Are noncoding sequences of Rickettsia prowazekii remnants of "neutralized"genes?

It has been hypothesized that a large fraction of 24% noncoding DNA in R, p rowazekii consists of degraded genes. This hypothesis has been based on the relatively high G+C content of noncoding DNA. However, a comparison with o ther genomes also having a low overall G+C content shows that this argument would also apply to other bacteria. To test this hypothesis, we study the coding potential in sets of genes, pseudogenes, and intergenic regions. We find that the correlation function and the chi (2)-measure are clearly indi cative of the coding function of genes and pseudogenes. However, both codin g potentials make almost no indication of a preexisting reading frame in th e remaining 23% of noncoding DNA. We simulate the degradation of genes due to single-nucleotide substitutions and insertions/deletions and quantify th e number of mutations required to remove indications of the reading frame. We discuss a reduced selection pressure as another possible origin of this comparatively large fraction of noncoding sequences.