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In 2023, researchers at the International Center for Biosaline Agriculture (ICBA)  in Dubai embarked on a groundbreaking genomic project. The study focused on the chromosome-level assembly and annotation of Citrullus colocynthis , a drought-tolerant wild relative of the domesticated watermelon ( Citrullus lanatus ). This research is significant as it provides critical insights into the genetic mechanisms underlying drought and salinity resilience, which is vital for the development of crops capable of thriving under increasingly harsh climatic conditions. The project aimed to leverage these genetic insights to improve the drought tolerance, disease resistance, and nutritional profiles of cultivated crops, thus contributing to global food security. The project, led by Dr. Anestis Gkanogiannis, Bioinformatics Scientist in ICBA, has resulted in the first genome to be officially linked to the ERGA as a Community Genome. This milestone not only highlights the importance of C. colocynthis  in global biodiversity but also serves as a motivating example for other researchers to contribute to the ERGA initiative. The research involved advanced genomic sequencing technologies, including HiFi, IsoSeq and Hi-C, to achieve a high-quality chromosome-level assembly and annotation of Citrullus colocynthis . The genome assembly revealed a genome size of approximately 366 Mb, characterized by low heterozygosity and significant repetitive content. Notably, the study identified 23,327 gene models that would enable researchers to uncover pathways associated with stress response mechanisms, which are key to the species' adaptation to arid environments. Being part of the ERGA community facilitated collaboration and resource sharing, which were instrumental in achieving the project's goals. Notable is the participation in the 2023 Elixir-Europe Biohackathon, along with fellow members of the ERGA annotation committee ( Click here to read more about it )The inclusion of this assembly in the ERGA project highlights its value to the broader scientific community, especially in the context of biodiversity conservation and crop improvement. This work will serve as a reference for future studies on plant adaptation and resilience, particularly in the context of climate change and food security This genome assembly's recognition as the first ERGA Community Genome is a significant achievement, setting a precedent for future contributions to the ERGA project. The data generated from this project has been made publicly available through ENA (umbrella BioProject PRJEB78362 ) with ERGA's stamp of approval, fostering collaboration and further research in the field of genomics. The success of this project is expected to inspire other researchers to contribute their own genomic data to the ERGA initiative, expanding the global understanding of biodiversity. Additionally, the insights gained from the Citrullus colocynthis  genome may inform breeding programs aimed at developing crops capable of withstanding extreme environmental conditions, thus contributing to global food security. This achievement would not have been possible without the collaborative efforts of the International Center for Biosaline Agriculture researchers, especially the Crop Diversification and Genetics Section under the Crop improvement and sustainable production Theme (Drs. Augusto Becerra, R. K. Singh and Hifzur Rahman) and ICBA's gene bank (Dr. Mohammad Shahid). About the Author Anestis Gkanogiannis  is a researcher at the International Center for Biosaline Agriculture, contributing to the ERGA Sequencing & Assembly and Annotation Committees. He is involved in genomics projects aimed at improving agricultural resilience through innovative crop breeding strategies. Related Links: https://www.biosaline.org/about-icba https://www.ebi.ac.uk/ena/browser/view/PRJEB78362 https://2023.biohackathon-europe.org/projects.html

The European Reference Genome Atlas (ERGA) Pilot Project reports its success in uniting researchers from across Europe to produce high-quality reference genomes for 98 species. This continental effort is setting the stage for a new, inclusive and equitable model for biodiversity genomics. Strength in (bio)diversity: Some of the European species selected for the ERGA Pilot Project. Photos by ©Mantonature, ©Cucu Remus, ©dadalia, ©scubaluna, ©Kristian_Nilsson, ©AlbyDeTweede, ©Carine Carnier, ©Daniel Jara from Getty Images via Canva.com In a new publication package , the European Reference Genome Atlas (ERGA) announces the success of its Pilot Project. This pioneering initiative assembled a large collaborative network of researchers and institutions across 33 countries to produce high-quality reference genomes of 98 European species. This marks a significant milestone in the quest to create a high-quality reference genome database for all European animals, plants, and fungi. The Pilot Project has provided valuable lessons and highlighted key challenges, positioning ERGA as a model for decentralised, inclusive, and equitable biodiversity genomics initiatives around the world, as reported in a new collection of research articles published today in npj Biodiversity. This collection provides a broad overview of the Pilot Project, the sample collection and processing procedures and insights into national node developments that resulted from the Pilot Project. The collection will continue to be added to as papers associated with the Pilot Project become available over time. Key Highlights of the Flagship Paper: Among many of the project's milestones are the first chromosome-level genome assemblies of species from Greece, one of Europe’s most biodiverse countries. Species such as the Cretan wall lizard and Aristotle’s catfish were sampled by local researchers in Greece to produce genomes that are now openly available for anyone across the world to access and study. This is a great example of what can be achieved by uniting an international community of biodiversity researchers, fostering collaboration between and within countries. The ERGA Pilot emphasised equity and inclusion, with the goal that genomic research and resources are accessible to all, regardless of geographical boundaries. For many of the participating researchers and countries, the project offered the first opportunity to actively engage in the generation of state-of-the art reference genomic resources for their native biodiversity. The ERGA Pilot was also successful in building momentum and bringing visibility to the growing importance of biodiversity genomics in Europe and beyond. Genomic data hold immense potential to inform conservation actions for endangered species and unlock discoveries in the fields of human health, bioeconomy, biosecurity and many other applications. Among the species sequenced by the project is for example the greater argentine - a commercially important fish species from the northern Atlantic. This new reference genome will enable scientists to make more accurate assessments of the genetic status of the species’ populations, ultimately guiding management decisions to ensure that fishing practices are sustainable and responsible. As the global scientific community strives to unlock the full potential of genomic data, the establishment of a Europe-wide collaborative network under the ERGA umbrella accelerates scientific progress and facilitates its translation into tangible benefits for biodiversity and society. Additionally, the network helps researchers at all career stages to find and share opportunities for training, partnerships, and funding Some of the advantages of joining forces as a large scientific community. Addressing Challenges ERGA is the European node of the global Earth BioGenome Project ( EBP ). In order to achieve its ambitious goal - to sequence all eukaryotic life on Earth - the EBP crucially needs worldwide participation and new, decentralised models of genome production. The ERGA Pilot was able to show that a fully distributed, collaborative, and coordinated genome production model is not only feasible, but effective - even at a continental scale and without a central source of funding available. In fact, most of the project budget came from grassroots efforts by individual members and partnering institutions, with additional support from sequencing partners and commercial sequencing companies providing grants, discounts and in-kind contributions. The ERGA Pilot project helped to identify and address the many challenges of working at the international scale. These challenges include dealing with the legal and logistical hurdles of shipping biological samples across borders, resource disparities between countries, and the search for balance between decentralisation and the need for standardisation to guarantee that only the highest possible quality reference genome assemblies, that met EBP metrics, were produced by the project. Future Directions ERGA’s decentralised approach holds great promise for the future of biodiversity genomics. The Pilot Project's success in building momentum and uniting researchers illustrates the power of this model. By fostering international collaboration and focusing on inclusivity and equity, ERGA is setting new standards for biodiversity genomics. The lessons learned and challenges addressed in the Pilot Project will guide future efforts, promoting robust and standardised workflows and a comprehensive genomic database for species in Europe and beyond. Mc Cartney, A.M., Formenti, G., Mouton, A. et al.  The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics. npj biodivers   3 , 28 (2024). https://doi.org/10.1038/s44185-024-00054-6 Quotes “ The ERGA Pilot Project attempted to scale the generation of high-quality reference genomes across an entire continent. An endeavour of such magnitude was made possible only through its commitment to the principles of inclusion, equity and collaboration as well  as the dedication of its diverse, transdisciplinary and cross sectoral participants. I feel incredibly lucky to have worked alongside such an amazing group of colleagues to help kickstart the construction of a genomics encyclopaedia of European species.” Ann McCartney , Member of the ERGA Pilot Committee - Assistant Researcher University of California Santa Cruz, and adjunct Ass. Prof at University College Dublin. “When we took on the leadership of this project, we didn't anticipate the extent of the work ahead. It was a challenging endeavour, but through perseverance and teamwork, we succeeded. We also had the invaluable support of sequencing centres, universities, and commercial companies who contributed to the ERGA Pilot Project, offering human resources for library creation, free sequencing, and in-kind products. This experience was truly one of a kind.”  Alice Mouton, Member of the ERGA Pilot Committee - former FNRS postdoctoral researcher, and scientific collaborator at the University of Liege, Belgium. “ERGA was all a dream, until it wasn't. Through this pilot project the prospect of uniting Europe under the flag of biodiversity genomics is now reality. We can be proud to have first established the process by which the genomes of many species will become available to the scientific community for conservation and beyond."   Giulio Formenti ,   Member of the ERGA Pilot Committee - Research Assistant Professor at the Rockefeller University. “The ERGA Pilot project is a radical step forward for the continent as it links researchers who need genomes sequenced with sequencing hubs ready to do just that. This exchange promotes sharing of tools, approaches, and understanding and has led to the successful bid for Europe-wide Horizon 2020 Biodiversity Genomics Europe funding. The pilot teams' enthusiasm has carried through to the wider project, and I am excited to see what they will accomplish in the future. ” Mark Blaxter , Head of the Tree of Life Programme, Wellcome Sanger Institute. “The ERGA pilot demonstrated the importance of a well-connected scientific community that is willing to cooperate to achieve a major common goal. This success marks a significant milestone for ERGA, illustrating that such an initiative can be highly inclusive while still maintaining the high standards set by the Earth BioGenome Project (EBP) for reference genome production. This ERGA pilot provides both an example and a roadmap for distributed efforts to build Biogenomes across Europe and potentially beyond.” Camila Mazzoni , former ERGA Chair and senior author of the article published and group leader at the Leibniz Institute for Zoo and Wildlife Research. “The ERGA Pilot project is a significant milestone in the Earth BioGenome Project (EBP) and a major step forward for biodiversity genomics in Europe. As the first biodiversity genomics project coordinated at a continental scale, ERGA has demonstrated two fundamental principles on which the EBP was built  — the first being that sequencing capacity will be geographically distributed, and the second being that any benefits derived from sequenced genomes would be shared equitably. ERGA is now poised to expand its goals to sequence thousands of genomes for conserving European biodiversity and the growth of a sustainable bioeconomy.” Harris Lewin , Chair of the EBP Executive Council and Research Professor at ASU . - For more information about the European Reference Genome Atlas (ERGA) and its Pilot Project, please visit erga-biodiversity.eu  and follow the initiative on social media ( X  and LinkedIn ). Join us in advancing the frontiers of biodiversity genomics and contributing to make the field more inclusive.

In March 2024, a team of researchers from various European institutions launched a collaborative project under the BGE-ERGA umbrella. This project, based at the University of Copenhagen and spanning multiple countries, involves a team of experts led by Assoc. Prof. Hernán E. Morales. The primary goal is to use advanced genomic tools to enhance the long-term viability and reduce the extinction risk of the little owl  ( Athene noctua)  in Europe. They aim to integrate comprehensive genomic and demographic data to inform effective conservation policies and strategies. Photo by Martha de Jong-Lantink - Flickr, CC BY-NC-ND 2.0 Research activities involve a large temporal dataset of samples spanning the last 100 years. This dataset is used to generate genomic sequences from modern (last 10 years), recent (1970s-1980s), and historical (over 100 years old) samples of little owls across Europe. This project will raise significant interest within the scientific community due to its potential to provide insights into the little owl's genomic erosion and adaptive potential.    The team is focusing on valuable sample archives curated by several researchers across Europe: Dr. Irene Pellegrino from the University of Piemonte Orientale, Prof. Cino Pertoldi and Prof. Torsten Nygård Kristensen from Aalborg University, and Dr. Peter Hosner from the National Natural History Museum of Denmark. Archived samples are mostly found in the form of feathers and small pieces of museum-preserved toe-pads. These materials contain minimal amounts of degraded DNA. Cutting-edge paleogenomics methods to extract whole genomes from these challenging samples are being used at the Globe Institute at the University of Copenhagen, a world-leading institution in ancient DNA research. Insights from this project will be crucial for understanding population decline's impacts and developing targeted conservation strategies. In addition to advancing our scientific understanding, this project illustrates the importance of genomics in the conservation of biodiversity. This project receives funding from the European Union under the European Union’s Horizon Europe research and innovation programme, co-funded by the Swiss Government and the British government, with additional support from the Danish foundation 15 Juni Fonden and collaborating institutions. We also thank the European Reference Genome Atlas (ERGA) for providing a collaborative platform that made this Photo 2 by Caroline Legg - Flickr, CC BY-SA 2.0 About the Author Hernán E. Morales is a council member of ERGA. He leads the Evolutionary and Conservation Genomics group at the Globe Institute, University of Copenhagen, focusing on the genomic consequences of population decline and the development of conservation strategies. You can learn more about his work and the team’s research at the University of Copenhagen's Evolutionary Genomics .

In June 2024, our project on the conservation genomics of the Atlantic bluefin tuna ( Thunnus thynnus ) started. Our primary goal is to explore the human-driven evolution of such species from a long-timescale dataset (up to 3000 BC) to better define the current health state of the stock.  We will provide stakeholders and policymakers with information to support sustainable conservation strategies. This project, granted by BGE-ERGA, will be led by Piergiorgio Massa and Alessia Cariani, from the University of Bologna (Italy). Piergiorgio will be supported by a team of 7 researchers from Italy (University of Bologna and Marche Polytechnic University) and Norway (Norwegian Institute for Water Research and Norwegian University of Life Sciences) who have extensive expertise in these areas. Tuna have been exploited as a source of food for human populations for centuries.  This new project will investigate the “genomic past” of tuna populations to better assess the current health of the stock. Our team member Adam Jon Andrews generated a low-coverage whole-genome dataset including tuna samples as old as 3000 BC. He has already found evidence of a decline in tuna populations caused by human activity since 1800. We expect this decline to leave selection footprints on the species’ genome. Hence, our research activities include increasing the sequencing depth of those samples to enable our planned genomic analyses. With this work, we’d like to showcase the importance of ancient DNA in conservation genomics studies, since it can provide a picture of the natural unimpacted state and improve estimates of impact time. Ancient tuna vertebrate used as the source material to obtain DNA. Investigating the genetic diversity of ancient populations can be very informative to conservation studies, since it can provide a picture of the natural unimpacted state. Photo by Fausto Tinti from the University of Bologna. Our project is a step forward in achieving the aim of the current UN Ocean Decade to “protect and restore ecosystems and biodiversity” by filling the gap caused by a lack of historical knowledge of how human exploitation has impacted the oceans and therefore what species should be restored. I am thankful for each member of the research team's dedication and expertise in supporting me in this ambitious project. I would also like to thank BGE-ERGA for providing a collaborative platform that made this research possible, for funding our project, and for helping us manage the project. This project receives funding from the European Union under the European Union’s Horizon Europe research and innovation programme, co-funded by the Swiss Government and the British Government. About the Author Piergiorgio Massa is a PhD student from the University of Bologna (Italy), he is part of the ERGA Italy and participates in the ERGA Data Analysis Committee .

Read the full interview with Diego de Panis below: 1. Can you briefly introduce yourself and how you became interested in reference genomes? My name is Diego De Panis, I’m a biologist and I coordinate the sequencing and assembly committee (SAC) of the European Reference Genome Atlas. As part of my PhD I started working with High-throughput sequencing, generating genome assemblies and using them as reference for comparative genomics and transcriptomics. At the time the sequencing technology landscape was a little bit different - long reads from PacBio were only starting to be used, so assemblies were mainly short-read based and we would use the long read data to improve the assembly as far as possible. Then as a postdoc I continued working with reference Genome generation. At the time High-C method was starting to be used for scaffolding assemblies and Nanopore data was also beginning to be adopted. I continued being involved in similar projects since then. So you can say that genomes have played a very important role in all my projects since my PhD. 2. Can you describe what are the main activities of the ERGA SAC? The sequencing assembly committee is also its community - there are not independent entities. Our activities mainly focus on community building, facilitating tools, standardising procedures, promoting discussions, supporting the scientific community, that kind of thing. For instance on the networking side, the activities are very connected to the goal of strengthening collaboration, reinforcing the network and expanding it and a very important part of this is knowledge sharing. We do this by promoting and providing places for the exchange of ideas, by presenting new methods and updates and also giving space for the community to show their work and to seek help or guidance. SAC also generates resources that stay available to the whole community. We produce some bioinformatic workflows - ways of running all different necessary programs in different combinations to produce the genome assembly and perform quality control on it. We test these workflows, write guidelines and we directly provide support to the community. All these workflows and guidelines contribute to the goal of establishing standards. For reference genomes to become high quality some quality standards must be met and it is easier to meet these quality standards if you follow standardized protocols and workflows, like the ones we share. So we play a role in this critical gatekeeping point. Related to that, we developed a new reviewing method that is completely open and based on standardized reports that show all the important metrics and quality controls so that community reviewers can check if the genome assemblies meet all relevant quality and define if it’s the final product ready to be shared with the scientific community. All this work is designed and produced with a lot of input from the community and by the community. This is the work of the network in action: coordinating from the community for the community. 3. Can you tell us about the most interesting and the most challenging aspects of being a part of SAC? It is super interesting to meet other researchers with similar interests and discuss current developments in the field of reference genomes. I also find it interesting to learn about the particular challenges that members are facing trying to generate a high quality genome assembly for a “weird” species or not so common genus. It is super rewarding to connect with people, transcending all sorts of boundaries - geographical, career, languages, resources - and meet all these different people and talk about applying scientific thinking to produce these amazing resources such as reference genomes. The challenging part is to move forward an agenda that is truly helpful and will make the community improve. It can be difficult to understand what people need, what will be helpful for them, or to identify when someone needs more space or time for a given matter to be properly addressed. It is also challenging to keep people engaged and avoid the zoom fatigue with so many online meetings. 4. What developments in the world of genome “sequencing and assembly” are you most excited about in the coming years? All the developments related to ultra low input protocols for sequencing library preparation are exciting. These methods already exist but they are quickly improving. Also protocols related to tricky samples or not “ideal samples” - this is something essential for the goal of generating genomes for all the eukaryotic biodiversity. These are some exciting developments that will bring a lot of progress in the field. Developments related to Oxford Nanopore sequencing and the production of ultra long reads are also very exciting. I think this technology is super cool and it will bring a lot of new possibilities. I have a lot of expectations about what will be finally delivered because this could make “telomere-to-telomere” (T2T) genome assemblies more accessible for the community. Finally of course developments related to Artificial Intelligence in general. This technology is proving pretty disruptive in other areas and I think this will happen in our field soon. 5. What are the next steps for the ERGA SAC Committee? There is a plan to open more space for discussions about sequencing, as we have been quite focused on the “assembly” part so far. So we should start having some dedicated meetings about this soon. I think that it could be useful for the community to have this dedicated space for exchanges between people across Europe. Other future steps are related to strengthening and expanding the sequencing and assembly Community by providing and promoting space for discussion, assisting the community and making useful resources available for all. Send an email to the Sequencing & Assembly Committee and learn more about how you can participate!

Tourism is the predominant economic force in Croatia. Consequently, coastal management strategies often focus on short-term solutions, resulting in unsustainable practices, particularly in highly populated or urban areas. For instance, Croatia's unique gravel beaches are currently managed without considering the natural resources they support. Furthermore, the lack of baseline knowledge about the biota residing on these beaches hinders the development of sustainable management strategies. In January 2024, a project led by Dr. Maximilian Wagner (YUFE4Postdoc scholar at the University of Rijeka) in collaboration with Prof. Hannes Svardal and Prof. Igor Ruzic began with the aim of investigating the biotic and abiotic relationships on both urban and pristine natural gravel beaches in Croatia. The project's overall goal is to help develop ecosystem-based beach management as part of sustainable long-term solutions for ongoing and future coastal management in Croatia. Rijeka is the third-largest city in Croatia and also home to endemic coastal species, such as the blunt-snouted clingfish - the project investigates long-term solutions for Specifically, within the framework of this BGE-ERGA case study, we will apply cutting-edge genomic techniques to investigate the role of natural (oceanographic) and artificial barriers in the larval dispersal of a key component of Mediterranean gravel beach fauna: the endemic blunt-snouted clingfishes . Two sympatric blunt-snouted clingfish (genus Gouania ) species exist in the area around Rijeka, providing the ideal setting for this study. While a reference genome for one of these species, G. adriatica , is already available, our first step will be to produce a reference genome for the second species, G. pigra . This will not only allow us to compare dispersal and connectivity patterns across both species, but it is also a prerequisite for achieving the high genomic resolution needed to study population processes on these unprecedentedly small spatial scales.  Hidden biodiversity - Clingfish are small and relatively poorly known. The comparison between the genomes of G. adriatica and G. pigra will bring new insights about the species and evolutionary processes occurring at a small spatial scale. Often, marine connectivity studies draw conclusions over large geographical scales, such as gyres and circulation systems. However, given the ongoing coastal development and the meagre dispersal abilities of some species, this study offers a unique opportunity to examine population-level dynamics at an exceptionally small spatial scale. This project not only aims to enhance our understanding of connectivity patterns in the marine realm but also highlights the importance of whole-genome investigations in assessing and understanding biodiversity across space and time.  We extend our gratitude to Duje Kalajzic, Prof. emer. Cedomir Benac, Dr. Marcelo Kovacic, Dr. Els de Keyzer, and Dr. Pascal Hablützel for their valuable contributions. This project is funded by the European Union under the European Union’s Horizon Europe research and innovation programme, co-funded by the Swiss Government and the British Government, with additional support from the Marie-Curie co-financed YUFE4Postdoc program. A challenging task: Researchers look for the tiny clingfish among the rocky beaches of Rijeka. Photos by Maximilian Wagner About the Author Maximilian Wagner is part of ERGA (Croatia) and participated in the creation and sampling of several reference genomes in the ERGA and VGP pilot phase. He is currently a YUFE4Postdoc funded PostDoc at the University of Rijeka working on the ecology and evolution of organisms (mainly fishes) living in gravel beaches. More information at: https://maximilian-wagner.org

In April 2024, the project “A new reference genome for the conservation of coastal species in the face of anthropogenic change” was selected in the ERGA-BGE call "Enhancing Biodiversity Genomics Applications for Ongoing Case Studies". The project involves researchers from the University of Barcelona (Barcelona, Spain) and the University of La Laguna (Canary Islands, Spain). This initiative is dedicated to generating a high-quality reference genome for D. curvisetae . This resource will significantly enhance our understanding of the genomic basis of adaptation and the mechanisms driving genetic diversity across species. The project, led by Prof. Julio Rozas, Dr. Sara Guirao-Rico, and Dr. Nuria Macías-Hernández, will accelerate the use of new high-quality reference genomes relevant for understanding, monitoring, and conserving biodiversity. Research activities include sampling campaigns to collect D. curvisetae  specimens from the coasts of Tenerife and the generation of a genome assembly and annotation. The group has a consolidated line of research that focuses on the radiation of animal species on oceanic islands based on the case study of the adaptive radiation of the spider genus Dysdera  in the Canary Islands. Previous research results include the identification of molecular targets of adaptive convergence in phenotypic traits related to trophic specialization in these islands. The current project is generating new reference genomes at the chromosome level for species that inhabit the intertidal zones of pebble beaches on seashores. The coastal areas of Tenerife have been one of the most degraded habitats in the last years, mainly due to urban development - can people and the native biodiversity coexist on the island’s shore? Species photo: Pedro Oromí This type of habitat is unique among the species of this genus, and only reported in some Macaronesian species. It represents a new case of ecological shift found in the genus Dysdera . This provides a great opportunity to investigate habitat specialization as a novel driver of species radiation, but more importantly, to envisage how these highly specialized organisms adapt to habitats particularly vulnerable to anthropogenic effects. The coastal areas of the Canary Islands have been one of the most degraded habitats in the last thirty years, mainly due to urban development, and this trend is still increasing. Members of the research team Julio Rozas, Sara Guiaro-Rico, Nuria Macías-Hernández, Vadim Pisarenco, Silvia García and Marta Olivé look  for spiders among the rocky sea shore of Tenerife. Photos by Julio Rozas and Sara Guirao-Rico This project will be the benchmark to boost knowledge of the genomic basis of convergent adaptation and the generation and maintenance of diversity associated with insular radiations. In addition, the results of this project will be important for predicting how factors such as coastal degradation, sea level rise, desalination, and other human-induced impacts will affect these organisms and their adaptive potential. Using the genomic information generated by this project, conservation initiatives can be implemented for a variety of species or evolutionary lineages exhibiting characteristics peculiar to coastal ecosystems that have traditionally been overlooked by conservation programs. The leading researchers of this project would like to extend their gratitude to all the members of the University of Barcelona and the University of La Laguna research team for their commitment and dedication, as well as to all the collaborators who participated in the sampling campaign. This project received funding from the European Union under the European Union’s Horizon Europe research and innovation programme, co-funded by the Swiss Government and the British Government, with additional support from national research grants. We also thank BGE-ERGA for providing a collaborative platform that made this research possible. About the Authors Prof. Julio Rozas, Dr. Sara Guirao-Rico, and Dr. Nuria Macías-Hernández are part of ERGA SPAIN. You can find more information about their research at   https://www.ub.edu/molevol/julio/  and https://portalciencia.ull.es/grupos/6542/detalle

This ERGA-BGE project, started in June 2024 and led by Dr. Justyna Kubacka, builds upon an ongoing study on the conservation genomics of the aquatic warbler, a threatened bird of highly fragmented central-European wetland. Under the ERGA-BGE umbrella, the project aims to whole-genome resequence around 20 individuals of the aquatic warbler from two populations. Samples were collected by Prof. Andrzej Dyrcz, Dr. Benedikt Giessing, Dr. Jarosław Krogulec, and Grzegorz Kiljan in the 1990s, and by Dr. Kubacka in the 2010s. The birds were sampled in one of the species' strongholds, the Biebrza Valley in the northeast of Poland, which hosts about 25% of the global population, and in the currently extinct breeding site in Western Pomerania at the Polish-German border. The two regions are approx. 600 km apart with only scarce breeding habitat in between. The project will focus on two populations of aquatic warbler: a larger population from the well-preserved Biebrza Valley marshes and a population from Western Pomerania that is currently extinct. Photos by Justyna Kubacka and Knyva. The ERGA-BGE project aims to complement the ongoing study with a more thorough evaluation of genomic inbreeding, effective population size, and genetic bottlenecks, as well as adaptive variation and population structure between the two distant populations. The results of the project will help us understand the extent of the loss of genetic diversity and its contribution to the decline of the aquatic warbler.  They will inform translocation of the species, which is being carried out to restore the extinct population in Western Pomerania.  Importantly, the ERGA-BGE project will use the recently finished chromosome-level reference genome of the aquatic warbler.    Looking for the tiny aquatic warbler across the vast landscape of the Biebrza Valley. Photo by Szczepan Skibicki. The research activities included fieldwork in remote mires to catch and blood-sample aquatic warblers. The samples collected in the 1990s were deposited in the Dresden Senckenberg Museum (Germany). Dr Kubacka extracted DNA from these samples on her visit to the Museum at the beginning of 2024. She is also curating a collection of aquatic warbler DNA samples, which will be used for the ERGA-BGE project. The project is expected to draw the attention of the scientific community as it will explore the past and present conservation genomics of a migratory bird that is a habitat specialist breeding in a vanishing wetland habitat. Handling and sampling small birds such as the aquatic warbler requires expertise and a lot of care. Photos by Irene Arnaldos Giner and Anna Dubiec. The study is funded by the German Ornithological Society (DO-G) and through EU Life programme resources awarded to Förderverein Naturschutz im Peenetal e.v., Germany, and the Baltic Environmental Forum, Lithuania. It is being carried out in collaboration with Prof. Michael Wink, Dr. Volker Salewski, and Dr. Martin Paeckert. It would not be made possible without the collectors, who laboriously obtained samples from breeding sites covering the whole breeding range of the species, including those as distant and remote as Western Siberia. The whole-genome resequencing part of the project will be performed thanks to funding from the European Union under the European Union’s Horizon Europe research and innovation programme, co-funded by the Swiss Government and the British Government. About the Author: Dr. Justyna Kubacka is an evolutionary ecologist and ornithologist. She works in the Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw. She belongs to the aquatic warbler genome team of the ERGA Pilot reference genome project.

We are pleased to announce the 20 projects that have been selected as part of the recent ERGA-BGE call "Enhancing Biodiversity Genomics Applications for Ongoing Case Studies" . The projects selected are on-going initiatives that leverage high-quality reference genomes to boost biodiversity conservation or to investigate how sustainably managed species contribute to our economy and health. The funding will be used to bring the relevant reference genomes up to Earth BioGenome Project (EBP)  standards or, for projects already meeting these criteria, to generate genomic data to enhance and complete the research - such as population re-sequencing data. Stay tuned for blog posts, updates and research outcomes of each of these projects reported here in the ERGA Blog! In the interactive map below you can explore the partner institutions distributed across Europe and the topic of each of the projects: This is a subcontracting task of the BGE Project and coordinated by the associated partner's team at the Swiss Institute of Bioinformatics . 📢 Stay tuned! In the coming weeks, we'll be introducing and highlighting the case studies through posts written by the scientists leading each project!

Every six years, the botanical community convenes for what has been called their “Olympic Games”: the International Botanical Congress . This year, the XXth congress brought over 3 000 attendees from all parts of the world from 21st to 27th July to sunny Madrid – during a major heatwave. Among them were several ERGA members, aiming to make contact among each other and to get more botanists involved in our initiative. Additionally, this was a great opportunity to exchange with other large-scale sequencing projects targeting plants, such as GAP  (Genomics for Australian Plants), 10KP  (Ten Thousand Plant Genomes) and DToL  (Darwin Tree of Life), putting ERGA on the map as the only cross-borders and community-driven initiative among them.  Katja inviting all IBC attendees to the ERGA satellite meeting at the end of her talk, which highlighted the importance of common standards and reproducibility in large-scale reference genome production. (Photo: Sophie Maiwald) Already on Tuesday evening, the symposium “Large-scale Generation and Utilisation of Reference-Quality Genomes from Plants”, organised by Peter Hollingsworth (Royal Botanic Garden Edinburgh) and Sean Graham (University of British Columbia), and the ensuing workshop of the 10KP project sparked heated discussions. These ranged from fair attribution and involvement of sample providers and other experts, open data access and findable vouchers, capacity building and “helicopter” science, i.e. the study of a country’s biodiversity without involving any local researchers, to the inequality of opportunities among the global North and South, which is further exacerbated by current technological limits such as the necessity of liquid nitrogen freezing. Specifically with respect to ERGA, several participants asked how they could contribute community genomes . The new ERGA badges served their purpose well and the ERGA satellite meeting was announced in all central places. (Photos: Katja Reichel) Although the meteorological conditions and a wave of COVID infections had somewhat diminished the field, over 20 attendees currently based e.g. in Spain, Portugal, France, Great Britain, Germany, Austria, Italy and Hungary – plus guests from China and Australia – also came to the ERGA plant specialists’ IBC satellite meeting on Wednesday afternoon. There, Katja Reichel gave an introduction to ERGA and to several current endeavours craving input from the plant community, such as the rogue genomes working group  and plant sampling SOP . About half of the group then stayed on to network and discuss general issues during plant reference genome production. This included topics as diverse as the lack of funding opportunities for big genomes (such as present in many plants), the missing overview of the species whose genomes are currently being sequenced (and by whom / prioritisation), the lack of software adapted e.g. to genomes of uneven ploidy or including huge repeat clusters which defy even long-read sequencing, the challenges of genome annotation , problems with high molecular weight (HMW) DNA extraction, as well as the isolation of plant genome scientists even within ERGA. However, the meeting also brought forth the expertise which already exists on some of these issues, and highlighted the need to connect and join forces. You can find the slides presented by Katja here .   Both from the meeting and from further conference break discussions arose several ideas for action. These include a more proactive, transparent communication on the aims and “rules” of ERGA within the (plant) science community and also towards partner projects such as DToL, the registration of ongoing reference genome sequencing projects, including community genomes, e.g. through GoaT , the establishment of a reporting standard for both successful and failed HMW DNA extractions alike, and a dedicated keybase channel for, as well as regular online / hybrid meetings of, the ERGA plant specialist community.    Hoping that these ideas will gradually be implemented, we thank Luisa Marins, Chiara Bortoluzzi and Christian de Guttry for help with the organisation and advertisement for the satellite meeting, all participants and discussion partners for their contributions, as well as the IBC organisers for giving us this opportunity to connect. About the Author Katja Reichel  is co-chair of the Sampling and Sample Processing Committee and regularly speaks out for plants within the ERGA community. At the IBC, she presented a bioinformatic pipeline  for the standardised generation of annotated plastid genomes from Illumina short reads. Her research on population and conservation genomics of partially clonal plants currently focuses on Arnica montana   and is partially financed by the Biodiversity Genomics Europe project.

In June 2024, Camille Cornet, researcher at the Swiss University of Neuchâtel , embarked on an exciting case study connected to Biodiversity Genomics Europe . This project is centred on the remarkable biodiversity of alpine butterflies, in particular the genus Erebia , whose species can be found throughout Europe. Some species are widespread, when others are localized and often endangered. Localized species are particularly threatened by climate change and land use, making this project important to implement future conservation measures. The primary goal of the project is to assess the functional genomic diversity of Erebia in the context of adaptation to environmental change. The results will be instrumental for conservation of Erebia  and will underscore the importance of genomic information for efficient biodiversity management. A great adventure: the team of scientists travelled all the way from France to Georgia in search of alpine butterflies to sample and study. After an idyllic yet intense period of fieldwork ranging from the French Massif Central over the Alps to the Caucasus in Georgia, the research team successfully sampled butterflies of a dozen Erebia  species, and sequenced and assembled their genomes. Preliminary results uncovered hidden genetic diversity as many species differ greatly in their number of chromosomal rearrangements. These substantial differences have been suggested to play a role in species diversification. To further elucidate the importance of genetic diversity for adaptation to climate change, the next stage involves annotating the genomes to pinpoint gene locations. This step is crucial to determine where important functional diversity exists within the genomes and whether they mediate genomic rearrangements. The 12 butterfly genomes sequenced revealed great genetic diversity within the genus Erebia - many species differ in their number of chromosomal rearrangements. This BGE Case Study on alpine butterflies highlights the importance of cutting-edge genomics research to provide the resources for their future conservation. As climate change coupled with habitat loss continues to threaten biodiversity, such investigations become essential. Stay tuned for more updates on our findings and their implications for conservation! This work would not be possible without the invaluable help of Tinatin Chkhartishvili and Giorgi Iankoshvili from Ilia State University in Georgia, and Yannick Chittaro and Andreas Sanchez from InfoFauna in Switzerland to collect specimens. This project has received funding from the European Union under the European Union’s Horizon Europe research and innovation programme, co-funded by the Swiss Government and the British Government. About the Author: Camille Cornet is a member of the ERGA community, participating in the ERGA effort by sequencing genomes of, among others, Erebia  butterflies. Camille is part of the Biodiversity Genomics Lab  at University of Neuchâtel. Photo credits: Camille Cornet and Giorgi Iankoshvili

Plant biologists from Umeå Plant Science Centre in northern Sweden are excited to be sampling the first individuals from a new collection of aspen trees. This will kick off a long-term project about genetic diversity in Nordic aspen trees (NordAsp). The NordAsp project studies natural genetic diversity in aspen, Populus tremula, along a climatic gradient across northern Norway and Sweden. Last summer, the roots of wild aspen trees were dug from more than 1200 locations spanning the Scandinavian peninsula, and new plants were propagated from those roots. Next year, 700 of these will be planted in new field experiments in both countries. Already this July, leaf samples will be harvested so that DNA can be extracted from representative trees to get advance knowledge about the genetic diversity of NordAsp. The NordAsp project studies natural genetic diversity in aspen, Populus tremula, along a climatic gradient across northern Norway and Sweden. Plants were sampled from root cuttings in 1200 locations and propagated in a greenhouse. The ERGA project investigates genetic variation in a selection of 40 individuals representing the sampling gradient. Photos Credit: Urška Klepec, Maxime Chantreau Previous research has shown that there is a huge amount of genetic variation among aspens on the landscape. Aspens are very heterozygous, meaning that individuals are genetically very different to each other – just like humans are. The DNA sequencing of the first 40 individuals of the NordAsp collection will give us the opportunity to look at variation in DNA sequences among representative trees growing along our east to west sampling transects. We will see how the trees differ as individuals, looking for contrasting patterns of inheritance in their genetic sequences. We will also get information that helps us plan the DNA sequencing of all 700 aspens in our new common garden experiments, for example which sequencing technologies to use. The data will lead us to a new wealth of knowledge about the biology of an ecological keystone species. Information about genetic variation along this extreme climatic transect will also help us predict the resilience of this species – and its dependent flora and fauna – when faced with future climate scenarios. The Aspen Across the Seasons: how resilient are the trees to a changing climate? The answer lies in their genes. This project was led by Prof. Stefan Jansson and was made possible by the sampling efforts of 35 researchers from UPSC and plant propagation by Skogfork, an essential stakeholder in this project. Leaves from the new plants will be sampled by Nathaniel Street and Kathryn Robinson, with DNA preparation by Vikash Kumar. We are grateful to the Trees for the Future (T4F, a subsidiary of Trees and Crops for the Future, TC4F), and the Biodiversity Genomic Europe (BGE) project for financial support.   About the Author: Nathaniel Street is Professor of Forest Tree Genomics at Umeå University and leader of the NordAsp BGE project. Visit our homepage , lab page and read more about the T4F project at https://www.slu.se/en/Collaborative-Centres-and-Projects/trees-and-crops-for-the- future/