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The long-term evolution of E. coli: promoting archeogenetics as a complement to experimental evolution approaches

Periodic Report Summary 1 - GECOLINOMICS (The long-term evolution of E. coli: promoting archeogenetics as a complement to experimental evolution approaches.)

The retrieval of ancient DNA sequences from long-dead organisms offers a unique perspective on the understanding of the past. The GEcoliNOMICS project has provided the opportunity to both significantly improve ancient DNA metholodology and answer historical and biological questions. Cutting-edge approaches in high-throughput DNA sequencing have been applied to a variety of ancient samples, with the aim to identify experimental conditions improving access to ancient DNA molecules from the extraction stage. Our optimized methods led to a reduction in sequencing costs of up to 100-fold. Enrichment methods have also been investigated, including the cutting-edge approach aimed to capture methylated regions of ancient genomes, facilitating access to ancient molecules but also revealing ancient epigenetic landscapes. Our methodological advances have had a significant and positive impact not only in the further development of the project, but also in the field of palaeogenomics as a whole, as improving the tool kit available for characterising ancient (epi-)genomes. We expect that these innovations will impact, in a very short term, on our understanding of the recent evolutionary trajectories humans, their pathogens, but also animals and plants. More specifically for the GEcoliNOMICS project, ancient horse samples have been investigated in order to understand the domestication process. In parallel, the presence of microorganisms in the samples studied was investigated through novel metagenomic approaches developed in the group, which allowed for the specific identification of depositional environments as well as for the detection of ancient pathogens. The most relevant results are reported in the group webpage at