Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species

Mitreva, Makedonka; Wendl, Michael C; Martin, John; Wylie, Todd; Yin, Yong; Larson, Allan; Parkinson, John; Waterston, Robert H; McCarter, James P

doi:10.1186/gb-2006-7-8-r75

Table 1 Summary of sequences used by nematode species

From: Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species

Clade	Code	Species	ESTs	Total number of clusters	Clusters or genes used		Codons	GC content (%)
					n	%
V	NA	Necator americanus ^a	4,766	2,294	1,784	78	192,756	46
	AC	Ancylostoma caninum ^b	9,079	4,203	3,207	76	305,036	48
	AY	Ancylostoma ceylanicum ^b	10,544	3,485	2,814	81	387,372	49
	NB	Nippostrongylus brasiliensis ^b	1,234	742	630	85	75,934	50
	HC	Haemonchus contortus ^b	17,268	4,146	4,102	99	584,513	47
	OO	Ostertagia ostertagi ^b	6,670	2,355	1,961	83	222,616	48
	TD	Teladorsagia circumcincta ^b	4,313	1,655	1,616	98	194,351	48
	CE	Caenorhabditis elegans ^c	-	-	22,254	100	9,784,215	43
	CB	Caenorhabditis briggsae ^c	-	-	19,528	100	8,007,053	44
	PP	Pristionchus pacificus ^c	8,672	3,690	2,597	70	297,605	51
IVa	SS	Strongyloides stercoralis ^a	11,236	3,635	2,803	77	367,308	33
	SR	Strongyloides ratti ^b	9,932	3,264	2,682	82	320,874	32
	PT	Parastrongyloides trichosuri ^b	7,712	3,086	2,457	80	284,785	40
IVb	PE	Pratylenchus penetrans ^d	1,908	408	338	83	45,802	46
	GP	Globodera pallida ^d	1,317	977	479	49	65,699	51
	GR	Globodera rostochiensis ^d	5,905	2,851	2,192	77	290,614	51
	HG	Heterodera glycines ^d	18,524	7,198	5,564	77	742,990	50
	MI	Meloidogyne incognita ^d	12,394	4,408	3,214	73	366,435	37
	MJ	Meloidogyne javanica ^d	5,282	2,609	2,086	80	203,135	36
	MA	Meloidogyne arenaria ^d	3,251	1,892	1,483	78	176,816	36
	MH	Meloidogyne hapla ^d	13,462	4,479	3,507	78	407,985	36
	MC	Meloidogyne chitwoodi ^d	7,036	2,409	1,906	79	205,612	35
	ZP	Zeldia punctata ^c	388	208	102	49	16,723	43
III	AS	Ascaris suum ^b	38,944	8,482	5,830	69	646,740	46
	AL	Ascaris lumbricoides ^a	1,822	853	508	60	42,919	47
	TC	Toxocara canis ^b	4,206	1,447	866	60	103,065	48
	BM	Brugia malayi ^a	25,067	9,511	6,483	68	561,296	39
	DI	Dirofiliaria immitis ^b	3,585	1,747	1,380	79	126,880	38
	OV	Onchocerca volvulus ^a	14,922	5,097	2,914	57	299,336	40
I	TS	Trichinella spiralis ^a	10,384	3,680	2,693	73	290,794	41
	TM	Trichuris muris ^b	2,713	1,577	1,179	75	147,995	49
	TV	Trichuris vulpis ^b	2,958	1,257	1,000	80	106,071	48

^aHuman parasite, ^banimal parasite, ^cfree-living, and ^dplant parasite. EST, expressed sequence tag.

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