A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution

Andersson, Jan O; Sjögren, Åsa M; Horner, David S; Murphy, Colleen A; Dyal, Patricia L; Svärd, Staffan G; Logsdon, John M; Ragan, Mark A; Hirt, Robert P; Roger, Andrew J

doi:10.1186/1471-2164-8-51

Table 2 Codon usage in highly and weakly expressed genes

From: A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution

		Spiro hi¹		Spiro weak²		Giardia hi³		Giardia weak⁴				Spiro hi¹		Spiro weak²		Giardia hi³		Giardia weak⁴
		#	RSCU⁵	#	RSCU⁵	#	RSCU⁵	#	RSCU			#	RSCU⁵	#	RSCU⁵	#	RSCU⁵	#	RSCU⁵
Phe	UUU	80	0.62	3520	1.21	51	0.41	3584	0.99	Ser	UCU	208	3.11	2235	1.51	75	1.20	3962	1.53
	UUC	180	1.38	2317	0.79	197	1.59	3689	1.01		UCC	114	1.71	1009	0.68	125	2.01	2559	0.99
Leu	UUA	62	0.77	3475	1.84	4	0.05	1394	0.44		UCA	38	0.57	2035	1.38	22	0.35	2218	0.86
	UUG	17	0.21	1639	0.87	27	0.32	2466	0.77		UCG	7	0.10	1027	0.69	77	1.24	1825	0.70
	CUU	184	2.30	2163	1.15	123	1.44	5060	1.59	Pro	CCU	142	2.27	1372	1.31	49	0.65	2177	1.05
	CUC	210	2.62	1470	0.78	239	2.80	4307	1.35		CCC	87	1.39	650	0.62	118	1.56	2010	0.97
	CUA	0	0.00	1220	0.65	15	0.18	2302	0.72		CCA	20	0.32	1570	1.50	41	0.54	2369	1.14
	CUG	7	0.09	1366	0.72	105	1.23	3601	1.13		CCG	1	0.02	608	0.58	94	1.25	1720	0.83
Ile	AUU	155	0.96	4600	1.52	92	0.62	4220	1.09	Thr	ACU	194	1.90	2206	1.36	45	0.53	2757	0.97
	AUC	302	1.87	1977	0.66	302	2.05	4272	1.11		ACC	170	1.66	1322	0.81	103	1.22	2811	0.98
	AUA	28	0.17	2476	0.82	48	0.33	3086	0.80		ACA	34	0.33	1929	1.19	57	0.68	3544	1.24
Met	AUG	164	1.00	2280	1.00	181	1.00	4180	1.00		ACG	11	0.11	1047	0.64	132	1.57	2306	0.81
Val	GUU	261	2.09	2782	1.61	98	0.77	3608	1.27	Ala	GCU	321	2.48	2448	1.27	118	0.82	3529	1.00
	GUC	140	1.12	1252	0.72	297	2.32	3375	1.18		GCC	143	1.11	1570	0.82	228	1.59	3738	1.06
	GUA	81	0.65	1668	0.97	27	0.21	1591	0.56		GCA	46	0.36	2233	1.16	96	0.67	4588	1.30
	GUG	18	0.14	1210	0.70	90	0.70	2819	0.99		GCG	7	0.05	1437	0.75	132	0.92	2310	0.65
Tyr	UAU	145	1.34	2703	1.31	59	0.55	3095	1.00	Cys	UGU	45	0.58	1943	0.80	28	0.39	1437	0.80
	UAC	71	0.66	1430	0.69	156	1.45	3110	1.00		UGC	110	1.42	2893	1.20	116	1.61	2137	1.20
Gln/TER ⁶	UAA	58	0.83	3576	1.67	21	1.91	54	0.94	TER	UGA	30	1.00	140	1.00	6	0.55	62	1.08
	UAG	44	0.63	1697	0.79	6	0.55	56	0.98	Trp	UGG	50	1.00	752	1.00	57	1.00	1458	1.00
His	CAU	70	0.85	1239	1.22	17	0.22	1595	0.85	Arg	CGU	235	3.37	764	0.99	100	1.18	1661	1.04
	CAC	95	1.15	796	0.78	136	1.78	2151	1.15		CGC	30	0.43	781	1.02	253	2.98	2403	1.51
Gln	CAA	30	0.43	1500	0.70	25	0.23	2676	0.73		CGA	1	0.01	392	0.51	19	0.22	1115	0.70
	CAG	147	2.11	1791	0.84	192	1.77	4640	1.27		CGG	1	0.01	352	0.46	7	0.08	1324	0.83
Asn	AAU	106	0.68	4502	1.28	61	0.43	3571	0.91	Ser	AGU	10	0.15	1269	0.86	15	0.24	1818	0.70
	AAC	208	1.32	2544	0.72	226	1.57	4291	1.09		AGC	24	0.36	1296	0.88	60	0.96	3171	1.22
Lys	AAA	191	0.59	5117	1.28	50	0.16	2778	0.53	Arg	AGA	141	2.02	1694	2.20	39	0.46	1575	0.99
	AAG	458	1.41	2902	0.72	565	1.84	7623	1.47		AGG	11	0.16	628	0.82	91	1.07	1459	0.92
Asp	GAU	208	1.28	3993	1.26	100	0.55	5063	0.97	Gly	GGU	345	3.03	2029	1.24	88	0.73	1923	0.79
	GAC	116	0.72	2333	0.74	264	1.45	5424	1.03		GGC	71	0.62	1672	1.02	215	1.77	2699	1.11
Glu	GAA	325	1.53	4444	1.24	53	0.24	4072	0.71		GGA	35	0.31	1816	1.11	59	0.49	2797	1.15
	GAG	101	0.47	2716	0.76	389	1.76	7431	1.29		GGG	4	0.04	1029	0.63	123	1.01	2342	0.96

¹⁾S. salmonicida genes represented by more than 10 ESTs (35 genes, 6948 codons)
²⁾S. salmonicida genes unrepresented among the ESTs (682 genes, 122846 codons)
³⁾G. lamblia homologs to S. salmonicida genes represented by more than 10 ESTs (33 genes, 7004 codons)
⁴⁾G. lamblia homologs to S. salmonicida genes unrepresented among the ESTs (172 genes, 184988 codons)
⁵⁾Relative synonymous codon usage; the most and least abundant codons for each amino acid are indicated with boldface and italic font, respectively.
⁶⁾UAA and UAG encode glutamine in Spironucleus, and are termination codons in Giardia [25, 26].

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ISSN: 1471-2164

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