Data from: Trace DNA from insect skins: a comparison of five extraction protocols and direct PCR on chironomid pupal exuviae

Insect skins (exuviae) are of extracellular origin and shed during
moulting. The skins do not contain cells or DNA themselves, but epithelial
cells and other cell-based structures might accidentally attach as they
are shed. This source of trace DNA can be sufficient for PCR amplification
and sequencing of target genes and aid in species identification through
DNA barcoding or association of unknown life stages. Species
identification is essential for biomonitoring programs, as species vary in
sensitivities to environmental factors. However, it requires a DNA
isolation protocol that optimizes the output of target DNA. Here, we
compare the relative effectiveness of five different DNA extraction
protocols and direct PCR in isolation of DNA from chironomid pupal
exuviae. Chironomidae (Diptera) is a species-rich group of aquatic
macroinvertebrates widely distributed in freshwater environments and
considered a valuable bioindicator of water quality. Genomic DNA was
extracted from 61.2% of 570 sampled pupal exuviae. There were significant
differences in the methods with regard to cost, handling time, DNA
quantity, PCR success, sequence success and the ability to sequence target
taxa. The NucleoSpin® Tissue XS Kit, DNeasy® Blood and Tissue kit, and
QuickExtract™ DNA Extraction Solution provided the best results in
isolating DNA from single pupal exuviae. Direct PCR and DTAB/CTAB methods
gave poor results. While the observed differences in DNA isolation methods
on trace DNA will be relevant to research that focuses on aquatic
macroinvertebrate ecology, taxonomy and systematics, they should also be
of interest for studies using environmental barcoding and metabarcoding of
aquatic environments.