DPSN：扩增子测序引物标准化命名数据库

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

摘要:

扩增子测序是目前用来衡量微生物多样性时使用最广泛的测序手段。因为其扩增的需要，所以选择合适的特定引物是必需的，且其对结果影响甚大。probeBase是目前最常用的记录了人工校正后的rRNA探针和引物的数据库。然而，我们发现probeBase中63.58%的引物存在不同程度的注释错误，包括命名重复、命名无规律以及匹配位置错误等。更严重的是，目前主流的短命名方式不具有唯一性，导致对应关系模糊不清。因此，我们定义了更简单可行的短命名标准并开发了新的引物科学命名数据库（DPSN），并对probeBase里的所有173个引物进行了校正，并新加入了4个新的改良引物以及38个针对大亚基的新引物。新的短命名规则包含3个基本要素：在正链5'端的位置、版本号和方向。此外在前面加入了识别大/小亚基以及主要针对的菌界的标志。使用DPSN，可以快速查找感兴趣区域对应的引物并比较不同版本的差异选择合适的引物。同时还能建立命名与序列的明确一一对应关系，避免歧义。

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.