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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 “Connections” posts, we explored how DNA technologies, collaborative networks, and international policies shape biodiversity genomics. Today, we turn to another key element: the important role that non-professionals can have in science, or what is often called citizen science . We will unpack what this term means, clarify common misconceptions, and highlight why citizen scientists are vital to projects like Biodiversity Genomics Europe (BGE). It is a story about terminology and teamwork. The term citizen science  is surprisingly recent. One early recorded use dates back to 1989, when 225 volunteers collected rain samples for acid rain awareness for a U.S. project ( Wikipedia ). The term “citizen science” was formally added to the Oxford English Dictionary only in 2014,  defining it as a “scientific work undertaken by members of the general public, often in collaboration with or under the direction of professional scientists and scientific institutions."  A citizen scientist, likewise, is defined as a member of the public who engages in such work alongside   professionals. Interestingly, “citizen” here simply means anyone; in other words, science by citizens of the world. Thus, a citizen scientist is anyone who is not a scientist but actively  participates in real research. Biodiversity genomics relies on citizen scientists because the task is far larger than any research team can achieve alone. As species are vanishing at record speed, only a constant stream of data will give us the power to detect and address threats in time. Volunteers support this reach in different ways, such as hobby entomologists who photograph and submit insects for DNA barcoding, park rangers and hiking clubs who keep Malaise traps operating, or even coastal residents who filter seawater to capture the eDNA of invasive species. Their local knowledge reveals hidden habitats, while the DNA they collect flows directly into reference libraries and genome databases. The exchange is two-way. Participants gain new skills, a genuine sense of ownership, and a front‑row seat to cutting‑edge science. In return, they become ambassadors who share information about genomics, conservation, and responsible sampling within their communities.  Instead of being an optional extra, citizen science now powers the large‑scale, inclusive approach that modern biodiversity genomics demands. Science conducted with the public, for the lasting benefit of both people and the planet. Stay tuned  for our next post, where we will continue to explore the ever-expanding connections in the world of biodiversity genomics. Within BGE, both ERGA and iBOL Europe carried out many activities involving citizen scientists, including, for instance, the Bioblitz in the Croatian Caves we talked about in our previous blog post . You can learn more about BGE’s involvement with citizen scientists here .

The White-spotted Yellow Wart Slug’s reference genome opens new doors to a better understanding of this unique Mediterranean species, its history, adaptations and factors threatening its survival. Photo by Miquel Pontes The White-spotted Yellow Wart Slug ( Phyllidia flava ) is a one-of-a-kind bright orange sea slug species only found in the warm waters of the Mediterranean. Biodiversity Genomics Europe has generated the first reference genome for this species with the help of citizens and researchers. In this article, we hear from Carles Galià Camps, the researcher who proposed the sequencing of the species and took part in the sampling campaign to find the tiny ocean dweller. Carles shares his enthusiasm about the species (and nudibranchs in general), explains how a reference genome can be used to support conservation and tells us how this project benefitted from collaboration between scientists and citizens who share a passion for the sea and its life forms. Watch the video for highlights of this conversation and read the full interview below: Carles Galià Camps is a Catalan young postdoctoral researcher at the Spanish National Museum of Natural History. He is a geneticist interested in knowing how species evolve and get adapted to new conditions. His heart was stolen by nudibranchs, also known as sea slugs, and since then he has been trying to generate new knowledge about them, specifically on their evolution and their phylogenetic relationships. Could you introduce Phyllidia flava and highlight some interesting facts about this species? Carles Galià Camps : To me, Phyllidia flava is one of the most unique nudibranchs (sea slugs) worldwide. This is because it has many unique characteristics. The first is that it is the only species of the genus in the Mediterranean Sea. All the other species of the same genus are found in the Indian and Pacific Oceans. This is because when the Tethys Sea closed, there were two different Phyllidia communities, being Phyllidia flava the last Phyllidia species on the Mediterranean side of the Tethys Ocean, whereas the genus was very successful in the Indian and the Pacific Oceans. That's something really unique. The other thing is that this sea slug species has a really close relationship with a sponge species, which it feeds on. Actually, this is not only a prey-predator relationship, but the sea slug is also capable of stealing some of the metabolites of the sponge. Because of this behavior, it is able to produce some metabolites which are deterrents and help the species disturb possible predators. Sometimes these sea slugs get stressed because they notice we are taking pictures of them and they start to secrete an orangish substance, which is this deterrent. That’s why you should never poke one of these! It’s really easy to see when you are annoying them and that they are defending themselves thanks to that sponge. In general, nudibranchs usually breathe through the skin because they are so small that they don’t need lungs or any specialized organ. In some cases, if they are large enough, they have gills, which are usually found near the anus, in the animal’s back. But this is not the case for Phyllidia and other Phyllididae species because they have a unique structure, which is a gill in the lower-lateral side of the body. And no other sea slug family besides this one has it. So it’s another unique characteristic of this species. Because of all of that, I think that Phyllidia flava is awesome, and it has lots of potential to teach us about evolution, sea biology, and many other topics. Photos by Whitepointer from Getty Images, NathalieGermain, yfhishinuma from Getty Images and Jackdrafahl from pixabay. Why is it so exciting to study nudibranchs? Carles: Nudibranchs are absolutely wild. If you’re not familiar with them, they’re basically mollusks - like snails - that have lost their shells. Normally, a shell provides physical protection against predators, but nudibranchs had to evolve other strategies to survive. So, in a way, they were like, Oh no, I need to figure something out! They’ve developed an incredible range of defense mechanisms, most of them chemical, such as P. flava ’s interaction with the sponge that I mentioned before. There are other nudibranchs that feed on anemones and corals. Instead of keeping the chemical metabolites, they actually store the nematocysts - the stinging cells from their prey - and can use them to sting predators. That’s insane! And then there are the sacoglossans, also known as the “solar-powered sea slugs", which actually are not “nudibranchs”. They feed on algae and are able to store chloroplasts in their bodies, potentially allowing them to photosynthesize, at least to some extent. While this ability still needs full scientific validation, what we do know is that they can store these chloroplasts long-term and digest them when needed. This adaptation is crucial because algae often have seasonal growth cycles, so these sea slugs have found a way to maintain a backup food source when algae aren’t available. Despite not being listed as endangered by the IUCN, Phyllidia flava is considered highly vulnerable. Can you explain the main threats to this species?   Carles:   There are two main factors that can be seen as threats to this species: the fact that it is naturally rare, and human-made impacts: The first one is that the species is rare, so there are not that many animals. And the sponge that it feeds on is also rare, so there’s a convergence of rareness and difficulties in finding it.  And then there are human-made effects. Among them there is ocean warming. We don’t really know yet how it will impact the species, but for sure, it will impact it, especially the population structure of the species. This sea slug is distributed across the whole Mediterranean, but some populations will disappear due to the warming, and some others may be enhanced. In any case, though, its genetic richness will drop, the population structure will change, and with this drop in genetic diversity, its resilience to climate change and changing environmental conditions will be diminished. So in the near future, I think that this will be the main issue that can threaten this species.  Another main human-made threat is trawling. This species lives on sponges but when there is trawling for fishing, they just take away lots of those sponges - and the regulation somehow doesn’t contemplate it.  As I said, the sponges are the main habitat of Phyllidia, and well… It's a vicious cycle. If we keep taking the food out of the sea along with some Phyllidia, Phyllidia will suffer more to find food, and eventually, I think that Phyllidia flava  will just disappear from the Mediterranean.   It’s a combination of all of these factors: the rareness of the sponge, the rareness of the nudibranch, climate change affecting populations and genetic diversity, and finally, human-made impacts that are eroding the original environmental conditions. How will the new reference genome help science address these threats? Carles:  I really love population genomics. As a scientist, that was the topic of my PhD thesis and what I’m working on.  What we’ve seen is that if you have a reference genome, your results improve significantly, and you can infer any pattern - any evolutionary pattern, any adaptation pattern… basically anything you may want.  Once there the reference genome is available, we can gather samples from the species across its distribution, across the whole Mediterranean, and try to understand the genetic richness of the species and the mechanisms it has to overcome unusual environmental conditions, such as marine heatwaves and salinity shifts. Then, there are many other issues that can be tackled with the help of the reference genome. Remember that this is the last remaining species of the genus Phyllidia in the Mediterranean - a true relic - because it split from all the others many years ago.   This makes it an important calibration point in phylogenetic analysis. In other words, you can determine when Phyllidia flava diverged from the other Phyllidia species, estimating that this split happened X years ago when the Tethys Sea closed. With this reference point, researchers can tackle broader questions related to evolutionary timelines and demographic changes.   Another fascinating aspect that can be explored with its genome is how Phyllidia flava absorbs deterrent molecules from its sponge prey and modifies them for its own defense. To me, that’s mind-blowing - this species not only uses its food source for nutrition but also repurposes it for self-defense.  This is something that many nudibranchs do, but Phyllidia flava stands out as a perfect model for studying this unique adaptation. It must have been difficult to sample such a tiny animal that lives deep underwater. Can you share the story of how the sampling happened and the role of citizen scientists in this?  Carles: When I first learned about ERGA-BGE's call for proposing species to have their genomes sequenced, I knew I wanted to participate. I study various animals, but my heart belongs to nudibranchs, and I wanted to sequence a nudibranch because there are not many reference genomes available for this group. I think this is one of the few, if not the first, chromosome-level assembled nudibranch genomes, which is top-tier.   However, I don’t scuba dive that much. My main research duties involve writing and analyzing data, and while I love that kind of work (field work), I don’t always have time to be in the ocean. When it’s time to go to the sea, I often can’t make it. I knew about Miquel Pontes - he is passionate about the ocean and has many initiatives related to nudibranchs. Right now, he’s moving into new fields, working with corals, collaborating with many people, and developing a network of ocean enthusiasts. Miquel even created a WhatsApp group where every week, he announces, “I’m going scuba diving. Who’s coming?” . He organizes trips, makes checklists of nudibranch species in different areas, and even explores pools in Barcelona to document biodiversity. Even though he’s not a scientist by training, he knows an incredible amount about marine life. Most importantly, he knows where to find the species. As a researcher, I only have the theory, but he goes to the sea every week and has seen Phyllidia flava  over and over again. He knows exactly where to look, which sponges to check, and how to spot them. For me, talking to him was essential. I had the idea and could go to the ocean, but my chances of finding Phyllidia flava on my own were much lower than if I worked with him. For the sampling campaign, it wasn’t just the two of us. We were looking for a tiny sea slug (about two centimeters) blending perfectly with orange sponges, making it really difficult to spot. So we used the WhatsApp group and invited people to join. They came, and we gave a short briefing. We explained what we were doing, why we were collecting Phyllidia flava , and the importance of sequencing its genome. They were super engaged and excited to be part of the project. Then, we jumped into the sea and started searching. In the first dive, we had four people. The second time, six. Both were unsuccessful. It wasn’t until the third attempt, with four people again, that we finally found it - It was a real mission! These dives were on different days in different locations. You never really know where to find these animals. On land, you can scout the area in advance, but underwater, it’s much harder. Unless you’ve been to the same place dozens of times, you’re relying on luck. That’s the challenge, but it also makes each discovery even more rewarding. But in the third attempt we finally found Phyllidia flava ! It was Miquel who spotted it, actually. His experience and sharp eye were key in locating it. Afterward, we celebrated. We went to a bar, had a beer, and talked even more about the species . It was a great moment. This experience showed me how important it is to have people like Miquel. He engages with others, bringing citizens together week after week. He shares his passion, but he also connects with scientists, combining our strengths to reach common goals. It’s important to gather people like him, because they can really help researchers, they enjoy what they do, and they spread awareness. In the future, the people involved in the sampling of the species will care about it and share their experiences with family and friends. It’s a great way to spread knowledge and raise awareness about marine life. Learn more: Genome Report: ERGA-BGE Reference Genome of Phyllidia flava (Nudibranchia: Phyllidiidae), a Relict Species Endemic to the Mediterranean Sea   Species fact sheet | Opistobranquis https://opistobranquis.info/en/guia/nudibranchia/doridina/doridoidei/phyllidioidea/phyllidia-flava/ Interview and editing by Luísa Marins

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.