DPSN: standardizing the short names of amplicon-sequencing primers to avoid ambiguity

Abstract:

Amplicon sequencing is the most widely used sequencing method to evaluate microbial diversity in virtually all environments. Thus, appropriate and specific primers are needed to amplify amplicon regions in amplicon sequencing. For this purpose, the community currently uses probeBase, which curates rRNA-targeted probes and primers. However we found that 63.58% of the primers in probeBase have problematic issues in the short name, full name, and/or position. Furthermore, the current convention for short names causes ambiguity. We here introduce our new Database of Primer Scientific Names (DPSN), which is a manually curated database for the 173 primers from probeBase and 42 new added primers complete with a new short name convention. Building on the work of probeBase, we provide a more user-friendly and standardized system. The new short primer naming convention has three basic components:5' position on the sense strand, version, and direction. An additional character for the name of the taxonomic group is also added in front of the name for convenient use. Furthermore, DPSN contains primers for large subunit as well. In order to separate them from the primers for small subunit, a header character is also recommended. All 173 primers in probeBase were corrected according to this new rule, and are stored in DPSN, which is expected to facilitate accurate primer selection and better standardized communication in this field.