Saproxylic beetles are important bioindicators of forest health but their enormous diversity
makes their identification challenging. As an example, the French fauna of saproxylic
beetles alone contains 2,663 species in 72 families. Recently, DNA barcoding was
proposed as a promising tool for the identification and monitoring of saproxylic beetle
species. However, the rate of DNA barcode recovery from specimens of natural history
collections using standard Sanger sequencing protocols remains low and challenges the
construction of reference libraries. In this study, we test the potential of high-throughput
sequencing (HTS) technology to reduce this shortfall by increasing sequencing success
rate and lowering processing cost per specimen. Using a dual-indexing strategy for library
construction and sequencing on the Illumina MiSeq platform, we successfully sequenced
the DNA barcodes of 286 dry-pinned saproxylic beetles out of 521 specimens aged
from 1 to 17 years and sampled in natural history collections. Age at sequencing did not
affect sequence recovery and the success rate (54.9%) of our approach is comparable
to that obtained using Sanger sequencing technology in another study targeting beetle
specimens from natural history collections, but the cost per specimen is significantly
reduced when using HTS. Finally, we shortly discuss how the newly produced DNA
barcodes contribute to the existing library and we highlight a few interesting cases in
which the new sequences question current species boundaries.