Search Results

ERGA  (European Reference Genome Atlas) and iBOL (International Barcode of Life) Europe  are pleased to announce the signature of a Memorandum of Understanding (MoU) to officialise their strategic alignment and shared aspirations for the future.  Both iBOL Europe and ERGA address biodiversity loss in Europe by accelerating the application of genomic science to enhance understanding of biodiversity, monitor biodiversity change, and guide interventions to address its decline.   iBOL Europe applies DNA barcoding, while ERGA advances the generation of reference genomes for European Biodiversity. The MoU includes concrete agreements on crucial strategic alignment aspects, especially cross-collaboration, knowledge exchange and network building. With both research-oriented initiatives focused on applying genomic science to better understand biodiversity, there are many natural synergies and complementary approaches to building shared knowledge. The MoU was signed on 10 October 2024 in Thessaloniki (Greece) by the representatives of each initiative.  We look forward to taking our collaboration forward.

In June 2024, researchers from the Centre for Ecology, Evolution, and Environmental Changes  (CE3C) at the Faculty of Sciences, University of Lisbon, Portugal, in partnership with Biodiversity Genomics Europe  (BGE), launched a groundbreaking project to improve the genomic annotation of the white crowberry ( Corema album ). This initiative seeks to deepen our understanding of this essential coastal plant species and address its conservation needs amid changing environmental conditions. Corema album  ssp. album  is an Iberian Peninsula endemic species with a recognised ecological value in its natural habitat. This dioecious perennial woody shrub is a key structural species of the dune systems and is only found in the Iberian Peninsula’s coastal dunes and pine tree forests. Its habitat holds a priority conservation status under Council Directive 92/43/EEC. Due to anthropogenic pressures and climate change, C. album  populations are declining, particularly populations inhabiting the southern limit of the distribution range, and the species is listed as a conservation concern in PROGEN by ICNF. Corema album population over the cliffs of Vila Nova de Milfontes, Portugal. (Photo credit: João Jacinto) The main target of this project is to produce a high-quality reference genome for Corema album , included in the ERGA Pilot Project, by conducting RNA sequencing (RNA-seq) on multiple tissues from both male and female plants. This effort will help annotate the reference genome, providing comprehensive insights into the species’ genetic diversity and adaptation mechanisms. Studying both male and female C. album  plants is crucial due to its dioecious nature, which is essential for understanding sex-based genetic diversity. A well-annotated reference genome will enable researchers to better understand the genetic basis of Corema album ’s adaptation to its coastal habitat, particularly aridity. By enhancing the genomic understanding of Corema album , this project aims to contribute significantly to the conservation of coastal dune ecosystems, ensuring their resilience and sustainability for future generations. This project also highlights the broader importance of genomics in biodiversity conservation, potentially guiding conservation strategies for other species in similar habitats. Close-up of a female Corema album plant bearing fruits. (Photo credit: Carla Alegria) Leading this endeavour is Manuela Sim-Sim and a dedicated team of researchers, including Helena Trindade, Vítor Sousa, Bruno Nevado, Carla Alegria and João Jacinto, combining expertise in systematics, taxonomy, genetics, molecular biology, bioinformatics, and ecology, actively participating in both ERGA and the Genome Team of the pilot project. By bringing together a diverse team and leveraging cutting-edge genomic techniques, this initiative represents a significant step toward integrating genomic data into effective conservation strategies, safeguarding the biodiversity of coastal dune ecosystems. 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, with additional support from CE3C’s FCT Unit funding UIDB/00329/2020 ( https://doi.org/10.54499/UIDB/00329/2020 ). By integrating genomic data into conservation efforts, this project aims to pave the way for more informed and effective strategies to protect and sustain biodiversity in coastal ecosystems. About the Author Manuela Sim-Sim , Helena Trindade , Vítor Sousa , Carla Alegria  and João Jacinto  are members of the Corema genome team for the ERGA pilot project. Additionally, Vítor Sousa participates in the Data Analysis Committee  and is also a member of the ERGA Council of Country Representatives . Manuela Sim-Sim, Vítor Sousa and Bruno Nevado are leaders of CE3C’s research groups Natural History Collections & Systematics  (NHC&S), Evolutionary Genomics and Bioinformatics  (EGB), and Speciation Genomics  (SG), respectively, and Helena Trindade, Carla Alegria and João Jacinto (PhD student) are members of CE3C’s Plant Functional Ecology  research group.

We are excited to announce the upcoming Genome Application Symposium , which will be held on September 30 and October 1, 2024. This two-day online  event promises to be an enriching experience, bringing together leading experts and enthusiasts in the field of genomics and promoting knowledge exchange. Focusing on the development of genome applications for the protection of biodiversity and stakeholder engagement , this symposium will provide opportunities for interdisciplinary interactions from basic to applied science.   Event Details: 📅 September 30 and October 1, 2024 ( click to add to your agenda! ) 🕘 9:00 to 16:45 CEST | ▶️ Venue: Zoom   A playlist with all recorded sessions is now available on Youtube: Participation is open to everyone. No registration is required, the event will be openly transmitted via Zoom   Overview of the program:

Imagine it’s June again – flowering time for Arnica! Except this year, June also saw the beginning of a pioneering research project on this well-known medicinal plant, which is currently disappearing from large parts of its native range in Europe. At the invitation of Dr Katja Reichel from FU Berlin, Arnica specialists from several European countries will join forces in the new BGE ERGA case study ArnicaSNP  and develop a scheme for monitoring diversity and changes in the species’ genome – through time and space. Quo vadis, Arnica? As populations decline and disappear in large parts of its range, the species faces an uncertain future. Photo by Katja Reichel. In the BGE project, Arnica serves as an example to show how the availability of reference genomes impacts the way conservation geneticists work. Currently, wild stands of the charismatic yellow-flowering herb are highly protected in some European countries, yet heavily exploited in others, since large-scale cultivation has so far failed. Populations in different parts of the species’ range thus face a variety of threats, from overharvesting to the abandonment of hay meadows, which used to be an important Arnica habitat type especially in the lowlands, but whose existence depends on mowing. These direct factors in the decline are overlaid by more complex effects of climate change, which may also impact the higher-up growth sites that gave Arnica its Latin name, Arnica montana , and Arnica’s composite reproductive system, including both sexual offspring from seeds and clonal “daughter” plants connected underground to their parent. The need to understand Arnica’s evolution to ensure the species’ effective protection has motivated a number of previous local conservation genetic studies, yet so far, no range-wide comparison exists. Arnica habitats at a glance. Photos by Katja Reichel, Aaron Pérez Haase and G. Mansion / A. Guggisberg. ArnicaSNP now takes Arnica conservation research to a new level: By jointly analysing genomic data from across Europe, based on DNA samples collected in previous studies and over a period of more than ten years, it will provide essential information to allow the repeated, range-wide measuring of the species’ natural diversity. This includes testing methodological questions, such as which sections of the genome evolve locally vs. in different parts of the plant’s range, or on which time scale to expect detectable changes. The Arnica reference genome, which is also being generated as part of the ERGA BGE project, will hereby serve as a “map” for smaller stretches of DNA (RADtags, SSR loci) sequenced in a total of over 400 samples. Moreover, the project will give future conservation scientists an opportunity to get their first experience with genomic data in the project’s equally important training and dissemination part. By bringing the European Arnica community together,  we hope that ArnicaSNP will be a hotbed of further ideas on the plants’ sustainable protection and equitable use, and inspire similar networks for other disappearing species.  This project is made possible by the support of the ERGA community, and 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, as well as from FU Berlin. About the Author Katja Reichel works at Freie Universität Berlin , doing research  on the population and conservation genetics of partially clonal (and other) plants, often – as for ArnicaSNP – in collaboration with the Berlin Botanic Garden and Botanical Museum . She is also the current co-chair of the ERGA Sampling and Sample Processing Committee.

The “Enhancing Biodiversity Genomics Applications for Ongoing Case Studies” call of BGE has triggered much of our interest at the beginning of 2024. We study an endangered small mammal species in Hungary, and we had already produced a short-read dataset, but long-reads and Hi-C data were missing to achieve a high-quality genome. So, we rapidly nominated our target species, the Hungarian birch mouse ( Sicista trizona ) of the Sminthidae family of Rodentia, arguably one of the rarest mammals in Europe. The nominal subspecies, S. trizona trizona , is extinct in Austria and Slovakia, most probably in Serbia, and has almost gone extinct in Hungary, where only a single population is known. Our research team formed by the researchers of the HUN-REN–UD Conservation Biology Research Group, the Evolutionary Genomics Research Group of the University of Debrecen, and the Hungarian Natural History Museum has won the opportunity to undertake this research under the umbrella of the HUN-REN Office for Supported Research Groups (Budapest, Hungary). The study will provide a high-quality reference genome for the Hungarian birch mouse, which will assist a population genomic study at the single locality, representing the only known population of the subspecies, managed by the Bükk National Park Directorate at the protected territory “Borsodi-Mezőség” Landscape Protection Area (Hungary). The Hungarian Birch-mouse ( Sicista trizona trizona) . Photo by Gábor Sramkó. During the annual monitoring survey of this species, we managed to collect enough blood samples from two animals for high-molecular-weight DNA extraction. One sample of individuals, coded as ST65, provided enough clear DNA samples with fragment size > 30kb. This will first be subject to Pac-Bio HiFi sequence data generation using a commercially available service provider based in the EU that should yield approximately 40× long-read coverage of the Hungarian birch mouse’s genome. Furthermore, we will also produce Hi-C data from samples collected during the second round of monitoring surveys at the known locality this autumn. All these data will make a perfect use for analysing genomic data originating from a reduced-representation genomic library technique RADseq. The latter data were collected from across the currently known range of the habitat of the subspecies, and thus we hope to deliver readily usable results for the effective preservation of the Hungarian birch-mouse on its last known site. Furthermore, this reference genome will be the first to represent the family Sminthidae, the basal clade of the mice suborder, Myomorpha. Therefore, we also expect our birch mouse genome to become a valuable resource in evolutionary research targeting research questions in mice (in a broad taxonomic sense). Photos by Gábor Sramkó. In summary, we feel privileged by the opportunity the BGE project provided to us: our favourite birch mouse, on the brink of extinction, can enormously benefit from a genomic resource that will lay down the genetic basis of a well-established management plan for this critically endangered taxon. We extend our gratitude to the Bükk National Park Directorate and personally to Péter Balázsi, for their invaluable help during the fieldwork and the project. We are highly indebted to the two PhD students of the PI, Virág Nyíri and Lajos Szatmári, for the high-quality work during the laboratory work. This project is funded by the Horizon Europe research and innovation programme, co-funded by the Swiss Government and the British government, with additional support from a national research grant awarded to the PI (NKFIH FK137962); and fieldwork supported by the GRASSLAND-HU LIFE IP. We also thank BGE-ERGA for providing a collaborative platform that made this research possible. About the Author Gábor Sramkó is part of the ERGA community from Hungary. He is contributing to the WP11 action in BGE, where he helps an ongoing ERGA case study  on the common hamster ( Cricetus cricetus ) as an evolutionary geneticist expert.  Gábor’s main interest lays in phylogenetics, phylogeography and conservation genetics at the genomic level among plants and animals. He is the head of the Evolutionary Genomics Research Group at the University of Debrecen, Hungary . Tamás Cserkész is part of the ERGA community from Hungary. He is contributing to the WP4 and WP11 action in BGE, where he coordinates an ongoing ERGA case study on the common hamster ( Cricetus cricetus ) as an mammalogist expert.  Tamás’s main interest lays in phylogenetics, phylogeography and conservation of mammals. He is the project coordinator at the Hungarian Natural History Museum, Hungary .

The Phycology Research Group at Ghent University contributes with a case study to the BioGenEurope "Enhancing Biodiversity Genomics Applications" program with a project started in June 2024. Within the project, we aim to establish reference genomes for two red macroalgae Porphyra dioica  and Porphyra linearis  to support ongoing research.  Porphyra dioica  and Porphyra linearis belong to an ancient red algae group, commonly known as bladed Bangiales. This order includes many fascinating species, some of which are well known, such as Nori sheets - an essential ingredient in sushi - but there are also others with a complex physiology that permits them to survive in the stressful intertidal environment. Besides tolerating quick changes in temperature and light intensity, they can also survive desiccation and freezing.  Porphyra dioica  and Porphyra linearis belong to an ancient red algae group, sequencing their genomes will help researchers to better understand their complex physiology and evolution.   Photo by By Emile Wuitner - Wuitner, Emile (1921) Algues Marines des Cotes de France (Manche et Ocean), Encyclopedie Pratique du Naturaliste. v.VII, Paris: Paul Lechevalier, Public Domain. With the help of these two genomes, we will be able to gain a better understanding of underlying fundamental processes in red macroalgal evolution, adaptation, and specific life cycle variation. In addition to providing fundamental knowledge about this ancient lineage of red algae, this new genomic data can assist in overcoming hurdles associated with the valorisation of European Porphyra. 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. Porphyra linearis  growing in its natural habitat. Photo by Jessica Knoop About the Author Prof. Olivier De Clerck and Dr. Jessica Knoop are from the Phycology Research Group at Ghent University, BE. The working group focuses on genetics, diversity, life cycle control of marine macroalgae. We address questions ranging from descriptive taxonomy over ecological studies forecasting the distribution of species in relation to environmental change to genomics. These fundamental biological questions are also used to solve more applied aspects - advancing seaweed cultivation in Europe. You can find more information about the research at https://phycology.ugent.be/

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