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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/

Read the full interview with Alice Mouton below: 1. Can you introduce yourself and how you got involved with ERGA and the Training and Knowledge Transfer Committee? My name is Alice Mouton and I’m a researcher based in Belgium. I got actively involved in the early stages of building the European Reference Genome Atlas (ERGA). Early on, I was actually engaging with the Belgian representative of the Cluster 6 of the Horizon Europe Work Program to make some modifications on the draft of the call for the future Horizon Europe project that would better fit ERGA and is now currently underway (BGE). I got naturally involved as well in the early stages of ERGA by being elected as one of the Belgian representatives in the ERGA Council. Back in 2021 I was mostly involved with the SSP (Sampling & Sample Processing) Committee and I started to supervise and coordinate the ERGA Pilot project with Ann Mc Cartney and Giulio Formenti. Because I was starting to have a heavy workload with the ERGA Pilot project on a voluntary basis while working on my postdoc project, I had to slow down my different activities in the other committees. I actually got involved in the TKT committee more recently around 2022. I helped with the submission and the organization of the EMBO course that was held in Belgium by another TKT member. That's how I put my foot into the TKT committee. I got hired through the Biodiversity Genomics Europe projects as a training and knowledge transfer officer. It  was quite evident that I would lead the TKT committee due to my position. 2. What are the main activities of the ERGA Training & Knowledge Transfer Committee? Our committee has several types of actions. We support the design and the implementation of learning and skill sharing activities. We also have the goal of collecting, promoting and developing training materials in biodiversity genomics - like webinars, workshops and other activities. We also receive more direct support requests from members who want to organize a workshop. We offer help promoting and organizing these community workshop. We have the goal of connecting and supporting members to develop proposals for financing activity related to Training and Knowledge Transfer. We have gained experience by submitting a few of those applications in the last few years. We are also building a knowledge hub where everyone will be able to find educational/learning materials, such as tutorials related to every step of the genome generation workflow: from genome assembly to how to request a permit and downstream analysis or how to involve stakeholders in the project. Right now, we are working on a guide with some tips and practical advice on how to organize events such as workshops, conferences, webinars, which will be openly available to everyone. 3. What are the most interesting and the most challenging aspects of chairing TKT? The most interesting part is actually seeing that we can make a difference. When we organize workshops they are free of charge and we have high attendance. So I think it's really exciting because it shows that there is a lot of interest in training activity around biodiversity genomics. Perhaps one of the challenges within ERGA is to make connections with the other committees. When other committees need help organizing workshops or webinars, TKT is here to offer support but sometimes there is a lack of communication. One of the challenges is making TKT visible to the other committees. 4. In your experience, what do you see as the most effective strategies to promote effective biodiversity genomics training and capacity building across Europe, considering the complexity of the task and great heterogeneity between countries? It really is a challenging task to promote training in biodiversity genomics across Europe. Mostly because genomic knowledge is not equally distributed across the continent, we have a strong bias: Western European countries generally having more experienced researchers in the field while Eastern European countries tend to have less people with training in genomics. So there is a bias that we should somehow address. There is also a strong financial barrier to access to knowledge and training because of access to funding. Access to adequate computational infrastructure is another challenge. When we offer free genomics workshops, they are often too short for the participants to fully grasp the complexity of a certain type of genomic analysis. Online workshops also require a stable internet connection and we have high demand and not that many spots can be offered. So I think maybe the most effective strategy to promote biologist genomics training would be first to have an European computer infrastructure that would be available to all researchers in the continent. This would solve a critical issue: when we organize a workshop we offer access to a high performance computer and then when the workshop ends the participant might not have access to this kind of resource. So they might learn how to do the analysis but they don't have access to the resources needed to perform this analysis with their own data. That’s why I think that one of the best strategies to really boost training in genomics in Europe would be to invest in infrastructure development. Another effective strategy to promote genomics training is to provide all of these tutorials and step by step tutorials free of charge. Currently a lot of knowledge and resources are kept private or within individual research groups. 5. What do you see as the next steps for the ERGA TKT Committee? I think the most important step right now for the TKT committee is to finalize the ERGA Knowledge Hub. This will be a really important resource for the biodiversity genomics community from Europe and beyond to have easy access to many step by step tutorials and other training materials. Send an email to the Training & Knowledge Transfer Committee and learn more about how you can participate!

by Andrei Ștefan The 2nd edition of the RoBioinfo Conference took place between 11-13 April 2024 in the lovely city of Cluj-Napoca, Romania. This event was organized by the Romanian Society of Bioinformatics and I was invited to give a talk about ERGA, as country representative in the ERGA Council. The conference mainly focused on clinical genomics and human health, but had a parallel session dedicated to ancient DNA and animal genomics. Roughly 100 people took part in the conference and the preceding workshops. The first part of the talk was about ERGA structure and organization and the second part focused on the sample workflow of the pilot-project, with an emphasis on the results. One of the species included in the pilot is Nepa anophthalma (a blind, hunting insect from Movile Cave) and the attendees were curious to find out more about it and its environment. The audience mostly comprised students and young researchers and were happy to hear that people in Romania are also conducting studies in biodiversity genomics. The following discussions were about obtaining sampling and shipping permits and the challenges of polyploidy in plant genomics. The conference presented a great opportunity to talk about ERGA and the results of the pilot-project and hopefully drive some students in the field of conservation genomics. I wish to thank Luísa and Chiara from the ERGA Media and Communications Committee for their help in setting up the presentation. Andrei Ștefan part of the ERGA Council representing Romania. He works in the molecular biology lab of the Natural History Museum in Bucharest. 🇷🇴 Would you like to connect with other researchers working on biodiversity genomics in Romania? Write to the country representatives in the ERGA Council: Romania@erga-biodiversity.eu

Working with genomes of "unconventional" taxa? Join the ERGA Rogue Genomes Workshop: What and why? We think that we should redefine what a high quality genome means in the larger context of eukaryote biodiversity, since for many lineages it won’t be possible to meet the standards of the Earth BioGenome Project (EBP) due to: Biological properties - the EBP standards are largely based on metrics from vertebrates. Eg, we know that many invertebrates have ‘different’ genomes (eg, parasites may have a high % of missing BUSCOs, etc). Methodological problems - eg, low quality of reads after sequencing, poliploidy leading to assembly problems, picoeukaryotes where WGA is necessary, etc. How to tackle this to make sure we are including under the ERGA umbrella reference genomes that may depart from the standards of EBP? Let's discuss it! Who? All ERGA members with expertise in species with rogue genomes are welcome to participate! The efforts will be coordinated by the Executive Board. When? 1st meeting: 30th April, 2:30pm to 4pm: Brainstorming and formation of working groups. 2nd meeting: 2-3 weeks afterwards (TBD): Group session to put together the ideas of the working groups, and discuss an output for the work done. How?

This month's session of the ERGA BioGenome Analysis & Applications Seminars will focus on comparative genomics, with a talk by Toni Gabaldón. Don't miss it! 🕚 Monday, April 29th 2024 - 12:00 CEST. Join us live on YouTube: Abstract Got a genome? get a phylome!: orthology and paralogy detection and the phylomeDB approach to newly-sequenced genomes Comparing the newly-sequenced genome of our species of interest with available ones can help us understanding the origin and evolution of traits of interest. A first necessary step is the determination of orthology (and paralogy) relationships across genes, for which a plethora of methods exists. The phylome approach (www.phylomedb.org) builds a gene phylogeny for every single gene encoded in your genome of interest across a set of compared species. This phylome is further processed to predict orthologs and paralogs, detect and date gene duplication events, infer past events of inter-species hybridization and horizontal gene transfer, as well as to uncover footprints of selection, introgression, gene conversion, or other relevant evolutionary processes. Here, I will describe this approach and showcase the PhylomeDB’s ERGA community support initiative. Speaker Toni Gabaldón Toni Gabaldón is ICREA Research Professor jointly affiliated to the Institute for Research in Biomedicine (IRB) and the Barcelona Supercomputing Centre (BSC), where he leads the Comparative Genomics group (www.cgenomics.org). His research focuses on understanding the complex relationships between genome sequences and phenotypes and how these two features evolve within and across species.