GC-compositional strand bias around transcription start sites in plants and fungi

BMC Genomics

Table 1 GC-skew in various eukaryotes

Group	Species	GC-skew	Mean	Std. Dev.	No. of sequences
Plant	Sorghum bicolor	++	0.126	0.278	4,482
	Oryza sativa	++	0.118	0.304	18,676
	Triticum aestivum	+	0.095	0.255	13,133
	Arabidopsis thaliana	+	0.094	0.303	18,714
	Gossypium	+	0.092	0.304	1,561
	Zea mays	+	0.075	0.247	7,904
	Glycine max	+	0.050	0.311	6,162
	Chlamydomonas reinhardtii		0.032	0.184	3,343
	Pinus luchuensis		-0.045	0.227	3,896
Fungus	Filobasidiella neoformans	++	0.222	0.341	243
	Neurospora crassa	++	0.184	0.276	2,763
	Coccidioides immitis	++	0.174	0.317	52
	Aspergillus nidulans	++	0.139	0.238	254
	Magnaporthe grisea	++	0.126	0.224	2,799
	Saccharomyes cerevisiae		-0.012	0.188	2,642
	Schizosaccharomyces pombe		-0.032	0.189	1,489
Protist	Eimeria tenella		0.046	0.195	300
	Tetrahymena thermophila		0.040	0.249	171
	Trichomonas vaginalis		0.037	0.167	47
	Dictyostelium discoideum		0.015	0.328	2,032
	Neospora caninum		-0.004	0.169	636
	Toxoplasma gondii		-0.019	0.184	1,328
	Sarcocystis neurona		-0.035	0.183	91
	Trypanosoma brucei	-	-0.080	0.230	231
	Plasmodium berghei	--	-0.102	0.308	86
	Cryptosporidium parvum	--	-0.124	0.259	70
	Plasmodium falciparum	--	-0.191	0.354	1,905
Animal	Caenorhabditis elegans		0.008	0.194	8,848
	Drosophila melanogaster		-0.011	0.170	14,310
	Amblyomma variegatum		-0.015	0.152	77
	Ictalurus punctatus		-0.017	0.216	382
	Rattus norvegicus		-0.023	0.193	12,594
	Danio rerio		-0.029	0.198	9,350
	Homo sapiens		-0.045	0.213	53,459
	Mus musculus		-0.045	0.217	50,029
	Xenopus laevis	-	-0.064	0.212	13,444
	Schistosoma mansoni	-	-0.088	0.230	195

The mean values and standard deviations (Std. Dev.) of the GC-skew values 100-bp downstream of the 5' -end were calculated in virtually assembled transcripts of nine plant species, seven species of fungus, 11 protist species and 10 animal species, which were downloaded from [16, 17]. The symbols + and ++ denote the predominance of C: ++ (≥0.10) and + (≥0.05). The symbols - and -- denote the predominance of G: -- (≤-0.10) and - (≤-0.05).

ISSN: 1471-2164