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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:

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 give a short introduction to both communities. In our first post , we introduced Biodiversity Genomics and its importance. Today, we highlight the two growing communities powering the Biodiversity Genomics Europe ( BGE ) project: iBOL Europe  and ERGA . Each of these pan-European networks brings its unique approach to understanding and protecting the living world, yet both share a common mission: to safeguard Earth’s biodiversity at a critical moment in our planet’s history. iBOL Europe  is the European regional node of the global International Barcode of Life consortium (iBOL) . Its core method, DNA barcoding , relies on short, standardised segments of DNA to identify species accurately and efficiently, much like human fingerprints can be used to identify individuals. With a broad network of more than 500 members from 173 institutions across 29 European countries, iBOL Europe is building an interconnected system that can rapidly detect and monitor species, offering critical insights into their distributions and interactions. iBOL Europe’s work also links into iBOL’s global BIOSCAN  initiative, which aims to track species worldwide, discover novel ones, and deepen our understanding of ecosystem dynamics. ERGA  (the European Reference Genome Atlas) tackles biodiversity from another angle: assembling high-quality reference genomes . As the European node of the Earth BioGenome Project (EBP ), ERGA’s goal is to coordinate the sequencing and assembly of the complete genomic “blueprints” of all eukaryotic species across Europe, offering extraordinary details about each organism’s genetic makeup. These chromosome-level genomes serve as foundational resources, allowing researchers to explore complex biological processes and evolutionary histories. Beyond generating genomes, ERGA’s pan-European community works on best-practice guidelines, training materials, and community-based actions that strengthen the entire biodiversity genomics ecosystem. Despite their distinct approaches, one focusing on rapid species identification through barcoding, the other on in-depth genomic assemblies, iBOL Europe and ERGA both endorse the urgent need to address biodiversity loss . Together, they form complementary pillars under the BGE project, accelerating our collective capacity to observe and protect life on Earth. In our next post, we will go deeper into how barcoding and reference genomes intersect, overlap, and collectively expand our understanding of biodiversity genomics. We hope you enjoyed this exploration of the two key communities, and we look forward to sharing more insights soon! 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 blog posts that explore the fascinating world of Biodiversity Genomics and the intersection of their communities. Biodiversity  is such a popular term that it’s easy to assume that it has been around for centuries, but, in fact, it is relatively new. The word "Biodiversity" was first coined in 1985 during the National Forum on Biodiversity  held in Washington, D.C. Before this, the term "biological diversity" was used but it was not until the Forum that the term "Biodiversity" took on its current meaning.  Biodiversity itself is a combination of two roots: " Bios " (Βίος), from the Greek word for life , and "Diversity," derived from the Latin word " Diversitas ," meaning variety or difference : Together, these two words describe the richness of life forms on Earth, including ecosystems, species - from plants and animals to bacteria, fungi, and microscopic organisms - and the genetic makeup of individual organisms. It is also about how life forms interact and build intricate communities, with each part contributing to something greater than the sum of its parts. While the concept of biodiversity has existed in scientific circles for years, it was not until the Earth Summit  in Rio de Janeiro (Brazil) in 1992 that it gained political traction. At the Summit, representatives from 150 countries signed the Convention   on   Biological   Diversity  (CBD). This marked a turning point, with biodiversity being recognised as an environmental issue and a critical factor in economic, social, and cultural well-being. The signing of the CBD was a major step in the international community’s commitment to the preservation and sustainable use of biodiversity, outlining three main objectives: the conservation of biological diversity, the sustainable use of its components, and the fair and equitable sharing of benefits arising from genetic resources. In 2022, the CBD was implemented to conserve the genetic diversity of all species within the Kunming-Montreal Global Biodiversity Framework – until then, it focused on domesticated and farmed species, cultivated plants, their wild relatives and other socioeconomically and culturally important species. What exactly is genomics ? Genomics is the study of an organism’s genome, which is its entire set of genetic material , and how this information influences its biology. Every single organism within the domain of Eukaryota (which includes plants, animals, fungi, and more) has a genome made up of DNA – the fundamental blueprint of life. Compared to genetics, genomics takes a broader scientific approach: it looks at all the DNA in an organism's genome, including both the genes that code for proteins and the non-coding regions that do not directly code for proteins but still play essential roles in gene regulation and function. What sets genomics apart from genetics is its comprehensive scope and the level of resolution it offers, allowing us to dive deeper into the complex genetic structure that defines every living being. However, it is worth noting that over recent years, the term genomics has been used more loosely to include areas of genetics and even DNA-barcoding research that use ‘genomics’ technologies. Genomics is closely tied to biodiversity because it helps us better understand a key overlooked component: "genetic diversity." In our next Connections blog post, we will take a closer look at how iBOL Europe and ERGA are advancing our understanding of biodiversity and genomics, shedding light on the complexity of life. We hope you have enjoyed this brief introduction to the concepts of "Biodiversity" and "Genomics." Stay tuned for more exciting insights in the upcoming posts!

At this month's ERGA Plenary meeting , taking place on Monday, May 19 at 15:00 CEST , Christina Hvilsom will present on national and international efforts to monitor genetic diversity, supporting policy goals and informed conservation. Abstract National and international efforts to monitor genetic diversity Genetic diversity is the foundation of biodiversity and essential for the long-term survival, adaptation, and resilience of populations, species, and entire ecosystems. While genetic diversity has long been neglected in biodiversity policy and management, the current Convention on Biological Diversity (CBD) Kunming- Montreal Global Biodiversity Framework (GBF) now includes genetic diversity monitoring, including for wild species. Tools and indicators to assess and monitor genetic diversity are available, but are rarely applied due to the gap in knowledge transfer between conservation science and application. GINAMO assesses and delivers science-based and co-designed best practices and guidelines for the use of genetic diversity indicators. This will enable the routine integration of genetic criteria and indicators into biodiversity monitoring and assessments, from policy at regional, national, and EU levels, to global conventions and obligations. A key component of GINAMO is the use of facilitated group decision-making processes to partner and co-decide from the outset with the stakeholder community, so that all resources produced meet their concerns, reporting duties, and monitoring needs, and are more likely to be adopted. Easy-to-apply, standardised and automated workflows will be co-created for assessing genetic indicators at various transboundary geographical scales. Speaker's Bio Christina Hvilsom Christina Hvilsom is based at Copenhagen Zoo where her main research area is applied conservation genetics, using genetics and genomics to enhance the success and sustainability of small populations and contrasting in- and ex-situ population management of endangered species. Her work has gradually shifted more into policy, lobbying, providing support and guidance for the uptake and use of genetic indicators by countries enabling them to monitor genetic diversity. Christina is involved in several international biodiversity consortia and networks facilitating collaboration across science, management and biodiversity policy-such as coordinating the EU Biodiversa+ project GINAMO . 🔔 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!

We are happy to announce that the Earth BioGenome Project ( EBP ) has formally recognised the European Reference Genome Atlas (ERGA) as its first regional node representing the European continent. This marks a significant milestone in the long-standing collaboration between the two initiatives and strengthens the biodiversity genomics community in Europe and beyond. The first EBP Regional Node Since the early establishment of ERGA in 2020, we have been connected to the EBP as part of the Network of Affiliated Projects . More recently, the EBP has defined a procedure for the establishment of Regional Nodes  - initiatives responsible for “coordinating EBP-related activities across broad geographical areas, including continents and political unions”. In the last years, ERGA has grown into a community of over 1000 members, taking a leading role as a hub for connecting hundreds of people and institutions, producing reference genomes for European biodiversity, and promoting valuable knowledge dissemination and exchange. The broad scope and inclusive nature of our community meant ERGA was well positioned to become the very first regional node of the Earth BioGenome Project. We are delighted to take on this role and excited about the opportunity of contributing to the EBP at a new level. ERGA as of May, 2025 - a growing community committed to the development of biodiversity genomics in Europe. *Genome assemblies linked to the ERGA umbrella bioproject at the European Nucleotide Archive produced by ERGA Affiliate Initiatives such as the Darwin Tree of Life, the Catalan BioGenome Project, the ATLASea Marine Genomes Project, the Biodiversity Genomics Project, and others. “The EBP is excited to designate ERGA as its first Regional Node, which encompasses biodiversity genomics research across the European continent. ERGA’s outstanding organization and state-of-the-art infrastructure will significantly contribute to the EBP’s goal of sequencing all 1.8 million named eukaryotic species in 10 years, providing solutions for species conservation and mitigating the effects of climate change on economically important plant and animal species.” Harris Lewin, EBP's Executive Council Chair. “As the EBP regional node, ERGA plays an important role in connecting and coordinating efforts in the region, from large-scale projects to individual researchers all contributing to assembling the atlas of reference genomes for biodiversity in Europe.” Robert Waterhouse , ERGA chair. “The official recognition of the European Reference Genome Atlas (ERGA) as the European node of the Earth BioGenome Project marks the culmination of years of dedication by a passionate and engaged community. From the initial brainstorming sessions during the pandemic—with over 100 participants—to the progress made through Biodiversity Genomics Europe and other initiatives, ERGA has grown into a well-known, inclusive community. Together with the growing number of projects under its umbrella, ERGA is now playing a pivotal role in democratising access to high-quality genomics for biodiversity research across Europe.” Camila Mazzoni , ERGA founding chair. Alignment of goals  The recognition of ERGA as an EBP Regional Node reinforces our community’s commitment to build and foster a global EBP network, aligning our goals and contributing to sequence the genomes of all living eukaryotic species on Earth. Following the requirements for EBP regional nodes, ERGA is committed to:  Coordinate activities with the EBP and EBP-affiliated projects as described in our governance document   Adhere to and promote recommendations and guidelines issued by EBP Committees, Councils, or the Secretariat. Click here  for a view of a model of the organisational structure of the EBP as a global network of interconnected communities. Click here  to learn more about the ERGA community and structure. Other Relevant Links EBP Regional Node Application The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

This month's ERGA BioGenome Analysis & Applications Seminar will feature three short talks on the topic of genomic erosion and biodiversity conservation. Learn more below about the featured talks and speakers: Hernán E. Morales, Samuel Speak, and Xuejing Wang. 🕚 Tuesday, April 29th 2025 - 11:00 AM CEST 📅 Add the seminar to your calendar Watch the recorded seminar: Genomic erosion and biodiversity conservation The seminar will be divided in three parts (around 15 minutes each): Using genomes through time to study diversity loss - Hernán E. Morales The biodiversity crisis is driving the loss of critical genomic diversity essential for species survival and adaptation. Even after population recovery, genetic diversity may continue to decline—a phenomenon known as "genetic drift debt." To investigate this, we compare whole genomes from pre-decline (100+ year-old museum specimens) and post-decline (modern) populations of endangered bird species with varied decline trajectories. We assess how population declines affect deleterious, functional, and neutral variation, and use simulations to evaluate how demographic history and conservation actions influence extinction risk and recovery. Our aim is to uncover the evolutionary dynamics of genomic erosion. Scoring deleterious alleles in endangered species – Samuel Speak Captive breeding programmes can act as insurance populations against extinction and to preserve genetic diversity of endangered species. However, due to their small size, the survival of these populations is threatened by inbreeding depression resulting from high genetic load. We developed the LoadLift pipeline which utilises Combined Annotation-Dependent Depletion (CADD) scores from model species to estimate the genetic load within ultraconserved elements (UCEs) of individuals. Six pink pigeons (Nesoenas mayeri) were analysed with LoadLift and in silico crossings, to identify optimal mate pairings expected to show the least inbreeding depression. LoadLift was further used to assess the genetic load of the whooping crane (Grus americana), to compare the methods of LoadLift and SNPeff, showing good correspondence in their classifications of deleterious mutations. LoadLift aims to maximise the potential of ex situ populations for species conservation and restoration by enabling captive-breeding managers to reduce inbreeding depression and maintain long-term viable populations. Genomic erosion through the lens of comparative genomics – Xuejing Wang The loss of genetic diversity and the species’ response can vary widely depending on their evolutionary histories, life-history traits and demographic trajectories. Comparative genomics offers a powerful framework to explore the dynamics of genomic erosion across species. We compared the genomes of three Mauritius birds with additional 36 birds spanning the avian phylogeny, to investigate the genomic consequences of their demographic collapses. We found that historical population sizes influenced current genetic health, with higher heterozygosity linked to greater heterozygous load and the ratio of effective to census population size predicted a species' conservation status. We also found significant differences in genetic load and genome structure between taxonomic groups, showing the value of multispecies comparisons. Speakers Hernán Morales studied Biology at UNAM, Mexico, and completed an MSc at the University of Groningen, Netherlands. He earned his PhD from Monash University, Australia, and joined the Globe Institute at the University of Copenhagen in 2019. In 2023, he established the Evolutionary and Conservation Genomics Group that utilizes (paleo)genomics, quantitative genomics, and evolutionary modelling methods to explore the mechanisms behind the generation, preservation, and loss of biodiversity. Samuel Speak is a Postdoctoral Research Scientist in the Haerty Group at the Earlham Institute, working to identify loci associated with aquaculture relevant traits related to environmental stress within Tilapia species. Prior to this position, he was a NERC ARIES DTP PhD student at the University of East Anglia, the Natural History Museum London and Chester Zoo working on the conservation genomics of endangered bird species in zoos. During which he focused on quantifying the genetic load of individuals in captive breeding programs using CADD scores within the ultraconserved elements of the genomes. Applying this to threatened species including the pink pigeon ( Nesoenas mayeri ) and the whooping crane ( Grus americana ). Xuejing Wang is a postdoc working in Evolutionary and Conservation Genomics Group in Globe Institute, University of Copenhagen. She currently works on the conservation genomics of Mauritius kestrel and other endangered birds, focusing on demographic history, temporal genetic dynamics and genetic load. During her PhD in University of Bern, she worked on the population genomics and evolution of an insular mammal, the Orkney vole.

At this month's ERGA Plenary meeting , taking place on Monday, April 28 at 15:00 CEST , Dr. Thomas Mathers will present his work on a Tree of Life pilot project focused on improving reference genome assemblies for challenging species, along with new insights from complete bird microchromosome assemblies. More details can be found below. Watch the recorded talk: Abstract Chromosomally complete reference genomes for challenging species: overcoming sequencing dropout in bird microchromosomes Large genome assembly projects aim to generate chromosomally complete reference genomes across the tree of life. Typically, these projects rely on PacBio HiFi long-read sequencing and HiC to deliver reference genomes at scale. This approach results in high-quality genome assemblies that meet or exceed gold standard metrics for most lineages. However, some species are recalcitrant to assembly and challenges remain to generate high-quality genome assemblies for all taxa. Within vertebrates, birds present a substantial assembly challenge due to the presence of tiny, hard to assemble, microchromosomes. These chromosomes have distinct genetic and epigenetic features and are highly fragmented in PacBio HiFi de novo  assemblies, to the extent that in many cases the full complement of chromosomes cannot be identified. In this talk, I present results from a Tree of Life pilot project to improve the reference genomes of 20 bird species using Oxford Nanopore long-read sequencing. We find that using PacBio HiFi reads for de novo  assembly results in up to 70% missing gene content on the 10 smallest bird chromosomes due to sequence coverage dropout. I will discuss the possible causes for this sequence dropout and highlight new insights from complete microchromosome assemblies. Speaker's Bio Thomas Mathers Tom is a former BBSRC Future Leader (Discovery) Fellow at the John Innes Centre where he studied the evolutionary genomics of crop pest host range and is currently a Senior Computer Biologist at the Welcome Sanger Institute working on the Tree of Life Project. At Sanger, Tom carries out genome curation, develops tools to support curation efforts and leads projects making use of Tree of Life genomes to improve genome assembly methods and gain insights into basic biology through genome analysis. Recent projects include assembly and comparative analysis of bird microchromosomes, identification and evolution of supernumerary B chromosomes and sex chromosome turnover in flies. 🔔 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!