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Last week, ERGA was present at the Vertebrate Genomes Project 2025 Conference , held at The Rockefeller University in New York City from September 30 and October 1. ERGA and VGP share a long-standing collaboration, working together on shared workflows for genome assembly and evaluation  and collaborating under the Biodiversity Genomics Project ( BGE ). So far, dozens of vertebrate genomes from species found across Europe have been sequenced under the ERGA umbrella, directly contributing to the VGP’s goal of sequencing all ~70,000 living vertebrate species. Discussing vertebrate genomes in the heart of New York City. Tom Brown, coordinator of the ERGA IT & Infrastructure Committee , presented the work within the BGE project on FAIR (Findable, Accessible, Interoperable, and Reusable) genome assembly publishing and establishing distributed models of genome generation across Europe. As the VGP and the Earth BioGenome Project (EBP) begin their journey into the Phase II expansions of each project, attention must be given to fully FAIR reporting and publishing of all outputs from sample to reference genome, and coordinated across all nodes of the EBP.  In New York, Tom presented ERGA’s solutions for  generating reports  for all genomes produced as part of the BGE project and sharing all bioinformatic workflows within WorkflowHub . Photos by Chul Lee . Relevant links VGP Website: https://vertebrategenomesproject.org/ Larivière, D., Abueg, L., Brajuka, N. et al. Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Nat Biotechnol 42 , 367–370 (2024). https://doi.org/10.1038/s41587-023-02100-3

This September, the heart of Tuscany beat to the rhythm of genomics!  From the 8th to 12th September 2025, Florence, Italy, welcomed researchers from around the globe for the third edition  of the EMBO Practical Course on Genome Sequencing, Assembly, Curation, and Downstream Analyses . This week-long event explored the entire workflow of reference genome projects - from sample preparation to sequencing, assembly and annotation and provided a key opportunity to showcase ERGA and how its collaborative infrastructures and shared standards support the generation of high-quality reference genomes across Europe. EMBO course instructors and participants enjoying a moment together in front of Florence’s Basilica di Santa Croc The course was designed for action. Participants worked hands-on with real datasets - PacBio HiFi, Oxford Nanopore, Illumina Hi-C and RNA-seq - to perform de novo assembly, scaffolding, haplotig purging, and genome annotation within the Galaxy platform , using the Training Infrastructure as a Service ( TIaaS ). Beyond technical exercises, the course offered insights into reproducible workflows, pangenome development, and AI-assisted functional annotation. ERGA workflows  and tools drew particular interest, showing how standardized approaches can streamline genome projects and make high-quality genomic data widely accessible. Participants at all career stages left with new knowledge and skills to apply these cutting-edge practices in their own research. This edition of the EMBO course was organized by Claudio Ciofi (University of Florence, IT) and Giulio Formenti (The Rockefeller University, US; ERGA Council member for Italy). The co-organizers and invited speakers included Aureliano Bombarely (IBMCP/CSIC, ES; ERGA Council member for Spain), Silvia Manrique (CSIC, ES), Jean-François Flot (Université libre de Bruxelles, BE), Nadège Guiglielmoni (University of Cologne, DE), Astrid Böhne (Museum Koenig Bonn, DE), Tom Brown (Leibniz Institute for Zoo and Wildlife Research, DE; Chair of the ERGA IT Committee), Kirsty McCaffrey (The Rockefeller University, US), Marco Sollitto (University of Florence, IT), Alice Mouton and Björn Grüning (University of Freiburg, DE), with assistance from Camilla Reginatto De Pierri (University of Florence, IT; Chair of the ERGA TKT Committee). Text by Camilla Reginatto De Pierri, from the ERGA Training & Knowledge Transfer Committee

This month's ERGA BioGenome Analysis & Applications Seminar will feature a talk by speaker Aleksey V. Zimin about EviAnn (Evidence-based Annotator), a novel evidence-based eukaryotic gene annotation system. Tuesday, September 23rd 2025 - 15:00 CEST Youtube link: https://www.youtube.com/live/n1usz4-mCXo 📅  Add the seminar to your calendar Abstracts Efficient evidence-based genome annotation with EviAnn For many years, machine learning-based ab initio gene finding approaches have been central components of eukaryotic genome annotation pipelines, and they remain so today.  The reliance on these approaches was originally sustained by the high cost and low availability of gene expression data, a primary source of evidence for gene annotation along with protein homology. However, innovations in modern sequencing technologies have revolutionized the acquisition of gene expression data, allowing scientists to rely more heavily on this class of evidence. In addition, proteins found in a multitude of well-annotated genomes represent another invaluable resource for gene annotation. Existing annotation packages often underutilize these data sources, which prompted us to develop EviAnn (Evidence-based Annotator), a novel evidence-based eukaryotic gene annotation system.  EviAnn takes a strongly data-driven approach, building the exon-intron structure of genes from transcript alignments or protein-sequence homology rather than from purely ab initio gene finding techniques. We show that when provided with the same input data, EviAnn consistently outperforms current state-of-the-art packages including BRAKER3, MAKER2, and FINDER, while utilizing considerably less computer time. Annotation of a mammalian genome can be completed in less than an hour on a single multi-core server. EviAnn is freely available under an open-source license from  https://github.com/alekseyzimin/EviAnn_release  and from Bioconda as “eviann”. Practical introduction to genome annotation with EviAnn In the second part of the presentation I will explain how to use EviAnn, to annotate genomes of small and large eukaryotes.  I will show how to find and download protein evidence from NCBI and describe inputs and outputs of EviAnn.  For demonstration purposes, I will run an annotation of a small fungal genome. Speaker Dr. Aleksey V. Zimin Research Scientist, Department of Biomedical Engineering Johns Hopkins University, USA I have been working in the field of Bioinformatics since 2002, beginning with my collaborations with The Institute for Genomic Research (TIGR) and Celera Genomics. The main goals of my research are (i) developing algorithms and software for de novo genome assembly and annotation for the latest generation sequencing data and (ii) applying the software to produce high quality annotated assemblies for the most challenging genomes. I lead the development of the open-source MaSuRCA genome assembly package, which is currently able to produce accurate high-quality assemblies from sequencing data produced by Illumina, PacBio, and Oxford Nanopore instruments. As of today, MaSuRCA was used to assemble over 2600 eukaryotic genomes submitted to NCBI GenBank. I played a leading role in producing assemblies for many challenging genome projects, including the 22 Gbp genome of Loblolly pine (Pinus taeda), the 17 Gbp genome of bread wheat (Triticum aestivum), the 3Gbp Atlantic salmon (Salmo salar), and many other plants and animals. In recent years, I was the leading author of several widely used bioinformatic software titles such as MUMmer4 sequence aligner, POLCA and JASPER assembly polishers, and SAMBA scaffolder. Most recently the focus of my research has encompassed transcriptome assembly, protein alignment and genome annotation algorithms. My most recent work includes a novel automated genome annotation package called EviAnn, which sets new standard for automated genome annotation software. The software titles that I develop and/or maintain are available under an open-source license from my github repository https://github.com/alekseyzimin and several titles are also available from Bioconda.

At this month's ERGA Plenary meeting , on Monday, September 15 at 15:00 CEST , Robyn Shaw will present on " Global genetic diversity loss and the power of conservation to restore species resilience ". Check more information below. Abstract Global genetic diversity loss and the power of conservation to restore species resilience Genetic diversity provides the foundation for species resilience and adaptive capacity. Yet, unlike species and ecosystem diversity, the global status of within-population genetic diversity has received less attention and has not been assessed comprehensively across the tree of life. In addition, the effectiveness of conservation actions in maintaining or restoring genetic diversity remains poorly understood. With 57 collaborators, we conducted a global meta-analysis of more than three decades of research, screening over 80,000 studies and extracting thousands of estimates from 628 species across 141 countries. Using meta-analytic methods, we compared genetic change across taxa, metrics, and study designs. We found widespread genetic diversity loss, particularly in birds and mammals, linked to threats such as habitat modification, disease, and exploitation. Importantly, some conservation actions were associated with positive outcomes. In particular, population supplementation (e.g. restoring connectivity or translocation) led to increases in genetic diversity over time. Our findings indicate that while genetic diversity is being lost globally, targeted conservation can restore it, providing an evidence base to guide genetic monitoring, inform biodiversity reporting, and support species resilience. Speaker's Bio Robyn Shaw is a postdoctoral research fellow at the University of Canberra, in the Centre for Conservation Ecology and Genomics. She uses genetics and field studies to explore the effects of fire, invasive species, land use and climate on animal populations; integrating this information into decision-making tools for conservation practitioners. 🔔 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!

Are you interested in bioinformatics and eager to connect with peers worldwide while working on projects with direct applications for the life sciences? Join this year’s BioHackathon Europe between 3–7 November 2025 . Online participation is free and registrations are still open! Face-to-face registration is currently full, but you can join the waiting list. “BioHackathon Europe is an annual event that brings together bioinformaticians and computational biologists from around the world. It’s organised by ELIXIR Europe , and offers an intense week of hacking, with participants working on diverse and exciting projects. BioHackathon is a community-driven event, which provides an opportunity for members of the life sciences community to meet and work together on topics of common interest. The goal is to create code that addresses challenges in bioinformatics research.”  This year, members of the ERGA community will lead two projects at the BioHackathon and are looking for more contributors to join their teams! The first project, proposed by the Data Analysis Committee , focuses on developing workflows for phylogenomics. The second project, developed by the Annotation Committee in collaboration with the Research Data Alliance, addresses FAIR metadata associated with genome annotations. Check out the project abstracts below and join the one that interests you most! Project 3: Automatic workflow for benchmarking BUSCO genes for phylogenomics Abstract Phylogenomics is a central aspect of biodiversity genomics, as it reveals the relationships among organisms and key evolutionary processes such as introgression and gene flow. Genome-scale datasets are increasingly a reality in phylogenomics due to the availability of genomes for an ever-growing number of species. BUSCO datasets (universal single-copy orthologs) have become standard in assessing genome assembly completeness and are fully integrated into the pipelines of large genome consortia such as ERGA. Due to their low-copy nature, BUSCO genes are also increasingly used in phylogenomics, from genome skimming data to high-quality chromosome-scale genomes. Yet, their phylogenetic performance has not been thoroughly explored. Preliminary analyses show that BUSCO genes can recover robust phylogenetic relationships, but their single-copy nature is challenged: most BUSCO genes display varying levels of paralogy when using biodiverse species sets, and failure to account for this can negatively affect phylogenetic reconstruction. This BioHackathon aims to build an automatic phylogenomics pipeline using the output of the BUSCO software. Contrary to existing pipelines, we aim to explicitly resolve paralogy events, thereby resulting in larger and more informative datasets. This pipeline will be used to benchmark the phylogenetic performance of the newly defined BUSCO lineage datasets, identifying not only the prevalence and evolutionary depth of the various paralogs but also resolving them for improved phylogenetic utility of BUSCO genes. This project will result in a fully-fledged FAIR-compliant phylogenomics pipeline based on BUSCO and an assessment of the phylogenetic performance of new BUSCO gene sets (version odb12). Leads: Tereza Manousaki, Iker Irisarri, Tom Brown Project 23: Streamlining FAIR Metadata for Biodiversity Genome Annotations Abstract Initiatives like the European Reference Genome Atlas (ERGA) and Australian Tree of Life (ATOL) comprise a scientific response to the current severe threats to biodiversity, generating thousands of reference genomes for species across the tree of life. Unfortunately, few solutions exist for structured reporting, quality assessment and persistent deployment of metadata pertaining to the annotation of functional and structural features along the assembled genomes. ERGA is developing a format and repository for annotation reports to support collection of metadata for genome annotations in line with the existing ERGA Assembly Reports (EAR). ATOL is currently building a ""Genome Engine"" capable of producing automated genome notes and INSDC submissions for genomic data. Similar initiatives exist in the context of other biodiversity projects. In parallel, the FAIRification of Genomic Annotations Working Group (FGA-WG) in the Research Data Alliance (RDA) has been developing a secondary, harmonised FAIR metadata model and infrastructure to improve discovery and reuse of publicly available genomic annotations/tracks, across biomedical and biodiversity fields. This project brings together – for the first time – participants from two disjoint BioHackathon projects, BH2024 project #31 and BH2023 project #20, across ERGA, ATOL, FGA-WG, Ensembl, EBP-Nor and other initiatives, to form a ""supergroup"" to tackle the metadata challenges pertaining to biodiversity genome annotations! For the 2025 BioHackathon, we will develop automated processing, validation and transformation of collected metadata consistently deployed across repositories for ERGA Annotation Reports and ATOL Genome Notes (primary metadata), and metadata harmonised according to the recommendations from the FGA-WG group (secondary metadata). Leads: Sveinung Gundersen, Alice Dennis, Tiffanie Nelson   Read about ERGA's participation in the BioHackathon Europe 2023 . #BioHackEU25

After a short summer break, Genomics Connections  is back! In this episode, Kasia and Christian chat with Ela Sari and Luísa Marins about science communication and the importance of disseminating information about biodiversity genomics to a variety of audiences. Ela is based at Naturalis Biodiversity Centre , and Luísa at the Leibniz Institute for Zoo and Wildlife Research , and both work as part of the communication team of BGE. 🎧 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

From the mighty blue whale to the humble baker’s yeast, scientists have barely begun to understand the vast genetic diversity among lifeforms. Of the 1.67m known species of animal, plant, fungi and protists, just 1% have been genetically sequenced.  In 2035, this figure could reach 100%.  Published in Frontiers in Science , this is the new ambition of the Earth BioGenome Project (EBP)—a global network of scientists sequencing the genomes of Earth’s eukaryotes. Its goal? To create a digital library of DNA sequences that will help us preserve and protect life on Earth and tackle rapid environmental change.  With a growing network of more than 2,200 scientists in 88 countries—including flourishing local and Indigenous research communities in the Global South—EBP is making discoveries that could help assure food security, advance medicine and agriculture, and drive a deeper global understanding of biodiversity to support conservation and pandemic prevention.  Biological ‘moonshot’  EBP began global DNA sequencing in 2020 and is now sequencing genomes 10 times faster.   New innovations to meet this ambitious ‘moonshot’ include portable ‘pop-up’ labs to expand sequencing capacity, as well as boosting engagement and inclusion in the world’s biodiversity-rich yet remote regions.   “As biodiversity loss gathers pace, so must our work,’ said senior author Prof Harris Lewin at Arizona State University , in the US. “Our growing digital ‘genome ark’ is shifting what’s possible in genomics from isolated, expensive sequencing efforts to a global, scalable, and inclusive enterprise.”    Strong roots By the end of 2024, EBP-affiliated projects had published 1,667 genomes covering more than 500 eukaryotic families. Network researchers also deposited a further 1,798 genomes meeting EBP standards, bringing the total number of genomes to 3,465.   These data have illuminated the origins and evolution of life on Earth, and the role of genetic diversity in species’ ability to adapt to change. For example, they have helped reveal how Svalbard reindeer adapted to Arctic conditions, and how chromosomes evolved in butterflies and moths. The project’s research methods are also helping to improve tools such as environmental DNA (eDNA), which uncovers new lifeforms through the genetic footprints they leave behind.   “We have laid the roots to build our digital ‘tree of life’—and our early outputs are already reshaping what we know about evolution, ecosystem function, and biodiversity,” said lead author Prof Mark Blaxter at the UK’s Wellcome Sanger Institute .  Ambitious goals  As EBP enters the second of its three phases, Phase II brings ambitious new goals that will rapidly accelerate the project’s work.   Building on Phase I, Phase II aims to sequence 150,000 species—half of all known genera—within four years. It will prioritize species that are important to ecosystem health, food security, pandemic control, conservation, Indigenous peoples and local communities.  It also aims to collect 300,000 samples, around half of which will form the basis of Phase III.  Achieving this will require sequencing 3,000 new genomes per month—more than 10 times faster than current rates. The authors say that advances in technology are on their side: genome sequencing is now eight times cheaper than just a few years ago, which means budgets stretch further and work can accelerate.  “It’s a biological moonshot in terms of the scale of ambition. As species vanish and ecosystems degrade, we aim to capture and preserve the biological blueprint of life on Earth for future generations,” said Prof Blaxter. "Understanding the origins and evolution of life on Earth is a human pursuit equivalent to understanding the origins and evolution of the universe."  Genome lab in a box The EBP’s authors highlight key challenges, including coordinating the global collection of 300,000 species and ensuring open, low-carbon data infrastructure.   Much of the Earth’s biodiversity is found in the Global South. Therefore, vast amounts of the species collection, sample management, sequencing, assembly, annotation, and analysis will be delivered by local EBP partners. This will also help to ensure equitable access and culturally appropriate practices, while reducing societal and environmental impact.   To accelerate sequencing in remote regions, the authors propose using self-contained ‘pop-up’ sequencing labs housed in shipping containers. Known as a ‘genome lab in a box’ (gBox), the labs could enable local and indigenous scientists, particularly in the Global South, to generate high-quality genomic data locally.  "Chile is one of the world’s biodiversity hotspots with many endemic species, but these are under threat," said co-author and local EBP community member Prof Juliana Vianna from The Chilean 1000 Genomes Project at Pontificia Universidad Católica de Chile . "In addition, our species are often studied only after samples are exported. With gBoxes, we can change that. Local teams can generate the data here, in context, and immediately connect it to the conservation and sustainable management challenges we face on the ground."  "Biodiversity scientists in low and lower middle-income countries confront daily the great irony of our species and our planet: that the lion’s share of funding and infrastructure for genomics is located at higher latitudes while the great bulk of biodiversity is found in the tropics,” said co-author and local EBP community member Dr Andrew J Crawford from Universidad de los Andes in Colombia . “The gBox would allow any nation on the globe to make its own choices, empower the next generation of researchers in biotech and computational biology, and impact national economies by asking novel questions and developing creative solutions."  “The gBox isn’t just a lab—it’s a symbol of equity in science. By equipping local and Indigenous researchers with advanced genomic tools, we’re empowering the Global South to contribute on equal footing to the Earth BioGenome Project. This shift ensures biodiversity science is inclusive, locally driven, and culturally informed,” said co-author and local EBP community member Prof Montserrat Corominas at Universitat de Barcelona .  Value for money  Since launching, EBP has created international standards, built a network of affiliated projects, and completed many of its Phase I targets.  The projected cost of Phase II is $1.1 billion. This includes a $0.5 billion Foundational Impact Fund to support local training, infrastructure, and applied research in the Global South.   The full cost of sequencing all 1.67 million named eukaryotic species in 10 years is estimated at $4.42 billion—less than the cost of the Human Genome Project or the Webb Telescope in today’s dollars.  The authors say this investment is “very reasonable for a global effort with such a lasting impact.”  Upcoming Event: Frontiers in Science Deep Dive Join the article authors—Prof Harris Lewin, Prof Mark Blaxter, and Dr Dr Federica Di Palma—to hear how EBP’s next phase will accelerate biodiversity research, support global conservation, and extend genomic benefits to underserved regions using mobile sequencing labs.   Alongside a panel of fellow experts, they will explore the importance of open data sharing, training local scientists, and sequencing at the source—ensuring inclusivity, capacity-building, and benefit-sharing, especially in the Global South.    This free webinar takes place on 18 September 2025, 16:00-17:30 CEST.  The Earth BioGenome Project Phase II: illuminating the eukaryotic tree of life | Register   -- The article is part of the Frontiers in Science multimedia article hub ‘ The Earth BioGenome Project: scaling up .'

For one week in August 2025, Barcelona became the European capital of evolution: the city hosted this year’s ESEB 2025 Congress , the biennial conference of the European Society for Evolutionary Biology. The event was a huge success, bringing together almost 2,000 attendees from around the globe to discuss topics spanning diverse aspects of evolutionary biology: from palaeontology to molecular evolution. The rapidly increasing quality and availability of reference genomes from species across the tree of life offers powerful new tools to evolutionary biologists. This was reflected in a programme full of talks and symposia related to biodiversity genomics. ERGA at ESEB 2025 Given the growing importance of reference genomes in evolutionary studies, it made sense for ERGA to have a strong presence at ESEB 2025. The conference offered a valuable opportunity to raise visibility, showcase our efforts, and share available resources with the evolutionary biology community. ERGA participated as an exhibitor with our own booth. The participation was made possible thanks to Biodiversity Genomics Europe ( BGE ) , funded by the European Union under Horizon Europe and co-funded by the Swiss and UK governments. Welcoming new members Throughout the five conference days, the ERGA booth was a lively space for discussion. Attendees stopped by during breaks to learn about our initiative, ask questions, and pick up ERGA stickers and other goodies. Over 20 people signed up on the spot, and we warmly welcome them to the ERGA community! The meeting was also a special opportunity for ERGA members who regularly meet and collaborate online but rarely meet face-to-face to connect in person, exchange ideas, and strengthen our community. During two lunch breaks, we gathered for group photos to capture the moment. ERGA members from many different countries, committees and projects gathered in the ERGA booth. Evolution takes to the streets In addition to our presence at ESEB, we also had the chance to take ERGA and BGE to the streets of Barcelona, engaging directly with the public. Thanks to a collaboration between ESEB 2025 and the science communication association La Ciència Al Teu Món (LCATM) , a series of outreach activities were organised during Les Festes de Gràcia , a traditional Barcelona street festival. On the colourfully decorated Carrer Perill  in the Gràcia neighbourhood, we interacted with festival visitors and invited them to play a science-themed board game. The activity, titled “DNA rules! Explore the building blocks and the future of biodiversity,”  introduced participants to European plants, animals, and fungi being sequenced as part of the BGE project. Players learned about threats to these species’ survival and how genomic knowledge can support their conservation. Click here to read more about the activity. Outreach activity during Les Festes de Gràcia. Photos by Arantxa Ajuria, Roberto Torres and Luísa Marins Thank you! We would like to thank everyone who visited the ERGA booth and joined the outreach activity. We look forward to many more opportunities to connect, both within our scientific community and beyond!

🗓️ 17 - 22 August 2025 📍 Barcelona, Spain This August, ERGA will be in Barcelona to participate in the Congress of the European Society for Evolutionary Biology ( ESEB 2025 ). This large and exciting conference is a great opportunity for many ERGA members to gather in person, exchange ideas, and connect! During the conference, visit the ERGA booth to learn more about our community, discover our many initiatives, and meet fellow members. We’ll be at stand #10 in the exhibitors’ area, near the food bars and posters. Feel free to stop by anytime and use the booth as a meeting point. We hope it becomes a friendly space where you can chat about genomics and connect with colleagues in the field. Are you presenting a poster, giving a talk, or hosting a symposium at ESEB? Send us an email at media@erga-biodiversity.eu , we’d be happy to help promote your work! We look forward to seeing you in sunny Barcelona! ☀️ #ESEB2025

The European Reference Genome Atlas ( ERGA ) and the European node of the International Barcode of Life ( iBOL Europe ), two international communities of scientists brought together under the Biodiversity Genomics Europe  Project, are joining forces for “Connections,” a series of blog posts that explore the fascinating world of Biodiversity Genomics  and the intersection of their communities. 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