Search Results

Author: Ann Mc Cartney (ERGA Pilot Project Committee) Originally written for the Research Data Alliance Blog The crisis In the midst of our sixth mass extinction, according to recent reports from IUCN a total of 41,000 of our known species are threatened with extinction. The extinction of Earth’s species is not confined to a particular taxonomic group, nor to a specific geographic area (Fig 1), but rather it is a global problem that has been considered by the Convention on Biological Diversity to be a “common concern” of all humanity. Despite the conservation and preservation of our biodiversity being a shared global problem, the solutions for each species, ecosystem, and geographic location will need to be tailored accordingly. Targeted universalism is one strategy proposed to achieve a shared mission through locally contextualized solutions. Genomes for conservation A key aim of the biodiversity genomics research enterprise is to provide a catalog of Earth’s biodiversity through genomic sequencing technologies, using this information to develop tools, metrics and indicators that can contribute to the conservation and preservation of species. Acknowledging the magnitude of work ahead, in 2018 the Earth BioGenome Project (EBP) was established. The EBP as an umbrella organization acts to synergize the efforts of biodiversity genomic initiatives across the globe. The organization is growing, with >50 affiliated initiatives to date. In 2021, the first regional node of the EBP was established, the European Reference Genome Atlas (ERGA). The mission of ERGA is to use DNA sequences to catalog and build our understanding of all Europe’s eukaryotes. For each species, a vast quantity of sequencing information will be produced - enough to cover the entire DNA record, or genome, of the species. This sequence information will then be carefully placed together, akin to placing the pieces of a jigsaw puzzle together. However, as there are typically many many more DNA sequences than jigsaw puzzle pieces, this is done through computational algorithms to ensure the sequences are put together in the correct order. After assembling the pieces of the sequence puzzle - the product is called a reference genome. Reference genomes are powerful tools yielding the ability to explore previously unknown aspects of the species we share our planet with. Genomes from the same species can be compared to understand the diversity within - an indicator of a species resilience to climate changes. Genomes from different species can be compared to better understand their evolutionary relationship, providing a more clear understanding of the branches that compose the tree of life. Genomes also contain genes that can be compared to identify genes that are associated with specific characteristics and can have huge implications for biodiversity and ecosystem health (including humans!), food-security, and ecosystem services. The breadth of applications made possible by reference genomes highlight the importance of investing resources into their generation for all species. Situating genomes in a socio-political context The creation of genomes is not outside of the socio-political realities that exist across the globe today. Generating data to create accurate and complete reference genomes requires expensive sequencing equipment, laboratory access, a skilled workforce, and significant computational resources. Just like the distribution of biodiversity, the resources to create reference genomes are not evenly distributed across the globe. For ERGA specifically, this is evident if one looks at the OECD reports on GDP per capita and the percentage investment in R&D per country in Europe. To address this and learn about how these structured inequities would manifest in ERGA, a Pilot Project (ERGA-Pilot) was established. From its outset, ERGA-Pilot recognised that the purposeful inclusion of segments of the population, Peoples, and communities that have and continue to be left outside of research was fundamental to the long-term success of the ERGA. The Project was also cognisant that the foundations built during the pilot phase would have huge implications on who was included, had access to, and benefitted from the production of genomes across Europe into the future. To this end, ERGA-Pilot undertook a critical evaluation of justice, equity, diversity and inclusion (JEDI) throughout all stages of the decision-making processes associated with the project design. Here, the intentional acknowledgement, recognition and participation of Indigenous Peoples and Local Communities (IPLCs) and respect for their sovereignty was considered a priority. By intertwining JEDI into the scientific mission of the ERGA-Pilot in this way, a strategy for establishing a decentralized, accessible, and scalable infrastructure that supported the production of reference genomes for all species, and was accessible to all researchers across Europe was designed. This infrastructure was designed to ensure that it was responsive to the rights codified in the United Nations Declaration on the Rights of Indigenous Peoples (UNDRIP), that outlines Indigenous Peoples’ right to exercise sovereignty over their genetic resources and data. Contemporising genome data governance for a more just, equitable and inclusive genomic future IPLCs have, and continue to be left outside of the research enterprise, specifically genomic research. Typically, when genomic research has been conducted with IPLCs, it is usually done on them, their knowledge systems, and resources for the benefit of an external project’s research agenda. Seldom does the research provide meaningful results back to the IPLC, and rarely does it sustainably include IPLCs as equal partners. IPLCs have grown tired of “gifting” their time, resources, and knowledge to research under the auspices of the “public-good” without involvement, benefits, and fair attribution. Many IPLCs are now taking this into their own hands. Indigenous digital technologies, data governance principles, and research organizations are being created to take agency over Indigenous research, samples and data. These processes and procedures are driven by Indigenous ways of knowing creating a new research ecosystem that responds to contemporary research needs but remains outside of, and free from colonial legacies. As a westernized project co-ordinated by white privileged researchers, ERGA-Pilot sought out opportunities to incorporate sovereignty in a way that implemented these creative and innovative tools already being produced by leading Indigenous Data Sovereignty experts. For this, a partnership with Global Indigenous Data Alliance (GIDA) and Local Contexts was established, and funded through an EOSC-Future Funding Platform Grant [RDA_OSF_EOSC-228]. The partnership focussed on developing novel strategies to operationalise the CARE principles for Indigenous data governance over samples and data generated for the purposes of reference genome production that had been collected from IPLC lands, air, and waters. Whilst evaluating the project design, it was determined that integrating the Local Contexts Traditional Knowledge and Biocultural Label and Notices system within the ERGA-Pilot as a standard of practice, would ensure that any Indigenous rights and interests could be disclosed and associated with all IPLC samples and data collected in partnership with ERGA. Contextualising Genomes The power of reference genomes is driven by the breadth of potential research applications it can support. In 2016, the FAIR principles were developed to provide researchers data-centric guidance for realizing the full potential of data, for their own research purposes and for secondary users. The principles have since become a dogma within the biodiversity genomics research community, and an almost equivalent value is now being placed on the contextual information associated with generating the genome data - the metadata. Similar to many research standards of practice, existing metadata standards such as Darwin Core are plagued by colonial legacies. This has resulted in the adoption of standardized metadata schemas that have prioritized the collection of information that has been deemed important to western and white researchers. Subsequently leading to the standardized erasure of information of importance to IPLCs from sample and data records. Local Contexts is an Indigenous led organization dedicated to rectifying this wrong through the development of a human- and machine- readable disclosure system that functions to streamline the inclusion of Indigenous permissions, protocols and provenance into metadata records, within digital environments. The method of disclosure is initialized by both the researcher and IPLC registering on the Local Context Hub. From here, the researcher can create a research project for the samples or data and assign a Biocultural Notice to the project. This Notice will be immediately sent through the Hub to the partnering IPLC. Upon receiving the Notice, the IPLC can validate the Notice and issue a customized Traditional Knowledge and/or Biocultural Label/s disclosing any provenance, protocol or permission information the community would like to associate with the project and their resources. Each registered project contains a unique permanent identifier that can be placed into the metadata record of the associated samples and data, providing a long-term link to the disclosed Indigenous interests. For ERGA-Pilot, generating genomes for European species by researchers across all Europe required the development of a comprehensive and robust metadata collection procedure that could ensure that all samples collected and data generated, were associated with all relevant contextual information. Here, an ERGA metadata schema was established along with a supporting standard operating procedure. The completion of a valid metadata schema was mandatory for participation in the ERGA-Pilot. Metadata completeness and validity for the project was inspected by COPO, a metadata brokering platform. During schema development, a new, controlled, and validatible field was generated to support the implementation of the Label and Notices’ unique permanent identifiers (Fig.2). A guidance document was also developed to offer support for researchers new to the Label and Notices system. Decolonising metadata schema across biodiversity genomic research Embedding Indigenous rights and interests as part of the ERGA-Pilot metadata collection standard of practice provided every participating researcher the opportunity to collect samples and generate genome data that are in alignment with both the FAIR and CARE principles. Making space for Indigenous rights and interests as a standard of practice during the metadata collection procedure in this way has consequently resulted in the inclusion of these fields into ERGA as it moves beyond its Pilot Phase. However, we hope that by utilizing the ERGA-Pilot as a regulatory sandbox showcasing the benefit of this approach, that it will motivate and inspire uptake by other biodiversity genomics initiatives, metadata standards, public digital repositories, and scientific journals to build a more just, equitable and inclusive future for the scientific research enterprise at large.

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)