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In June 2024, a collaborative project started between the Centre for Ecology, Evolution, and Environmental Changes (CE3C) , at the Faculty of Sciences, University of Lisbon, Portugal, and Biodiversity Genomics Europe (BGE) . The project is led by Octávio S. Paulo and André F. Henriques and aims at evaluating, in three regions of Portugal, the potential impact of Small-Scale Farming (SSF) on the genetic variability and adaptation of three wild bee species: Andrena flavipes  (Panzer, 1799), Bombus terrestris  (Linnaeus, 1758), and Lasioglossum malachurum  (Kirby, 1802). Our hypothesis posits that Small-Scale Farming landscapes may positively influence the genetic diversity of these three common wild bees species, thereby promoting their adaptation to the crop mosaic seen in these landscapes. Using data from ESRI | Sentinel-2 Land Cover 2022 we chose three regions of Portugal with suitable areas for two contrasting landscapes: low agriculture landscapes (LoA) and Small-Scale Farming landscapes (SFF). An extensive field work was done across these three regions of Portugal, where samples from the three target species were collected. These samples will be processed in the CE3C facilities, in Lisbon, to obtain high-quality genomic DNA and subsequently shipped to state-of-the-art laboratories to perform next-generation sequencing of pooled samples (Pool-seq).  In search of native bees: The project included extensive field work to collect samples from the three target species. | Photo taken by Eduardo Sousa. To test our hypothesis, we will combine high-quality reference genomes and the pool-seq data for the three species, to compare, within each region and between the three different regions, the SSF and LoA landscapes. Preliminary results based on RAD-seq data seem to support our hypothesis. This innovative project not only enhances our scientific understanding of the genetic status of three important wild bee species but also highlights the importance of genomics in biodiversity conservation. Should our hypothesis prove correct, the results could be relevant for designing a conservation plan for wild bees, guided by genetic and genomic principles and the capacity of these species to adapt to small-scale farming landscapes. 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 national research grants FCT 2022.14424.BD awarded to André F. Henriques and FCT Unit funding UID/BIA/00329/2019. We also extend our gratitude to BGE-ERGA for providing the collaborative platform that made this research possible.   About the Authors: Octávio S. Paulo and André F. Henriques are members of the ERGA Portugal and participate in the ERGA Sequencing & Assembly , Annotation and Data Analysis Committees. Octávio S. Paulo leads the CoBiG2 group of CE3C and André F. Henriques is a PhD student in the same group. More information can be found at CoBiG2 group. Photo credits: Lasioglossum malachurum : By James Lindsey at Ecology of Commanster, CC BY-SA 2.5 Andrena flavipes : Fritz Geller-Grimm, CC BY-SA 3.0 , via Wikimedia Commons Bombus terrestris : Paulo Costa, CC BY-SA 3.0 , via Wikimedia Commons

Are you a plant specialist interested in boosting genomic resources for the European flora? ERGA will host a satellite meeting during this year's International Botanical Congress  on July 21 - 27 in Madrid, Spain. Join us - in presence or online - to learn more about ERGA, meet other members and network with researchers with similar interests. More details: ERGA plant specialist meeting 🕒 Wednesday July 24th, 15:00 - 18.00 📍 Room N107+8 🔗 Zoom link for remote participants The European Reference Genome Atlas (ERGA) is a continental-scale initiative under the umbrella of the Earth Biogenome Project (EBP), bringing together researchers across all taxonomic groups and experts on all stages of reference genome generation, for the common aim of producing high-quality reference genomes for all eukaryotic species inhabiting Europe. This meeting shall be an in-person get-together for all plant scientists within ERGA, with the possibility of virtual participation for those who could not make it to the IBC. We particularly welcome plant scientists of all career stages who are not yet members, but interested in learning more about ERGA and in joining our initiative. Agenda 1) Short introduction to ERGA + ways to participate 2) Ongoing ERGA plant community projects 3) Ideas and plans Please reach out to Katja Reichel ( katja.reichel@fu-berlin.de ) if you would like to support the organization of this meeting, give a short account about your participation in ERGA, co-chair part of the event, or add more ideas to the agenda..

The ERGA Knowledge Hub  is live! The main goal of this new portal is to gather and share educational materials on genomics and related topics, lowering access barriers and promoting knowledge exchange across Europe and beyond. Links to various types of training materials are available in the Hub, including lectures PDFs, videos, GitHub pages, interactive content. The Hub will collect content covering all steps relevant to production and application of reference genomes and genomic data  - from data generation and analysis to the ethical and social aspects that the workflow entails. This collection of educational materials is built based on the community’s input and everyone is welcome to submit their own educational materials or those from others - as long as a licence that allows free distribution and sharing with or without accreditation is provided. All the material available in the Hub is curated by a team of ERGA committee coordinators, ensuring the high quality of the content.  The ERGA Knowledge Hub was made possible thanks to Biodiversity Genomics Europe  (BGE) funded by the European Union under the Horizon Europe research and innovation program, co-funded by the Swiss and British governments. The portal was developed by the ERGA Training & Knowledge transfer Committee  in collaboration with the Swiss Institute for Bioinformatics.  Contribute! To submit a link to the collection, you just need to click on “ Contribute !” on the upper right corner of the Knowledge Hub.  You’ll need to select the type of license associated with this resource - if no licensing information is available on the page, you can try contacting the authors and ask if they agree to have their materials linked in the Hub. ⏯️ To learn more about the ERGA Knowledge Hub watch the Camila Mazzoni's presentation introducing the Hub to the Earth Biogenome Community: -- If you have any questions or suggestions related to the ERGA Knowledge Hub, please contact us at training@erga-biodiversity.eu.

June saw the annual meeting of Galaxy  developers and users at the Galaxy Community Conference 2024  in Brno, Czechia. This year over 150 participants came together to share updates to the Galaxy platform and present use-cases showing how Galaxy has enabled high-quality science through providing computational infrastructure and software support. Galaxy has established open computational servers in the United States , Europe  and Australia  alongside a suite of tools to give scientists the opportunity to process and analyse data of any size without the need to establish or use a local High Performance Computing service.  During the 4-day conference ERGA, the Vertebrate Genomes Project  and the wider Earth BioGenome Project  were well-represented, demonstrating how Galaxy fits into a distributed model of reference genome generation. Updates to the VGP pipeline were presented by Delphine Lariviere and Linelle Abueg, showcasing how they have used a Galaxy server at the Vertebrate Genomes Lab to assemble over 150 species. They also introduced the efforts made to assist manual curation of the assemblies.  The VGP uses their published pipelines and training material to give instructional workshops on how anyone can use Galaxy to assemble a genome without access to an HPC or even needing to install any software. Within the ERGA framework, Tom Brown presented how collaborators from Galaxy EU are helping ERGA to establish a review system for genome assembly via the ERGA Assembly Report ( EAR ) and assist the genome annotation community in installing necessary tools and developing workflows that enable researchers to annotate their favourite genome using best-practice tools and pipelines. You can learn more about the VGP’s efforts to assemble vertebrate genomes in their paper published in Nature Biotechnology  and read about ERGA’s efforts to benchmark annotation tools and workflows on a diverse range of organisms in their report from last year’s BioHackathon Europe . Click to check the poster and slides presented at the conference: The Galaxy Community Conference 2024 presented a fantastic opportunity for developers, systems administrators and researchers from the genomics, astronomy and material science communities to come together and hear about the latest advancements in Galaxy and its uses. Many thanks to the organisers and especially Björn Grüning and Anton Nekrutenko for their support given to the biodiversity genomics community. About the Author Tom Brown is the coordinator of the ERGA IT & Infrastructure Committee and also participates in the ERGA Sequencing & Assembly and Annotation Committees .

Dozens of scientific institutions and laboratories open their doors and invite visitors to discover their current research by interacting with scientists in an informal, playful atmosphere - that’s the spirit of the Lange Nacht der Wissenschaften  (“Long Night of Science”) which happens every summer in Berlin. On Saturday, June 22nd, 2024, Biodiversity Genomics Europe and ERGA participated in the event for the first time with a stand organised by the BGE team from the Leibniz Institute for Zoo and Wildlife Research  at Haus der Leibniz-Gemeinschaft in the heart of the German capital. Our main goal was to spread information about BGE and the European Reference Genome Atlas  (ERGA), highlighting the urgent need for conservation efforts for European species and discussing how state-of-the-art genomic technologies are helping to improve our understanding of biodiversity and advance its protection. We developed an interactive guessing game that allowed visitors to test their knowledge about some of the species that are having their genomes sequenced by BGE - with a particular focus on those of conservation concern.  Some snapshots of a very busy evening at the Haus der Leibniz-Gemeinschaft. You can find more photos of other activities here . Photos: Donat Agosti and Diego de Panis The board game attracted visitors of all ages - including families with children, young adults, and senior citizens - through the duration of the event and promoted an exciting dialogue with this varied audience. “When I think of corals, I immediately picture Australia. I had no idea such beautiful species were also present here in Europe!” - said one of the visitors, referring to the Yellow Gorgonian ( Eunicella cavolini), a common species in the Mediterranean Sea classified as “Near Threatened” by the International Union for Conservation of Nature (IUCN).   Another case that surprised the visitors was the charismatic and critically endangered European mink ( Mustela lutreola ). Once widespread in Europe, its range has suffered a drastic reduction by over 85% since the mid-19th century due to habitat loss and illegal hunting. Only a few fragmented populations still exist and its genome, sequenced as part of the ERGA Pilot project, will bring insights that can support and guide management and conservation actions. The Yellow Gorgonian coral, the Spanish moon moth and European White Elm illustrate the broad diversity of species sequenced by BGE and ERGA.  Photos: albert kok, CC BY-SA 3.0 , via Wikimedia Commons ;  Banco de imágenes del CNICE - MEC, CC BY-SA 2.5 ES, via Wikimedia Commons; Christian Fischer, CC BY-SA 4.0 , via Wikimedia Commons. Many other fascinating species captivated the audience, such as the smallest bat species found in Europe ( Pipistrellus hanaki), the beautiful Spanish Moon moth ( Graellsia isabellae ), and the gigantic European White Elm . The   Long Night of Science offered a great opportunity to reach out to citizens and tell them a bit about what we do at BGE and ERGA and why. Science communication events like this one are a rewarding two-way street, allowing us to learn from each other and gather diverse perspectives that guide us forward as a community of researchers, advancing and advocating for the development of biodiversity genomics in Europe. We thank everyone who stopped by our stand and the organisers of this year’s Long Night of Science and look forward to participating again next year! — About I’m Luísa Marins, and I coordinate communication actions for the European Reference Genome Atlas. If you want to know more about this event or the game, or if you would like help organizing a similar stand or any ERGA/BGE outreach activity across Europe, please reach out to media@erga-biodiversity.eu . References https://www.iucnredlist.org/species/50012182/50606230 https://www.berlin.de/en/events/2096550-2842498-long-night-of-the-sciences.en.html https://globalconservation.org/endangered-species/european-mink

ERGA, in collaboration with the Global Genome Biodiversity Network (GGBN) and the Earth Biogenome Project (EBP), held a webinar on Access and Benefit Sharing (ABS) with a special focus on the Nagoya Protocol on April 8th, 2024. We organized this seminar in response to frequent questions from the ERGA community regarding this topic, which highlights its complexity and relevance. ERGA’s goal for this seminar was to enhance understanding and provide clarity on ABS regulations, especially in relation to the Nagoya Protocol, an agreement that governs the fair and equitable distribution of profits arising from the utilization of genetic resources. The main speaker, Scarlett Sett (CSIRO ACDP), delivered an outstanding presentation, shedding light on the complexities and necessities of ABS in biodiversity research. The event was a success with over 90 participants from 29 countries around the world. Participating researchers from a few countries were working with genetic samples originating from over 50 different countries. This underscores the global nature of biodiversity research and highlights the critical need for clear and effective ABS regulations. However, the seminar also revealed that the bureaucracy associated with these regulations can significantly slow down research projects. This is particularly concerning during this period of the sixth mass extinction when swift scientific progress is essential. While the seminar focused on raising these challenges, it set the stage for future discussions on how to streamline bureaucratic processes without compromising the Nagoya Protocol goals. We recognised the necessity of highlighting the concrete benefits of the Nagoya Protocol for researchers, local communities, indigenous people, and stakeholders. Europe lacks comprehensive information on these benefits. We encourage the community to share their insights and experiences regarding the positive impacts of the Nagoya Protocol: How has it benefited your research, local communities, or indigenous groups in Europe? What successes or improvements have you witnessed? If you have insights or data on these benefits, please contact us at elsi@erga-biodiversity.eu . Your contributions can help demonstrate the value of ABS regulations and support ongoing research and conservation efforts globally. The benefit should outweigh the bureaucratic burden, which has been highlighted by Italian researchers' negative experiences: “Italy adhered to the Nagoya Protocol on June 23, 2011, at the same time as the European Union and 11 of its member states. Although the Nagoya Protocol entered into force on October 12, 2014, coinciding with the holding of COP 12 of the Convention of Biological Diversity (CBD), Italy has not yet ratified the Protocol. As a result, as of today, access to all genetic resources present on Italian soil is not regulated, meaning that any violation of the Nagoya Protocol does not result in any legal prosecution. As the Nagoya Protocol has not yet been ratified, researchers are facing challenges in complying with the principles of Access and Benefit Sharing (ABS), challenges that are further exacerbated by the absence of an authority to consult either at the university level, regional level, or national level. This has led to very unclear and opaque guidelines, that are often unclear to the experts themselves, who are often unwilling to answer clarification requests, as they do not want to take responsibility for misleading or misguiding researchers. As researchers are in dire need of clarification and guidelines, a “do-it-yourself” approach has started to be applied for the most studied species. Although this approach should be discouraged, it seems researchers must go with it while waiting for the establishment of a centralised authority for the regulation of the Nagoya Protocol. The lack of abundant resources in academia has also led researchers to be protective over the data collected or generated throughout the research, hampering the full compliance of ABS. Research findings are also not often communicated to the lay public and local communities as this step in the research process is not considered a priority. Early signs of improvement have emerged since the implementation of the National Recovery and Resilience Plan (PNRR), but only the coming years will tell whether these improvements have been successful or not.“ The seminar on ABS and the Nagoya Protocol was a productive event, providing a deeper understanding among participants and emphasizing the importance of efficient and fair access to genetic resources. We extend our gratitude to Scarlett Sett for her fantastic presentation, to GGBN for their collaboration in organizing this seminar, and to Amber Scholz (DSMZ) who made this webinar possible. For those who missed the event, the slides are available here and a recording of the presentation is available on YouTube. About the Authors The Ethical, Legal, and Social Implications Committee of ERGA. Social Media Dissemination Follow us for more updates: ERGA Twitter, ERGA LinkedIn, ERGA Mastodon For any questions, feel free to reach out to us at elsi@erga-biodiversity.eu or through our #ELSI channel in Keybase.

This month's session of the ERGA BioGenome Analysis & Applications Seminars will focus on phylogenomics, with talks by Iker Irisarri and Maaike Bierenbroodspot. Don't miss it! 🕚 Monday, May 27th 2024 - 12:00 CEST (Add the seminar to your calendar) Join us live on YouTube: Abstracts About the speakers Iker Irisarri Iker did his PhD at the Museo Nacional de Ciencias Naturales in Madrid. He was a postdoc at the Universities of Konstanz (Germany), Uppsala (Sweden), and Göttingen (Germany), and at the Museo Nacional de Ciencias Naturales (Spain). Since 2022, he is a group leader at the Leibniz Institute for the Analysis of Biodiversity Analysis and the Museum of Nature, Hamburg. He will soon join the Museo Nacional de Ciencias Naturales as a Ramon y Cajal fellow. Iker is passionate about phylogenomics and major evolutionary transitions, particularly the conquest of terrestrial environments, which he has studied in both vertebrate animals and plants. Maaike Bierenbroodspot Maaike studied life sciences at Utrecht University. She pursued her master's degree in Molecular Life Sciences at the University of Göttingen, where her interests shifted from wet lab work to computational analyses. Currently, she is pursuing her PhD in the group of Prof. Jan de Vries in Göttingen, whose primary focus is to understand the molecular adaptation to land in plants. Here, she helped establish a phylogenomic pipeline using genomic and phylotranscriptomic data.

We're happy to announce that the Global Genome Biodiversity Network (GGBN) and ERGA with the support of Digital Sequence Information (DSI) network are organizing a two-part webinar series focused on ABS (Access and Benefit Sharing), the Nagoya Protocol and DSI this April. Join us by filling the registration form below! Spots are limited. First Session (April 8th 2024, 09:00 - 11:00 CET) An introduction to Access and Benefit Sharing (registrations closed) This session will concentrate on the Nagoya Protocol, intended as an introductory guide tailored to our communities. It will be structured in two parts: a theoretical segment, which will be recorded, followed by an interactive Q&A segment, which will not be recorded. We invite members from EBP, GGBN, ERGA, and Africa BP to join this enlightening discussion. Speaker: Scarlett Sett (CSIRO-ACDP) Second Session (April 24th 2024, 17:00 - 19:00 CET) Digital Sequence Information (DSI) & the Convention on Biological Diversity This session will dig deeper into Access and Benefit-Sharing (ABS), Digital Sequence Information (DSI), and the Convention on Biological Diversity. It is designed to build on the foundational knowledge from the first session and provide deeper insights into DSI-related topics. Speaker: Amber Scholz (Leibniz Institute DSMZ) Further details: Each webinar is designed to accommodate up to 300 participants. Registration for each session will close two days prior to the first seminar. Access to the webinar, including the Zoom link, will be exclusively provided to those who have registered. In collaboration with the ERGA ELSI committee, we've decided to offer a certificate of attendance. Recorded talks are now available on the ERGA Youtube channel: Slides for download:

At this month's ERGA Plenary meeting (Monday, May 27 at 15:00 CEST) Vice-chair Olga Vinnere Pettersson gave an interesting talk about her experience at a sequencing facility producing reference genomes for non-model organisms. Find details and the recorded talk below: Abstract Since 2013, the Genomics Platform at SciLifeLab has been operating PacBio and ONT instruments. However, there still were many challenges of applying these technologies to non-model genomes. Our team spends lots of effort to understand and mitigate some of these challenges. In this talk, I will present the layout of a reference genome generation process from sampling to sequencing and introduce the auditorium to the main challenges of long-read sequencing of non-model species. Sequencing procedure and chemistry will be explained and some real-life examples will be presented. Speaker's Bio - Olga Vinnere Pettersson Mycologist, PhD in Molecular Evolution. Sequenced my first reference genome in 2009. Since 2012 - sequencing technology consultant / project coordinator at the National Genomics Infrastructure, a part of Genomics Platform of SciLifeLab: the center of excellence in molecular biosciences in Sweden. Currently, I am leading the SciLifeLab – Uppsala University involvement in the Biodiversity Genomics Europe (BGE) consortium, an initiative founded by the EU Horizon Europe program. Together with the Sanger institute, we are leading the effort of sequencing reference genomes of the European eukaryotic biodiversity and creating a de-centralized infrastructure to carry out this work on our continent. Vice-chair of ERGA, member of ERGA SSP and EBP Sampling Committee. To receive the Zoom link and join this and our upcoming plenary meetings, register as an ERGA member.

On the 18th of June, Biodiversity Genomics Europe will organise a panel discussion at the World Biodiversity Forum 2024 that will take place next 16-21 June in Davos. 👉 The topic of the panel will be ‘Unleashing biodiversity's secrets through integrated and scaled genomic science solutions’. The panel discussion aims to bring together experts from both the DNA barcoding (iBOL Europe) and full-genome sequencing (ERGA) stream in an open forum to: Introduce the current state-of-the-art to the wider community of stakeholders in biodiversity research and policy; Debate the priorities for addressing challenges and seizing opportunities needed to accelerate and integrate genomic science solutions into practices. Interested in participating? 📩 Registration is open until June 7: https://worldbiodiversityforum2024.org/registration/ Please note that the event is in-person only. — More information about BGE’s panel discussion (look for PD-2): https://worldbiodiversityforum2024.org/workshops-and-panel-debates/ More information about the programme: https://worldbiodiversityforum2024.org/session-program/