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This month's ERGA BioGenome Analysis & Applications Seminar will feature a talk by speaker Pío Sierra about a new tool, pantera, which allows faster identification of Transposable Elements in genome assemblies. 🕚 Tuesday, July 8th 2025 - 11:00 CEST 📅 Add the seminar to your calendar Youtube link: https://www.youtube.com/watch?v=gTCUd1SIxa8 Watch the recorded talk: Abstracts Faster identification of Transposable Elements in full genome assemblies New high quality genomes, together with faster whole genome alignment methods, have opened the possibility of identifying new Transposable Element (TE) families by their polymorphic character in different genome sequences, in contrast to previous methods based on repetitiveness, homology and structural features. We have developed a new tool, pantera, which can leverage this capability and the availability of new genome assemblies to improve our knowledge about transposable elements and the roles that they play in genome evolution. In this presentation I will explain how it works and some results from applying it to several species across the tree of life. Speaker Pío Sierra ,  Research Assistant, Karam Teixeira Group - Department of Genetics, University of Cambridge I am a computational biologist from Spain that came to bioinformatics a little late, or just in time, depending on how you look at it. I just obtained my PhD and I specialized in analysis of transposable elements.

In a new publication, the European Reference Genome Atlas (ERGA) members call the biodiversity genomics research community to harmonise practices in the assessment of genome-wide genetic diversity. Standardisation is needed to improve the integration of genomics-informed insights into conservation efforts and better meet the needs of stakeholders such as policymakers, conservation practitioners, and local communities. The invited review entitled “Biodiversity Genomics Research Practices Require Harmonising to Meet Stakeholder Needs in Conservation” is published as part of Molecular Ecology’s special issue “Conservation Genomics - Making a difference”. The main message of the publication is that to fully realise the potential of genomics in biodiversity conservation, the scientific community must develop and adopt harmonised, stakeholder-informed standards that encompass not only the production and management of genomic data, but also downstream analysis and interpretation. The paper calls for a collaborative, inclusive, and practical approach to embed genomic tools into conservation policy and practice globally and highlights the ERGA community’s ongoing efforts towards this goal. The publication was made possible thanks to funding from the Biodiversity Genomics Europe Project, which aims to advance the use of genomics in conservation and policy-making. Examples of successful stakeholder engagement in biodiversity genomics leading to improved conservation outcomes across the tree of life: root-associated fungal species in Sweden, butterflies in Switzerland, and the keystone European Aspen in Scandinavia. Photos: Wylius (via Getty Images), Jean-Paul Boerekamps, and Игорь Загребин (via iNaturalist). Identifying the problem Despite the widely recognised importance of genetic diversity estimates to assess factors relevant to species’ conservation, such as their adaptability and resilience, the application of genomics-informed insights into concrete conservation actions is still limited. In this invited review, the authors make the point that this limitation is partly due to widespread inconsistencies in the ways genomic data used for genetic diversity estimates are generated, analysed, and interpreted. While state-of-the-art genomic tools, like whole-genome (re)sequencing (WGS), provide high-resolution insights into genetic diversity, they also require consistent methodologies across time and space to ensure stronger conservation impact. The effective translation of genomic insights into concrete conservation measures is also limited due to known challenges of the scientific community in connecting, communicating, and engaging with other relevant stakeholders - policymakers, conservation practitioners, and local communities; and the uneven access to genomic technologies across the globe.  Taking action The authors make the case that in order to meaningfully integrate their science into conservation, the biodiversity genomics community must make an effort to co-create their research projects with active participation of other stakeholders every step of the way.  The paper presents successful examples of this co-creation process: three case studies that concretely demonstrate how the early involvement of stakeholders in conservation projects leads to better adoption and practical application of genomics data. On the other hand, the paper also presents the results of surveys and workshops promoted within the ERGA community, which highlight that there is a critical need to build capacity amongst scientists and improve their skills in identifying and effectively engaging relevant stakeholders.  Figure from Buzan, Guttry et al., 2025, Molecular Ecology, CC BY 4.0. A framework for enhancing consistency and comparability of genetic diversity assessments through improved harmonisation and standardisation of key steps from study design to data archiving. A call to the research community Based on the issues identified, the authors launch a call to action: while a lot of ongoing efforts aim to standardise the production of reference genomes (and other reference resources),  it’s time to also create and promote standards for downstream genomic diversity assessments . Such standard metrics and best practices will greatly enhance accuracy and comparability across studies and increase their accessibility and uptake by other stakeholder groups, leading to better conservation outcomes. Solutions proposed to achieve this harmonisation include several community-driven actions such as developing consensus guidelines and analytical pipelines for genomic data, promoting training and capacity-building initiatives for scientists and other stakeholders, and strengthening inclusive and equitable data practices aligned with FAIR and CARE principles. Buzan, E., Guttry, C. D., Bortoluzzi, C., Street, N., Lucek, K., Rosling, A., ... & Waterhouse, R. (2024).  Biodiversity Genomics Research Practices Require Harmonising to Meet Stakeholder Needs in Conservation. Molecular Ecology, 2025. DOI: https://doi.org/10.1111/mec.70001 For more information about the European Reference Genome Atlas (ERGA), please visit erga-biodiversity.eu  and follow the initiative on social media. Join us in advancing the frontiers of biodiversity genomics and contributing to make the field more inclusive.

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. What is a Biodiversity Hotspot? 🔥 Biodiversity hotspots are regions that are exceptionally rich in endemic species  (those found nowhere else), into relatively small areas, but face important threats. Consequently, these Hotspots are global conservation priorities because they harbour a large portion of Earth's biodiversity. The European continent hosts such hotspots, and Biodiversity Genomics Europe, under a dedicated partnership agreement led by CSIC, the Spanish National Research Council, chose six priority countries to boost the generation of genomic resources for their most distinctive species: What is a BioBlitz? ⚡ BioBlitzes, coordinated sampling efforts that unite taxonomists, genomicists, and volunteers, are beneficial in two ways. First, they act as a field classroom, immersing citizen scientists, from local residents to school students into science, strengthening community awareness. Second, DNA barcodes  generated during an event provide information about which species are present, while reference-quality genomes  built from those same species help us understand how they work, adapt, or decline. Data from barcodes and genomes are tightly coupled: barcodes provide real-time monitoring, while genomes reveal functional variation that informs management. Click to learn more about barcoding and reference genomes . Croatia - Genomes in the dark - collecting in a hidden biodiversity hotspot The Dinaric mountain range of Croatia is home to the world’s richest subterranean biomes and is the historical cradle of biospeleology (cave biology).  Cave species evolved in remarkably stable conditions, which makes them highly vulnerable to rising temperatures and other disturbances. Their subterranean habitats are isolated, and the organisms cannot survive on the surface, leaving them with no migration possibilities when the environment changes. This ecological trap makes genomic studies and the protection of their subterranean refuges increasingly urgent. Did you know?   So far, 900+ cave species have been found in the Dinarides, with over 150 new ones reported in Croatia since 2002.  Two cave-focused BioBlitzes took place in April and October 2024, one on the island of Mljet, the other in Velebit’s Cerovac caves. Participants learned how to locate invertebrates, recognize different species, and preserve specimens for barcoding and genome sequencing. More than forty cave species were secured. In addition, park staff and school groups were introduced to biodiversity genomics and learned more about how genomic resources can support biodiversity assessment, conservation, and restoration efforts by providing scientific evidence for informed management decisions. This outcome demonstrates how local partnerships and the use of genomic data can advance subterranean biodiversity conservation. Photos by Martina Pavlek, Iva Cupic, Jana Bedek, TIn Rozman, Alen Kirin and Nikolina Kuharic.

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 #6 - Biodiversity Hotspots & how to study them Press Releases ERGA at ESEB 2025 Events Genomic Connections #3 - DNA Metadata and FAIR Play Press Releases

socialjustice@erga-biodiversity.eu < Back Social Justice Committee socialjustice@erga-biodiversity.eu Co-chairs Fabrizio Ghiselli James Fleming Head to the committee page >> Connection #6 - Biodiversity Hotspots & how to study them Press Releases ERGA at ESEB 2025 Events Genomic Connections #3 - DNA Metadata and FAIR Play Press Releases

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 #6 - Biodiversity Hotspots & how to study them Press Releases ERGA at ESEB 2025 Events Genomic Connections #3 - DNA Metadata and FAIR Play Press Releases