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Authors: Christian de Guttry, Robert Waterhouse and Camila Mazzoni Considering the unprecedented biodiversity crisis facing our planet, comprehensive efforts to understand, protect, restore, and conserve species and their ecosystems are more important than ever. The European Reference Genome Atlas (ERGA) emerges as a community response of scientists contributing to this endeavour by using DNA to study biodiversity. In alignment with the Earth BioGenome Project (EBP), this pan-European initiative aims to coordinate the production of high-quality reference genomes of European eukaryotic biodiversity. In an exciting development, researchers from the ERGA community describe their vision & principles in a short Correspondence published at Nature, entitled "Biodiversity: assembling an atlas of European Reference Genomes", marking a significant milestone in ERGA’s mission. The ERGA Initiative: At the heart of ERGA lies a diverse community of scientists, driven by a shared vision to optimise reference genome generation. ERGA seeks to unlock the potential of genomics technologies for biodiversity research and conservation by developing common protocols, workflows, and resources. Our collaborative effort involves researchers from a variety of fields and institutions throughout Europe, all committed to advancing our understanding and preservation of our rich biological heritage. Guiding Principles: ERGA's governance is rooted in a set of core principles that shape its actions and decisions. Scientific excellence forms the bedrock, ensuring that research conducted under ERGA's umbrella meets the highest quality standards. Distributed expertise and infrastructure across Europe enable access to a broad range of specialised knowledge and cutting-edge technologies. ERGA strives for balanced taxonomic, geographic, and habitat representation, recognizing the importance of preserving biodiversity in all its forms. The initiative adheres to FAIR guidelines (Findable, Accessible, Interoperable, and Reusable) for data generation and release, enabling wide accessibility and facilitating collaborations within the scientific community. Furthermore, ERGA places a strong emphasis on prioritising eukaryotic species that require immediate attention, ensuring that resources allocated generate benefits in the short-term to both research and society. Funding and Collaboration: To achieve its ambitious goals, ERGA receives support from the European Union and associated countries (Switzerland and United Kingdom) as part of the Biodiversity Genomics Europe (BGE) project. This funding not only highlights the importance of ERGA's work but also underscores the commitment of European nations to biodiversity research and conservation. Join the Journey! ERGA's mission to compile a European atlas of reference genomes holds immense promise for biodiversity protection and restoration. Through collaboration, knowledge sharing, and the application of cutting-edge genomics technologies, ERGA seeks to make a tangible difference in preserving Europe's natural heritage. With more than 800 ERGA members to date, we invite you to join us on this collective journey as we continue to take significant steps towards advancing the use of genomics approaches for the safeguarding of our planet's incredible biodiversity for generations to come. Read the correspondence: www.nature.com/articles/d41586-023-02229-w

"G-BiKE's WG4 organizes a webinar on novel genomic tools for conservation for scientists, practitioners, managers, and decision-makers on Thursday, June 22 2023 at 15:00 CET! What new technological advancements have been seen as opportunities for conservation by some and are highly controversial among others on synthetic biology? Who are the people, institutions, practitioners, and external actors who gravitate around these questions and challenges? This is a simple question whose answer can be articulated more than we might realize! Your contribution to the discussion is essential, as the results will be used to open one of the first windows of feasibility for current and future potential conservation applications." Click here for more information.

ERGA will host a paralllel session during the annual meeting of the Society for Molecular Biology Evolution this July in Ferrara, Italy. We are excited to gather together so many ERGA members in person for the first time! In this ERGA session we invite the community to brainstorm the future of genome generation workflows. There is still time to register for the conference and participate! You will find more details about the session below: As one of the key steps for cataloguing biodiversity across Europe, a consortium of scientists launched the European Reference Genome Atlas initiative in 2020. The consortium builds upon growing numbers of reference biogenome initiatives around the world and is the European node of the global umbrella Earth BioGenome Project (EBP, www.earthbiogenome.org). ERGA is working towards the creation of a distributed genome generation infrastructure across Europe and fostering the exchange of genomics expertise so that high-quality reference genomes can be generated for all eukaryotic species on the continent. Since a large number of ERGA Members will be attending SMBE23, we invite the community to a brainstorming session regarding the challenges and opportunities of reference genomes. We aim to define and answer outstanding questions about the genome generation workflow (from sampling to sequencing, assembly, annotation, and beyond) and how to amplify genomics knowledge across the scientific community and society. Further details will be circulated to ERGA Members through our mailing lists and community chat forum. Not an ERGA Member? You can sign up here: https://www.erga-biodiversity.eu/contact-us Questions? You can contact ERGA Coordination via contact@erga-biodiversity.eu or check out these short introductory videos explaining the organisation of ERGA, the ERGA Council, and the ERGA Committees: https://www.youtube.com/@erga-consortium1001

In a new paper recently published in the Journal Trends in Genetics, members of the European Reference Genome Atlas (ERGA) advocate for reference genomes as fundamental resources in biodiversity conservation, showcasing genomics as an emerging powerful tool for species conservation. The review illustrates that reference genomes have the combined power of speeding up genomic analysis and making results more reliable: exactly what is needed in conservation science. Genomes for biodiversity conservation - the connection between these might not be evident at first, but genetics provides critical evidence for scientifically informed management decisions. In a paper recently published in the Journal Trends in Genetics, a group of researchers affiliated to the European Reference Genome Atlas reviews the potential of genomic data in safeguarding global biodiversity, emphasising the advantages of reference genomes for increased speed and reliability of results. Biodiversity is the variety and variability of life on Earth, a prerequisite for ecosystem functioning and health. Human actions have resulted in the ongoing extinction wave which poses a significant threat not only to other living creatures, but to humanity itself. To effectively protect biodiversity, we must first understand it. Scientists have known for a long time that the origin for all the astonishing variation we see in living species - from shape, size, colour, behaviour and many other characteristics - is encoded in their genomes. The genome of an organism is the complete set of its genetic material (usually DNA) stored inside its cells. The genetic material serves as a “blueprint” for the construction and organisation of the organism's body, containing the instructions for it to function and allowing it to pass its characteristics onto the next generations. In spite of being the basis for all other levels of biodiversity, this underlying genetic diversity has often been neglected in biodiversity assessments and conservation efforts. “Many factors can explain this neglect, including lack of awareness, technical limitations, costs and the complexity of studying genetic diversity”, explains Kathrin Theissinger, Researcher at LOEWE centre for Translational Biodiversity Genomics in Germany and one of the first co-authors of a recently published paper that reviews the application of genomic tools to conservation efforts. “Despite these challenges, the importance of genetic diversity is now widely recognized, and even mentioned as a central goal in the recent COP15 conference. Conservation efforts are increasingly incorporating genetic information into their assessments and planning. Advances in technology and methods for studying genetic diversity have made it easier and more affordable to assess genetic variation, and there is a growing awareness of the importance of maintaining genetic diversity for the long-term survival of biodiversity.” complements Theissinger. In recent years the accelerated technological advances in the field of genomics have indeed made the goal of obtaining the complete genome of each species on the planet seem more feasible than ever. While it took humanity over ten years and around $300 million dollars to sequence the first human draft genome, a high-quality reference genome of comparable size can now be obtained in a matter of weeks for around 5,000 dollars. Of course, sequencing all life is still a very ambitious goal, and scientists across the world are connecting through the Earth BioGenome Project (EBP) - an extensive multinational network - to tackle this collective challenge. At a regional level, researchers have formed the European Reference Genome Atlas (ERGA), the European node of EBP. “ERGA is a scientific consortium that aims to promote the generation of high-quality reference genomes for European eukaryotic biodiversity while building a distributed genomic structure across Europe and facilitating the exchange of genomics expertise across the whole continent”, says Camila Mazzoni, group leader at the Leibniz Institute for Zoo and Wildlife Research and chair of ERGA. ERGA has a strong conservation genomics component and was recently funded through a Horizon Europe call on Biodiversity and Ecosystem Services. In the coming years the consortium will be generating hundreds of genomes ranging from endangered species, species of importance for ecosystem function and stability, to key species for agriculture, forestry, and fisheries, but also non-model organisms from underrepresented groups that make up a huge yet overlooked proportion of biodiversity. Sequencing complete high-quality genomes for multiple individuals is still not feasible for most endangered species, but as highlighted in the review, one or a few excellent quality genomes can take species conservation a long way. This is because a single high-quality reference genome can be used to support and enhance an array of different analyses, based on data that can be obtained at lower cost. “Genomics allows geneticists and managers to arrive at more precise study of parameters which have been in focus for decades such as the genetic consequences of fragmentation on diversity, divergence and inbreeding.” explains Jacob Höglund, Professor of Animal Conservation Biology at the Uppsala University and corresponding author of the paper. “It also opens up for new conceptual advances and new questions concerning the study of these issues. For example the interaction between population size and isolation, genetic load, inbreeding depression, evolvability and extinction.” Conclusions drawn from analysing a species' genomic diversity can then be applied to the real world in multiple ways. “Genomic data provides a powerful tool for understanding the genetic basis of biodiversity, giving a high-resolution insight into the genetic composition and therefore the adaptive potential of a species, a population or a community, and can be used to inform and guide conservation efforts in the Anthropocene.” says Theissinger. This knowledge can for example help practitioners decide which areas should be prioritised as conservation units or which individuals to include in a breeding program in order to optimise the genetic outcomes for the species. “Genomic knowledge in threatened species opens up numerous future possibilities for research and application, including the characterization and management of functional variation and genetic load, and the design of improved genetic rescue programs.” says Carlos Fernandes, a wildlife genetics scientist at the University of Lisbon and one of the first co-authors of the paper. Overall, this review provides a valuable resource for those who wish to obtain a first grasp of the interface between genomics and conservation. As Giulio Formenti, one of the paper’s first authors and a founding member of ERGA, puts it: “This collective work provides an excellent review on how reference genomes and genomics in general can aid conservation efforts. As such, it will constitute an essential resource to train the next generation of conservation genomicists.” Fernandes complements: “We hope that our work can contribute to bridging the gap and increase dialogue and synergies between conservation genomicists and practitioners for the sake of biodiversity conservation." Publication Kathrin Theissinger, Carlos Fernandes, Giulio Formenti, Iliana Bista, Paul R. Berg, Christoph Bleidorn, Aureliano Bombarely, Angelica Crottini, Guido R. Gallo, José A. Godoy, Sissel Jentoft, Joanna Malukiewicz, Alice Mouton, Rebekah A. Oomen, Sadye Paez, Per J. Palsbøll, Christophe Pampoulie, María J. Ruiz-López, Simona Secomandi, Hannes Svardal, Constantina Theofanopoulou, Jan de Vries, Ann-Marie Waldvogel, Guojie Zhang, Erich D. Jarvis, Miklós Bálint, Claudio Ciofi, Robert M. Waterhouse, Camila J. Mazzoni, Jacob Höglund, How genomics can help biodiversity conservation, Trends in Genetics, 2023, ISSN 0168-9525, https://doi.org/10.1016/j.tig.2023.01.005. (https://www.sciencedirect.com/science/article/pii/S0168952523000203)