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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.

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