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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 01:03:27 Efficient evidence-based genome annotation with EviAnn - Aleksey V. Zimin More information, including abstract: https://www.erga-biodiversity.eu/post/efficient-evidence-based-genome-annotation-with-eviann Speaker: Dr. Aleksey V. Zimin - Research Scientist, Department of Biomedical Engineering, Johns Hopkins University, USA --- 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 15:09 Global genetic diversity loss & the power of conservation to restore species resilience - Robyn Shaw https://www.erga-biodiversity.eu/post/global-genetic-diversity-loss-and-the-power-of-conservation-to-restore-species-resilience 🧬 Learn more about #ERGA & join us today! https://www.erga-biodiversity.eu Play Video Play Video Genomics for Biodiversity Conference - from genomes to impact More information & link to the program: https://www.erga-biodiversity.eu/post/genomics-for-biodiversity-conference-from-genomes-to-impact This conference will bring together researchers and other stakeholders interested in applied biodiversity genomics and will showcase how it can have an impact on real-world issues, focusing primarily on biodiversity conservation and the bioeconomy. Learn more about ERGA & BGE at: https://www.erga-biodiversity.eu/ and https://biodiversitygenomics.eu/ Play Video Play Video 36:03 Faster identification of Transposable Elements in full genome assemblies - Pío Sierra More information, including abstract: https://www.erga-biodiversity.eu/post/faster-identification-of-transposable-elements-in-full-genome-assemblies Speaker: Pío Sierra, Research Assistant, Karam Teixeira Group - Department of Genetics, University of Cambridge, United Kingdom --- 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 55:27 Target capture sequencing approaches to the study of plant evolution More information, including abstracts: https://www.erga-biodiversity.eu/post/target-capture-sequencing-approaches-to-the-study-of-plant-evolution Speakers: Lisa Pokorny, Ramón y Cajal Researcher at Real Jardín Botánico (RJB-CSIC), Spain Pol Fernández Mató, Institut Botànic de Barcelona (IBB, CSIC-CMCNB), Catalonia --- 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 15:23 The ERGA Community Genome Report Collection at Pensoft RIO - Robert Waterhouse https://www.erga-biodiversity.eu/post/the-new-erga-community-genome-report-collection-at-pensoft-rio The new ERGA Community Genome Report Collection at Pensoft RIO The new European Reference Genome Atlas (ERGA) Community Genome Reports collection at Pensoft's Research Ideas and Outcomes journal provides a single platform to collate publications from the ERGA Community describing their reference genomes. An ERGA Genome Report is a technical description that clearly presents the methodologies employed for sequencing and assembling genomes, together with standard quality metrics and relevant metadata, and genome annotation information if available. The ERGA Genome Reports preprinted and/or published through this collection follow a standardised format to ensure consistent quality and facilitate data findability and reuse. Genome Reports published elsewhere will be considered for inclusion in this collection if they (1) align with the ERGA Genome Report standards and (2) clearly acknowledge ERGA in the manuscript. Through collating Genome Reports from across ERGA affiliated projects and members, this collection provides an open-access resource that promotes high standards, supports comparative analyses, and drives advances in genomics research. Play Video Play Video 04:18 Embia tyrrhenica genome - Giobbe Forni Learn more about BGE: https://biodiversitygenomics.eu/2025/06/10/community-driven-reference-genomes/ Play Video Play Video 02:00 The ERGA Knowledge Hub - Intro Video https://knowledge.erga-biodiversity.eu - visit the ERGA Knowledge Hub and contribute today! 🧬 Learn more about #ERGA & join us today! https://www.erga-biodiversity.eu

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 Connection #8 - Bioinformatics: reassembling the book of life ERGA meets VGP in New York City ERGA at the EMBO course in genome sequencing, assembly, curation, and downstream analyses EVENTS Genomics for Biodiversity Conference - from genomes to impact Faster identification of Transposable Elements in full genome assemblies ERGA at ESEB 2025 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

Executive Board Council of Countries Committees Our Partners Pilot Project Former Contributors top OUR COMMUNITY ERGA is an bottom-up initiative based on people, consisting of hundreds of scientists across the entire European continent and beyond. Research institutions, infrastructure facilities as well as partner genome projects will play an important role within ERGA. Finally, ERGA will have a focus on societal needs particularly related to Biodiversity conservation. For that purpose, ERGA will work engaging governmental and non-governmental entities and will closely involve citizens in different actions. Executive Board Executive Board executive-board@erga-biodiversity.eu Robert Waterhouse Chair Ann Mc Cartney Vice Chair Olga Vinnere Pettersson Vice Chair Rosa Fernández Scientific Officer Elena Bužan Partnership Officer Chiara Bortoluzzi Dissemination Officer Lada Lukić Bilela Social Integration Officer Camila Mazzoni Funding Opportunities Officer Jaakko Pohjoismäki Genomic Outreach Officer List of Former Executive Board Members > Council of Country Representatives Contact the national representatives for more information on the ERGA community in your country! Andorra Andorra@erga-biodiversity.eu Manel Niell List of Former Council Members > Council of Countries Committees SSP - Sampling & Sample Processing samples@erga-biodiversity.eu More > DAC - Data Analysis Committee analysis@erga-biodiversity.eu More > Media & Communications media@erga-biodiversity.eu More > Social Justice Committee socialjustice@erga-biodiversity.eu More > SAC - Sequencing and Assembly Committee assembly@erga-biodiversity.eu More > ITIC - IT & Infrastructure Committee itinfra@erga-biodiversity.eu More > CS - Citizen Science citizenscience@erga-biodiversity.eu More > Annotation Committee annotation@erga-biodiversity.eu More > ELSI - Ethical, Legal, and Social Issues elsi@erga-biodiversity.eu More > TKT - Training and Knowledge Transfer training@erga-biodiversity.eu More > Committees Our Partners Our Partners ERGA is the pan-European partner of the Earth Biogenome Project (EBP) Affiliated Initiatives Associated Partners Pilot Project Pilot Project Committee Coordinators pilot@erga-biodiversity.eu Giulio Formenti Alice Mouton Ann Mc Cartney Learn more about the Pilot Project Former Contributors SSP - Sampling & Sample Processing Committee Filter by Type Astrid Böhne (Former Committee Chair) Former Contributors

citizenscience@erga-biodiversity.eu < Back CS - Citizen Science citizenscience@erga-biodiversity.eu The Citizen Science and Outreach Committee aims to facilitate collaboration and communication between scientists, stakeholders and citizens to increase trust in the scientific process and ensure that genomics research reflects the needs and perspectives of the broader community. By engaging a broad range of stakeholders, including policy makers, non-governmental organisations, industry representatives and citizens, the Committee seeks to foster a fruitful multi-stakeholder dialogue and support the traditional community knowledge through the use of citizen science and stakeholder perspectives. To achieve its goals, the Committee works to engage citizens and stakeholders in the research process and to promote public understanding of genomics through various public events and other activities. In addition, the Committee supports policies that support genomics research and its translation into practical applications for the benefit of society. (V.1.0 02.05.2023) Chair Elena Buzan Coordinators Christian de Guttry Luísa Marins Steering Committee Jacob Höglund Lino Ometto Svein-Ole Mikalsen Chiara Bortoluzzi Connection #8 - Bioinformatics: reassembling the book of life ERGA meets VGP in New York City Events ERGA at the EMBO course in genome sequencing, assembly, curation, and downstream analyses Events

Glossary This page provides explanations about terms and acronyms often used within ERGA and in the context of Biodiversity Genomics. You can filter the terms alphabetically or according to categories: Annotation Citizen Science Data Analysis ELSI IT & Infrastructure Media & Communications Other Sampling & Sample Processing Sequencing & Assembly A B C D E F G H I J K L M O P R S T V W References > (Genome) annotation The process of identifying the functions of different pieces of a genome. This includes genes that code for proteins and non coding features (e.g. intron-exon structure of protein coding genes, promotors, transposable elements). Typically performed using computational methods, followed by manual curation. (Genome) assembly A genome assembly is a representation of an organism’s genome that is made using computer programs to turn (assemble) raw sequence data into longer, continuous sequences. (Genome) completeness An estimate of how well a reference genome represents the complete sequence of the target organism. A complete genome should equal the haploid genome size of the target, but may be defined when ‘all chromosomes are gapless and have no runs of 10 or more ambiguous bases, there are no unplaced or unlocalized scaffolds, and all expected chromosomes are present.’ (https://www.ncbi.nlm.nih.gov/assembly/). There are different approaches to estimate the completeness, like BUSCO, analysing K-mers, etc. ABS Access & Benefit Sharing BGE Biodiversity Genomics Europe. The BGE Project has received funding through a Horizon Europe call on Biodiversity and Ecosystem Services. The overarching BGE project includes two streams of genomic research: reference genomes and barcoding, in an effort to establish ERGA and BIOSCAN as the European nodes of the Earth Biogenome Project and of the International Barcode of Life (IBOL), respectively. BUSCO A bioinformatic method (Benchmarking Universal Single-Copy Orthologues) used to estimate the completeness of the coding fraction of an organism’s genome based on the proportion of (lineage specific) single copy orthologous genes that are found in a genome assembly. Biodiversity genomics The application of genomic methods to research biodiversity. CARE Principles The CARE principles for Indigenous data governance (https://www.gida-global.org/care) provide a governance framework that supports the recognition of rights and interests Indigenous Peoples’ to their physical and digital data as well as their Indigenous Knowledges. CBD Convention on Biological Diversity COPO The Collaborative OPen Omics (COPO) platform is for researchers to publish their research assets, providing metadata annotation and deposition capability. It allows researchers to describe their datasets according to community standards and broker the submission of such data to appropriate repositories whilst tracking the resulting accessions/identifiers. Learn more about COPO in this article by the Earlham Institute. CS Citizen Science Committee Chromosome-level assembly the process of generating a contiguous sequence of all chromosomes of a genome, often aided by genetic maps or proximity ligation techniques (3C-seq, Hi-C); term also used to refer to the resulting genome sequence. Council meetings During the monthly ERGA council meetings, the representatives of countries and other genome projects associated with ERGA meet to discuss and vote on important matters related to ERGA’s governance and actions. The council is the main decision making body of the consortium. Learn more about ERGA's structure in our Governance Document. DAC Data Analysis Committee DSI Digital Sequence Information - learn more: https://www.cbd.int/dsi-gr/ DToL The Darwin Tree of Life Project aims to sequence the genomes of 70,000 species of eukaryotic organisms in Britain and Ireland. EBP The Earth BioGenome Project EBP Genome assembly quality standard 6.C.Q40 Minimum reference standard of 6.C.Q40, i.e. megabase N50 contig continuity and chromosomal scale N50 scaffolding, with less than 1/10,000 error rate. For species with chromosome N50 smaller than a megabase this will be C.C.Q40. Additional recommendations include K-mer completeness >90%, BUSCO complete single-copy single >90%, BUSCO complete single duplicate < 5%, and Gaps/Gbp <1000. EC European Commission ELSI Ethical, Legal, and Social Issues (Committee) ENA The European Nucleotide Archive (https://www.ebi.ac.uk/ena) is a global repository for sequence data and provides resources that support management and access to sequence data. ERGA European Reference Genome Atlas ERGA Plenary Our plenary meetings are open to all registered ERGA members and generally include short updates given by committee chairs and one invited talk on various themes connected to biodiversity genomics (watch the previous ones here). ERGANews ERGA’s monthly newsletter, includes important updates about the consortium, each of the committees and associated projects. Our newsletters are usually published on the first Tuesday of each month. All editions of the newsletter are stored here. Equity Deserving According to the Canadian Council (https://canadacouncil.ca/glossary/equity-seeking-groups) equity deserving groups are those individual researchers, communities, Peoples, regions or countries that have identified barriers to equal access, opportunities, and resources due to disadvantage and/or discrimination and that are actively seeking, and deserving of social justice and reparation. The discrimination experienced could be caused by attitudinal, historic, social, and environmental barriers that could be based on a plethora of characteristics that are including (but not limited to) sex, age, ethnicity, disability, economic status, gender, gender expression, nationality, race, sexual orientation, and creed. FAIR Principles A set of principles to guide appropriate management and curation of scientific data (https://www.go-fair.org/fair-principles/) that emphasise data accessibility and use by ensuring that data are Findable, Accessible, Interoperable, and Reusable. Due to the increasing amount of scientific data being reposited, FAIR guidelines promote a data format that is amenable to automated computational access of data by stakeholders Galaxy Galaxy is an open source, web-based platform for data intensive biomedical research. Genome Report A genome report is a technical publication that describes all the steps taken to produce a reference genome: sampling, sequencing, assembling, annotating. They often have a standardised format and structure that allows readers to quickly and easily understand the quality of the genome and how it was generated. GoaT Genomes On A Tree HE Horizon Europe , sometimes refers to the BGE project funded under HE HSM Hierarchical Storage Management is both a data management and data storage technique which transparently manages the movement of data between the different layers of a tiered storage based on file size thresholds, usage and I/O pressure. Usually, a tiered storage is composed of one or more layers of disk arrays, ordered by capacity, latency, redundancy and storage cost. A slow but economically effective archival layer is at the bottom, composed of magnetic tape libraries and automated tape robots, with the highest capacity and latency. The movement between layers is automatically triggered. Haplotype A haplotype refers to the collection of genetic material within an organism that is inherited together. Haplotype may be used to describe a few loci or any number of chromosomes (a chromosome-scale haplotype). Hi-C Sequencing-based method used to study three-dimensional interactions among chromatin regions by measuring the frequency of contact between pairs of loci. Since contact frequency is related to the distance between a pair of loci, Hi-C linking information is used to help with scaffolding stages during a genome assembly process. Hi-C map / graph production The occurrence and frequency of Hi-C contacts are analysed and used in assembly scaffolding. They are typically visualised in Hi-C 2D heatmaps with the full genome sequence on the X and Y axis and a markup for each observed contact. HiFi reads HiFi (High Fidelity) PacBio reads are produced by taking multiple sequences of the same molecule to provide a consensus sequence that is usually 12-20kbp long and has a low error rate (>99.9 % consensus accuracy). INSDC International Nucleotide Sequence Database Collaboration (https://www.insdc.org/) is an initiative between the DDBJ, EMBL-EBI and NCBI that together act as a global repository of sequence data and associated metadata, and provide tools and services that allow access to genomic resources. ITIC IT & Infrastructure Committee IsoSeq This is a sequencing protocol developed by PacBio that aims to sequence full-length transcripts using the accurate, long read capabilities of PacBio HiFi technology. IsoSeq data facilitate analysis of transcriptomes and genome annotation by identifying full-length isoforms of transcripts. JEDI / DEIJ Justice, Equity, Diversity, and Inclusion Subcommittee K-mer A K-mer is a DNA sequence of length k; for example, the sequence AGCT contains the 3-mers (K-mers of length 3) AGC and GCT. Library DNA, cDNA, or RNA that has been prepared for NGS within (usually) a specific size range and containing adapters, which are designed to be appropriate for (a) specific sequencing platform(s). M&C Media & Communications Committee Metadata A collection of data that provides contextual information about multiple characteristics of other, corresponding original data. ONT Oxford Nanopore Technologies (ONT; https://nanoporetech.com/) is a next generation sequencing technology whereby sequence data are generated from the changes in current that occur as single-stranded DNA or RNA molecules pass through nanoscale protein pores (nanopores). ONT provides long read data (up to several megabases) that facilitate genome assembly. Omni-C Modified version of Hi-C that uses a sequence-independent endonuclease during its protocol to produce more even sequence coverage increasing overall resolution. Open data Open data are freely accessible and unrestricted data that can be accessed, used,reused and shared with third parties for any purpose. PUID A permanent unique identifier is a unique label for an object that does not change, such as the Digital Object Identifier (DOI) attached with a scientific publication. PacBio Pacific Biosciences (PacBio; https://www.pacb.com/) is a single-molecule, real time (SMRT) next generation sequencing technology in which sequence data are generated by fluorescent light emission that occurs when a DNA polymerase adds nucleotides. PacBio produces long read data (tens of kilobases) that facilitate genome assembly. RNA-Seq RNA-Seq is a technique that determines the complete or partial RNA sequence using NGS. The RNA expression profiles vary in different tissues of the same organism and can be influenced by physiopathological circumstances. RNA-Seq data facilitate genome assembly by providing empirical evidence for annotation of transcribed regions. Reference genome An accepted standard representation of an organism’s DNA sequence. High-quality reference genomes typically have high completeness (chromosome-level with few gaps in sequence), few errors, and are annotated and accessible. A reference genome serves as a tool for alignment-based analyses, such as variant calling or RNAseq, and has many other applications, for example, phylogenetics and evolutionary relationships, identification of genes and variants, functional analysis and comparative genomics. Reference genomes referred to as “drafts” are those that are under active construction and refinement, and not yet finalised through manual curation. SAC Sequencing and Assembly Committee SOP A standard operating procedure (SOP) is a document that provides detailed instructions on how to perform an activity, outlining the step-by-step process required for its execution. SRA Sequence Read Archive SSP Sampling & Sample Processing (Committee) TKT Training & Knowledge Transfer Committee References The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics (Glossary)- bioRxiv 2023.09.25.559365; doi: https://doi.org/10.1101/2023.09.25.559365 How genomics can help biodiversity conservation; doi: https://doi.org/10.1016/j.tig.2023.01.005 Refererences

socialjustice@erga-biodiversity.eu < Back Social Justice Committee socialjustice@erga-biodiversity.eu Co-chairs Fabrizio Ghiselli James Fleming Head to the committee page >> Connection #8 - Bioinformatics: reassembling the book of life ERGA meets VGP in New York City Events ERGA at the EMBO course in genome sequencing, assembly, curation, and downstream analyses Events

training@erga-biodiversity.eu < Back TKT - Training and Knowledge Transfer training@erga-biodiversity.eu The Training and Knowledge Transfer (TKT) committee aims to support the design and implementation of learning and skill-sharing activities in the field of biodiversity genomics research. Our committee actively engages with all ERGA committees to collect, promote, and develop training materials, including webinars, workshops and activities, and make them available to the ERGA community. We work with the ERGA community to connect experts interested with members wishing to learn new skills and improve their knowledge of the chain of steps required for reference genome generation. We also connect and support members to collaboratively develop funding proposals for financing TKT-related activities, and we coordinate the programme for the monthly ERGA Plenary meetings. V.1.0 02.05.2023 Chair Camilla Reginatto De Pierri Coordinator Christian de Guttry Steering Committee Alice Mouton Lino Ometto Nadège Guiglielmon Robert Waterhouse Spiros Papakostas Jean-François Flot Connection #8 - Bioinformatics: reassembling the book of life ERGA meets VGP in New York City Events ERGA at the EMBO course in genome sequencing, assembly, curation, and downstream analyses Events

annotation@erga-biodiversity.eu < Back Annotation Committee annotation@erga-biodiversity.eu Annotations transform genomes into larger sources of knowledge and offer critical added value to genome assemblies. They serve as a direct link between the genome sequence and function and facilitate comparisons across taxa, both on a large and small scale. The ERGA Annotation Committee is composed of researchers and bioinformaticians who have experience in using computational methods to predict the structural and functional composition of whole genomes. We strive to understand and use the most advanced analytical methods for annotating genomes, to develop new methods for annotation and its evaluation, and to align with the standards set by the EBP. We are committed to promoting the best possible annotation pipelines are available to and used by the annotation community and new researchers entering this field. The committee meets regularly to review the progress of the annotation in ERGA-genomes, discuss current issues and challenges, and propose changes to improve the annotation process. (V.1.0 16.05.2023) Chair Alice Dennis Coordinator Christian de Guttry Steering Committee Aureliano Bombarely Hugues Roest Crollius Henrik Lantz Fergal Martin Florian Maumus Committee Resources Structural Annotation Guide Pre-trained AUGUSTUS models 💡ERGA Knowledge Hub Pipelines BRAKER3 Protein-Coding Annotation Pipeline Connection #8 - Bioinformatics: reassembling the book of life ERGA meets VGP in New York City Events ERGA at the EMBO course in genome sequencing, assembly, curation, and downstream analyses Events

ERGA Calendar

Social Justice Committee Social Justice Committee Definition Generating high-quality eukaryotic reference genomes is transforming our understanding of biology and evolution. The process of developing this resource so that it has long-term utility is complex and intricate, requiring not only technical and scientific expertise but also the integration of social justice principles. These data will have a significant impact on society, making the incorporation of social justice principles essential. In the ERGA community research setting, social justice means treating everyone fairly and ensuring that individuals from all backgrounds can benefit from our research. Key components of this process include diversity in research participation, fair distribution of research benefits, adherence to high ethical standards, dissemination of research findings to a broad audience, and fostering an inclusive and supportive research environment. The ERGA Social Justice Committee is dedicated to embedding justice, equity, diversity, and inclusion principles into every aspect of eukaryotic genome production, from sampling to results dissemination. This committee serves as an ethical compass for ERGA members, guiding the community to ensure that every step in the genome generation pipeline is conducted with social responsibility and respect for diversity. We aim to ensure both scientific rigor and social responsibility in our guidelines for generating high-quality reference genomes by integrating these principles. Authors in alphabetical order Chiara Bortoluzzi, Christian de Guttry, James Fleming, Fabrizio Ghiselli, Jennifer Leonard, Rebekah Oomen Objectives Promoting Diversity In ERGA, diversity is multifaceted, encompassing the composition of research teams with individuals from diverse backgrounds and expertise, the variety of taxa sequenced and their geographical origins, as well as the involvement of stakeholders and citizen scientists. This approach ensures research methodologies and outcomes reflect nature's extensive diversity. Ensuring Equity Equity in ERGA is about providing equal access to resources and opportunities across all individuals, communities, countries, and research institutions. It particularly aims to include those historically underrepresented or marginalised. Transfer of Knowledge is integral to this effort, ensuring broad participation in this research. Advancing Inclusion Inclusion involves creating a research environment that values and welcomes the contributions of all, aiming to promote a setting in which every participant can thrive and deliver their maximum potential. To achieve this, we focus on enhanced communication tools, aiming to ensure everyone feels comfortable and supported. Upholding Justice ensuring genomic research processes are available to interested researchers. It also means recognizing and addressing traditional social inequalities affecting current research practices. Application in High-Quality Reference Genome Generation Diversity Sequencing: Allocate sequencing capacity to underrepresented taxa to broaden biodiversity knowledge. Collaboration: Establish diverse consortia to ensure broad geographic representation in genomic research initiatives. Promote gender equality in research teams and leadership positions within genomic projects. Outreach: Develop educational materials on genomics tailored to different academic backgrounds, ages, cultures, and languages. Equity Sample collection : Ensure equitable access to the benefits from genetic resources for source countries and communities, in line with the Access and Benefit Sharing framework (ABS) and the Nagoya Protocol. Ensuring, where possible, equitable access to the field for researchers with diverse needs. Wet lab: Partner with local labs in sample-origin countries to build capacity and share expertise. Sequencing : Offer training programs and protocol sharing in sequencing techniques for scientists from all backgrounds. Genome assembly: Provide open-source software and pipelines together with cloud-based computational resources for researchers who need access to bioinformatic support and computing power. Publishing : Encourage open access availability, either through open access publication or deposition of versions of papers in open access repositories. Technology transfer: Facilitate the transfer of cutting-edge genomic technologies to laboratories in low-income countries; Provide legal and technical assistance to navigate regulations. Inclusion Sample collection: Implement informed consent protocols that respect Indigenous and local communities' rights and traditions. Empower the efforts of local taxonomic experts alongside those communities throughout the sample collection process. Publishing: Adopt open-access policies for publishing results, making information freely available to the community as soon as possible. Data sharing: Facilitate and encourage the rapid sharing of data in global databases that are freely accessible and FAIR (Findable, Accessible, Interoperable, and Reusable), promoting data democracy. Capacity building: Establish mentorship programs connecting established scientists with emerging European-based researchers. In this way, we aim to encourage the development of a new generation of scientists with a representative and diverse mix of abilities, genders, ethnicities, cultural and economic backgrounds, and geographical origins. Community engagement: Acknowledging the diverse contributions made beyond those in academia - universities/ museums/ research institutions - particularly those from local communities and underrepresented groups at all steps of the process from sampling to genome generation and appropriately recognizing their participation. Outreach: Host public science events in biodiversity genomics in diverse geographical locations to spread awareness and foster interest. Ensuring scientific events are organised in a way that is inclusive and accessible, both physically and socially. Social Justice Relevance: Acknowledging that both research and its outcomes could disproportionately affect specific communities within Europe, we commit to responsibly using outreach, engagement, and communication channels to center local communities impacted by biodiversity loss and anthropogenic environmental change, which are directly addressed in the ERGA remit. Personal data sharing: Ensure that data-sharing practices respect the privacy and rights of individuals and communities represented in the data. Ethics: Regularly review external bodies' ethical guidelines to address emerging issues related to social justice in genomics and strive to position ERGA to be as inclusive as possible. Sustainability: Research and implement sustainable laboratory and computational practices to reduce waste and energy consumption; Evaluate the long-term environmental impact of genomic research activities and develop strategies to mitigate negative effects. Conclusion Achieving the broad goals of social justice, diversity, equity, and inclusion in genomic research presents significant challenges. One major hurdle is the intrinsic resource and infrastructure disparities across different European regions. This discrepancy limits access to advanced genomic technologies, computational resources, and skilled personnel. This widens the gap between well-funded institutions in Strengthening countries and less-funded ones in Widening countries. It is also imperative to note that the historical underrepresentation of some groups and species in genomic studies poses ethical and logistical challenges when redressing these imbalances. The complexities of integrating diverse biological samples, especially from Indigenous and marginalised communities, require sensitive, informed consent processes and benefit-sharing arrangements that respect both legal frameworks and ethical considerations. Furthermore, incorporating a wide range of species and their geographical origins into research necessitates a collaborative effort, which geopolitical, financial, and linguistic barriers can hamper. There are as many solutions to these challenges as there are issues themselves. Fostering international collaborations sharing resources, knowledge, and skills is a key strategy for building capacity in underrepresented regions and marginalised groups. Initiatives like cloud-based computational resources, open-source software, and open-access publishing models can democratise access to genomic research tools and findings. Furthermore, engaging local communities in the research process, from planning through to publication, ensures that projects are culturally sensitive and ethically sound, while also facilitating the equitable sharing of benefits. Education and outreach, tailored to diverse audiences, can raise awareness and foster a more inclusive next generation of genomic researchers. Ultimately, the path to achieving Social Justice in genomic research is ongoing and requires a commitment to continuous reflection, adaptation, and action towards these ideals.

ERGA Library Filter by Category Select Category Publication Biodiversity Genomics Research Practices Require Harmonising to Meet Stakeholder Needs in Conservation Year: 2025 DOI/URL: https://onlinelibrary.wiley.com/doi/10.1111/mec.70001 Next Publication A chromosome-level genome assembly of the European green toad (Bufotes viridis) Year: 2025 DOI/URL: https://doi.org/10.1093/g3journal/jkaf002 Next Publication Chromosome-level reference genome assembly for the mountain hare (Lepus timidus) Year: 2025 DOI/URL: https://peercommunityjournal.org/articles/10.24072/pcjournal.514/ Next Publication The genome sequence of the Violet Copper, Lycaena helle (Denis & Schiffermüller, 1775) Year: 2025 DOI/URL: https://doi.org/10.12688/f1000research.156485.1 Next Publication Nuclear and mitochondrial genome assemblies for the endangered wood-decaying fungus Somion occarium Year: 2025 DOI/URL: https://doi.org/10.1093/gbe/evaf003 Next Publication Chromosome-scale genome assembly and de novo annotation of Alopecurus aequalis Year: 2024 DOI/URL: https://doi.org/10.1038/s41597-024-04222-y Next Publication A Faroese perspective on decoding life for sustainable use of nature and protection of biodiversity Year: 2024 DOI/URL: https://doi.org/10.1038/s44185-024-00068-0 Next Publication The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics Year: 2024 DOI/URL: https://doi.org/10.1038/s44185-024-00054-6 Next Publication Building a Portuguese coalition for biodiversity genomics Year: 2024 DOI/URL: https://doi.org/10.1038/s44185-024-00061-7 Next Publication Contextualising samples: supporting reference genomes of European biodiversity through sample and associated metadata collection Year: 2024 DOI/URL: https://doi.org/10.1038/s44185-024-00053-7 Next Publication First Chromosome-Level Genome Assembly of a Ribbon Worm from the Hoplonemertea Clade, Emplectonema gracile, and Its Structural Annotation Year: 2024 DOI/URL: https://doi.org/10.1093/gbe/evae127 (Funded by the Research Council of Norway project “InvertOmics—phylogeny and evolution of lophotrochozoan invertebrates based on genomic data” (project number: 300587 to T.H.S.) Next Publication The genome sequence of the Violet Carpenter Bee, Xylocopa violacea (Linnaeus, 1785): a hymenopteran species undergoing range expansion Year: 2024 DOI/URL: https://doi.org/10.1038/s41437-024-00720-2 Next 1 2 3 1 ... 1 2 3 ... 3

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: