0.78
B. C. exaltata Cumulative Codon Usage
Phe	UUU	769	1.41	Ser	UCU	355	1.55
	UUC	321	0.59		UCC	214	0.94
Leu	UUA	627	1.9		UCA	260	1.14
	UUG	424	1.29		UCG	149	0.65
Tyr	UAU	517	1.62	Cys	UGU	150	1.46
	UAC	123	0.38		UGC	55	0.54
ter	UAA		0	ter	UGA		0
ter	UAG		0	Trp	UGG	322	1
Leu	CUU	405	1.23	Pro	CCU	263	1.33
	CUC	130	0.39		CCC	187	0.95
	CUA	264	0.8		CCA	201	1.02
	CUG	128	0.39		CCG	139	0.7
His	CAU	350	1.48	Arg	CGU	242	1.22
	CAC	122	0.52		CGC	102	0.51
Gln	CAA	530	1.52		CGA	273	1.37
	CAG	168	0.48		CGG	117	0.59
Ile	AUU	753	1.5	Thr	ACU	428	1.67
	AUC	271	0.54		ACC	210	0.82
	AUA	482	0.96		ACA	280	1.09
Met	AUG	385	1		ACG	105	0.41
Asn	AAU	684	1.5	Ser	AGU	299	1.31
	AAC	226	0.5		AGC	93	0.41
Lys	AAA	860	1.56	Arg	AGA	326	1.64
	AAG	243	0.44		AGG	135	0.68
Val	GUU	372	1.42	Ala	GCU	464	1.73
	GUC	132	0.5		GCC	186	0.69
	GUA	378	1.44		GCA	292	1.09
	GUG	165	0.63		GCG	133	0.49
Asp	GAU	571	1.55	Gly	GGU	395	1.2
	GAC	167	0.45		GGC	173	0.53
Glu	GAA	716	1.48		GGA	462	1.4
	GAG	254	0.52		GGG	288	0.87
C. C. obtusiflora Cumulative Codon Usage
Phe	UUU	649	1.51	Ser	UCU	262	1.56
	UUC	213	0.49		UCC	138	0.82
Leu	UUA	559	2.14		UCA	203	1.21
	UUG	292	1.12		UCG	108	0.64
Tyr	UAU	392	1.71	Cys	UGU	112	1.53
	UAC	67	0.29		UGC	34	0.47
ter	UAA		0	ter	UGA		0
ter	UAG		0	Trp	UGG	264	1
Leu	CUU	323	1.24	Pro	CCU	207	1.41
	CUC	88	0.34		CCC	109	0.74
	CUA	215	0.82		CCA	185	1.26
	CUG	92	0.35		CCG	88	0.6
His	CAU	245	1.54	Arg	CGU	188	1.39
	CAC	73	0.46		CGC	80	0.59
Gln	CAA	425	1.51		CGA	202	1.49
	CAG	138	0.49		CGG	62	0.46
Ile	AUU	593	1.59	Thr	ACU	358	1.85
	AUC	189	0.51		ACC	121	0.62
	AUA	339	0.91		ACA	208	1.07
Met	AUG	310	1		ACG	88	0.45
Asn	AAU	543	1.53	Ser	AGU	240	1.43
	AAC	167	0.47		AGC	57	0.34
Lys	AAA	697	1.58	Arg	AGA	207	1.53
	AAG	188	0.42		AGG	74	0.55
Val	GUU	282	1.46	Ala	GCU	348	1.61
	GUC	137	0.71		GCC	151	0.7
	GUA	235	1.22		GCA	253	1.17
	GUG	119	0.62		GCG	114	0.53
Asp	GAU	399	1.53	Gly	GGU	338	1.4
	GAC	123	0.47		GGC	126	0.52
Glu	GAA	548	1.48		GGA	345	1.42
	GAG	194	0.52		GGG	160	0.66

Calculations were made from all coding regions combined. Due to difference in genome content, the total number of codons was different for all taxa.

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