Distribution Patterns of rRNA Copy Number Repeats in Prokaryotic Genomes

Abstract

Unlike tandem repeats in eukaryotes, ribosomal RNA (rRNA) operons across prokaryotic genomes are widely distributed. Here, I examined the distribution of 16S ribosomal RNA gene copies using all entries from the Ribosomal RNA Operon Copy Number Database with a copy number of 2 or greater, using a metric--normalized range--that allows for comparisons between copy number. Normalized range varied across rRNA copy number, with the greatest distribution of rRNA gene copies in prokaryotic accessions with a copy number of 5. There was a significant phylogenetic signal for both bacteria and archaea (p<0.05). Archaea had higher normalized range than bacteria, even when comparing bacteria with comparable copy number (n=2-5) (p<0.05). Normalized range varied across bacterial phyla (p<0.05), with Cyanobacteria having the largest normalized range and Chlamydiae the smallest. Furthermore, normalized range was predicted by copy number, tRNA number, and pseudo-gene number, after correcting for phylum. When restricted to low bacterial copy numbers (n=2-5), normalized range was predicted by genome size, GC content, tRNA number, coding gene number, and pseudo-gene number. For archaea, normalized range was predicted by genome size, GC content, and tRNA number. Comparisons of bacteria and archaea suggest different mechanisms for rRNA copy distribution and maintenance across genomes.