Ancient Environmental Genomics Initiative for Sustainability (AEGIS)

Building a more sustainable and secure food production system while also preserving biodiversity in cropping systems under climate change, through the power of genomic sequencing.

The past is a roadmap to a sustainable future

The Ancient Environmental Genomics Initiative for Sustainability (AEGIS), jointly funded by the NovoNordisk Foundation and the Wellcome Trust, is a global consortium led by the Globe Institute at the University of Copenhagen. AEGIS aims to develop the essential science and methodology to use ancient environmental DNA (eDNA) – coupled with other ancient and modern biomolecule-based approaches – to identify important organismal associations and genetic adaptations in natural and agro-ecosystems that will improve future food security under climate change.

AEGIS will do this through:

• Studying how climate change and human activities have affected the types of species and their genetic makeup in natural ecosystems over time.
• Looking at how food crops and farming systems have changed as the climate and farming methods have evolved.
• Identifying useful genetic traits and ecosystem processes from the past that could help create more resilient crops and farming systems in the future.
• Using these climate-adaptive genetic traits to develop new strategies for improving the productivity, resilience, and sustainability of modern farming systems.

Modern reference genomes to interpret ancient DNA

The Tree of Life Programme at the Wellcome Sanger Institute is a major contributor to the Earth Biogenome Project’s mission to generate reference genome sequences for all named eukaryotic species. As part of AEGIS, the Tree of Life Programme will substantially enhance the available reference library to support eDNA analysis, through targeted sequencing of agroecosystem species and relevant soil metagenomic samples.

The species chosen for reference genome generation will represent the known and expected members of agricultural, grassland and riparian ecosystems, including dominant and keystone species, crop pathogens, rhizosphere symbionts and soil invertebrates. Additionally, sequencing near relatives of crops and revealing their ecosystem adaptations may inform analysis of crop resilience.

The Tree of Life will also build rich metagenomic assemblies of the prokaryotic and eukaryotic biota present in modern sediments and soils, by applying deep long-read and Hi-C approaches. These will significantly enhance the existing prokaryotic reference library with the genomes expected to be found in ancient soil and sediment eDNA.

Open data release

All sequence data generated by the project will be made publicly available. All raw and assembled reference genome data will be deposited in the European Nucleotide Archive (ENA) public database. Our intention is to rapidly publish all submitted assemblies as Wellcome Open Research notes, which can be cited. Genome annotations will be presented through Ensembl. For more information, please see the AEGIS Open Data Release Policy.