1.1.1 Overarching goal

Biodiversity Genomics Europe plus (BGE+) will harness the power of genomic science and DNA-based reference resources to strengthen taxonomic approaches for biodiversity in Europe, enhancing understanding of species and genetic diversity, widening participation, building skills, developing protocols and solutions, enhancing policy uptake, and developing the foundations of a European biodiversity genomics system. The project capitalises on developments in genomics, previous work performed at European level, and large community participation, to catalyse transformative change in the characterisation, conservation, and sustainable use of biodiversity.

• Objective 1. Mobilise the distributed network of taxonomists and genomic researchers across Europe to scale up production and use of DNA barcode and genome sequence data to expand geographical coverage and participation, and deliver novel insights into species and genetic diversity.
• Objective 2. Address rate-limiting steps in generating, managing, and analysing Barcode and Whole Genome Sequence (WGS) data to remove technical barriers to data production and deployment.
• Objective 3. Increase the policy uptake, use, and impact of genomic data to support environmental management, environmental risk assessment, and sustainable use of biodiversity.
• Objective 4. Establish the foundations of a comprehensive biodiversity genomics system in Europe to ensure long-term sustainable service provision, harnessing the power of genomics for biodiversity characterisation, conservation, and use.

BGE+ will provide a step change towards a distributed, inclusive, and quality-enabled biodiversity genomics infrastructure and community in Europe, leveraging our leadership of the established networks of the International Barcode of Life Europe (iBOL-E Link: https://iboleurope.org/) (Hollingsworth et al. 2026, Kaitetzidou et al. 2026), the European Reference Genome Atlas (ERGA Link: https://www.erga-biodiversity.eu/) (Mazzoni et al. 2023, Mc Cartney et al. 2024), and the Consortium of European Taxonomic Facilities (CETAF Link: https://cetaf.org/).

To deliver our objectives, we will:

• Establish a cascade grants mechanism (WP2) and wider training programme (WP3) encompassing the iBOL-E, ERGA, and CETAF communities, in order to mobilise the distributed network of taxonomists and genomic researchers across Europe to scale up production and use of DNA barcode and genome sequence data;
• Undertake innovative Research and Development (R&D) activities to develop new laboratory protocols (WP4) and informatics solutions (WP5) in order to address rate-limiting steps in generating, managing, and analysing barcode and WGS data;
• Develop strategic partnerships, harmonised genomic-application road-maps, and a synthesis of relevant policy needs (WP6) in order to increase the policy uptake, use, and impact of genomic data;
• Strengthen and grow the iBOL-E (WP8) and ERGA (WP9) communities, and develop long-term biodiversity genomic infrastructure plans (WP7) in order to establish the foundations of a comprehensive biodiversity genomics system in Europe.

The outputs of this project will provide immediate benefits in terms of skills, capacity, data, protocol development, and solutions to policy needs, and a long-term foundation for integrating biodiversity genomics into the European Research Infrastructure landscape.

1.1.2 Project premise and approach

The Project Premise

Despite more than 300 years of research in biosystematics, our understanding of life on Earth remains limited. Current estimates refer to 2.3 million extant species on the planet, recognised by taxonomists (Mora et al. 2011). Although this number has grown substantially over the years, it is impressively low in relation to the scale of biological diversity still to be described. Many published models project between 10 and 20 million species still unknown to science, with arthropods representing the largest group of undescribed species. At the same time, the need for evidence-based decisions in nature conservation has become a prerequisite for effective policymaking. Increasingly, European and international biodiversity goals, such as those emerging from the Kunming-Montreal Global Biodiversity Framework (GBF) (Convention on Biological Diversity 2022) or the European Nature Restoration Regulation (European Commission 2025), underscore the need for more and higher-quality evidence. These nature-related policies are only as good as the completeness and quality of the information they rely upon. Given the gap in taxonomic knowledge and the aspirational policy and science goals ahead of us, it is clear that to deliver on the promise of taxonomy to our societies, we must accelerate the production of biodiversity knowledge. For such acceleration, it is crucial to mobilise, connect, and consolidate all available resources and expertise, and deliver a robust and sustainable research infrastructure, as a distributed system, that enables researchers to scale up their taxonomic knowledge.

The Project Approach

New technologies, including high-throughput genomics and the application of Artificial Intelligence (AI), open up avenues of opportunities for scaling up taxonomic and biodiversity knowledge production. Significant progress has been made in the field of biodiversity genomics, where the scientific and technological readiness has reached a very high level of maturity. Large international initiatives have formed around the two major strands of biodiversity genomics: DNA barcoding [iBOL Link: https://ibol.org/ - International Barcode of Life, (Ratnasingham and Hebert 2007, Hebert et al. 2016)] and whole-genome sequencing [EBP Link: https://www.earthbiogenome.org/ - Earth BioGenome Project, (Lewin et al. 2018, Blaxter et al. 2025)], aiming to connect and support distributed global efforts. In Europe, scientific networks have formed, including iBOL-E Link: https://iboleurope.org/ for DNA barcoding and ERGA Link: https://www.erga-biodiversity.eu/ for whole-genome sequencing, which connect European communities to global efforts. In alignment with iBOL and EBP goals, the BGE+ approach is focused on the representative coverage of described eukaryotic biodiversity, excluding microbes where different methodologies are required.

In our journey to scale up biodiversity knowledge through the use of genomics, it is equally important to scale out and thereby benefit from the distributed efforts taking place through various-sized barcoding and whole-genome projects across the continent. These projects involve a large number of individual researchers and research labs, underscoring the importance of biodiversity genomics in the collective vision for a genomically enabled biodiversity knowledge space. Variation in approaches to sampling, wet-lab methods, and data curation practices and tools affects the comparability and interoperability of results, reducing the collective impact these distributed efforts could bring if they were better connected and consolidated. These challenges hinder the European community of biodiversity scientists from connecting, aggregating, and ultimately accelerating knowledge production, which is required to understand, characterise, protect, and sustainably use Europe's natural capital.

The BGE+ Project directly addresses the challenges described above, aiming at advancing the work already undertaken to establish a truly pan-European, genomically enabled knowledge production system. The project continues on the foundation established through the European project BGE1 (2022-2026) (Koureas et al. 2026).

1.1.3 BGE+ main Objectives

To achieve the project ambitions and deliver the expected topic outcomes of HORIZON-CL6-2025-01-BIODIV-03 Area B, BGE+ has defined four key objectives, their relevance to the call in terms of expected outcomes and scope, and their Key Performance Indicators (KPIs) to measure and verify the results. These objectives, and their relations to the project Work Packages (WPs) are presented here:

Objective 1. Mobilise the distributed network of taxonomists and genomic researchers across Europe to scale up production and use of DNA barcode and genome sequence data to expand geographical coverage and participation, and deliver novel insights into species and genetic diversity.

What we will do

Use cascade grants (WP2) to widen participation and expand geographic and taxonomic coverage of reference barcode libraries and reference genomes, with clear standards for open data, interoperability, and local capacity building. Provide targeted training and knowledge-transfer (WP3) to equip researchers and end-users with laboratory and bioinformatics skills, translating methods and tools into practice across Europe.

How we address Topic expectations (Area B)

• Widen participation. BGE+ widens participation and improves accessibility of genomic data by mobilising distributed teams and delivering structured training and knowledge transfer.
• Establish a comprehensive biodiversity genomics system in Europe. Through the cascade-funded projects, BGE+ pilots the orchestration of a future, scaled-out, interconnected European system for genomically enabled taxonomic research.
• Develop strategies and roadmaps for capacity building and knowledge transfer. BGE+ co-designs national/regional capacity plans with partners and embeds them in a shared roadmap and training curriculum.

KPIs: Number and diversity of new participating researchers, institutions, projects, regions, countries; Number of local follow-up initiatives, publications, and new collaborations. Increased generation and use of reference barcodes and genomes. Number of training events delivered and their geographic coverage; Number of participants reached; Diversity of training offered; Number of training materials shared/used/translated.

Objective 2. Address rate-limiting steps in generating, managing, and analysing Barcode and Whole Genome Sequence (WGS) data to remove technical barriers to data production and deployment.

What we will do

Deliver step-change protocols and workflows for distributed wet-lab operations (WP4) and improve open, FAIR-by-design (Findable, Accessible, Interoperable, and Reusable) bioinformatics tools, data standards and pipelines (WP5) that connect data, metadata and knowledge for routine, interoperable use and reuse. Build on and extend established infrastructures and data systems with enhanced standardisation to connect data, metadata, and knowledge, making them accessible for use and reuse in downstream applications.

How we address Topic expectations (Area B)

• Consolidate and enhance the uptake/use/impact of genomic data. BGE+ works towards the definition of a commons (a set of agreed-upon tools and practices) that helps consolidate the landscape of distributed efforts and lowers the access barrier to genomic and other interconnected data for taxonomists and other biodiversity scientists.
• Remove rate-limiting steps to boost uptake and impact. BGE+ streamlines lab steps (batchable protocols) and bioinformatics (containerised, reproducible pipelines), and trials AI-assisted modules where they add value.
• Ensure data are FAIR. Improve (meta)data standards, data curation practices and tools to enhance FAIR-by-design, whilst promoting the use of open data repositories (the European Nucleotide Archive, ENA; the Barcode of Life Data System, BOLD; the Global Biodiversity Information Facility, GBIF), ensuring community-produced datasets are described/annotated and deposited to the corresponding aggregators.

KPIs: Number of new reference barcodes and genomes produced through distributed community efforts; Diversity of ecosystems and new taxa covered; Amount of institutional investment, e.g. sequencing done locally. Increase in datasets and tools meeting FAIR principles; Decrease in time from data production to mobilisation; Increase in interoperability across platforms, e.g. machine-actionable metadata.

Objective 3. Increase the policy uptake, use, and impact of genomic data to support environmental management, environmental risk assessment, and sustainable use of biodiversity.

What we will do

Promote and showcase the integration of genomic tools into real-world biodiversity science and monitoring programmes; co-develop and test use cases that generate policy-relevant evidence on species, populations, and habitats; and strengthen interfaces with regulators and managers to support decision-making and reporting (WP6).

How we address Topic expectations (Area B)

• Cooperate with policy interfaces and observation initiatives (Knowledge Centre for Biodiversity - KCBD, BioAgora, citizen science, large-scale observations). BGE+ aligns outputs and formats with these interfaces and establishes regular exchange to support uptake.
• Ensure representative coverage, including lesser-known taxa and climate-indicator groups. BGE+, through the cascade-funded projects, selects target sites and taxa that close coverage gaps and brokers to bring together the results of these projects in policy making and conservation practices.
• Generate decision-ready evidence on species status, intra-species diversity and ecosystem condition. BGE+ co-develops policy-facing use cases with agencies and produces traceable indicators and briefs for management and risk assessment.

KPIs: Number of new tools/protocols in use; Improved resolution/accuracy; Adoption by environmental agencies; Number of new species/ecosystems monitored/assessed using genomics. Number of use cases with policy relevance; Number of policy briefs; Number of policies integrating genomics evidence/tools; Number of outcomes from engaging stakeholders.

Objective 4. Establish the foundations of a comprehensive biodiversity genomics system in Europe to ensure long-term sustainable service-provision, harnessing the power of genomics for biodiversity characterisation, conservation, and use.

What we will do

Define user needs and a service portfolio for a European distributed system; assess options for integration into one or more European Research Infrastructures (WP7). Strengthen and expand iBOL-E and ERGA as Europe’s nodes for DNA barcoding and whole-genome sequencing, connecting communities, standards, and facilities, and ensuring bi-directional knowledge flow (WP8, WP9).

How we address Topic expectations (Area B)

• Establish a comprehensive biodiversity genomics system in Europe and connect to existing global and European biodiversity data infrastructures. BGE+ surveys the needs of taxonomists and biodiversity scientists, and provides a roadmap for the future upgrade of existing ESFRI (European Strategy Forum on Research Infrastructures) Research Infrastructures. It does so by working directly with the infrastructures DiSSCo (The Distributed System of Scientific Collections) and ELIXIR (Europe's distributed research infrastructure for life science data), and engaging with others, such as LifeWatch and eLTER (European Long-Term Ecosystem Research).
• Establish a European network of taxonomy and genomics experts. Widens participation in iBOL-E and ERGA networks, improves governance, and the national nodes organisation. In collaboration with CETAF it strengthens the links between the genomics and taxonomic communities.
• Develop coordinated capacity-building strategies and roadmaps. Through iBOL-E, ERGA, and CETAF, it outlines development and engagement roadmaps, mapping long-term needs and promoting standard procedures and practices across the involved communities.

KPIs: Increased iBOL-E and ERGA membership, especially in underrepresented regions; Number of guidelines, best practices, and standards shared/used by the communities, and joint outputs with global networks. Deliver infrastructure design study; Pilot distributed service network; Number of facilities connected, standard procedures adopted, and stakeholders engaged.

1.1.4 Helping the community go beyond current limitationsInnovation supporting the consolidation and enhancement of genomics uptake

To prepare a future system capable of scaled-out biodiversity genomics knowledge production, BGE+ invests in innovation efforts by: (a) Understanding which tools, services, and procedures enable system-level change; (b) Surveying current capacity and readiness across Europe; and (c) Innovating to close the highest-value gaps.

Understanding. BGE+ will define what “good enough at scale” means for barcoding, metabarcoding, and reference-genome workflows, and what interoperability, provenance, and comparability are required for routine, distributed use. Starting with knowledge requirements derived from national and international biodiversity policy frameworks, BGE+ will identify the shared components necessary to support the critical path for delivery at scale in a cross-border (transnational) European system for scaled-up biodiversity genomics.

Surveying. BGE+ will use these technical baselines to map existing services and tools, understand their robustness and sustainability, as well as their interoperability. This mapping exercise will then highlight the areas that need to be strengthened so that these technical baselines can be served in the future.

Innovating. Where the mapping identifies gaps, BGE+ will deliver targeted, reusable solutions. These solutions will cover, among others, a) laboratory practices and protocols, b) data informatics pipelines and data curation and management tools and c) data infrastructure components.

Together, this sequence - understanding requirements, surveying readiness, and innovating where it matters - supports a purpose-driven approach to BGE+, scaling and consolidation efforts, aimed at the future operation of a European distributed system for biodiversity genomics as a research infrastructure.

Beyond technical and infrastructure barriers, comprehensive uptake of biodiversity genomics solutions in Europe is limited by challenges of translating genetic data into regulatory indicators, calibration with existing methods, inertia around change from traditional approaches, and slow regulatory acceptance of new methods. These barriers will be explored within the BGE+ project, and roadmaps will be produced for operationalising biodiversity genomic approaches to meet the needs of policy and practice.

Continuing efforts towards a sustainable future for Biodiversity Genomics

BGE+ builds on the success of the BGE1 Project (2022-2026) (Koureas et al. 2026), a direct response to the call by the European Commission to deliver European capacity in the field of biodiversity genomics and strengthen European presence in the global landscape. Specifically, BGE1 had three objectives a) Establish functioning biodiversity genomics networks at the European level to connect and grow community capacity to tackle the biodiversity crisis using genomic tools, b) Establish and implement large-scale biodiversity genomic data generation pipelines for Europe to accelerate the production and accessibility of genomic data for biodiversity characterisation, conservation, and biomonitoring and c) Apply genomic tools to enhance understanding of pan-European biodiversity and biodiversity declines to improve the efficacy of management interventions and biomonitoring programmes.

BGE1 work delivered scientific and systemic impact across the European taxonomic and biodiversity genomics communities. Systemic changes focused on increasing the rate of production of genomic data across communities and borders, and improving the efficacy of management interventions and biomonitoring programmes with sound genomic tools. Scientific impact focused on establishing positive feedback loops between scientific knowledge and policy needs. BGE1 presented proofs of concept demonstrating how cross-border collaboration can support entire value chains, including field sampling, sequencing, analysis, and application. The project specifically focused on establishing the necessary international collaborations, networks, and practices to enable such scaled-up operations. BGE+ is taking a further step in this direction of systemic and scientific transformation, examining the required mechanisms that will enable such cross-border collaboration and consolidation to be effective, sustainable, and impactful in the long term (Table 1).

1.2.1 Overview of BGE+ methodology

The structure of the BGE+ work programme builds on previous community efforts (namely the BGE1 project), advancing the work towards the delivery of a European distributed system for biodiversity genomics. The overview of the BGE+ methodology is linked to the work areas (Table 1) as follows (Fig. 1).

Figure 1.  

BGE+ work programme and connections with previous work (BGE1 2022-2026) and hand-over/sustainability plans (Biodiversity genomics European system - Research Infrastructure).

Scaling-out - Strengthening Participation & Skills (WP2 & WP3) The project focuses on widening participation (scaling out), emulating and assessing future continental-scale orchestration and collaboration models for a highly distributed system for biodiversity genomics knowledge production. WP2 deploys cascade grants to mobilise researchers across Europe, aligning activities with local conservation, bioeconomy, and policy needs. The cascade grants will facilitate interoperable outputs contributing to the consolidation of the landscape. WP3 converts methods and tools into practice through targeted training and knowledge transfer, onboarding cascade-funded teams and end-users, and feeding back capacity needs that guide the innovation WPs.

Innovation (WP4 & WP5) Linked to the content delivery branch is the innovation branch of BGE+. WP4 and WP5 focus on innovation activities that aim to raise the effectiveness and complementarity of distributed efforts by improving the interoperability of produced data, lowering the entry barrier to available technology and tools, and developing best practices and community standards. WP4 and WP5 serve the innovation branch, focusing on step-change laboratory protocols and improving open bioinformatics tools and services, respectively.

Translation to Policy & Practice (WP6) WP6 synthesises outputs from WP2–WP5 into policy-aligned roadmaps and use cases for biodiversity monitoring and management, covering both barcodes/metabarcoding and whole-genome applications.

Operations as a distributed system & Community engagement (WP7, WP8, & WP9) WP7 maps user needs, audits existing services. It develops an options analysis and service portfolio for long-term integration within the European Research Infrastructure landscape, drawing evidence and priorities from the preceding WPs. WP8 (iBOL-E) and WP9 (ERGA) maintain the project’s interface with the broader communities. They co-develop standards and best practices, host knowledge hubs, and ensure a bi-directional flow between BGE+ and European nodes of global initiatives. They also provide scientific support to cascade projects and channel community feedback to WP3–WP5, strengthening coherence across strands.

Coordination, ethics, and DEC (WP1) WP1 provides scientific and administrative coordination, ethics oversight and the dissemination-exploitation-communication (DEC) framework, including the Knowledge Platform. Through the Scientific Steering Board (SSB), WP1 aligns cascade-grant governance and ensures that WP synergies remain tight and purposeful.

1.2.2 Detailed methodology

WP1 Project management, communication and ethics

WP1 coordinates the Project in both administrative (T1.1) and scientific aspects (T1.2). The WP further provides support to Project partners with communication, dissemination, and exploitation activities (T1.3). Guided by the strategic Dissemination, Exploitation, and Communication plan, T1.3 will refine, update, and expand the mechanisms put in place by BGE1 while adding new tools designed to serve the new endeavour. Such is the case of the Knowledge Platform, which will be expanded to accommodate the new project’s outputs, the project’s communication impact assessment report, and the BGE+ final event that focused on application and science-policy connection. T1.4 oversees the alignment of project activities with ethical standards, particularly in relation to diversity and inclusion, personal data protection, the use of AI, and the handling of biological material and digital sequence information (DSI) in compliance with the Nagoya protocol and Access and Benefit Sharing (ABS) obligations. Relevant ethical standards will be identified with Project members at the beginning of the project through a survey. A Project Code of Conduct will be established to provide information about the ethical aspects and guidance for high ethical integrity throughout the diverse Project activities. Follow-up surveys will be conducted to monitor partners’ ethics-related practices, and the Code of Conduct will be updated as needed. A Project ombudsperson will be selected to provide just resolution of potential issues in an impartial, confidential, and independent manner. The WP will also take responsibility for the co-organisation of the Synergy Alignment Group (connecting to the project funded for Area A of the Topic) and the SSB (the BGE+ governance body to support the definition and implementation of the cascade-funded projects framework).

WP2 Community support for knowledge production

WP2 plays a pivotal role in achieving the BGE+ objective O1 by its work to scale up production and use of DNA barcode and genome sequence data. Its focus is community support for knowledge production (a) increasing geographical and species coverage in reference barcode libraries and improving the biodiversity monitoring toolkit for ecological assessments, (b) producing reference genomes for conservation and monitoring applications, and (c) providing novel insights into species and genomic diversity, detailed in section 1.2.3 below. WP2 will establish a comprehensive framework for the Cascade Grants mechanism, guiding calls for proposals, evaluation, and project selection aligned with BGE+ objectives. Secondly, WP2 will act as a broker connecting cascade-funded project outputs with WPs and Tasks across the BGE+ work programme, essentially amplifying the impact of individual cascade-funded projects. To achieve this, we will develop a robust framework that ensures open access, data harmonisation, local capacity building, and adherence to best practices (T2.1). This framework will be operationalised through the selection and evaluation of cascade-funded projects, which will be onboarded and monitored for their implementation, progress, and impact (T2.2). To ensure alignment across other WPs, we will establish the selection and evaluation criteria, as well as topic areas for the projects to be funded under T2.2, in conjunction with representatives of other WPs and the BGE+ SSB. This will enable the publication of calls and the successful onboarding of selected projects. Our framework will facilitate the integration of new participants into the BGE+ distributed infrastructure, expanding the ERGA and iBOL-E networks and enhancing data production and applications of reference genomes and barcodes for biodiversity research (T2.2). A detailed report (D2.2) will summarise the integration of new partners into the BGE+ distributed infrastructure, highlighting their contributions to the project’s goals. Furthermore, we will assess the added value of cascade projects, evaluating their individual and collective impacts and integrating them into BGE+ outcomes in a policy brief (D2.3). This will enable us to understand the effectiveness of the cascade grants mechanism and make informed decisions for future project development. Through WP2, we aim to create a sustainable and inclusive community that supports knowledge production, driving the advancement of biodiversity research and conservation, enabled by the cascade funding. By establishing a robust framework for cascade grants, we will foster collaboration, innovation, and impact, ultimately contributing to the Project’s overall objectives.

WP3 Training and knowledge transfer for scientists and end-users

WP3 plays a central role in ensuring that the project’s strategic goals can be realised by building the human and institutional capacity necessary for biodiversity genomics in Europe. To address the uneven distribution of expertise across the continent, the work package will deliver targeted training and knowledge transfer and will directly support objective O1 (mobilise the distributed network of taxonomists and genomic researchers across Europe to scale up production and use of DNA barcode and genome sequence data). The activities will begin with a systematic mapping of the current training landscape, carried out through surveys and community engagement, to identify gaps in capacity and priority needs within the iBOL-E and ERGA networks (T3.1). Based on this evidence, WP3 will design a roadmap for structured capacity building, ensuring that resources and training efforts are deployed strategically across the European research community. Training events will incorporate and cover wet lab and dry lab topics on sample collection and processing, library construction and sequencing, genome assembly, curation and annotation, barcode production and curation (T3.2). The training courses will respond to the needs of the community, including the cascade-funded projects. The translation of new protocols and pipelines emerging from WP4 and WP5 into accessible training materials will directly contribute to O2, lowering technical barriers to the production and analysis of genomic data. Capacity building initiatives will be designed as field-based, class-based, laboratory-based, and online events. Training activities will be delivered at multiple levels, ranging from introductory courses that establish essential background knowledge to advanced and highly targeted modules that address specific methodological challenges and project needs. This tiered approach will ensure that cascade-funded projects and community partners can adopt best practices in both wet-lab and bioinformatics methods, while also creating opportunities for stakeholders from management and industry to acquire the skills needed to use genomic data in real-world applications. In this way, WP3 contributes directly to O3 by fostering the policy uptake and societal impact of biodiversity genomics. To ensure sustainability and a long-term legacy, WP3 will develop a Capacity Building Resource Platform, providing a central point of access to the training programme and its outputs via an established GDPR-compliant (General Data Protection Regulation) tool (T3.3). This will build on and expand the existing ERGA Knowledge Hub (EKH 2026) and create a new iBOL-E Knowledge Hub, both of which will serve as enduring community resources beyond the lifetime of the project. By embedding training materials and outputs into these open infrastructures, WP3 will help lay the foundations for a European biodiversity genomics system that can continue to grow and evolve in the future, thus contributing to O4 and ensuring that the skills and knowledge base underpinning the Project remain a permanent asset for European research and society.

WP4 Improving laboratory protocols and approaches

WP4 serves as the laboratory innovation engine of BGE+, directly addressing multiple Project goals through systematic cost reduction and standardisation. The primary focus of WP4 is objective O2, working to address rate-limiting steps in generating, managing, and analysing Barcode and Whole Genome Sequence (WGS) data. This includes catalysing decentralised production of reference barcodes and genomes through multiple complementary approaches, including revolutionising specimen utilisation by facilitating easy to use protocols for fresh specimen barcoding (T4.1), optimising historical DNA protocols for museum collections (T4.2), breaking expensive cold chain dependencies through room-temperature preservation methods (T4.3), and enabling genome sovereignty through cost-effective reference genome production using portable sequencing platforms (T4.4). The work package also delivers a laboratory intercalibration framework (T4.5) for meta-barcoding-based biomonitoring studies. This laboratory-based standardisation enables reliable integration of innovative genomic tools into real-world biomonitoring programmes, providing the quality assurance necessary for evidence-based environmental reporting and management decisions, and supports the delivery of O3, to increase the policy uptake, use, and impact of genomic data. All protocols, workflows, and training materials will be designed as FAIR resources, openly shared through established platforms. This modular, community-supported approach ensures protocols remain current while facilitating widespread adoption and adaptation across the European research landscape and beyond. Through systematic benchmarking across taxonomic groups, preservation methods, and sequencing scales, WP4 will provide the methodological foundation early in the Project to ensure cascade-funded projects in WP2 benefit from validated methods. This comprehensive approach aims to support the transformation of biodiversity genomics from a high-cost, centralised activity into an accessible, distributed capability that can be deployed anywhere, anytime, by anyone. Thus, WP4 also contributes to O1 by removing the primary barriers (complexity and cost) that limit access to genomic technologies. WP4 democratises DNA barcoding (T4.1), museum specimen genomics (T4.2), and reference genome sequencing (T4.3, T4.4) by developing ultra-low-cost, fully documented and modular open access workflows that accommodate both resource-limited users and high-throughput laboratories. The work package contributes to O4, to establish the foundations of a comprehensive biodiversity genomics system in Europe through its commitment to open science and standardisation.

WP5 Improving bioinformatic tools and services

The primary focus of WP5 is to tackle critical informatic challenges to address rate-limiting steps in generating, managing, and analysing Barcode and Whole Genome Sequence (WGS) data (O2). Thus WP5’s focus on informatics complements WP4’s focus on laboratory methods. The specific goals of WP5 are to enhance bioinformatic tools, data management systems, and integrate research infrastructures to support broader engagement in biodiversity genomics across Europe. This WP will build on previous efforts under BGE1 (Heil et al. 2026) and other European projects, and will develop innovative work in three major areas: (i) Scaling up reference library production for genome and barcode generation and curation. A comprehensive framework for benchmarking genome workflows will be developed (T5.1), and assembly and annotation pipelines will be improved to democratise community access (T5.2). Current bioinformatic barriers in reference barcode generation and curation pipelines will be addressed to facilitate wider use and standardisation (T5.3). (ii) Improving biodiversity genomics infrastructure and FAIR data management systems. The WP will build on emerging standards, e.g., RO-Crates (Soiland-Reyes et al. 2022), and align with international best practices to improve the capture of provenance and source information, and develop metadata curation systems that increase interoperability between genomics and other biodiversity infrastructures (T5.4). Reference library data access via dedicated data portals and scholarly publications will be streamlined in line with FAIR-by-design principles (T5.5). (iii) Developing frameworks for downstream analysis for biodiversity monitoring. The focus will be on the analysis of intra-specific genomic data and the standardisation of genetic composition metrics (T5.6), as well as on prototyping a scalable system for metabarcoding data analysis to ensure data comparability across European biodiversity monitoring surveys (T5.7). The work of this WP will contribute to BGE+ objectives O1, O3, and O4 by supporting the cascade-funded projects (WP2), resulting in the production of guidelines and best practices to be shared with the communities (WP8, WP9). These guidelines will be converted into training materials for capacity building in WP3. Data produced in WP4 will be integrated into the developed bioinformatic pipelines, while the biodiversity application framework tasks (iii) will support the roadmaps for genomics uptake in biodiversity monitoring (WP6). The technical developments and enhancements of RI services in the biodiversity landscape will help address gaps identified in WP7. Overall, the results of WP5 will support the iBOL-E and ERGA communities (WP8 and WP9) in data production, analysis, management, and publication in a distributed system for biodiversity genomics.

WP6 Biodiversity genomics knowledge exploitation - Science and Policy cases

The focus of WP6 is to increase the policy uptake, use, and impact of genomic data (O3). It will promote the use of cutting-edge genomic tools in biodiversity assessment and monitoring, in support of European biodiversity policy frameworks (O3), connected to existing initiatives and infrastructures. It aims to advance the application of genomics, from barcodes to whole genomes, to address the European Union’s critical biodiversity objectives, including species and ecosystem assessments, as well as restoration efforts. Identifying and using high-impact application use cases, WP6 will contribute to establishing biodiversity genomics as a fundamental pillar for evidence-based decision-making across Europe. The activities of WP6 will be strategically integrated into the European landscape of biodiversity initiatives, stakeholders and policies, aligning goals, avoiding redundancy of actions and enhancing complementarity. To achieve this, WP6 activities will establish such a foundation through a comprehensive effort to identify, prioritise, and connect with key European biodiversity policies, directives, projects, initiatives, and stakeholders who can most benefit from genomic applications (T6.1), aligning with the EU Biodiversity Strategy for 2030 (European Commission 2020) and the Nature Restoration Regulation (European Commission 2025). This will result in a report on the strategic integration of genomic applications in biodiversity policies, programmes, and stakeholder networks (D6.1). WP6 will build two complementary roadmaps, based on use cases, that aim to detail the paths for the practical integration of genomic methodologies. The first roadmap (T6.2) focuses on the adoption of DNA barcoding and metabarcoding for widespread biodiversity monitoring, addressing major current gaps in coordinated organisational structures, harmonised workflows, and interoperable infrastructure required for coherent implementation across countries. It will benefit from key innovations developed in WP4 and WP5 to define essential components for cross-border application. Alignment with stakeholder needs will be achieved through consultation, utilising interviews and targeted workshops. Simultaneously, a second roadmap (T6.3) will be developed for the strategic application of whole-genome-based data, specifically addressing intra-species genetic diversity. It leverages gold-standard use cases with extensive genomic data across different taxonomic groups and will benefit from harmonised bioinformatics pipelines (implemented in WP5) to establish cost-efficient workflows for generating and analysing WGS data to derive meaningful Essential Biodiversity Variables (EBVs) (Pereira et al. 2013), providing clear guidelines for scientists, biodiversity managers, and policy makers from sampling to policy uptake. These roadmaps will integrate relevant results from cascade-funded projects (WP2) that expand the reach of use cases, and align with the strategic development of a pan-European system for biodiversity genomics (WP7). It will result in two complementary guidance documents, each one focused on a specific dimension of the genomic methods to be employed (D6.2 and D6.3). The conclusions of stakeholder mapping and the two complementary roadmaps will feed the final phase, which consolidates the strategic role of genomics by proposing a governance-oriented framework (T6.4). Through consultation with stakeholders, the task will refine implementation scenarios, resulting in a strategic synthesis report (D6.4) with actionable recommendations for institutional coordination and the sustained integration of genomic tools into European biodiversity monitoring and policy. Stakeholder consultations in T6.1 and roadmap development (T6.2, T6.3) deliberately bring together genomics researchers, taxonomists, environmental managers, and policy advisors. These consultations produce technical requirements that guide innovation priorities in WP4-5 and identify training needs for WP3, creating a bidirectional flow between data generation and application.

WP7 Towards a European distributed system for Biodiversity Genomics

WP7 will undertake options appraisals to drive decisions regarding the development and operation of a pan-European research infrastructure on biodiversity genomics. It addresses the current gap between research needs and the infrastructure services required to operate at scale, and directly addresses BGE+ Objective O4 to establish the foundations of a comprehensive biodiversity genomics system in Europe.

1. Users, needs, and current landscape (T7.1, T7.2). WP7 will define priority user groups (research, monitoring, and policy actors), map existing infrastructures and services, assess their maturity and accessibility, and identify gaps in relation to real-world use cases. Through this work, the WP will deliver a User Needs Assessment (D7.1) and a Service Scope & Gap Analysis (D7.2). Both reports will be used in the subsequent steps in the evaluation of the options for a future RI on biodiversity genomics.
2. Scientific and technical case (T7.3). Following the work on user needs, WP7 will develop a proposal on a suitable service portfolio - covering data generation and access, analytical tools, training, application support, and interoperability/policy requirements - through participatory workshops and interviews. As part of this work, the WP will deliver a Technical Service Portfolio (D7.3) report. The Report will help in understanding which of the existing RIs in the ESFRI landscape could potentially provide any of the services identified.
3. Following the mapping of infrastructure and users, WP7 will evaluate, through a series of thematic workshops (T7.4), the potential integration of the proposed biodiversity genomics service portfolio into one or more existing European RIs. Building on the mapping, WP7 will co-design solutions with existing RIs via thematic workshops, assess feasibility and upgrade routes (ESFRI-aligned), and deliver Actionable Recommendations for Integration (D7.4). BGE+ has already engaged with several RIs in the landscape to ensure willingness for engagement in the process, including DiSSCo, ELIXIR, and others (Arvanitidis et al. 2025). The approach of the WP includes a close collaboration with WP4 & WP5 (laboratory and bioinformatics developments) to ensure the service catalogue is grounded on current community practices; WP6 (policy roadmaps) so that proposed services meet regulatory and reporting needs; and WP2, WP8 and WP9 to align with cascade-funded activities and the iBOL-E and ERGA communities for broad, equitable uptake. By delivering a user-grounded service catalogue (D7.1–D7.2), a co-designed technical portfolio (D7.3), and integration recommendations (D7.4), WP7 provides the evidence base for decision making and will enable one or more ESFRI RIs to engage in delivering a distributed European biodiversity genomics system.

WP8 Network enlargement and support to iBOL-E

WP8 focuses on supporting, strengthening, and expanding the work of the DNA barcoding community in Europe via iBOL-E (Hollingsworth et al. 2026, Kaitetzidou et al. 2026), the European node of the International Barcode of Life (iBOL) (Ratnasingham and Hebert 2007). This work directly addresses O4, working to establish the foundations of a comprehensive biodiversity genomics system in Europe. WP8 will provide the secretariat support for iBOL-E, and coordinate and manage the activities of the network (T8.1). Through supporting, developing and/or establishing national or regional DNA Barcoding Nodes of iBOL (T8.2), WP8 will also develop model approaches for the set-up and roll-out of distributed low/medium throughput sequencing laboratories in Europe, to democratise access to data generation, and capitalise on the availability of low-cost portable DNA sequencing machines (T8.3). WP8 also serves to connect the DNA barcoding community to taxonomic experts linking sequence data and morphology, to enhance the quality of DNA barcode reference libraries as a resource for species identification, species discovery, and biomonitoring (T8.4). Collectively, these activities all contribute to the development of the European biodiversity genomics landscape (Kaitetzidou et al. 2026). WP8 has synergies across the BGE+ project, acting as the nexus between the consortium and the wider DNA barcoding community. The continually updated understanding and in-depth knowledge of the DNA barcoding landscape in Europe, as provided by WP8, will inform the appraisal of biodiversity genomics infrastructure options in WP7, further supporting the delivery of O4. Likewise, WP8 has been designed to closely align in structure and intent with WP9 (Network enlargement and support to ERGA), promoting synergies through joint efforts that support the delivery of a pan-European biodiversity genomics system. Beyond O4, WP8 supports O1, O2, and O3 by connecting iBOL-E community support to cascade-funded projects (WP2). Likewise, identified community needs will be fed through to WP3 (training), WP4 (laboratory protocols), and WP5 (data and informatics). In turn, the outputs of these other WPs will be made available to the iBOL community, creating a positive feedback loop.

WP9 Network enlargement and support to ERGA

WP9 is dedicated to consolidating and extending the ERGA network (Mazzoni et al. 2023) driving the production and exploitation of reference genomes for eukaryotic biodiversity, representing the European bioregion’s participation in global efforts of the Earth BioGenome Project (EBP) (Lewin et al. 2018, Blaxter et al. 2025). Thus, WP9 (genomes), is designed to be complementary to WP8 (barcodes), to support delivery of objective O4: establish the foundations of a comprehensive biodiversity genomics system in Europe. WP9 goals are centred on a community support framework that: Widens participation and increases the accessibility and use of genomics data for biodiversity management through scientific direction and support for the ERGA community to scale distributed production (T9.1 & T9.2); Empowers researchers to generate high-quality reference genome resources efficiently through community-based support systems with an open forum to build methods consensus, share expertise, and implement genomics-based biodiversity assessments (T9.2 & T9.3); Grows and aligns the network of genome production hubs and application/use actions through coordination efforts to cultivate synergies and harmonise translational actions supporting country and researcher needs with respect to biodiversity monitoring and reporting (T9.3 & T9.4); Strengthens taxonomic expertise in applying genomics technologies for biodiversity identification and monitoring, including genetic diversity within and between populations (T9.4). WP9 thus consolidates the coordination role of ERGA as the European node of the EBP, as well as contributing to broadening the impact of BGE+ objectives O1, O2, and O3. This community support framework also forms a bridge between the tasks and activities of BGE+ and the ERGA network. This involves guiding members in designing projects that leverage expertise to secure financial support for increased biogenome production and exploitation, as well as providing and directing technical support services to cascade-funded projects (WP2) through Community and BGE+ resources. Monitoring training and capacity building needs will inform the work of WP3, and relevant outputs of WP3 will be disseminated by WP9. Similarly, WP9 will disseminate the outputs from WP4 supporting field and laboratory work, and from WP5 providing data and informatics solutions, as well as feeding back needs to WP4 and WP5. For WP6, leveraging community expertise and experiences will inform stakeholder engagement tasks, particularly in relation to policy and decision-making, as well as the harmonisation and standardisation of whole-genome data and analyses to support biodiversity assessments, especially for intra-species diversity. WP9’s support of the forum and network of expertise for reference genomes provides the means for identifying existing biodiversity genomics services and understanding user needs to support the work of WP7. Finally, as part of the mission to build and maintain a strategic partnership with iBOL-E, joint actions with WP8 will promote synergies and alignments of efforts, as well as support a unified approach to delivering a distributed system for biodiversity genomics in Europe.

1.2.3 Financial Support to Third Parties (Cascade Grants) - Enlarging and consolidating the biodiversity genomics community

Scope

Financial Support to Third Parties - FSTP (cascade grants) is a core BGE+ instrument for connecting currently dispersed efforts in biodiversity genomics and piloting the operating model of a distributed, pan-European knowledge-production system. A multitude of teams across Europe already generate Barcode and WGS data. When aligned on common methods, standards, and data services, these efforts can deliver cumulative impact, address priority knowledge gaps, and create economies of scale. BGE+ will also strengthen capacity in genomic taxonomy in data-limited areas, such as Central and Eastern Europe, the Mediterranean, and outermost regions, linking genomic evidence production to species discovery, local conservation, and biodiversity management needs. Cascade-funded projects are to specifically support the following areas:

Addressing gaps in biological knowledge

• Filling priority gaps in reference libraries (barcodes and genomes) across taxa, biogeographic regions and ecosystems, explicitly targeting so far under-represented regions and groups. Groups, such as alien or endangered species and species of economic importance, including pollinators, will be specifically targeted, as well as species groups of policy relevance for biomonitoring. Additionally, taxonomic groups underrepresented in current national or international barcode and genome reference databases will be prioritised. The results will contribute to filling specific regional and national biological knowledge gaps.
• Translating data to policy-ready baselines that can be directly mobilised into monitoring and management roadmaps. Projects could also contribute to the development of regional or national baselines, providing the required background knowledge for future monitoring of shifts in population sizes and richness.

Addressing gaps in innovation and best practices - additionally to the reference libraries production efforts, cascade-funded projects may also:

• Contribute to improving the public offering of tools and resources at the national or European level.
• Contribute to the development of best practices and Standard Operating Procedures, as well as the dissemination of such products through iBOL-E, ERGA, and CETAF networks.
• Improve metadata quality and taxonomic efforts (provenance, sampling, vouchers, legal compliance), which increases reuse and reliability for downstream analyses.

For cascade-funded projects managing samples and data in a transnational manner a pre-award ABS/DSI compliance requirement will be included in the proposal templates. As an underlying premise, BGE+ will ensure, through a list of criteria for awarding and evaluating the cascade grants, that each project will:

• Make use of standard, shared services and tools that ensure the comparability of knowledge outputs and interoperability of all produced data;
• Curate, annotate, and deposit all data produced to agreed-upon open public data repositories (e.g. ENA, BOLD, GBIF, DiSSCo, etc.);
• Receive practical support for training personnel and onboarding them to the European communities of iBOL-E, ERGA, and CETAF;
• Connect their work and results to BGE+ work programme;
• Use citizen science activities for co-creation efforts, engaging local communities when possible and applicable.

Cascade-funded projects connected to the rest of the BGE+ work programme

BGE+ connects the cascade-funded projects to the objectives of the project by design (Fig. 2). Facilitated by the work in WP2, WP3 to WP9 are consulted in the process of the definition of the requirements, expected outcomes and conditions for the Topics to be funded under the FSTP scheme (T2.1). Furthermore, the participants in these WPs also provide support and guidance as needed to the grant recipients (T2.2). Finally, the outputs of the cascade-funded projects are connected to the WPs (T2.3) while simultaneously being integrated into the ERGA, iBOL-E, and CETAF networks, as well as the distributed infrastructure and policy applications. This framework ensures that the FSTP scheme is used not only to widen and consolidate participation but also to provide distributed capacity in the innovation and exploitation agenda of BGE+.

Figure 2.  

Role of the Financial Support to Third Parties (cascade-funded projects) scheme in BGE+. The diagram is showing inputs for the definition of the cascade grant calls, the support provided during implementation, and the connection of the outputs to BGE+ WPs. WP2 Tasks provide brokerage, facilitation, administration, and monitoring functions in the process.

Building on BGE1 and network experience

In BGE1, subcontracting was used to engage external teams. These teams took on parts of the BGE1 content-delivery pipeline - field sampling, taxonomic identification, sample processing, and sequencing. In BGE+, as we scale out the content delivery, this previous experience will be used to set clear requirements, deliverables, and performance standards for the cascade-funded projects.

1.2.4 Connecting BGE+ to relevant initiatives and projects

Aligning efforts to increase taxonomic capacity (Connecting to the project in area A of the Topic)

In addition to BGE+ serving as the primary carrier for the advancement and development of iBOL-E and ERGA, it aims to contribute directly to CETAF’s taxonomy agenda. As such, BGE+ will work closely with the project selected for funding in Area A of the same Topic (HORIZON-CL6-2025-01-BIODIV-03). Specifically, together with the selected project, BGE+ will form a Synergy Alignment Committee. The role of this committee will be to work towards the harmonisation of morphological and genomic data streams, strengthening interoperability and adoption of genomics-informed approaches in taxonomic work. Forming and operating the committee will be under shared responsibility between BGE+ and the project selected in Area A. Preliminary agreements are already in place regarding this approach with consortia addressing Area A of the Topic. Alignment activities have already started between the projects BGE1 and TETTRiS and shall continue as the projects mature. CETAF (leading partner in TETTRiS) is also a core partner in BGE1 and BGE+, which streamlines communication and allows for planning of joint activities.

Biodiversity Meets Data (BMD) Project (HORIZON-CL6-2024-BIODIV-01: Digital for Nature)

The BMD project Link: https://www.bmd-project.eu/ represents a significant investment in consolidating and organising available biodiversity data at a level of granularity that would enable detailed spatio-temporal biodiversity analyses. BMD will “create a centralised digital platform, referred to as a Single Access Point (SAP), for managers of natural resources and policymakers to support biodiversity conservation across Europe”. BGE+ and BMD will work together in a) using the BMD SAP for developing and offering analytical pipelines, where those rely on the availability and combination of spatio-temporal biodiversity data, and b) curate and serve all produced data from BGE+ to the BMD data infrastructure (directly or through mediating aggregators, such as GBIF or BOLD). Furthermore, BGE+ and BMD will work together to identify additional services and resources that could rely on the BMD infrastructure to serve the genomics community. BGE+ and BMD share a significant number of partners (including the coordinator - Naturalis), ensuring that such efforts will be prioritised from both projects.

Connecting to ESFRI Research Infrastructures

BGE+ is looking into a sustainable long-term future of service provision through the lens of our European Research Infrastructures. During BGE1, the community clearly supported this vision. As the first step, the community surveyed the landscape of RIs, their position, and the possibility of them offering added-value services that address the needs of biodiversity genomics for taxonomy and conservation purposes. In this context, RIs that have been previously identified as candidates for taking on the biodiversity genomics user needs are now direct partners in BGE+, including DiSSCo and ELIXIR. A dedicated WP (7) is tasked with assessing the technical, financial, and organisational feasibility of a major upgrade of one or more of those RIs so that they will be able to develop the necessary (to be defined also during the project) services and offer them as part of the portfolio to the European community of biodiversity scientists. In addition to DiSSCo and ELIXIR, WP7 will consider service portfolios of other Environmental RIs, including LifeWatch and eLTER (Arvanitidis et al. 2025).

Collaboration with other Projects under other relevant Topics

The BGE+ consortium is especially interested in connecting with the projects selected for funding under the Topics (i) HORIZON-CL6-2025-01-BIODIV-02: Strengthening the capacity of citizen science in biodiversity observation and (ii) HORIZON-CL6-2025-01-BIODIV-04 on large-scale biodiversity observations. Specifically, for (i) significant investments in engaging local communities in biodiversity genomic surveys have been made in the BGE1 project. BGE+ is committed to continuing to engage these local communities, as co-creation efforts are necessary for acceleration and impact delivery. As it is now expected that a dedicated project on citizen science will be funded, BGE+ is exploring the potential to leverage its previous investments (BGE1) through collaboration with the new project under 01-BIODIV-02. Regarding (ii), BGE+ expects that projects selected for funding in this Topic will propose the integration of (meta)barcoding methods for delivering high-throughput local biodiversity observation solutions. As such, it is expected that the need for engaging with local actors and supporting them in sample collection, management and processing, as well as lowering barriers to high-throughput sequencing or low-cost sequencing methods, would be a prerequisite to scaling up any future continental-scale in situ observation systems. In this context, BGE+ will connect with the projects under this Topic and establish a dialogue to understand the needs for capacity and access to resources and tools. These needs will be taken into account in establishing the requirements and designing the future European system (research infrastructure) for biodiversity genomics, as planned in BGE+.

1.2.5 Integrating efforts: Connecting the taxonomic, barcoding, and reference genome communities

As the European nodes of the iBOL and EBP global initiatives advancing the comprehensive application of genomic science to biodiversity research, iBOL-E and ERGA represent the two communities of practice operating in the European bioregion. As Europe’s network of biological and geological collections, CETAF brings together natural history museums, botanical gardens, and biodiversity research centres holding a wealth of biological collections, including animals, plants, fungi, and genetic resources. Aligning efforts through leadership and participation of these communities in the BGE1 Project has laid the foundation for closer collaborations through integrative taxonomy approaches and the development of a joint vision to transform how Europe organises, coordinates, and delivers genomics data for biodiversity research, monitoring, and policy applications. The commitment to work towards common goals, leveraging genomic science, was formalised in 2024 with the signing of the Memorandum of Understanding between iBOL-E and ERGA, establishing the basis for the development of a shared scientific and societal mission. The communities recognise the importance of facilitating the completion of reliable barcode and genome reference libraries for European taxa, which form the foundation upon which genomics-enabled biodiversity science and impact are delivered. Their complementarity forms a natural partnership contributing to breadth - broad-scale biodiversity assessments using DNA barcoding and metabarcoding for species discovery, monitoring, and ecosystem diagnostics - and depth - whole genome data supporting evolutionary research, conservation, and precision genetic composition monitoring - across a variety of applications. Building on the experience and achievements to date, BGE+ serves to advance the work of the communities towards the long-term goals of establishing an integrated European biodiversity genomics landscape. The identification of shared challenges and opportunities present clear areas of convergence: they require well-curated, legally compliant, and taxonomically verified samples; harmonised standards for field metadata, laboratory protocols, informatics workflows, and data deposition; they depend on skilled researchers across taxonomy, genomics, bioinformatics, and data science; demonstrating the utility and importance of integrating genomics and taxonomy into biodiversity monitoring and assessments is also a common goal. By delivering best practices in genomics BGE+ will equally serve to the overarching goal of building a robust integrative taxonomic system, aligning efforts and ensuring cross-fertilisation among ERGA, iBOL-E, and CETAF networks. A core feature of BGE+ is the co-development of standardised, interoperable components that promote reusability, consistency, and integration across the biodiversity genomics value chain: from Standard Operating Procedures (SOPs) for sample collection and data generation steps to shared metadata frameworks compliant with international standards, as well as from common best practices and technical implementations for data processing, submission, and analysis to centralised knowledge hubs, documentation platforms, and training materials to serve the communities and foster widespread adoption. By aligning distributed efforts under a common framework, BGE+ ensures that local activities contribute to regional and global goals, while respecting national priorities and expertise, creating a federated yet coordinated system that captures the strength of distributed European biodiversity genomics infrastructures.

1.2.6 Gender dimension

The Project Consortium commits to promoting gender equality in research and innovation throughout all phases of the Project’s implementation in alignment with Horizon Europe’s inclusivity objectives. With the support of the Advisory Board and T1.4 Ethics, we will oversee our performance and strategy for addressing gender and wider inclusivity and diversity. In training, communication, and community and stakeholder engagement activities, we will emphasise our aim to reach underrepresented groups, including women, local communities, and early-career researchers. Through this approach, we strive to improve gender representation and equity across European research with a focus on the biodiversity genomics and taxonomy communities. In scientific content, the only meaningful gender dimension of biodiversity genomics data is that we will seek to sample the heterogametic sex for reference data generation, containing both sex chromosomes where they exist and are relevant.

1.2.7 Open Science Practices

BGE+ is committed to implementing open science practices that align with Horizon Europe requirements and community best practices in biodiversity genomics. Our approach follows the principle of “open science, open data, open source” while acknowledging necessary provisions for quality assurance and publication processes. The project will deliver a Data Management Plan (DMP) that will refine the specific practices within the project. Still, the points of departure for data, metadata, source code and other computational deliverables, and provenance records are outlined below. All sequencing data generated will be deposited in established FAIR data repositories according to data type specifications. Genomic data and raw sequencing reads will be submitted to the European Nucleotide Archive (ENA) (O’Cathail et al. 2024), while DNA barcoding sequences will be deposited in the Barcode Of Life Data Systems (BOLD) (Ratnasingham and Hebert 2007). Occurrence records derived from metabarcoding analyses will be made available through the Global Biodiversity Information Facility (GBIF), ensuring broad accessibility for the research community. Additional project data, including analytical outputs and processed datasets, will be deposited in generic FAIR repositories such as Zenodo, preferably using the Creative Commons Public Domain (CC0) or Attribution (CC-BY) open licences. Data and metadata will conform to established community standards, including FASTA format for barcode and genome sequences, FASTQ for raw reads, GFF3 (Generic Feature Format Version 3) for genome annotations, BCDM (Barcode Core Data Model) for enriched barcode datasets, and DarwinCore for metabarcoding occurrences. Tabular data generated within the project (e.g. various types of analytics during data processing or downstream statistical analysis) will be packaged as FAIR digital objects using RO-Crate (Soiland-Reyes et al. 2022) with applicable data profiles and frictionless data standards to ensure interoperability. All computational deliverables will be developed as open source software using OSI-compliant (Open Source Initiative) licences, meeting Horizon Europe requirements for software accessibility. Source code will be made available through appropriate repositories based on the deliverable type. For example, Python packages will be published via PyPI, executable tools and wrappers through BioConda, workflow implementations via WorkFlowHub (Gustafsson et al. 2025) for Snakemake pipelines, and Galaxy-deployed tools through the Galaxy ToolShed (The Galaxy Community et al. 2026). Physical protocols for laboratory and field procedures will be documented and deposited in suitable repositories such as WorkFlowHub, ensuring methodological transparency and reproducibility across the research community. The project will maintain provenance records for computational analyses using standards-compliant formats, for instance, RO-Crates with workflow run profiles. These records will be deposited and linked to associated data in FAIR repositories, enabling reproducibility of research outputs. This approach ensures that analytical processes can be independently understood, verified, and built upon by other researchers. While maintaining our commitment to open science principles, the project acknowledges the need for short-term embargoes in specific circumstances. These may be applied to ensure data quality validation or to accommodate publication timelines for research outputs currently under review. Such embargoes will be minimal in duration and clearly justified, with all data ultimately made publicly available in accordance with FAIR principles. In cases where the datasets cannot be publicly shared, the reasons will be mentioned in their metadata description (e.g., ethical rules of personal data, intellectual property, commercial, privacy-related, security-related).

BGE+ advances the mission and methodology of BGE1 towards our ultimate goal of establishing a distributed European system for biodiversity genomics. As such, BGE+ builds on the experience and developments of BGE1 also in Dissemination, Exploitation, and Communication (DEC). BGE+ will refine, update, and expand the mechanisms put in place by BGE1 while adding new tools designed to serve the new endeavour.

The Project dissemination, exploitation, and communication measures associated with the expected results and aligned with the specific needs are summarised in Table 9, expected impacts from Project outcomes are summarised in Table 10.

BGE+ brings together Europe’s two principal biodiversity genomics communities - iBOL-E for DNA barcoding and ERGA for reference genomes - complemented by CETAF to anchor taxonomy and policy engagement. iBOL-E is represented by its coordination group (RBGE, Sanger, Naturalis) and the secretariat hosted by Naturalis; ERGA by members of its Executive Board (UU, UP, IZW) and the secretariat at SIB. CETAF is represented through its secretariat team. These networks connect BGE+ to >250 European institutions and to the global nodes (iBOL via UGuelph, EBP via ASU). The consortium comprises 22 partners across 17 countries, spanning biodiversity science, genomics, informatics, research infrastructures and policy application, and is committed to open and equitable science.

Naturalis — Experience/expertise: Coordination of large interdisciplinary EU and national programmes; RI development (DiSSCo); national-scale monitoring and digital infrastructure (ARISE, eDentity); host of European BOLD; strong stakeholder brokerage and data-interoperability practice. BGE+ contributions: Lead WP1 (management, DEC, ethics); support WP2 cascade framework; contribute to WP3 capacity building; WP4&5 innovation delivery; WP7 RI planning and WP8 community engagement.

LIB — Experience/expertise: Managing competitive funding schemes; metabarcoding wet/dry-lab capability; long experience with taxonomic data infrastructures and metadata; interoperability solutions for sequence repositories and infrastructure. BGE+ contributions: Lead WP2 (cascade grants); contribute to WP4–WP5 technical pipelines; channel user requirements to WP7; support ERGA applications in WP9.

CETAF — Experience/expertise: European network of natural science collections; ABS/Nagoya and ethics guidance; routes to national authorities; community standards and policy interfaces; TETTRIs project lead - taxonomy innovation, cascade grants scheme. BGE+ contributions: Lead ethics monitoring (WP1); support WP2–WP3; co-lead stakeholder engagement and policy translation in WP6.

NTNU — Experience/expertise: Long-running training programmes (ForBio); advisory role to national nature management; proven hands-on curricula translating methods to routine practice; NorBOL coordinator. BGE+ contributions: Lead WP3 (training); co-lead open barcoding framework in WP4; contribute to WP6–WP8.

UNIFI — Experience/expertise: Scaling genome/barcode production in small–medium labs (BGE1); WGS metrics; active in ERGA/iBOL-E; experience with TETTRIs/DiSSCo alignment to RI practices. BGE+ contributions: WP3 capacity building; WP4 optimisation of metabarcoding/genome pipelines; WP5 metrics harmonisation; WP7 RI integration; WP9 network engagement.

NHMUK — Experience/expertise: Museomics; multi-national programmes lead (DiSSCo-UK, UKBOL); high-throughput digitisation; strengths in taxonomy and HMW DNA extraction. BGE+ contributions: Lead WP4 (wet-lab innovation); deliver WP3 training; develop user-centred tools in WP5; support iBOL-E practice adoption.

Sanger — Experience/expertise: Large-scale genome production (DToL, BIOSCAN UK; >3,000 assemblies); robust QC and assembly validation. BGE+ contributions: Innovate sampling to eliminate cold-chain needs (WP4); contribute to WP3 training; benchmark genome/annotation workflows in WP5; community engagement WP9.

EMBL-EBI/ELIXIR — Experience/expertise: Operation of ENA/Ensembl; data standards and long-term archiving; ELIXIR Platforms/Communities; policy engagement and equitable access. BGE+ contributions: Lead WP5 (informatics innovation); WP3 training; lead service-portfolio planning in WP7; sustain BGE+ data flows.

IZW — Experience/expertise: Wildlife conservation genomics; BeGenDiv; field-to-lab workflows; delivery in low-infrastructure contexts; Europe–Latin America links. BGE+ contributions: Grow communities (WP3, WP9); advance genomes/analytics (WP4–WP5); contribute to policy pilots (WP6) and RI design (WP7).

CIBIO — Experience/expertise: Evidence-to-policy translation; DNA-based monitoring; ancient DNA and HPC; track record in Teaming, EuropaBON and agency partnerships. BGE+ contributions: Lead WP6 (policy-relevant applications); lead metabarcoding intercalibration (WP4); lead ERGA applications network (WP9); contribute to WP3 training and WP5 informatics.

UP — Experience/expertise: EOSC/EEA/EUA policy work; international genomics projects; governance schemes; practitioner and citizen-science engagement. BGE+ contributions: Lead WP7 (towards a sustainable distributed system); support WP2 cascade grants design and WP6 operationalisation in policy context.

RBGE — Experience/expertise: Plant/lichen barcoding; HMW DNA extraction at scale; IUCN groups; national strategies and reporting. BGE+ contributions: Lead WP8 (iBOL-E enlargement/support); deliver WP3 training; contribute WP4 lab skills, WP6 translation and WP7 RI strategy.

SIB — Experience/expertise: Bioinformatics for life sciences; ERGA secretariat; online knowledge hubs; population-genomics data publishing. BGE+ contributions: Lead WP9 (ERGA enlargement/support); operate WP3 hubs/registration systems; co-manage WP2 cases; align WP5 innovations with ERGA; support WP6–WP7.

UGuelph — Experience/expertise: iBOL global secretariat and BOLD; >15M curated specimens; high-throughput barcoding; global capacity building. BGE+ contributions: Support WP3–WP4 training and protocol adoption; advance BOLD alignment with ABS; strengthen iBOL-E via WP8.

ASU/EBP — Experience/expertise: EBP secretariat coordinating ~60 projects; cross-project standards and ethics frameworks; global governance. BGE+ contributions: Strengthen alignment with global genomics through WP9; share best practices and governance models.

UU — Experience/expertise: SciLifeLab host; state-of-the-art genomics, bioinformatics services and training; robust data management; broad user support. BGE+ contributions: Deliver WP3 training; contribute to WP4–WP5 innovation; support WP7 RI options and WP9 network development.

CNAG — Experience/expertise: Large-scale long-read WGS; accredited short-read sequencing (ISO 17025) with ISO 9001/27001; LIMS and secure data stewardship. BGE+ contributions: Genome protocols and pipelines development (WP4–WP5); support WP3 training and WP7 services and resources assessment.

PENSOFT — Experience/expertise: Open-access publishing; informatics platforms; communications for >30 EU projects; data-paper workflows; BgBOL co-founder, wet-lab expertise. BGE+ contributions: Map training needs (T3.1); streamline FAIR access (T5.5); support knowledge exploitation (WP6); iBOL-E communications (WP8).

AU — Experience/expertise: End-to-end genomics hub; TurkBOL founder; extensive WHO/FAO/iBOL/COST/ERC workshops; reproducible pipelines; national/international project delivery. BGE+ contributions: Lead cost-effective reference-genome enablement (T4.4); contribute WP3–WP4 training/democratisation; build networks via WP8–WP9.

UNIMAN — Experience/expertise: RO-Crate; FAIR provenance; workflow packaging across HPC/cloud; community training. BGE+ contributions: WP5 workflow/provenance solutions; WP3–WP4 training, knowledge sharing and innovation; strengthen interoperability and open access practices.

UniLodz — Experience/expertise: (Meta)barcoding, integrative taxonomy and biomonitoring; PoLBOL coordination; citizen-science mobilisation. BGE+ contributions: Advance barcoding democratisation and national capacity (WP3, WP8); contribute to WP4 wet-lab innovation and WP6 biomonitoring applications.

AUTh — Experience/expertise: Bioinformatics, GAP analysis and large-scale sampling; GrBOL leadership; stakeholder engagement. BGE+ contributions: Build capacity (WP3, WP8); deliver innovation and application in both barcodes and genomes (WP4, WP6); support WP7 RI establishment.