LIRBase: a comprehensive database of long inverted repeats in eukaryotic genomes

Abstract

Abstract Small RNAs (sRNAs) constitute a large portion of functional elements in eukaryotic genomes. Long inverted repeats (LIRs) can be transcribed into long hairpin RNAs (hpRNAs), which can further be processed into small interfering RNAs (siRNAs) with vital biological roles. In this study, we systematically identified a total of 6 619 473 LIRs in 424 eukaryotic genomes and developed LIRBase (https://venyao.xyz/lirbase/), a specialized database of LIRs across different eukaryotic genomes aiming to facilitate the annotation and identification of LIRs encoding long hpRNAs and siRNAs. LIRBase houses a comprehensive collection of LIRs identified in a wide range of eukaryotic genomes. In addition, LIRBase not only allows users to browse and search the identified LIRs in any eukaryotic genome(s) of interest available in GenBank, but also provides friendly web functionalities to facilitate users to identify LIRs in user-uploaded sequences, align sRNA sequencing data to LIRs, perform differential expression analysis of LIRs, predict mRNA targets for LIR-derived siRNAs, and visualize the secondary structure of candidate long hpRNAs encoded by LIRs. As demonstrated by two case studies, collectively, LIRBase bears the great utility for systematic investigation and characterization of LIRs and functional exploration of potential roles of LIRs and their derived siRNAs in diverse species.