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Updated: Oct 2, 2025

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons
Published on: August 29, 2014
RiboGrove: a database of full-length prokaryotic 16S rRNA genes derived from completely assembled genomes
Maxim A Sikolenko1, Leonid N Valentovich2
1Center of Analytical and Genetic Engineering Research, Institute of Microbiology, National Academy of Sciences of Belarus, Kuprevich Str., 2, 220141, Minsk, Belarus; Department of System Analysis and Computer Modelling, Faculty of Radio Physics and Computer Technologies, Belarusian State University, Nezalezhnasci Ave., 4, 220030, Minsk, Belarus.
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.
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