rrndb: the Ribosomal RNA Operon Copy Number Database

TLDR

The Ribosomal RNA Operon Copy Number Database (rrndb) is an online resource that compiles annotated rRNA operon copy numbers for prokaryotes, addressing the lack of readily accessible data on rRNA gene counts and sequences despite their widespread use in 16S rRNA-based identification. The study aims to elucidate the evolutionary implications of rRNA operon redundancy by providing a phylogenetically organized report of rRNA gene copy numbers across diverse prokaryotes. The database presents each organism’s rRNA operon copy number in a phylogenetically arranged format, linking entries to external resources such as the Ribosomal Database Project, GenBank, PubMed, and culture collections. The rrndb data will aid researchers in microbial ecology and evolutionary studies that rely on 16S rRNA gene sequences. The database is available online at http://rrndb.cme.msu.edu.

Abstract

The Ribosomal RNA Operon Copy Number Database (rrndb) is an Internet-accessible database containing annotated information on rRNA operon copy number among prokaryotes. Gene redundancy is uncommon in prokaryotic genomes, yet the rRNA genes can vary from one to as many as 15 copies. Despite the widespread use of 16S rRNA gene sequences for identification of prokaryotes, information on the number and sequence of individual rRNA genes in a genome is not readily accessible. In an attempt to understand the evolutionary implications of rRNA operon redundancy, we have created a phylogenetically arranged report on rRNA gene copy number for a diverse collection of prokaryotic microorganisms. Each entry (organism) in the rrndb contains detailed information linked directly to external websites including the Ribosomal Database Project, GenBank, PubMed and several culture collections. Data contained in the rrndb will be valuable to researchers investigating microbial ecology and evolution using 16S rRNA gene sequences. The rrndb web site is directly accessible on the WWW at http://rrndb.cme.msu.edu.