RiboGrove: a database of full-length prokaryotic 16S rRNA genes derived from completely assembled genomes

Abstract

16S rRNA gene is frequently used for the identification of prokaryotic organisms and for phylogeny inference. Several specialized public databases exist that contain complete and partial sequences of 16S rRNA genes. In this paper, we present RiboGrove: the first publicly available database that comprises only full-length sequences of 16S rRNA genes originating from completely assembled prokaryotic genomes deposited in RefSeq. Despite being strongly biased towards frequently sequenced genomes, RiboGrove is a useful complement to existing 16S rRNA resources and allows for analyses that would not be possible using amplicon-derived gene sequences. For instance, the absence of partial gene sequences in RiboGrove allowed us to make a summary of prokaryotic organisms, which lack core anti-Shine-Dalgarno sequence in their 16S rRNA genes. In this study, we describe the collected sequence data and present the results of exploratory data analysis of 16S rRNA gene sequences.

Keywords: DNA primers; Intragenomic variability; Metagenomics; Nucleotide composition; Shine–dalgarno sequence; Small ribosomal subunit.