Data from: 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 employed in another available software for that purpose, ecoPCR.
3. We used PrimerMiner to download cytochrome c oxidase subunit I (COI)
sequences for 15 important freshwater invertebrate groups, relevant for
ecosystem assessment. By processing COI markers from both databases, we
were able to increase the amount of reference data 249-fold on average,
compared to using complete mitochondrial genomes alone. Furthermore, we
visualized the generated OTU sequence alignments and describe how to
evaluate primers in silico using PrimerMiner. 4. With PrimerMiner we
provide a useful tool to obtain relevant sequence data for targeted primer
development and evaluation. The OTU based reference alignments generated
with PrimerMiner can be used for manual primer design, or processed with
bioinformatic tools for primer development.