Intra-genomic 16S rRNA gene heterogeneity in cyanobacterial genomes

The ability of the small ribosomal subunit (16S) rRNA to infer fine scale phylogenetic relationships is, in principal, impaired by the presence of multiple and variable gene copies within the same genome. This study investigated the extent of intra-genomic 16S rRNA gene heterogeneity in cyanobacteria. Using bioinformatics, all available sequenced cyanobacterial genomes were screened for microheterogeneity between their paralogous ribosomal genes. As a result, cyanobacteria were found to commonly contain multiple ribosomal operons and the numbers of copies were relatively proportional to genome size. Moreover, intra-genomic paralogous 16S rRNA gene copies often contain point-mutations that were validated by secondary structure modeling to be true point mutations rather than sequencing errors. Although microheterogeneity between paralogous 16S rRNA genes is relatively common in cyanobacterial genomes, the degree of sequence divergence is relatively low. We conclude that cyanobacterial intra genomic 16S rRNA gene heterogeneity generally has a relatively small impact on species delineation and inference of evolutionary histories of cyanobacteria.