HSDatabase – a database of highly similar duplicate genes from plants, animals, and algae

Abstract

Gene duplication is an important evolutionary mechanism capable of providing new genetic material, which can help organisms adapt to various environmental conditions. Recent studies, for example, have indicated that highly similar duplicated genes (HSDs) are involved in adaptation to extreme conditions via gene dosage. However, HSDs in most genomes remain uncharacterized. Here, we collected and curated HSDs in nuclear genomes from a diversity of species and indexed them in an online, open-access sequence repository called HSDatabase. Currently, this database contains 117,864 curated HSDs from 40 eukaryotic genomes, and it includes information on the total HSD number, gene copy number/length, and alignments of gene copies. HSDatabase also allows users to download sequences of gene copies, access genome browsers, and link out to other databases, such as Pfam and KEGG. What's more, a built-in Basic Local Alignment Search Tool (BLAST) option is available to conveniently explore potential homologous sequences of interest within and across species. HSDatabase is presented with a user-friendly interface and provides easy access to the source data. It can be used on its own for comparative analyses of gene duplicates or in conjunction with HSDFinder, a newly developed bioinformatics tool for identifying, annotating, categorizing, and visualizing HSDs.