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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.

At this month's ERGA Plenary meeting , on Monday, June 16 at 15:00 CEST , Robert Waterhouse will introduce the new ERGA Community Genome Report Collection at Pensoft's Research Ideas and Outcomes (RIO) journal . Abstract 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. 🔔 To receive the Zoom link and join this and our upcoming plenary meetings, register as an ERGA member . ▶️ You can watch all previous ERGA Plenary talks here . If you would like to suggest a speaker or topic for a future plenary session, please contact us at training@erga-biodiversity.eu . We welcome your input!

This month's ERGA BioGenome Analysis & Applications Seminar will feature two talks on the use of target capture sequencing to study plant evolution. Learn more about these exciting presentations by Lisa Pokorny and Pol Fernández Mató below. 🕚 Monday, June 23rd 2025 - 12:00 PM CEST 📅 Add the seminar to your calendar Watch the recorded seminar: Abstracts Target capture sequencing approaches to the study of plant evolution - Lisa Pokorny Understanding plant evolution requires integrating data across micro- and macroevolutionary scales to uncover the processes shaping biodiversity. Advances in HTS have transformed evolutionary research, providing unprecedented resolution for studying these evolutionary processes and the patterns they result in. However, many plant species have extremely large genomes (often polyploid and with an overabundance of repeated elements), making WGS impractical. Hyb-Seq, a HTS approach that combines target capture sequencing with genome skimming, offers an efficient alternative by selectively recovering both highly-conserved nuclear loci (e.g., orthologs) and broader genomic content (high-copy number regions). Hyb-Seq is particularly powerful for integrating natural history collections into biodiversity research, expanding the scope of evolutionary studies. Target capture sequencing and the challenge of the largest Eukaryotic genomes: insights from Tmesipteris - Pol Fernández Mató Building on the basics of target capture sequencing, this case study explores its application in Tmesipteris , a fern genus with the largest known genomes among all eukaryotes. We demonstrate how custom target capture sequencing strategies can overcome the challenges posed by extreme genome size and polyploidy, enabling the study of the previously untapped lineages to obtain novel evolutionary insights. Speakers Lisa Pokorny , Ramón y Cajal Researcher at Real Jardín Botánico (RJB-CSIC), Spain. Lisa graduated ( B.Sc . in Biological Sciences) from Autonomous University of Madrid (UAM, Spain), where she also got her M.Sc . in Evolutionary Biology and Biodiversity. She got her PhD in Biology from Duke University (Durham, NC, USA). Her postdoctoral trajectory spans RJB-CSIC, Royal Botanic Gardens, Kew (Richmond, UK), ICBGP (UPM-INIA/CSIC, Madrid), and BB (CSIC-MCNB, Catalonia). Her research focuses on understanding of the mechanisms driving the origin, maintenance or loss of biodiversity across spatiotemporal scales. For this she implements molecular HTS approaches (target capture sequencing) and bioinformatic HPC workflows (phylogenomics and population genomics) to bridge evolutionary scales and to unravel biogeographic patterns in land plants (and other organisms).  Pol Fernández Mató , Institut Botànic de Barcelona (IBB, CSIC-CMCNB), Catalonia  Graduated in Biology from the Universitat de Barcelona (UB). He later received a "la Caixa" scholarship to pursue a master's degree in the Erasmus Mundus programme TROPIMUNDO and is currently completing his thesis at the Institut Botànic de Barcelona (IBB, CSIC-CMCNB) under the supervision of Jaume Pellicer on the Evolution of Giant Genomes in Plants, funded by the Spanish Ministry of Universities through an FPU grant.

🗓️ 17 - 22 August 2025 📍 Barcelona, Spain This August, ERGA will be in Barcelona to participate in the Congress of the European Society for Evolutionary Biology ( ESEB 2025 ). This large and exciting conference is a great opportunity for many ERGA members to gather in person, exchange ideas, and connect! During the conference, visit the ERGA booth in the main hall to learn more about our community, discover our many initiatives, and meet fellow members. More details about the booth programme coming soon! Are you presenting a poster, giving a talk, or hosting a symposium at ESEB? Send us an email at media@erga-biodiversity.eu — we’d be happy to help promote your work! We look forward to seeing you in sunny Barcelona! ☀️ #ESEB2025

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. ERGA and iBOL Europe have been working together to bring biodiversity genomics closer to you through a collaborative blog series, “ Connections .” Now, we’re thrilled to announce that this collaboration is expanding into a new format: 🎙️ Genomic Connections – a podcast about the science, stories, and people behind biodiversity genomics. Starting in April 2025, a new episode of Genomic Connections  will be released every month. The podcast will be hosted by Christian de Guttry  (ERGA Project Manager) and Kasia Fantoni  (iBOL Europe Community Manager), who will dive into key topics in biodiversity genomics alongside special guests from the BGE community — scientists and experts working at the forefront of this exciting field. Each episode will explore a different step of the genomic workflow, always highlighting the many connections between our two genomic communities and the advantages of joining forces for better outcomes for biodiversity. You’ll hear directly from the people who are helping boost genomic science and infrastructure in Europe — the challenges they face, the innovations they develop, and the impact of their work. Whether you're a scientist, student, or simply curious about how genomics is helping us understand and protect life on Earth, Genomic Connections  is the right podcast for you! 🔔 Click here to follow Genomic Connections on Spotify to make sure you never miss an episode! #GenomicConnections Episode 1 ❄️ Frozen Futures: The role of biobanking in Biodiversity Genomics with Jonas Astrin and Camilla Di Nizo In the very first episode of Genomic Connections, Kasia and Christian spoke to Jonas Astrin & Camilla Di Nizo, both from The Leibniz Institute for the Analysis of Biodiversity Change ( LIB ), about the role of biobanking  in Biodiversity Genomics. 🎧 Listen to the episode to learn more about their day-to-day work and the basics of biobanking: what it actually means and why is it so important for biodiversity research? Do you have any suggestions about how we can improve the podcast or biodiversity genomic-related topics you would like us to cover? Send us a message! media@erga-biodiversity.eu Read the other posts in the series:

In the third episode of Genomic Connections , Kasia and Christian chat with Joana Pauperio, Biodiversity Project Manager at the European Nucleotide Archive, in the European Bioinformatics Institute ( EMBL-EBI ). They discuss the concept of “metadata,” why it is crucial to ensure high-quality research, and some best practices scientists should follow to ensure the data they produce is FAIR - Findable, Accessible, Interoperable, and Reusable. 🎧 You can listen to Genomic Connections on Spotify and PocketCast . 🔔 Click here  to follow Genomic Connections on Spotify to make sure you never miss an episode! Do you have any suggestions about how we can improve the podcast or biodiversity genomic-related topics you would like us to cover? Send us a message! media@erga-biodiversity.eu

The ERGA Plenary Meetings are the main monthly gatherings of our community, when announcements are made and discussions and debates are conducted on topic-oriented presentations. The plenaries happen on the third Monday of each month at 15:00 CET. To receive our regular emails with the links to join the meetings you simply need to register as an ERGA member . The meetings always include updates by the ERGA committees and at least one presentation on various topics related to the genome generation workflow. Check the playlist to watch previous plenary talks: 📅 Check the #ERGACalendar to stay up-to-date with all events and meetings

Did you know that the Biodiversity Genomics Europe ( BGE ) project is producing genomes with the help of hundreds of scientists across Europe?  This endeavour was made possible through open calls during the early phase of the project, where researchers were invited to propose their "favorite" species for genome sequencing. The resulting wishlist included over a thousand species! Choosing which ones to prioritise required a selection process developed by BGE - click here  to learn all about it. Some of the species suggested for genome sequencing by the European research community. Photos by P. Oromi, Miquel Pontes, Frederic Zuberer, V Decroocq, Tetiana Derevenko. The selection process was essential to prevent duplicated efforts and to prioritize species based on various criteria, including taxonomic and geographic representation, as well as scientific, cultural, or economic significance. This was a crucial step to ensure that the biodiversity sequenced under BGE was truly diverse and not only charismatic species like birds and mammals were sequenced, but also a variety of lesser studied organisms that also deserve the spotlight, such as algae, worms, and fungi. All BGE genomes are being produced following the guidelines and standards established by the European Reference Genome Atlas ( ERGA ) - the European node of the Earth BioGenome Project ( EBP ) - to achieve high levels of quality and completeness.  To learn more about all the species currently being sequenced under ERGA-BGE, we invited the researchers who proposed them to give brief talks addressing: What makes the selected species so interesting? What key questions are scientists most excited to explore with its genome? Watch the videos below to find out!  Playlist: Community-driven Reference Genomes - Biodiversity Genomics Europe Several of these genomes are already openly available for anyone to use!  🧬 Check the collection of ERGA-BGE genomes at the European Nucleotide Archive >> 🌍 Check the distribution of all genomes sequenced under the ERGA umbrella >> 📑 Check the collection of ERGA-BGE Genome Reports already available >> Learn more: What is a reference genome and what does it mean to sequence it? What is the European Reference Genome Atlas? How are ERGA and BGE connected?

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