PrimerMiner: an R package for development and in silico validation of DNA metabarcoding primers

1. DNA metabarcoding is a powerful tool to assess biodiversity by amplifying and sequencing a standardized gene marker region. Its success is often limited due to variable binding sites that introduce amplification biases. Thus the development of optimized primers for communities or taxa under study in a certain geographic region and/or ecosystems is of critical importance. However, no tool for obtaining and processing of reference sequence data in bulk that can serve as a backbone for primer design is currently available.

2. We developed the R package PrimerMiner, which batch downloads DNA barcode gene sequences from BOLD and NCBI databases for specified target taxonomic groups and then applies sequence clustering into operational taxonomic units (OTUs) to reduce biases introduced by the different number of available sequences per species. Additionally, PrimerMiner offers functionalities to evaluate primers in silico, which are in our opinion more realistic then the strategy employe...

1. DNA 元条形码（DNA metabarcoding）是通过扩增并测序标准化基因标记区域以评估生物多样性的有力工具。其应用效果常因可变结合位点引发扩增偏好性而受限。因此，针对特定地理区域和/或生态系统中的研究群落或分类群开发优化引物，至关重要。然而，当前尚无能够批量获取并处理参考序列数据、可作为引物设计核心支撑的工具。
2. 本研究开发了R软件包PrimerMiner，该工具可针对指定的目标分类群，从生命条形码数据平台（BOLD）与美国国家生物技术信息中心（NCBI）数据库中批量下载DNA条形码基因序列，并通过将序列聚类为操作分类单元（OTUs），降低因单个物种可用序列数量差异带来的偏好性。此外，PrimerMiner还提供计算机模拟（in silico）评估引物的功能，我们认为该方案相较于现有策略更贴合实际应用场景。