Genomic DNA from animals shows contrasting strand bias in large and small subsequences

BMC Genomics

Table 3 Correlation of (G - C) versus (A - T) in subsequences taken at random from unmasked genomes

Scientific name	Common name	Correlation from 500 base window	Correlation from 500 kb window	Difference (Col 3 - Col 4)
Gallus gallus	Chicken	+0.032	-0.952	+0.983
Homo sapiens	Human	+0.216	-0.672	+0.889
Pan troglodytes	Chimpanzee	+0.233	-0.609	+0.841
Macaca mulatta	Rhesus macaque	+0.244	-0.696	+0.940
Mus musculus	Mouse	+0.158	-0.556	+0.715
Rattus norvegicus	Rat	+0.094	-0.608	+0.703
Canis familiaris	Dog	+0.301	-0.268 (A)	+0.569
Bos taurus	Cow	+0.306	-0.628	+0.934
Monodelphis domestica	Opossum	+0.501	-0.019	+0.519
Tetraodon nigroviridis	Puffer fish	+0.149	+0.045	+0.103
Danio rerio	Zebra fish	-0.045	-0.338	+0.293
Oryzias latipes	Medaka fish	+0.100	-0.143	+0.242
Ciona intestinalis	Sea squirt	-0.088	-0.277	+0.189
Drosophila melanogaster	Fruit fly	-0.014	-0.308	+0.295
Anopheles gambiae	Malaria mosquito	-0.035	-0.324	+0.289
Caenorhabditis elegans	Nematode	+0.313	+0.490	-0.177

In each case the sample size is 4000. The figures in the difference column have a statistically significant difference from zero, (Z test on difference between corrrelation coefficients after Fisher transformation; Z ≥ 4.7 (value for puffer fish); for example Z = 46 for human; n₁ = n₂ = 4000). The results are more pronounced for the higher organisms, with the result for chicken for 500 kb windows being close to 1.0. Note (A) For dog there is a small subpopulation which are outliers from the main part of the sample: when these observations are removed the correlation is -0.735. The corresponding analysis on the previous assembly gave -0.695.

ISSN: 1471-2164