Search Results

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:

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 posts that explore the fascinating world of Biodiversity Genomics  and the intersection of their communities. In the second episode of Genomic Connections , Kasia and Christian chat with Claudio Ciofi - Professor at the University of Florence and founder of the Florence High-Throughput Sequencing Facility. They ask Claudio about the many ways DNA information is empowering biodiversity research and improving conservation outcomes, the top methods and technologies for obtaining high-quality genomic data, his first-hand experiences working in the field to collect samples from fascinating species such as Komodo dragons and Galápagos tortoises, and, finally, his vision for the future of the rapidly evolving field of biodiversity genomics. 🎧 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 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 our earlier posts, we celebrated the technical wizardry that empowers iBOL Europe’s DNA barcoding and ERGA’s reference-genome pipelines. Today, we zoom out from benchtop and bioinformatics queues to the rules  for using those pipelines responsibly. The conversation here is based on two elements: the Nagoya Protocol on Access and Benefit Sharing (ABS)  and the debate over Digital Sequence Information (DSI) . Both are under the umbrella of the United Nations Convention on Biological Diversity ( CBD ), and both are poised to shape every barcoding run and every reference genome we produce. The Nagoya Protocol , adopted in 2010 and enforced in 2014, translated the Convention’s promise of fair and equitable benefit‐sharing into operational obligations. Field teams who collect specimens must secure Prior Informed Consent and negotiate Mutually Agreed Terms before any genetic resource crosses a border. These administrative steps aim to curb scientific colonialism, foster respect for Indigenous knowledge systems, and channel royalties or capacity‐building back to the nation where the specimen was collected. iBOL Europe and ERGA already navigate this protocol daily, because each barcode voucher and each specimen used for the generation of a reference genome must carry a transparent legal pedigree. Source: https://www.cbd.int/convention/articles/default.shtml?a=cbd-01 The CBD  entered into force in 1993, and the boom of sequence databases soon revealed a gap in the Convention. Indeed, the CBD focuses on physical samples, while genomic data travels instantly across digital platforms. The policy community coined the term Digital Sequence Information (DSI) to highlight this distinction - DSI refers to raw reads, assemblies, and barcodes. Since 2016, Parties to the Convention have sought a mechanism that extends benefit-sharing to these 'files' without impairing open science principles. Negotiators progressed at the Kunming–Montreal Conference of the Parties in 2022. This process led to the establishment of the Cali Fund for the Fair and Equitable Sharing of Benefits from the Use of Digital Sequence Information on Genetic Resources during COP16 in 2024/2025, aimed at collecting contributions from commercial users of DSI. COP16 laid the groundwork for implementing these mechanisms, and ongoing discussions will continue to fine-tune the system. ABS permits are NOT “boring compliance forms" to rush through on the eve of submission. They are architectural blueprints for an equitable, reproducible, and future-proof research culture. The sooner biodiversity researchers integrate Nagoya thinking and prepare for DSI benefit-sharing, the smoother the path for publishing, sharing, and reusing our data sets will be. So, the next time you plan a field expedition or start assembling a genome, remember: ethics is not a speed bump; it’s the on-ramp to a legacy of science that everyone can share.

The new ERGA Community Genome Reports Collection  hosted at Pensoft’s RIO Journal offers an open and inclusive space for Genome Reports produced by the ERGA community. With clear guidelines and a shared platform for creating standardised reports, we hope to reduce the effort required from individual researchers. In doing so, we aim to support the production of more high-quality Genome Reports, increasing visibility, recognition, and reusability across the entire community. The RIO Journal platform allows preprinting at no cost and publishing following a standardised format for an affordable fee. The collection also accepts Genome Reports published elsewhere - so if you wish to publish in a different journal the report can still be displayed in the ERGA collection. More details about the process are outlined below. Several genome reports are already available in the ERGA Community Genome Reports Collection .  What is a 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 follow a standardised format and structure  that allows readers to quickly and easily understand the quality of the genome and how it was generated. Genome reports are “data papers” - unlike classical research papers, they generally do not include any type of downstream analysis or evolutionary interpretation of results. A Genome Report will typically include a brief introduction about the species sequenced, a detailed description of the methodology used to obtain the genome (from sampling in the field to the bioinformatic steps) and plots and statistics that summarise the quality of the resulting genome assembly. Why are Genome Reports encouraged by ERGA? They allow for the proper recognition  of everyone who contributed to the production of the reference resource in a citable manner. They support open and reproducible science  - by providing all the methodological details that are often cut or condensed in traditional research manuscripts. They allow crucial information to be shared soon after the genome assembly is ready - well before downstream analyses, which can take months or years, are completed. This helps accelerate the use and application of the data. There are different ways of contributing to the ERGA Community Genome Reports Collection: [1] Link a Genome Report published elsewhere to the Collection (free of charge) Click on “Add document to collection” ⇒ confirm you have consent of all authors ⇒ import (add) and confirm publication metadata (authors, etc.) ⇒ submit request ⇒ editors check requirements ⇒ accept ⇒ appears in the Collection linked to the source publication No cost [2] Add a preprint PDF to the Collection (free of charge) Click “Start manuscript” ⇒ confirm you have consent of all authors ⇒ complete publication metadata (authors, abstract, etc.) ⇒ upload your PDF ⇒ submit request ⇒ editors check requirements ⇒ accept ⇒ appears in the Collection as a preprint No cost, Community can comment on the preprint [3] Write and submit your manuscript for Peer-Review publication in the Collection  Using the ARPHA Platform  to create your Genome Report. You can then submit it for peer-review Click “Start manuscript” ⇒ write and submit your manuscript using the ARPHA Writing Tool ⇒ submit request ⇒ editors check requirements ⇒ peer-review ⇒ accept ⇒ appears in the Collection as a peer-reviewed publication  Publication cost: EUR 270 - 330, fully semantically published article with DOI at RIO What are the requirements for adding a Genome Report to the collection? The requirements and recommendations for a Genome Report publication to be included in this collection are detailed here . Each submission to the Collection will be evaluated by the Collection Editors, to decide whether the Genome Report satisfies the criteria for inclusion. Watch this talk by Robert Waterhouse for more details about the collection. If you have any questions about the collection, please contact   robert.waterhouse@gmail.com The creation of this collection was supported by the Biodiversity Genomics Europe (BGE) project through the Horizon Europe Framework Programme of the European Union under grant agreement No. 101059492, funded by Horizon Europe under the Biodiversity, Circular Economy and Environment (REA.B.3); co-funded by the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number 22.00173 and 24.00054; and by the UK Research and Innovation (UKRI) under the Department for Business, Energy and Industrial Strategy’s Horizon Europe Guarantee Scheme.

In the fourth episode of Genomic Connections , Kasia and Christian chat with Amber Hartman Scholz, microbiologist and Head of the Science Policy & Internationalization Department at the Leibniz Institute DSMZ in Braunschweig, Germany. They dive into the topic of Digital Sequence Information, or DSI, and the ongoing global discussions on how to ensure equitable access to and fair sharing of benefits arising from the use of genetic information from biodiversity. 🎧 You can listen to Genomic Connections on Spotify and PocketCast . Interested in this topic? Learn more about the Nagoya Protocol on Access and Benefit Sharing (ABS) and the debate over Digital Sequence Information (DSI): https://www.erga-biodiversity.eu/post/dna-rules-fair-play 🔔 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

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.

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