Pseudogenes, junk DNA, and the dynamics of Rickettsia genomes

Studies of neutrally evolving sequences suggest that differences in eukaryo tic genome sizes result from different rates of DNA loss. However, very few pseudogenes have been identified in microbial species, and the processes w hereby genes and genomes deteriorate in bacteria remain largely unresolved. The typhus-causing agent, Rickettsia prowazekii, is exceptional in that as much as 24% of its 1.1-Mb genome consists of noncoding DNA and pseudogenes . To test the hypothesis that the noncoding DNA in the R. prowazekii genome represents degraded remnants of ancestral genes, we systematically examine d all of the identified pseudogenes and their flanking sequences in three a dditional Rickettsia species. Consistent with the hypothesis, we observe se quence similarities between genes and pseudogenes in one species and interg enic DNA in another species. We show that the frequencies and average sizes of deletions are larger than insertions in neutrally evolving pseudogene s equences. Our results suggest that inactivated genetic material in the Rick ettsia genomes deteriorates spontaneously due to a mutation bias for deleti ons and that the noncoding sequences represent DNA in the final stages of t his degenerative process.