Heir to the Biodiversity Genomics Europe project, the new Biodiversity Genomics Europe Plus (BGE+) will harness the power of genomic science and DNA-based reference resources to transform how biodiversity is monitored, protected, and sustainably used across Europe. Building on advances in genomics and the success of previous European collaborations, BGE+ aims to strengthen taxonomic research, improve understanding of species and genetic diversity, and, more importantly, lay the foundations for a long-term European biodiversity genomics system.

DNA technologies and genomic science now offer a step-change in how nature can be managed, conserved and utilized. The ability to use DNA to measure and monitor diversity at the species and genetic levels opens up a multitude of applications for which reference libraries of DNA barcodes and genomes are crucial. BGE’s policy brief makes the case for sustained investment and support for building reference libraries of European biodiversity, and offers a long term vision for the future.

BGE+, heir to BGE, has been selected for funding. This amazing news means that our consortium will have support for its long-term objective of a European research infrastructure for biodiversity genomics.  

BGE: proof of concept

If there is one thing BGE has demonstrated, it is that coordinated, transnational efforts can overcome logistical, technical, and policy challenges and create operational pipelines for sampling, sequencing, data management, and application across Europe. In fact, by piloting joint initiatives and sharing expertise and investments, BGE has indeed built a model for scaling genomic knowledge production. Now, the question remains: scale up how? Where should we go from here?

Well, the answer to those questions has been kind of in the air in recent times, mostly expressed like this: “we need to create an integrated and sustainable European biodiversity genomics ecosystem to allow the research community to deliver scientific, policy, and potentially political impact.”

But it was during our recent policy roundtable Biodiversity Innovation: Enabling technology for Nature and Green Growth (Brussels Oct. 25) that Costas Kadis, European Commissioner for Fisheries and Oceans, uttered the words we all in BGE were waiting for: there is a need for a biodiversity genomics infrastructure in Europe.

BGE’s Biodiversity Innovation: Enabling technology for Nature and Green Growth roundtable (October 2025)

BGE+: focus on infrastructure

Biodiversity Genomics Europe plus (BGE+) aims to take us there. The new project will muster pan-European collaboration to scale up the production and uptake of genomic evidence for taxonomy, monitoring and policy. It will widen participation, standardise methods, and prepare a distributed European system for biodiversity genomics.

BGE+ has four objectives:

(1) broaden participation and capacity across Europe;

(2) make distributed genomic data production interoperable and FAIR by design;

(3) translate evidence into practice through co-designed use-case roadmaps; and

(4) define the service portfolio and assess financial and technical feasibility for a future European research infrastructure in biodiversity genomics.

The consortium unites iBOL Europe (DNA barcoding), ERGA (reference genomes) and CETAF (taxonomic research and natural history collections) to align end-to-end workflows from field sampling to application.

Laboratory work at Naturalis Biodiversity Center (The Netherlands)

A project with opportunities or all

Through targeted cascade grants (Financial Support to Third Parties) and hands-on training, BGE+ will enlarge community capacity while converging on shared protocols and standard practices, improving data interoperability and consolidating community efforts. Building on previous work, BGE+ will carry forward the communities’ long-term vision: turning fragmented efforts into a coherent, scalable system that delivers reliable genomic evidence for taxonomy and policy.

The final act of the BG Connects event, last October, convened a group of key policymakers, researchers, and civil society actors to explore how biodiversity genomics can support Europe’s response to biodiversity loss, drive innovation and contribute to the goals of the EU Biodiversity Strategy 2030 and the European Green Deal. The roundtable, titled “Biodiversity innovation: Enabling technology for nature and green growth”, counted on the presence of Costas Kadis, European Commissioner for Fisheries and Oceans.

At the core of the EU’s Biodiversity Strategy for 2030, and a pillar of the European Green Deal, nature conservation and green growth require innovative, cost-effective and scalable solutions. However, Europe still struggles to turn fragmented and complex biodiversity-related data into actionable insight and sustainable solutions.

Costas Kadis, who gave the introductory remarks, highlighted the need for a biodiversity genomics infrastructure in Europe. The idea, very much in line with BGE’s vision, and discussed during the symposium that preceded the experts’ roundtable, resonated throughout the conversation. Participants agreed on the need to explore mechanisms for a pan-European integrated approach to service delivery for biodiversity genomics. There was also ample consensus on the need to further break down data silos across Europe in favor of a larger knowledge pool, operating in sync.

Science Business, collaborator of BGE in organising the roundtable, has just released a detailed report with the main conclusions from the meeting. You can access it by clicking on the button below.

There are complex “upstream” challenges involved in generating high-quality reference genomes, essential for modern biodiversity research. Drawing on the practical experiences of the European Reference Genome Atlas (ERGA) community, a new BGE publication, “From Permits to Samples: Addressing Key Challenges for High-Quality Reference Genome Generation in Europe” highlights that, while sequencing technologies have advanced, the logistical steps leading up to sequencing remain a significant bottleneck. The paper aims to provide a comprehensive guide for researchers around a number of areas, covering the critical workflow from navigating legal permits to the physical handling of samples, ensuring that biodiversity genomics initiatives can scale effectively across regions and taxa.

Following a “workflow-based” order, the article focuses first in the intricate landscape of ethics and permits, particularly within the European context. Next, the interest shifts to the physical collection of samples and the rigorous planning that is needed to ensure the viability of the material for sequencing and the prevention of DNA/RNA degradation.

Other areas of interest in the paper include the challenges involved in the extraction of nucleic acids -e.g. where standard commercial kits may fail-, the value of biobanks and natural history collections as sources of genomic material, and the need for close collaboration between field biologists, taxonomists, legal experts, and bioinformaticians. 

This paper was published by Molecular Ecology Resources.

About the ‘ERGA iBOL Europe Connections’ series

The European Reference Genome Atlas (ERGA) and the European node of the International Barcode of Life (iBOL Europe), two international communities of scientists brought together under the Biodiversity Genomics Europe Project, are joining forces for “Connections,” a series of blog posts that explore the fascinating world of Biodiversity Genomics and the intersection of their communities. 

Blog 8 – Bioinformatics: reassembling the book of life

In our previous posts, we compared DNA to a book: barcodes help us identify which book we are holding, while reference genomes enable us to read every page. But here is the twist: by the time DNA leaves the wet lab, the book is broken as if we have run the pages through a “paper–shredder”. DNA extraction, library preparation, and DNA sequencing all turn the long DNA sequence into millions of pieces (Check the Connections blog #3 for an overview of these different steps of the genomic workflow). Bioinformatics is the art of turning that pile of shreds back into something we can read, search, and compare. It is the art that turns barcodes and reference genomes into usable knowledge.

Image 1: Informatics and advanced computing are necessary to analyse the huge amount of data generated for genomic research.

Bioinformatics is the product of molecular biology meeting computing. Bioinformatics facilitated the development of the first sequence alignments and substitution matrices, dynamic programming, the creation of searchable databases, and the first “find-it-fast” tools that supercharged homology searches. As sequencing scaled, assembly algorithms emerged, followed by hybrid approaches for long-read platforms. Alongside the algorithms came various file formats (FASTA/FASTQ/BAM/CRAM/GFF/GTF), workflow engines, and the hard-won lesson that reproducibility matters more than quick fixes.

For barcoding, the task is targeted: extract a standard marker (or “abstract”), check its quality, align it against a trusted database, and report the most accurate match with confidence. Think of well-indexed catalogues and fast look-ups, ideal for monitoring and quick assessments. For reference genomes, the task is editorial. Correct sequencing errors, assemble the million pieces into chromosomes, phase haplotypes, polish with multiple evidence tracks (long reads, linked reads, Hi-C, RNA-seq), and annotate genes and repeats.

That finished “book” enables population genomics, local adaptation, and conservation genomics studies.

Figure 2: Examples of some common bioinformatics tasks when working with genomic data from across the tree of life. Bioinformatics is the art that turns raw data into knowledge with useful applications for biodiversity.

Modern analyses involve dozens of steps, quality checks, trimming, deduplication, mapping, variant calling, assembly, scaffolding, annotation, all wrapped in containers and workflows to make sure a colleague can re-run them on Tuesday and get an answer on the same day. Good metadata is the structure that holds all the pages: sample, permit, locality, preservation, instrument, kit, and version numbers (Check this episode of the Genomic Connections Podcast to learn more about the importance of metadata). Without that structure, even the finest assembly becomes a vague curiosity.

A few field notes from the trenches

Everyone has a story of a 2 a.m. run that failed because a file was called final_FINAL_reallyFinal.fastq.gz. We have all been rescued by checksums, saved by containerised toolchains, and learned never to delete intermediate files before the multi-QC report is green. We name scripts after pets, we comment our code (eventually), and we celebrate the day a 500 GB BAM shrinks elegantly into a reproducible VCF.

Why does this matter to BGE? For iBOL Europe, robust bioinformatics means clean barcode libraries, sound assignments, and credible trend analyses. For ERGA, it means reference genomes that stand up to re-analysis and can power subsequent population, functional, and comparative genomics, the applications stakeholders care about (from conservation planning to bioeconomy uses).

Bioinformatics is not an afterthought: it is a research field itself! It is the bridge from sequencer output to decisions. Treat pipelines as publishable methods, treat metadata as data, and treat your future self as a collaborator who deserves clarity. In the next post, we will demonstrate how these computational foundations are applied in practical settings, including monitoring, policy, and management, without losing sight of the overall context (or the pages).