Symmetries in the genome structure of Bacillus subtilis shown by doublet frequency maps

摘要

A method of visualisation of sequence patterns in genomes was applied on the study of the structure of the genome of the Gram-positive bacterium Bacillus subtilis. The information stored in more or less strong noised symmetries, strange sequence parts and other features of DNA sequences related to the evolution of genomes can be visualised by a graphical representation of doublet frequency distributions. The method gives an insight in the weak relationships between different parts of the genome. A very clear subdivision of the genome in two parts of nearly equal size (about 2 million bp) is reflected by the distribution of doublet frequencies. The pattern also shows the inclusion of the known prophages and prophages-like structures as strips of strange sequence segments in the matrix pattern. The method is particularly suiteable for the visualisation of translational symmetries. The doublet frequency maps show clearly segments, which are doubled or multiplied in the genome. Sequence segments with a comparatively low degree of relations become visible beside identical sequence parts. A sequence segment of about 5,5 kb existing 9 times was found in four single, a double and a triple arrangement. Hexaplet correlation maps and maps of the correlation of doublet frequencies of coded amino acids are suitable well for the detection of symmetries in the genome of Bacillus subtilis and supply an increased contrast in case of noised duplications of larger sequence segments. In summary, the visualisation reflects obviously the evolution of the genome by an hierarchy of insertions and duplications with characteristically doublet contents in a matrix of more homogenous distributed doublet frequencies.