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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. In this blog post, we discuss some commonalities between the genomic approaches followed by our two communities: DNA barcoding and reference genome sequencing. In our first post, we explored the importance of biodiversity genomics. In the second post, we met iBOL Europe and ERGA, the two communities that power the Biodiversity Genomics Europe project ( BGE ) by studying biodiversity using different but complementary genomic techniques. Today, we will look at how these two communities perform many similar steps to achieve their goals. This includes collecting biological samples, analyzing genomic data, and applying their findings to support biodiversity conservation initiatives. Field Sampling: Both iBOL Europe and ERGA start with the first step of collecting material in the field. For iBOL Europe, this involves obtaining tissue samples from both museums and the field, where environmental DNA (eDNA) samples from soil and water are also gathered in addition to flying insects from tools like Malaise traps. Alternatively, ERGA typically obtains tissue samples (for example, leaf cuttings, biopsies, or whole organisms) that require immediate freezing, often in liquid nitrogen, to keep the biological material as intact as possible. This extra layer of care ensures the highest-quality DNA available for in-depth genomic analyses. From the top of the Alps (left) to the lowlands of the Biebrza Marshes (right), finding samples for barcoding and  DNA sequencing often feels like an adventure. However, field sampling must always be carried out with an extra layer of care to ensure that specimens are stored in the most appropriate ways to optimise the time and costs associated with field sampling. This is exemplified by the small tank filled with liquid nitrogen shown on the left-hand figure, which is used to transport and preserve the precious samples down the mountain. Photos by Brad Carlson and Szczepan Skibicki. Sample Processing:  Once in the lab, both communities make use of molecular techniques to extract DNA. However, while barcoding involves DNA extractions from both individual specimens and bulk or environmental samples (that contain multiple organisms), reference genome sequencing is solely focussed on high quality DNA extractions from individual specimens. DNA from individual specimens.   Sequencing: After DNA extraction, both initiatives use next-generation sequencing platforms to decode the genetic material. iBOL Europe often relies on targeted DNA sequencing approaches, but also uses short-read ‘skimming’ for museum specimens, to generate DNA barcodes from environmental samples and reference samples. Meanwhile, ERGA leverages several different types of short-read and long-read data to assemble chromosome-level reference genomes that capture complex genomic regions more effectively. Sequencing centers, along with the sequencing machines depicted here, are crucial components of the infrastructure needed to support biodiversity genomics initiatives such as BGE.  Data analysis: Both iBOL Europe and ERGA handle large amounts of genomic data. Artificial intelligence (AI) methods increasingly help compare unknown DNA snippets against huge digital libraries or refine the final genome assembly. For iBOL Europe, the goal is to generate DNA barcode reference libraries and use these for accurate species identifications to enable presence/absence monitoring at scale. For ERGA, the data analysis aims at unraveling full genomic architectures from reference genomes, offering clues for evolutionary studies and potential “genetic rescue” strategies for threatened species . Biodiversity conservation impact: ultimately, the information obtained from both DNA barcoding and reference genome assembly informs conservation actions. DNA barcoding data can help pinpoint hotspots of species diversity or track the spread of invasive species. On the other hand, ERGA’s high-quality genomic resources can guide genetic rescue efforts, revealing which populations have enough genetic diversity to adapt to pressing environmental changes. Although iBOL Europe and ERGA focus on different levels of detail, their workflows share many parallels,  with high quality references central to both endeavours, underscoring the collaborative spirit of the BGE project. Following similar steps, from field sampling to sequencing and analysis, these two communities bring diverse genomic data under one roof. Thus, biodiversity is understood faster and deeper, and there is a stronger scientific basis for protecting life on Earth. Stay tuned for our next post, where we continue to explore the synergies between DNA barcoding and reference genomes. Read the other posts in the series:

Triplefin blenny in the Adriatic Sea ©Sandra Bracun This BGE case study, led by the Svardal Lab at the University of Antwerp, builds upon two recently sequenced chromosome-level reference genomes from the ERGA pilot project. The project involves multiple European research institutions, including the Marine Biology Station Piran, the University of Graz, and the Natural History Museum Rijeka. It focuses on the widespread Triplefin Blenny ( Tripterygion tripteronotum ) and the vulnerable brackish-to-freshwater Adriatic Dwarf Goby ( Knipowitschia panizzae ). While high-quality genomes for both species have been sequenced, RNA sequencing is the next crucial step to complete the genomic work and support conservation efforts. Triplefin blenny - Photos by Sandra Bracun. The Triplefin Blenny ( Tripterygion tripteronotum ) is an ideal model for speciation studies due to its isolation by Adriatic Sea currents and its role in research on vision-related behavior for predator avoidance. In contrast, the Adriatic Dwarf Goby ( Knipowitschia panizza e) and its relatives face significant conservation challenges due to taxonomic uncertainties, habitat loss, and climate change. Whole-genome re-sequencing, leveraging high-resolution genomic resources, will clarify taxonomy and population distribution, providing essential data for conservation.  Sampling the Adriatic Dwarf Goby in the estuaries of Koper, Slovenia. ©Maximilian Wagner As we gather more information, understanding the genomic basis of adaptation is essential for comparing and elucidating biodiversity patterns. By sequencing the transcriptomes of both species, we will not only complete the genomic dataset but also provide unprecedented insights into the genomic pathways that drive and sustain biodiversity in these species. This project also highlights the ERGA community’s expertise in high-quality genome production. We extend our gratitude to those involved, including Dr. Marcelo Kovacic, Dr. Domen Trkov, Dr. Maximilian Wagner, and Henrique Leitão. About the Authors At the Svardal lab  we investigate the development and changes in Earth's natural diversity through genome sequencing and mathematical modeling. By studying genomic variations, we gain essential insights into evolutionary history, population connections, demographic patterns, and adaptations.

At this month's ERGA Plenary meeting , taking place on Monday, March 17 at 15:00 CET , Ancuța Fedorca will introduce the new COST Action Genetic Nature Observation and Action (GENOA). More details can be found below. Watch the recorded talk: https://youtu.be/SkrTubd818s?si=4QBk_-l5WIHTK0Ex Abstract Genetic Nature Observation & Action - GENOA CA23121 Genetic diversity is fundamental for adaptation and essential to species survival, hence for nature’s contributions to people. Furthermore, genetic knowledge supports the effective use of resources to ensure the holistic protection of biodiversity. While genetic diversity data and indicators are available, they are often not integrated into species management and monitoring schemes in Europe due to a lack of capacity. Furthermore, current national policies and practices have not yet ‘adapted’ to the new Global Biodiversity Framework. In order to better understand genetic diversity in species and their populations and actively use it to monitor and safeguard biodiversity, there is an urgent need to refine, assess, inform and facilitate the implementation of genetic diversity data and indicators across European countries. This implementation of genetic diversity data should be achieved by including practitioners, companies, policymakers and the wider public. The needs of all these stakeholders should be investigated and taken into account in order for collaborations to be inclusive and effective, as such, building knowledge, capacity and trust among partners. Hence, GENOA will co-create and improve the procedures, methods and data on genetic diversity (indicators) and co-develop tailored dissemination packages to reach out to and exchange with targeted stakeholders to enable a better understanding of genetic diversity information. In addition, the monitoring, reporting and application of genetic data will improve, which will contribute to the conservation of biodiversity at all levels. 🔗 https://www.cost.eu/actions/CA23121/ Speaker's Bio Ancuța Fedorca Ancuța Fedorca is a leading expert in conservation genetics and the sustainable use of biological diversity. She has played a key role in numerous international and national research projects, driving advancements in environmental research and integrating genetic diversity into conservation policy. As an internationally recognized scientist, she has contributed to high-impact scientific publications, furthering global understanding of genetic diversity and its role in conservation. Currently, Ancuța leads COST Action GENOA (CA23121), a dynamic network of scientists, practitioners, and decision-makers working together to enhance genetic diversity assessment. In this initiative we are spearheading efforts to refine methodologies, improve genetic diversity indicators, and develop targeted dissemination strategies to bridge the gap between research and policy. 🔔 To receive the Zoom link and join this and our upcoming plenary meetings, register as an ERGA member .

The European Reference Genome Atlas (ERGA) initiative is a pan-European scientific response to current threats to biodiversity. Reference genomes provide the most complete insight into the genetic basis that forms each species and represent a powerful resource in understanding how biodiversity functions. With approxima HOME A GENOME ATLAS OF EUROPEAN BIODIVERSITY The European Reference Genome Atlas (ERGA) initiative is a pan-European scientific response to current threats to biodiversity. Reference genomes provide the most complete insight into the genetic basis that forms each species and represent a powerful resource in understanding how biodiversity functions. With approximately one fifth of the ~200,000 European species at risk of extinction, we need to act fast and together to generate high-quality complete genome resources in large scale. Science needs genomes to understand biodiversity, biodiversity needs to be understood to be protected. HIGHLIGHTS Celebrating the “Mouse of Hungary” - the endangered Hungarian Birch Mouse is selected as Mammal of the Year 2025 Meet iBOL Europe and ERGA Plenary talk - Genetic Nature Observation Action (GENOA) EVENTS Plenary talk - Genetic Nature Observation Action (GENOA) Structural Variation in the Barley Pangenome and the TRITEX Pipeline for Plant Genome Assembly Pangenome graphs and their applications in biodiversity genomics Open to Collaborate ERGA is committed to the development of new modes of collaboration, engagement, and partnership with Indigenous peoples for the care and stewardship of past and future heritage collections. Calls OUR MISSION 1/3 1/3 1/3 1/3 WHAT WE DO Establishing high-quality reference genomes requires an interdisciplinary workflow From species to genomes … and beyond. From species selection to data analysis, the process of creating reference genomes for the entire biodiversity will involve a deep synergy among museums, research institutes, universities, sequencing centres, bioinformatics and computational groups. Citizens will also play an important role supporting the inclusion of all types of species. WHAT WE AIM FOR Creating and consolidating a collaborative and interdisciplinary network of scientists across Europe and associated countries Connecting relevant infrastructure across Europe following a distributed model that can dynamically increase Propagating guidelines for state-of-the-art genome establishment through training and knowledge transfer Next La comunidad ERGA tiene como objetivo optimizar la producción de genomas de referencia mediante el desarrollo y el intercambio de protocolos y flujos de trabajo, brindando acceso a recursos y apoyando el desarrollo de capacidades a través de la transferencia de conocimientos - para mejorar y ampliar el uso de datos genómicos para la protección y restauración de la biodiversidad Next OUR PROJECTS ERGA Pilot The Pilot Project was launched to demonstrate the feasibility of continent-wide collaboration. It was established, funded, and driven entirely by its members. Read more >> Biodiversity Genomics Europe ERGA has recently been funded as part of the Biodiversity Genomics Europe project through the European Union's Horizon Europe Research and Innovation Action. Read more ERGA Community Genomes Are you planning or developing a reference genome project of a European species? Join the growing family of ERGA Community G enomes! Read mo re “Species conservation is urgent and demands deep knowledge of the genetic features of their populations. A coordinated effort to generate complete reference genomes for all European biodiversity, such as what we are proposing with ERGA, can give us the whole picture about the adaptive differences and extent of a need for genetic rescue among populations and species.” Dr. Camila Mazzoni, Founding Chair, ERGA. Research Group Leader Leibniz Institute for Zoo and Wildlife Research Berlin, Germany

Community Guidelines Data & Tools Sampling Resources ERGA Library Media Community Guidelines & Documents ERGA Governance Document The ERGA Governance Document builds on the initial consortium structure guidelines and defines ERGA bodies, procedures, roles, and responsibilities. On registration, ERGA Members agree to be bound by both the ERGA Code of Conduct and this Governance Document . View More Code of Conduct ERGA is a bottom-up, open and inclusive community. ERGA membership is open to any individual who supports ERGA’s objectives, registers as a member, and agrees to be bound by the ERGA Code of Conduct. View More Privacy Policy As a community connecting researchers working in the field of biodiversity genomics, ERGA is committed to protecting privacy and respecting privacy regulations, as outlined in the ERGA Privacy Policy . View More Open Data Policy This document outlines the Open Data Policy (ODP) for ERGA. This includes all data and metadata produced as part of the activities within and/or associated with ERGA. View More ERGA Publication Project Code of Conduct This document sets out concepts, best practices, and expectations for ERGA Members to follow when engaged in collectively developing publication projects that involve the ERGA community. View More ERGA Glossary This page provides explanations about terms and acronyms often used within ERGA and in the context of Biodiversity Genomics. View More Community Guidelines Sampling Resources ERGA Sample Manifest ERGA aims to promote and facilitate ethical and legal sampling practices that are also complete and comprehensive so as to fully document the provenance of all samples. The ERGA Sample Manifest serves as the community standard for documenting sampling. View More Community Interest Species Survey From late 2021 to early 2023 ERGA conducted a community-wide survey to identify species of interest and potential sample providers; the archived list contains ~1700 species of interest. View More sampling-resources Data & Tools ERGA Data Portal Access the Data Portal and Status Tracker here . These resources are developed together with EMBL-EBI and provide the latest information about data available at the European Nucleotide Archive for all species registered under the ERGA umbrella project. View More ERGA Genome Tracking Console (GTC) The purpose of this tool is to facilitate the tracking of samples, sequencing status, assembly and annotation status, and facilitate the deposition of data into the ENA by keeping track of accession numbers. View More ERGA GoaT Page The Genomes on a Tree (GoaT) platform is mantained by the Wellcome Sanger Institute. GoaT helps coordinate efforts across the Earth Biogenome Project (EBP) Network at all stages from planning through sequencing and assembly to publication. View More ERGA GitHub Through community contributions, ERGA is working towards collecting computational workflows, pipelines, and tutorials in the ERGA GitHub Repositories . View More ERGA WorkflowHub Space Through community contributions, ERGA is working towards collecting computational workflows, pipelines, and tutorials in the ERGA WorkflowHub space. View More Galaxy / Genome Assembly View More Structural Annotation Guide A step-by-step guide on how to annotate protein-coding genes in your genome. Developed by the Annotation Committee. View More Guidelines on data submission - ENA This document provides summary of the key steps for submitting raw reads and genome assemblies (including annotations) to the European Nucleotide Archive. Developed by the IT and Infrastructure Committee. View More data-software Media For more information regarding the ERGA brand or other media inquiries please contact us at media@erga-biodiversity.eu. Logo - Transparent PNG ERGA Poster ERGA Banner ERGA YOUTUBE CHANNEL In the ERGA YouTube Channel you will find a number of resources such as recordings of previous seminars, workshops and interviews. Don't forget to subscribe to our channel to stay updated about upcoming events! media-resources ERGA-Consortium Play Video Play Video 50:29 Structural Variation in the Barley Pangenome and the TRITEX Pipeline for Plant Genome Assembly More information, including abstracts: https://www.erga-biodiversity.eu/post/structural-variation-in-the-barley-pangenome-and-the-tritex-pipeline-for-plant-genome-assembly Speakers: Martin Mascher and Marina Pupke Marone from the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK). --- The ERGA BioGenome Analysis and Applications Seminar Series is a joint initiative of the ERGA Data Analysis Committee (DAC) and the BGE-ERGA WP11-Genome Applications. The purpose of this seminar series is to promote knowledge exchange on state-of-the-art genomic analyses and applications and to create a space for connection and analysis-oriented discussion for ERGA members and the broader genomics research community. These seminars will provide opportunities for interdisciplinary interactions that explore emerging scientific trends, providing a platform for cutting-edge research, novel ideas, and insightful discussions. Learn more about ERGA & BGE at: https://www.erga-biodiversity.eu/ and https://biodiversitygenomics.eu/ Play Video Play Video 18:02 Pangenome graphs and their applications in biodiversity genomics - January 2025 https://www.erga-biodiversity.eu/post/pangenome-graphs-and-their-applications-in-biodiversity-genomics Play Video Play Video 03:36 Xanthium orientale subsp. italicum - Salvatore Tomasello Learn more about ‪Biodiversity Genomics Europe (BGE) at biodiversitygenomics.eu https://www.erga-biodiversity.eu/ Play Video Play Video 07:47 Interview with the Social Justice Committee Chairs - James Fleming & Fabrizio Ghiselli Read the full interview: https://www.erga-biodiversity.eu/post/5-questions-to-fabrizio-ghiselli-and-james-fleming-chairs-of-the-social-justice-committee Learn more about the ERGA Social Justice Committee: https://www.erga-biodiversity.eu/social-justice. Interested in joining our activities? Send us an email: socialjustice@erga-biodiversity.eu Play Video Play Video 21:57 The Journey of the Citrullus colocynthis Genome - Anestis Gkanogiannis ERGA Plenary Talk - January 2025 Learn more about ERGA Community Genomes: https://www.erga-biodiversity.eu/erga-satellite-genomes Title: From Community Contribution to ERGA Recognition: The Journey of the Citrullus colocynthis Genome Speaker: Anestis Gkanogiannis Abstract: This talk will explore the journey of the Citrullus colocynthis genome assembly, from its initial creation to its acceptance as the first ERGA-community genome. I will discuss the quality assessment process defined by ERGA, the challenges faced, and the steps taken to ensure compliance with ERGA’s standards. This case study highlights the pivotal role of community-led initiatives in expanding the ERGA genomic database beyond the pilot project. It also reflects on the collaborative potential of ERGA's "satellite" genome framework, which integrates contributions from the broader research community. Attendees will gain insights into the submission and review process, as well as the significance of Citrullus colocynthis as a model for drought-resilient crops within ERGA's biodiversity objectives. Play Video Play Video 02:56 Yellow gorgonian (Eunicella cavolini) - Didier Aurelle Learn more about ‪Biodiversity Genomics Europe at biodiversitygenomics.eu https://linktr.ee/erga_biodiversity Play Video Play Video 02:04 Biodiversity Genomics Europe Workshop @ BeGenDiv - Berlin 2024 The BGE Workshop @ BeGenDiv happened in September 2024. More information: https://biodiversitygenomics.eu/2025/01/14/a-recap-of-the-bge-workshop-at-the-berlin-center-for-genomics-in-biodiversity-research/ Play Video Play Video 23:11 What happened at the UN Biodiversity Conference COP16 on Digital Sequence Information?- Amber Scholz ERGA Plenary talk - December 2024: "What happened at the UN Biodiversity Conference (COP 16) on Digital Sequence Information? Can I still use open public genetic sequence data?" More information and abstract: https://www.erga-biodiversity.eu/post/what-happened-at-the-un-biodiversity-conference-cop-16-on-digital-sequence-information-can-i-stil

OUR PARTNER PROJECTS ERGA is the pan-European partner of the Earth Biogenome Project (EBP) Regional Partners: French Atlas of Marine Genomes (ATLASea) Earth Biogenome Project Norge (EBP-Nor) Swedish Earth BioGenome Project Worldwide Partners: