Small noncoding RNAs (sRNA/sncRNAs) are generated from different genomic loci and play important roles in biological processes, such as cell proliferation and the regulation of gene expression. Next-generation sequencing (NGS) has provided an unprecedented opportunity to discover and quantify diverse kinds of sncRNA, such as tRFs (tRNA-derived small RNA fragments), phasiRNAs (phased, secondary, small-interfering RNAs), Piwi-interacting RNA (piRNAs) and plant-specific 24-nt short interfering RNAs (siRNAs). However, currently available web-based tools do not provide approaches to comprehensively analyze all of these diverse sncRNAs. This study presents a novel integrated platform, sRNAtools (https://bioinformatics.caf.ac.cn/sRNAtools), that can be used in conjunction with high-throughput sequencing to identify and functionally annotate sncRNAs, including profiling microRNAss, piRNAs, tRNAs, small nuclear RNAs, small nucleolar RNAs and rRNAs and discovering isomiRs, tRFs, phasiRNAs and plant-specific 24-nt siRNAs for up to 21 model organisms. Different modules, including single case, batch case, group case and target case, are developed to provide users with flexible ways of studying sncRNA. In addition, sRNAtools supports different ways of uploading small RNA sequencing data in a very interactive queue system, while local versions based on the program package/Docker/virtureBox are also available. We believe that sRNAtools will greatly benefit the scientific community as an integrated tool for studying sncRNAs.

ABSTRACT: In plants, 24 nucleotide small interfering RNAs (24-nt siRNAs) account for a large percentage of the total siRNA pool, and they play an important role in guiding plant-specific RNA-directed DNA methylation (RdDM), which transcriptionally silences transposon elements, transgenes, repetitive sequences and some endogenous genes. Several loci in plant genomes produce clusters of 24-nt RNAs, and these loci are receiving increasing attention from the research community. However, at present there is no bioinformatics resource dedicated to 24-nt siRNA loci and their derived 24-nt siRNAs. Thus, in this study, Pln24NT, a freely available web resource, was created to centralize 24-nt siRNA loci and 24-nt siRNA information, including fundamental locus information, expression profiles and annotation of transposon elements, from next-generation sequencing (NGS) data for 10 popular plant species. An intuitive web interface was also developed for convenient searching and browsing, and analytical tools were included to help users flexibly analyze their own siRNA NGS data. Pln24NT will help the plant research community to discover and characterize 24-nt siRNAs, and may prove useful for studying the roles of siRNA in RNA-directed DNA methylation in plants. AVAILABILITY AND IMPLEMENTATION: http://bioinformatics.caf.ac.cn/Pln24NT . CONTACT: [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.