Short segmental duplication: parsimony in growth of microbial genomes

Abstract

We compare the distributions of occurrence frequencies of oligonucleotides two to ten bases long (2 to 10-mers) in microbial complete genomes with corresponding distributions obtained from random sequences and find that the genomic distributions are uniformly many times wider in a universal manner, that is, the same for all microbial complete genomes. The difference increases with decreasing word length, with the genomic spectral width about 40 times wider for 2-mers. We show that the observed genomic properties are characteristic of sequences generated in a simple growth model, where a very short initial random sequence (less than 1 kb) grows mainly by maximally stochastic duplication of short segments (of about 25 b). We discuss a number issues related to the findings and the model, including the proposition that life began in an RNA world before the birth of proteins.