GECOLINOMICS · The long-term evolution of E. coli: promoting archeogenetics as a complement to experimental evolution approaches
FP7 — People (Marie Curie Actions)
- Duration
- 2014-04-01 → 2016-03-31
- EU contribution
- €221,155
- Participants
- 1
- Scheme
- MC-IEF
Lines connect the coordinator with its partners.
Results in brief
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 http://geogenetics.ku.dk/research_groups/palaeomix_group
Data: CORDIS, © European Union
Project objective
The retrieval of ancient DNA sequences from long-dead organisms offers a unique perspective on evolutionary biology. In this proposal, we aim to take advantage of cutting-edge approaches in next-generation sequencing, together with the contributions of other fields, including medicine, experimental biology and microbiology, in order to access the complete genome sequences of ancient E. coli organisms that lived several hundreds to thousands of years ago. DNA enrichment coupled with high-throughput DNA sequencing will be implemented and several lines of evidence will be used to demonstrate the authenticity of the ancient E. coli sequences recovered.The wide knowledge of modern E. coli genomes will be compared to ancient strains for the first time and the plasticity of E. coli genomes will be analyzed over millions of generations, at evolutionary scales that encompass by several orders of magnitude the scope of what is accessible with standard approaches in experimental evolution, promising to reveal important features about the evolutionary mechanisms of adaptation and selection as well as the origin of the variety of modern E. coli populations. In parallel, we aim at characterizing the prevalence of virulence factors (i.e. Shiga toxin) that still cause the onset of serious outbreak of foodborne illness in Europe and in the United States. This information will reveal the importance of E. coli digestive outbreaks in past human populations and could contribute in monitoring outbreaks in current populations.We are confident that the present project, which represents a perfect synthesis of the applicant education and will be carried out under the supervision of an internationally recognised researcher within the fields of paleogenomics and hosted in one of the world’s leading centres for ancient DNA research, will push the limits of archaeogenetics and receive a wide international and general public attention.
Original text from CORDIS.
Participants
- KOBENHAVNS UNIVERSITET · KOBENHAVNCoordinatorDenmark
Links
Data: CORDIS, © European Union