Biodiversity Genomics Europe

Project Information

BGE

Grant agreement ID: 101059492

DOI

10.3030/101059492

Project closed

EC signature date 7 June 2022

Start date 1 September 2022

End date 28 February 2026

Funded under

• Food, Bioeconomy Natural Resources, Agriculture and Environment

Total cost

€ 17 159 391,25

EU contribution

€ 17 080 738,00

Coordinated by

STICHTING NATURALIS BIODIVERSITY CENTER
Netherlands

Periodic Reporting for period 2 - BGE (Biodiversity Genomics Europe)

Reporting period: 2024-03-01 to 2025-02-28

Summary of the context and overall objectives of the project

The Biodiversity Genomics Europe (BGE) Project aims to accelerate the application of genomic science to enhance understanding of biodiversity, monitor biodiversity change, and guide interventions to address its decline. BGE coordinates and upscales DNA barcoding and reference genome generation in the context of European biodiversity. The Project develops synergies by aligning efforts and resources of the DNA barcoding and genome sequencing communities across the continent. The BGE objectives with derived ambitions: CAPACITY: To establish functioning biodiversity genomics networks at the European level to connect and grow community capacity to use genomic tools to help tackle the biodiversity crisis With the ambition to (a) Future-proof our networks on biodiversity genomics research, (b) lower access thresholds to biodiversity genomics research, and (c) promote co-creation and citizen engagement. PRODUCTION - To establish and implement large-scale biodiversity genomic data-generating pipelines for Europe to accelerate the production and accessibility of genomic data for biodiversity characterisation, conservation and biomonitoring With the ambition to (a) establish distributed and inclusive capacity, (b) build economies of scale and (c) connect previously disjoined resources to deliver relevant knowledge. APPLICATION - To apply genomic tools to enhance understanding of pan-European biodiversity and biodiversity declines to improve the efficacy of management interventions and biomonitoring programmes. With the ambition to (a) improve the use of biodiversity genomics data in science policy and (b) establish European-wide large scale biodiversity genomics research mechanisms. The BGE Consortium comprises 33 partners across 20 countries and brings together, for the first time at this scale, the two communities for barcoding and reference genome to implement its aspirational programme.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Enhancing Research Capacity and Collaboration
The project has successfully established European nodes for key global biodiversity initiatives, integrating the DNA Barcoding and Genome Sequencing communities. This achievement has fostered a cohesive network that enhances collaboration and knowledge exchange among European researchers. Through these efforts, BGE has facilitated a series of webinars and panel discussions, growing a vibrant program of community events that encourage ongoing dialogue and collaboration within the biodiversity genomics community.

Advancements in Genomic Production
BGE has made significant strides in establishing robust frameworks for collecting and processing biological samples, vital for accurate genomic analysis. This includes the development of a comprehensive sample supply framework that encompasses museum specimens, field-collected specimens, and bulk samples for biomonitoring. The project has also made headway in species prioritization and the development of testing protocols that ensure the quality and reliability of genomic data.
A network of sequencing centres across Europe now collaborates closer, sharing methodologies and data more efficiently. This network has also explored new sequencing protocols to accommodate diverse taxa, particularly those with unique challenges. This collaborative approach has streamlined the sequencing process and enhanced genomic data quality.

Practical Applications of Genomic Tools
Regarding practical applications, the project has developed standardized workflows and protocols that are now used in various biomonitoring studies. These methodologies allow for more precise identification and biodiversity monitoring, providing essential data for conservation strategies. Additionally, case studies have been conducted to demonstrate the utility of reference genomes in biodiversity conservation, enhancing the bioeconomy and aiding disease research.

Integration and Data Management
A significant effort has been made to align the DNA Barcoding and Genome Sequencing activities, especially regarding data and metadata management. This alignment has facilitated joint community training and standardized sampling and analysis practices, which are crucial for maintaining consistency and reliability in data collection and interpretation.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Curated Reference Libraries and Metadata Management
Creating a curated reference library for pollinators, including a new atlas of mitochondrial diversity for butterflies, has significantly advanced our understanding of lepidopteran diversity. This contribution is crucial for developing reliable resources for biodiversity monitoring and conservation. Establishing standard operating procedures for sample collection and submission in population genomics has set new standards for metadata management. This enhances genomic data quality and ensures consistency and reproducibility in biodiversity research.

Enhancements in DNA Metabarcoding and Genomic Sequencing
Advancements in sample processing for DNA metabarcoding have been particularly impactful. The work on European terrestrial biodiversity using bulk samples has provided a deeper understanding of biodiversity patterns and their underlying genetic foundations. The optimization of DNA extraction and PCR amplification methods has streamlined the sequencing process, ensuring high-quality data that is critical for accurate species identification and ecological assessments.

Best Practices and Policy Recommendations
The project has been instrumental in establishing best practices across various facets of genomic research. This includes sampling, which is vital for maintaining ecosystem health and biodiversity. A series of best practices have also been codified as policy recommendations, such as the ERGA Open Data Policy and guidelines for biobanking. These policies not only advocate for transparency and accessibility but also foster a culture of standardization and rigorous scientific inquiry within the genomics community.

Infrastructure and Community Engagement
Significant infrastructure developments have been achieved, including the launch of the iBOL Europe website and the ERGA website. These platforms are central hubs for sharing information, fostering collaboration, and showcasing genomic achievements, enhancing community engagement and outreach. The ERGA Knowledge Hub Portal and various workshops, such as those focusing on genome annotation and assembly tools, have substantially improved the skills and knowledge within the community, further empowering researchers and enhancing the collective research capacity.

Genomic Data Production and Accessibility
The production of reference genomes and the development of community annotation workflows have enabled deeper insights into genomic structures and functions across diverse species. They contribute to the scientific community and have potential applications in conservation strategies, ecological monitoring, and environmental assessment. The ERGA Data Portal provides an intuitive platform for accessing a wide array of genomic data, significantly accelerating research and applications in biodiversity genomics.
These advancements collectively signify a step forward in integrating and applying genomic technologies in biodiversity research.

Biodiversity Genomic Europe