Abstract
Resting stages of aquatic organisms that accumulate in the sediment over
time are an exceptional resource that allows direct insights into past
populations and addressing evolutionary questions. This is of particular
interest in taxa that have recently faced environmental changes such as
the Daphnia longispina species complex, a keystone zooplankton
group in European freshwater ecosystems. However, genomic analysis might
be challenging as many of these resting stages are very small and the
DNA might be degraded. To reliably allow the resequencing of single
Daphnia resting eggs from different sediment layers and
characterize genomic changes through time, we performed whole genome
amplification to obtain DNA amounts suitable for genome re-sequencing
and tested multiple protocols involving egg isolation, whole genome
amplification kits and library preparation. A pre-sequencing
contamination screening was developed to quickly assess possible
contamination. In total, we successfully amplified and sequenced nine
genomes from Daphnia resting eggs that could be identified as
Daphnia longispina species. We analyzed the genome coverage and
SNP calling of these samples to optimize this method for future projects
involving population genomic investigation of the resting egg bank.