ena-STUDY-UNIVERSITY OF HAMBURG-17-01-2021-15:33:52:186-27
Next-generation sequencing of DNA from resting eggs: signatures of eutrophication in a lakeâ€™s sediment
Here, we investigated DNA sequences isolated directly (i.e. without hatching) from Daphnia resting eggs found in the sediments of Lake Constance spanning pre-, peri-, and post-eutrophication. We chose a Poolseq approach, where ~120 resting eggs from 4 different sediment layers were pooled together before building sequencing libraries. We expected genome-wide changes but also specifically changes in alleles related to pathways involved in mitigating effects of cyanobacterial toxins. We used pairwise FST-analyses to identify transcripts that showed strongest divergence among the four different populations and a clustering analysis to identify correlations between allele frequency shifts and changes in abiotic and biotic lake parameters. In a cluster that correlated with the increased abundance of cyanobacteria in Lake Constance we find genes that have been reported earlier to be differentially expressed in response to the cyanobacterial toxin microcystin and to microcystin-free cyanobacteria. We further reveal the enrichment of gene ontology terms that have been shown to be involved in microcystin-related responses in other organisms but not yet in Daphnia and as such are candidate loci for adaptation of natural Daphnia populations to increased cyanobacterial abundances.  In conclusion this approach of investigating DNA extracted from Daphnia resting stages allowed to determine frequency changes of loci in a natural population over time.
Here, we investigated DNA sequences isolated directly (i.e. without hatching) from Daphnia resting eggs found in the sediments of Lake Constance spanning pre-, peri-, and post-eutrophication. We chose a Poolseq approach, where ~120 resting eggs from 4 different sediment layers were pooled together before building sequencing libraries. We expected genome-wide changes but also specifically changes in alleles related to pathways involved in mitigating effects of cyanobacterial toxins. We used pairwise FST-analyses to identify transcripts that showed strongest divergence among the four different populations and a clustering analysis to identify correlations between allele frequency shifts and changes in abiotic and biotic lake parameters. In a cluster that correlated with the increased abundance of cyanobacteria in Lake Constance we find genes that have been reported earlier to be differentially expressed in response to the cyanobacterial toxin microcystin and to microcystin-free cyanobacteria. We further reveal the enrichment of gene ontology terms that have been shown to be involved in microcystin-related responses in other organisms but not yet in Daphnia and as such are candidate loci for adaptation of natural Daphnia populations to increased cyanobacterial abundances.  In conclusion this approach of investigating DNA extracted from Daphnia resting stages allowed to determine frequency changes of loci in a natural population over time.