SmallBARNA 2026: a kingdom-wide bacterial sRNA resource.

Abstract

Bacterial small RNA are important context-sensitive regulators of gene expression, especially in highly pathogenic bacteria, often controlling virulence. The number of predicted small RNA (sRNA) entries in public repositories has grown exponentially, contrasting with the linear growth of functionally validated sRNAs. While there are databases maintaining sRNA records from single bacterial species or taxonomic groups, a central repository of bona fide sRNAs for all bacteria with evidence, alignment, and RNA expression information is missing. Such a repository is a critical starting point for both wet lab biologists validating sRNA function as well as bioinformaticians creating new models for sRNA prediction. In this paper, we hand-curate 1117 articles from the literature to find 746 sRNAs that have been confirmed by northern blotting, quantitative polymerase chain reaction (qPCR), mutagenesis, or other functional validation methods. We map these sRNA sequences to QC-filtered bacterial genomic assemblies from NCBI, obtaining 3.8 million hits from 44 789 chromosomes and 10 884 plasmids. Finally, we also quantify these sRNAs in a filtered subset of 5292 isolates with available RNA-seq data from the Sequence Read Archive. The bona fide set, alignment, and expression information is available for download and interactive exploration at https://web.ccb.uni-saarland.de/smallbarna/.