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Read the full interview with Tereza Manousaki below: 1. Can you introduce yourself and why you decided to participate in ERGA and the Data Analysis committee? My name is Tereza Manousaki and I'm a researcher at the Hellenic Center for Marine Research in Greece. My research focuses on evolutionary genomics and on how genome evolution is linked to species phenotypic evolution and diversification. I have followed the genome papers from the era of the Nature paper until the era of the genome note and I have been really amazed by the progress of the field. While working with genomes I have been involved in different aspects of the downstream analysis, such as population genomics, aquaculture genomics, comparative genomics and pipeline development. So it's really an amazing time to be working with genomes. ERGA has been really fundamental in spreading the use of genomics to a wider community. It has shared knowledge and resources across many European countries, regardless of the existing capacity and infrastructure and it has been a real example of collaboration at the scientific and at the European level. Based on my background, I have decided to take a more active role within the ERGA Data Analysis Committee (DAC). I believe it is one of the most important committees because reference genomes provide the basis for a number of downstream applications which lead to a deeper understanding of species biology and evolution. 2. What are the main activities of the ERGA Data Analysis Committee? What the ERGA Data Analysis Committee has done since the beginning was to launch questionnaires trying to map the community's interests. Since mid-2023 we also launched a very interesting seminar series called “ERGA BioGenome Analysis and Applications Seminars” organised in collaboration with the project Biodiversity Genomics Europe. This seminar series is focused on the use of genomes in the areas of populations genomics, phylogenomics, comparative dynamics and functional genomics, which are the 4 scientific areas that the DAC is focused on. The interesting thing about our seminars is that they include a main presentation introducing the topic,  and focusing on the scientific question and how it was answered; and then there is a second session which dives deeply into the problems and the difficulties that scientists faced to answer the question. So these sessions have a strong focus on the actual analysis that took place, not only on the scientific findings. Everyone is welcome to join the seminars and participate in the discussions. They are livestreamed openly through the ERGA Youtube channel, where you can also re-watch all the previous sessions. We have also recently started DAC Community meetings which gather a very diverse group of scientists. With these meetings we aim, on one hand, to build a guide with solutions to the most important downstream application of reference genomes. On the other hand, we expect that these meetings help identify interesting topics that the community considers critical, identify gaps and grey areas, and work altogether in filling these gaps. The meetings are also open and anyone is welcome to join! Playlist: ERGA BioGenome Analysis & Applications Seminars. (Re)watch the talks at any time. 3. What are the most interesting and the most challenging aspects of chairing DAC? The most interesting aspect is at the same time the most challenging one: the heterogeneity of the members that are part of the community. It's an amazing privilege to have in the same group people that work on conservation, comparative genomics, phylogenomics and on functional genomics. This diversity has a great potential and we need to take advantage of it. 4. What are the developments in the analysis or practical applications of reference genomes that you are most excited about? What I'm really excited about is the number of reference genomes that are being sequenced and made publicly and openly available by large consortia. It’s amazing how these reference genomes are covering the tree of life, which brings biology to a new era and makes us reconsider the term "non-model” species. It’s also really interesting that now species that are rarely studied or considered “strange” organisms are having their genomes sequenced. So we don't see the favourite groups getting all the attention, but we see genome references being generated across every phylum, bringing many more opportunities in studying them. 5. What do you see as the next steps for the ERGA DAC Committee? The next steps for the data analysis committee in the following months would be: First, to develop and offer best practices for genomic downstream analysis. And, second, to engage the community and identify gaps in the 4 particular scientific areas we're working on and then work all together to fill them. The other thing we want to do is to continue connecting researchers with different backgrounds. We need to connect scientists that are working on software development to those who apply these softwares. And we have to go even one layer higher, reaching researchers that actually never used genomics or know very little about it. That’s the goal. Send an email to the Data Analysis Committee and learn more about how you can participate!

[This call is now closed, outcome to be announced] Through exploiting genomics technologies, we can make significant progress in preventing biodiversity loss and protecting our ecosystems. This is the mission at the heart of the Biodiversity Genomics Europe (BGE) ERGA stream, and we're inviting you to join us! Are you conducting research on biodiversity conservation or investigating how sustainably managed species contribute to our economy and health (bioeconomy)? If so, we have exciting news for you. We are pleased to announce a call for financial support for ongoing projects focusing on European eukaryotic species. We are looking for initiatives that leverage high-quality reference genomes in their research. This is a subcontracting task of the BGE Project aims to support the acceleration of your projects, enhancing their contribution to biodiversity and sustainability. The funding can be used to bring your reference genome up to Earth BioGenome Project (EBP) standards or, for projects already meeting these criteria, to generate genomic data to enhance and complete your research. For more information read the complete call (attached, and linked here) and submit your proposal using the link provided in the call description. Note that the applicant and all team members must be ERGA Member. To become a member, simply fill our registration form here. Note also that as this is a subcontracting task of the BGE Project, researchers affiliated to institutions that are funded partners of BGE (see: https://biodiversitygenomics.eu/the-project/network/) are not eligible to apply. Remember, only submissions received before March 13th, 2024 23:59 CET will be considered.

The production of any genome starts with a sample or, as scientists commonly refer to it, a specimen. A sample is a piece of the organism we wish to study- or, depending on the size of the organism, its whole body! From this sample, we are able to extract the DNA molecules that make up the genome. Since in the European Reference Genome Atlas we are interested in studying the biodiversity of Europe, sampling usually requires going to the field to find and collect the organisms in their natural habitats. This step - also known as fieldwork - is one of the favourite activities for many biologists as it provides an opportunity to spend time in nature. In some specific cases and depending on how rare the species is, the sample might be obtained from botanical gardens, zoos or even museums - that’s one of the many reasons these institutions are so central to biodiversity research: they not only guarantee fun weekend trips, but also play a role in storing and safeguard the genetic heritage of our planet. In general, biologists go to the field to find the species they wish to study. In some cases, however, it is more practical to obtain specimens from botanical or zoological gardens collections. Sequencing the entire DNA of an individual requires fresh, high-quality samples. For this reason, sampling can be one of the most challenging steps in the whole process of generating a genome. When we assemble a reference genome, the goal is to accurately uncover the true genome that  exists inside each cell. Depending on the conditions of storage and transport after sampling, the DNA can start to degrade, meaning that the long strings of DNA will slowly be fragmented into smaller pieces. Assembling a genome is like putting together a puzzle: the tinier the pieces, the more difficult it becomes. That’s why fresh samples are so important, so that we can obtain high quality DNA that will later ease our work when placing the pieces back together. Check the glossary to explore the concepts highlighted in bold and many others!

Jaakko Pohjoismäki, Professor in molecular biology and genetics, Department of Environmental and Biological Sciences, University of Eastern Finland There are six to eight species of hares in Europe, depending on one’s view on the certain subspecies and the geographical boundaries of the subcontinent. Two of the species, the mountain hare (Lepus timidus) and the brown hare (Lepus europaeus), are widespread and extend their range also to the Nordic countries, including Finland. As evident from the name, mountain hares are adapted to cold and snowy environments, having wide snowshoe feet and white winter pelage. In the barren winter landscapes of the high north, mountain hares can feed on twigs and saplings of local willow and birch species that are low in nutrients but full of harmful chemicals, which render the plants inedible for most plant-eaters. Consequently, mountain hares dominate the higher latitudes and mountainous regions of Europe, as well as exist as ice age relict populations in the British Isles. The brown hare is in contrast a more temperate climate adapted species, originating from the open grasslands of southwestern Eurasia and relying much on herbaceous plants also in their winter diet. Therefore, it is not surprising that the species has benefitted from the agriculture and cattle induced changes in the European landscape. During the last couple of decades, the brown hare’s distribution has been expanding northward with increasing speed, a change largely explained by the climate change driven shortening of the snow-covered season. This range expansion brings brown hares increasingly in contact with the mountain hares, whose numbers are simultaneously decreasing. The plight of the mountain hare is both due to increased predation because of camouflage mismatch during shortened winters but also because of direct competition by the brown hares. In southwestern Finland the situation is exemplified by the gradual extinction of the mountain hare populations on the mainland, whereas the populations on the Finnish Archipelago islands, not yet colonized by brown hares, are still thriving. Although the species have slightly different habitat preferences, mountain hares and brown hares coexist in many places in Finland, including urban areas. Photo by Mervi Kunnasranta. One aspect of the competition is highly intimate, as the two species can pair and produce fertile hybrid offspring. Curiously, this interaction is one-sided as the brown hare seems to be able to obtain locally adapted gene variants from the mountain hare whereas for the mountain hare hybridization appears to be a dead-end. While this unidirectionality can be driven by demographic factors or mate competition, our research group in the University of Eastern Finland has been interested in investigating whether genetic compatibility could help  explain the phenomenon. This is particularly interesting as these mechanisms could give an insight into speciation mechanisms at the genome level. At some stage of their history, species originate from the same ancestral population but develop following independent evolutionary trajectories, where their genetic makeup is independently moulded by local selective pressures and random genetic drift. Through time, the genetic differences accumulate from population differences to species differences, such as we see them in both the phenotype and the genotype of mountain hares and brown hares, separated from their common ancestor some three million years ago. Although the schoolbook definition of species as “ a group of individuals that actually or potentially interbreed in nature” emphasizes the reproductive isolation between them, the reproductive isolation can be governed by many mechanisms. One of these is genetic compatibility, allowing the embryonic development and birth of viable, fertile hybrids. As the incompatibilities develop gradually during evolution, they are not dichotomous and can exhibit substantial variation. The mountain hare – brown hare couple is especially interesting as the large lifestyle differences reflect significant differences in how their bodies function, including some basic cellular processes. Because of their adaptation to the harsh winter conditions, mountain hares are more prepared for resource conservation compared to brown hares. This shows also in the life history strategy of the two species, with mountain hares resourcing more into ageing rather than reproduction, especially compared to the brown hares. Consequently, mountain hares are longer lived (up to 18 years!) but have lower reproductive capacity than brown hares. This difference is also seen at the cellular level. Brown hare fibroblast cells grow and migrate faster than those of mountain hares, a difference that is explained by the differences in the relative lengths of certain cell cycle phases. Similarly, mountain hare cells have certain interesting and specialized biochemical pathways, which probably enable cold adaptation with the expense of having fewer resources to anabolic metabolism - that is, fewer resources that allow them to build-up more complex molecules from simpler ones. It can well be that certain types of adaptations are not permissive for changes caused by the genes from another species. In this context, the brown hare would represent a genetically flexible species, capable of incorporating mountain hare genetic components as a part of its normal physiological processes, whereas the incorporation of brown hare features into mountain hare background will cause a breakdown of the hybrids. While the Mountain hare's snowshoe feet are a highly characteristic adaptation to the long snow covered season, the narrow hind feet of the brown hares can cause major difficulties for the animals to move and find food when the snow is soft and deep. Photos by Jaakko Pohjoismäki. Our group has generated the reference genomes for both the brown hare and the mountain hare as a part of the ERGA pilot project. For us, these genomes are akin to the Rosetta stone, allowing us to decipher the exact nature and the information content of any gene in the two species. They enable us to pinpoint the genes underlying the observed species differences and experimentally test the role of individual genes in any cellular process. This is particularly interesting when trying to understand metabolic adaptation, the evolution of life history strategies and how these contribute to the compatibility of the hybridization. Mountain hare and brown hare species pair in Finland represents an exciting natural experiment, which – with the help of the species genomes – allows us to understand broader evolutionary processes. They also vividly exemplify how climate change is reforming animal populations and effects the species interactions. The brown hare has already experienced and will continue to benefit from human impacts on the environment. Only time will reveal the resilience of its arctic cousin in confronting the challenges that lie ahead. --- The annotated genome assembly of the brown hare has been published and is openly available (Read the publication pre-print). The mountain hare genome has been assembled and is currently undergoing the annotation process.

The ERGA Plenary Meetings are the main monthly gatherings of our community, when announcements are made and discussions and debates are conducted on topic-oriented presentations. The plenaries happen on the third Monday of each month at 15:00 CET. To receive our regular emails with the links to join the meetings you simply need to register as an ERGA member. The meetings always include updates by the ERGA committees and at least one presentation on various topics related to the genome generation workflow. Check the playlist to watch previous plenary talks: 📅 Check the #ERGACalendar to stay up-to-date with all events and meetings

Read the full interview with Alice Dennis below: 1. Can you introduce yourself and how you got involved with ERGA and the Annotation committee? My name is Alice Dennis and I am a lecturer at the University of Namur in Belgium. I've been here for about 2 years and I've been working with ERGA for even longer. I started in the early days, maybe around January, 2021 when it was coming together and I was really interested in this idea of constructing genomes from more diverse taxa. One of my main motivations was that I work on a snail in a group of pulmonates that is very underrepresented in the literature, and so I was trying to help build up enthusiasm for sequencing close relatives and things like this. When I first joined ERGA, I volunteered to start helping the annotation committee with this idea of increasing biodiversity representation and I've been here ever since. 2. What are the main activities of the ERGA Annotation Committee and why should someone consider joining? At the annotation committee, we have monthly meetings where everyone is welcome to see our discussions about tools for genome annotation and challenges we are facing. And I really would like to see greater participation across ERGA because this is the step in genome assembly that is often forgotten. So, annotation tools are lagging behind those for assembly. And even more so, we are missing the tools for evaluating our annotations. And so these are the things we're interested in at the annotation committee. We also have experts from different aspects of annotation who are much more versed than me and things like repeat prediction and gene family evolution and these sorts of very interesting analyses of course. And so everyone is welcome to come to our meetings and see what we're talking about, but I would also like to start making room for people to bring their annotation problems and projects. And so we can create space within all of our meetings or even have larger efforts if people want to approach us to know how their projects are going or to get specific feedback. Video: Alice presenting the work of the Annotation Committee during the Biodiversity Genomics Conference 2023 3. What is the most challenging aspect of chairing the Annotation Committee? So I think that one of the main challenges is that we are still having trouble finding good pipelines. We really highlighted this recently. A group of us went to the BioHackathon in November 2023. Mostly people from the annotation committee at ERGA or people we had found through there, but also researchers from around the world via the biohackathon. And we sat down and we really found some of the hurdles to creating annotation and a lot of this is in gathering the right amounts of evidence, things like RNAseq and protein data. And this is really lacking in a lot of systems. And so I think this sort of resource building is the main challenge. And from my own work in molluscs we see that the lack of close relatives really limits our ability to work with homology based approaches. So we really need to improve our taxonomic representation. 4. What developments in the world of genome annotation are you most excited about in the coming years (new promising technologies, software…) I think the most exciting thing in the coming years is that we're going to have more genomes to compare. And so this is free of technologies, but it is of course enabled by projects like the genome assembly going on in ERGA because having more close relatives will mean that we can improve our annotation and we can have much better predictions of genes and gene features and other structural aspects of genomes. This will be a huge leap forward in annotation. I really also think this will be improved by having more user friendly tools and these are under development by lots of people. And so I hope we as a committee can help facilitate this and bring to the forefront the best tools for each different taxonomic group, but hopefully to standardize this as much as possible across taxa. And lastly, I think with the long read technologies that are coming out, we are going to have better annotations. And so as these become cheaper and have fewer errors, we can really utilize long reads to improve genome annotation. 5. What do you see as the next steps for the ERGA Annotation Committee? I hope in the next months and years we can really try and bring in more of the ERGA community to see how important annotation is. I would like to bring in more recommended packages for people to use if you go to our web page now, there is one or 2 pipelines recommended as well as an overview of the steps and annotation. So I hope we can increase and improve these resources for people and try to make these available to everyone. And like I mentioned, I think the next thing we really want to do is be available for people who would like feedback and help with their annotations. Everyone is welcome to join our committee and ways to get in touch with us are varied. We are on KeyBase and we check that regularly. We have a mailing list if you would like to join that and receive reminders of all of our meetings. Or if you would just like more information, you can email (annotation@erga-biodiversity.eu). And I hope to see you all at our meetings, which are currently on Monday afternoons, just once a month. Find Alice on Mastodon @AliceDennis@genomic.social Send an email to the Annotation Committee and learn how you can contribute!

Reference genomes are becoming a new fundamental tool in biodiversity and evolutionary research and as a result, the number of reference genome initiatives is increasing, as demonstrated by the growing number of international initiatives to make genomes available across the tree of life, such as the Earth BioGenome Project. Training and access to knowledge on genome assemblies are becoming critical for the whole scientific community. After the successful first edition of the EMBO course in Bruxelles at the Université libre de Bruxelles in September 2022, the second edition of the EMBO course on genome sequencing, assembly, and downstream analyses took place for a full week in Valencia in January 2024 within the Polytechnic University of Valencia (UPV). During this week, around 30 participants from everywhere in the world got equipped with theoretical knowledge and practical know-how to enable them to sequence their genome of interest and analyze it all the way to publication. This course covered the whole life-cycle of a reference genome sequencing project, from library preparation, DNA sequencing to genome assembly, assembly evaluation and assembly improvement and all the way to annotation. The workshop's participants, speakers and organizers On the first day, the speakers covered topics such as the importance of vouchering and metadata and high-quality DNA to start a genome project, followed by a broad overview of sequencing methodologies and associated cost and how to design sequencing experiments. On the following days, participants followed practicals about de novo genome assembly, assembly scaffolding, haplotig purging and annotation using the Training Infrastructure as a Service (TIaaS) implemented in the European Galaxy Server. The participants worked on PacBio HiFi and Oxford Nanopore  datasets, Hi-C reads and Illumina RNA-seq coming from a nematode species belonging to the Panagrolaimidae family. The last few days, the speakers also gave enlightening talks about the importance of Galaxy for reproducible science, the future of pangenomes, the presence of reference genome initiative in the UK, in Europe, and in the US as well as the use of IA to infer functions of unknown protein. All the materials related to the course will be available in the upcoming ERGA Knowledge Hub. Meet our nematode Propanagrolaimus JU765  kindly provided by Nadège Guigliemoni (University of Cologne, Germany) The invited speakers for this course were Olga Vinnere Petterson (Uppsala University, SE), Rosa Fernández (Institute of Evolutionary Biology (IBE) (CSIC-UPF), ES), Kamil Jaron (Wellcome Sanger Institute, UK), Jennifer Leonard (Doñana Biological Station - CSIC, ES) and Linelle Abueg (The Rockefeller University, US). This EMBO course was organized by Aureliano Bombarely (Institute of Plant Molecular and Cellular Biology (IBMCP)(CSIC-UPV), ES) , Silvia Manrique (Valencia Polytechnic University, ES),  Giulio Formenti (The Rockefeller University, US), Jean-François Flot (Université libre de Bruxelles, BE), Alice Mouton (University of Florence, IT), Nadège Guiglielmoni (University of Cologne, DE). Text by Alice Mouton

The first week of November was busy for some members of the ERGA Annotation Committee. They participated in the Elixir BioHackathon Europe 2023. This year, the event took place in Barcelona and brought together 180 scientists from all over the world to work on 35 different bioinformatics projects. The project, led by Annotation committee members Jèssica Gómez-Garrido and Alice Dennis, focused on Genome annotation and other post-assembly workflows for the tree of life. Annotations are an essential component of reference-genomes, as they transform genomes into larger sources of knowledge and link the sequences with their functions, facilitating comparisons within and across taxa. Together, the team managed over 50 annotation runs, focusing on 7 different species and a dozen different annotation tools and pipelines. The main goals of the Hackathon were to: (1) test software in a number of infrastructures to ensure they are reproducible, (2) test tools in as wide a range of taxa as possible, (3) perform annotation on the same organism, but with varying amounts of input information to determine in which organisms and under which conditions annotation tools perform better or worse, and (4) bring together developers and users for direct interaction and to assist in software implementation. The Elixir BioHackathon presented a fantastic opportunity for researchers from the genome annotation community to come together and work on this project. We thank Alice and Jèssica for their work in organising the project and Elixir for their support.

Outcome of the call for Sampling reference genomes of eukaryotic species from biodiversity hotspots in Europe to support the mission of Biodiversity Genomics Europe Selected Hotspots: From the received expressions of interest, the BGE evaluation committee has selected six biodiversity hotspots in Europe. This strategic decision shows BGE commitment to biodiversity conservation in areas of exceptional ecological significance. With these projects, BGE is demonstrating its commitment to fostering biodiversity preservation across the European Widening regions (there is no hierarchy in the order of the projects): Georgia. Multiple habitats, covering areas of high endemicity with species-rich and under-sampled/under-explored ecosystems: the Borjomi-Kharagauli glacial area, the upstream areas of Rioni River / Racha, the Tekhuri river valley area (Lebarde), and the Javakheti Range. Presented by Dr. David Tarkhnishvili (Ilia State University). Cyprus. Covering Natura 2000 sites (https://ec.europa.eu/environment/nature/natura2000/index_en.htm) with high levels of endemism, that extend along the central mountain range of the island and host the five endemic priority habitat types: a) Troodos National Forest Park; b) Paphos forest; c) Machairas National Forest Park; and d) Madari-Papoutsa. And sampling for terrestrial, freshwater and marine arthropod taxa at the following protected coastal areas: e) the Akamas Peninsula National Park in the NW; f) the Cape Greco National Forest Park in the SE; g) the Akrotiri peninsula in the South. Presented by Dr. Anna Papadoupoulos (University of Cyprus). Bulgaria. Covering two terrestrial ecosystems largely understudied but of major biodiversity importance for Bulgaria and the Balkan region: Strandzha Nature Park, and a network of key cave ecosystems across the country. Presented by Dr. Stefaniya Kamenova (National Museum of Natural History at the Bulgarian Academy of Sciences). Croatia. Focused on the Dinarides, a karstic mountain chain in the western Balkans recognised as a global hotspot for cave biodiversity. Presented by Dr. Martina Pavlek (Ruđer Bošković Institut, Zagreb). Portugal. Focused on true flies of Madeira’s laurisilva, a UNESCO world heritage site and the world’s largest surviving remnant of laurel forest. Presented by Dr. Dora Aguín-Pombo (University of Madeira). Hungary. Covering four biotopes of two areas within Hungary: Western Transdanubia (Dél-Zala Sandland: alluvial and Molinia meadows, closed pannonic sand steppe, and Keszthely Hills: rupiculous pannonic grassland, pannonic oakwoods) and Kiskunság, lowland between Danube and Tisza River (Pirtó Sandland: open pannonic sand steppe and inland dunes - Kelemen-szék: salt meadow and salt steppe. Presented by Dr. Tibor Kovacs (Hungarian Biodiversity Research Society). Calls for tenders for projects focused in these areas are now open!

This month's session of the ERGA BioGenome Analysis & Applications Seminars will focus on genomics applied to the assessment of population vulnerability, featuring invited speakers Orly Razgour and Chris Barratt. 🕚 Wednesday, February 28th - 11:00 CET. Join us live on YouTube: Abstracts Speakers Orly Razgour Orly Razgour is a Senior Lecturer in Ecology at the University of Exeter, leading the Global Change Genetics group. Orly got a PhD from the University of Bristol and has held research fellowships at the University of Stirling, University of Bristol and the University of Southampton. Orly’s research integrates genomic, ecological and modelling approaches to understand biodiversity responses to global environmental changes, with a focus on bats, though not exclusively. Much of Orly’s research is applied, aiming to inform conservation management under environmental change. Orly is the Editor in Chief of the journal Diversity and Distributions, a trustee of the Bat Conservation Trust, a Scientific Advisor for the UNEP Agreement for the conservation of European bats (Eurobats), and the Chair of the British Ecological Society Climate Change group. Chris Barratt Chris Barratt is a postdoctoral researcher within sDiv, the synthesis centre of iDiv, and also a guest researcher at Naturalis. Chris's obtained his PhD from the University of Basel, Switzerland and has had research fellowships at the Max Planck Institute for Evolutionary Anthropology and iDiv. He integrates genomics, spatial modelling and ecological data and models to predict population level responses to global change. He primarily focuses on amphibians in Europe and Africa but also works with other vertebrate and plant species around the world.