Achieving the Global Biodiversity Framework (GBF) goals and targets for genetic diversity depends on our capacity to assess and monitor the genetic health of species with precision, consistency, and scalability. Reference genomes - high-quality, chromosome-level assemblies generated for representative individuals of a species - are rapidly becoming foundational to this effort. Within the European Reference Genome Atlas (ERGA), research groups, infrastructures, and conservation actors are collaborating to generate such genomes across Europe’s biodiversity. These genomic resources are transforming the toolkit available for genetic monitoring and provide direct support for implementing CBD-aligned conservation actions.
Reference genomes underpin reliable genetic diversity indicators by greatly improving the accuracy of downstream analyses. Their use enables far finer resolution than traditional markers, allowing quantification of, among others, inbreeding, genetic diversity, and patterns of local adaptation. These metrics complement and reinforce the GBF Headline Indicator A.4., which assesses whether population sizes are large enough to maintain long-term adaptive potential. By anchoring population-level genomic data to a reference, demographic reconstructions become more robust, effective population size estimates gain precision, and early warning signals of genetic erosion can be detected before declines become visible through demographic or ecological trends.
Beyond supporting headline measures, reference genomes open the door to a suite of additional DNA-based indicators relevant to restoration success, connectivity planning, and climate change resilience. They facilitate the meaningful integration of environmental DNA, museum genomics, and Earth Observation data, providing scalable approaches for biodiversity surveillance across landscapes and taxa. ERGA’s coordinated standards for sampling, sequencing, analysis, and data stewardship aim to ensure that these resources are interoperable and accessible to national monitoring programmes.
As countries develop and refine strategies to meet GBF targets, reference genomes offer a future-proof and affordable investment: one genome enables decades of genetic monitoring and can be re-analysed as tools and indicators advance. By presenting current progress and case studies from ERGA, this presentation will highlight how reference genomes are becoming a practical and powerful component of conservation decision-making - helping nations monitor, restore, and secure genetic diversity for the long term.