Data from: Lessons from genome skimming of arthropod-preserving ethanol

Field-collected specimens of invertebrates are regularly killed and
preserved in ethanol, prior to DNA extraction from the specimens, while
the ethanol fraction is usually discarded. However, DNA may be released
from the specimens into the ethanol, which can potentially be exploited to
study species diversity in the sample without the need for DNA extraction
from tissue. We used shallow shotgun sequencing of the total DNA to
characterize the preservative ethanol from two pools of insects (from a
freshwater habitat and terrestrial habitat) to evaluate the efficiency of
DNA transfer from the specimens to the ethanol. In parallel, the specimens
themselves were subjected to bulk DNA extraction and shotgun sequencing,
followed by assembly of mitochondrial genomes for 39 of 40 species in the
two pools. Shotgun sequencing from the ethanol fraction and read-matching
to the mitogenomes detected ~40% of the arthropod species in the ethanol,
confirming the transfer of DNA whose quantity was correlated to the
biomass of specimens. The comparison of diversity profiles of microbiota
in specimen and ethanol samples showed that ‘closed association’ (internal
tissue) bacterial species tend to be more abundant in DNA extracted from
the specimens, while ‘open association’ symbionts were enriched in the
preservative fluid. The vomiting reflex of many insects also ensures that
gut content is released into the ethanol, which provides easy access to
DNA from prey items. Shotgun sequencing of DNA from preservative ethanol
provides novel opportunities for characterizing the functional or
ecological components of an ecosystem and their trophic interactions.