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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.

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.

Read the full interview with Torsten Struck below: 1. Can you introduce yourself and how you got involved with ERGA and the Sampling & Sample Processing (SSP) committee? I'm Torsten Struck and I work at the Natural History Museum of the University of Oslo. I've been working my whole academic life with marine invertebrates and with genomic data for a long time already. I started this work early on in Germany, initially with transcriptomic data. And nowadays my focus has shifted to genomic data. I got involved with ERGA because I am also part of the community of the Norwegian Earth BioGenome Project (EBP-Nor). When I became an ERGA member, I was asked where I would like to contribute and I chose two topics which I find most interesting: sampling and sample processing and sequencing and assembly. I was interested in the sampling topic because we gathered some previous experience with other projects and knew how challenging it can be for the species we work with in my group. And that’s how I got more involved with the SSP. 2. What are the main activities of the ERGA SSP and why should someone consider joining the committee? The first activities of the SSP committee were related with the ERGA pilot project, we worked a little bit with species selection for the project but mainly developing the Sampling Code of Conduct and from that we developed guidelines on how to collect all the necessary metadata associated with the samples. We were also involved in developing the sampling manifest in close cooperation with the Darwin Tree of Life project. At this stage, we also organised that all the countries in Europe learned about the (Pilot) project, especially the Nagoya focal points of each country. We reached out so they could learn about ERGA to hopefully make the permitting process easier. Another important activity last year was the development of criteria of how to select species for genome sequencing. Since all projects are limited, somehow there needs to be a decision on how to select the species and usually this is a top down process - whoever “owns” a project decides about the selection procedure. But we made it bottom up and developed it as a committee. Everybody who was interested could join and could bring in what they thought was important. Based on this we developed the procedure and then the final decision was made by the ERGA council, but it was really a bottom up process. Right now we are working on standard operating procedures on how to sample different taxonomic groups to get data for genomic analysis and we are also working on a paper on what challenges one can face when sampling for genomics. Video: Presention of the species selection procedure developed by the SSP. I think this variety of activities is one of the main reasons why it might be really interesting to join the group. We are a quite diverse group and we address a broad portfolio of different topics related to sampling. And so members can really get into different topics, on what interests them even within the SSP. It’s not just one topic, but there are different possibilities of how to participate and bring in your expertise. 3. What are the most interesting and the most challenging aspects of chairing the SSP? What I find most interesting about being part of the committee and now also as a chair is that I get to meet many people with different taxonomic expertise and I think that’s the beauty of the group. But we are not all taxonomists, we also have lab folk with different backgrounds in the committee. That makes the work with the SSP really interesting, because you learn a lot. Before joining the committee, I was aware of the challenges I face sampling and studying marine invertebrates, but there are many other challenges I didn’t know about. For example, with mammals it can be really challenging to be even allowed to sample and sometimes you are not allowed to provide the sampling locality, if the species is endangered - which I was not aware of. Or how to sample plants, fungi, or lichens - lichens are more “meta” organisms and are very hard to process. You really have to tweeze them apart. Also I learned a lot about all the different aspects one has to consider while sampling and what metadata are most important for the different taxonomic groups.  I also learned much about the challenges that come with the permits, given the different countries we are in or with logistics. Here in Norway it’s relatively easy to get to ship material, but that’s not always the case. There are also many aspects that we need to consider for the species selection process that I had never thought too much about before joining ERGA. Such as JEDI (Justice, Equality, Diversity and Inclusion) and important principles such as FAIR (Findable, Accessible, Interoperable and Reusable) and Open science data. Other people in our committee had much more experience with these topics, and it was quite interesting to also learn about that. All these different aspects are also reasons why I think it’s so interesting to join our committee. Because you learn a lot and start thinking about topics you haven’t thought about before. The most challenging aspect I face as a chair is to coordinate all these many different tasks and to push them forward. Time is a challenge, since we only meet once a month. And it requires a lot of engagement by everybody and that can be challenging to keep up. 4. Sampling can be one of the most difficult steps in the reference genome generation pipeline, which can create critical bottlenecks in the effort to sequence all life on Earth. What do you see as the solutions to this in the European context? I mean if we really think about it, sampling all life is difficult because we need to reach places like the deep sea or other remote areas, and many species are rare or can only be found through a certain time period. And I think the main reason sampling is so often seen as a challenge is because as of now we're doing very targeted sampling to sequence reference genomes. This is because there are really high standards of what kind of sample is needed to produce a reference genome and to fulfil them you need to collect at a very high standard: samples need to be flash frozen, for example. Generally, people will only follow these high standards when it's really necessary - when they know for sure that that specimen will be sequenced at the reference genome-level. Just doing it because maybe in the future the specimen might be sequenced takes a lot of time away. But I think there are several solutions to this: First of all, we need to really invest in research and development to find ways to get reference genomes starting from lower-quality, not so well preserved specimens. This would also allow us to maybe use material that was collected in the past but not perfectly preserved. It might also ease the hurdle of logistics, as it's not always easy to ship these deep frozen samples across borders, even across European ones. So having the opportunity to work for example with ethanol preserved samples or dry material could be helpful. Maybe now with a growing body of reference genomes available that might be possible, if we can use them as “guides” to facilitate the assembly process. The other thing is that we also need to engage more with other initiatives which are already out there doing fieldwork, such as ecological studies. In Norway for example there's the Artsdatabanken - they fund five to six projects each year which only go out to map different taxonomic groups across the Norwegian Coastline or the Norwegian landscape. The barcoding community hooked up really early with them. When people apply to obtain this funding, one of the requirements is that they agree to barcode all the species. With that, they managed to increase the number of barcodes for Norwegian species substantially. Maybe we could do something similar: that we hook up with these initiatives and ask that when they go to the field they should also collect samples that we can use to produce reference genomes. And we provide them not only with the knowledge but also the infrastructure by providing access to liquid nitrogen or at least dry ice, shipment and storage afterwards. So that’s another idea that I think might allow us to scale-up, besides being able to use lower quality samples/data, to hook up with this type of initiative. 5. What are the next steps for the ERGA SSP Committee? We will continue working on the Standard Operating Procedures for sampling that I mentioned earlier. We need to develop them in more detail, and that means also taxonomically in more detail. At the moment we often work in very large groups of organisms. The other thing would be what I just mentioned about how we can overcome the bottleneck: that maybe the SSP could do some lobbying for this research and development topic of using lower quality material and maybe also more challenging taxa in general. On the other hand, the SSP can also act by building bridges. Since we have so many taxonomists in the group, they could be bridges to reach all these other initiatives which go sampling so that we can collaborate with them opportunistically. So that whatever they sample, they remember to sample also for genomics. And we as SSP maybe are the ones who can at least help building these bridges because we actually know what's going on at the national level. And the other thing is what SSP needs to do is to keep up the engagement. It is still very good but on the other hand we need also to see that people get something concrete out of this work. If you invest a lot of time and you don't have papers or at least get a genome out of it in the end it's not very helpful for your career, especially for younger ones. We need to find ways to be able to do that. One way in which we do that is by writing papers together. We always try to work at least on a paper once in a while and everybody's free to join as they see fit. So if you like to work on samples of different taxonomic groups and how to sample them feel free to join us. We are a very open community and we are happy about everybody who's keen on working with us! Learn more about the work of Torsten and the "Comparative and Evolutionary Genomics” (CEG) Research Group on their blog: Send an email to the Sampling & Sample Processing Committee and learn how you can contribute!

Guilherme Roxo, CIBIO-Azores, Universidade dos Açores O arquipélago dos Açores é um dos segredos mais bem guardados de Portugal. O solo vulcânico das ilhas permite a plantação de vários tipos de alimento, desde o chá que as avós tomam até ao ananás que as crianças gostam. Contudo, não são apenas os produtos gastronómicos que caracterizam o arquipélago, na verdade, um dos seus segredos mais bem guardados é a sua flora. Por entre os pastos verdejantes e as cidades de arquitetura única escondem-se florestas que já cá existiam muito antes do povoamento. É exatamente nestas florestas onde ocorrem plantas únicas e de extrema beleza. Uma dessas plantas é o Agrião dos Açores (Cardamine caldeirarum). Paisagens em diversas ilhas do arquipélago de Açores. O agrião endémico dos Açores pertence à família das Brassicaceae, grupo esse que engloba espécies de extrema importância na alimentação, entre os quais as couves, nabos, brócolos entre outros. O que diferencia este agrião dos demais é que esta espécie cresce somente neste arquipélago, com a excepção da ilha Graciosa. Uma das principais características deste agrião é que cresce apenas em sítios que estejam permanentemente húmidos (Schäefer, 2021). No ano de 1838 o cientista suiço, Heinrich J. Guthnick, recolhe uma amostra durante a sua visita ao arquipélago, e esta vem a ser descrita pela primeira vez pelo botânico alemão Moritz August Seubert em 1844 (Seubert, 1844). Em 1897 o botânico americano William Trelease descreve a espécie que encontrou na ilha de São Miguel que se diferencia das outras pelas suas flores que contam com maior dimensão (Trelease, 1897). Estudos genéticos nesta espécie, realizados por uma equipa DIVERGE da Universidade dos Açores liderada pela Professora Mónica Moura, já indicam a possibilidade da existência de várias espécies crípticas ao longo do arquipélago. Espécies crípticas, são, portanto, duas ou mais espécies que, apesar de sua aparencia (externa) semelhante, são consideravelmente diferentes a nível genético. Agrião dos Açores no seu habitat natural e detalhe das suas flores com um possível polinizador. O ERGA (European Reference Genome Atlas, traduzido como “Atlas Europeu de Genomas de Referência”) é uma iniciativa pan-europeia que tem como objetivo sequenciar genomas de referência de qualidade para todas as espécies europeias. O genoma é o conjunto de toda a informação genética de um indivíduo ou de uma espécie, sequenciá-lo é, portanto, determinar a ordem dos nucleótidos (os blocos de construção do ADN) de uma molécula de ADN. A sequenciação de espécies necessita de máquinas extremamente caras que não existem nos Açores. De modo a construirmos genomas de referência de alta qualidade é necessário manter a planta o mais saudável possível até o momento da extração do ADN. E porque é que será importante sequenciar uma espécie? Sendo o genoma toda a informação genética de um indivíduo, a sequenciação de uma espécie pode nos revelar diversas descobertas que podem ser utilizadas para saúde humana, estimular a economia, fonte alimentar, biossegurança, entre muitos outros. Um exemplo pode ser a transferência de genes desta espécie para por exemplo um agrião tornando-o mais resistente a certos stresses aumentando a sua produção ou até aumentando o seu valor nutricional. O agrião dos Açores foi umas das escolhidas para o projeto piloto do ERGA. Os habitats onde o Agrião dos Açores ocorre encontram-se degradados e a presença desta espécie é cada vez mais rara. Assim sendo, em um domingo em julho desloquei-me ao vale das Lombadas em São Miguel de modo a colher as amostras necessárias. Estava um dia chuvoso e para chegar ao local é por uma estrada de pedra antiga e o carro já derrapava. Ao chegar ao local é necessário entrar pela ribeira adentro e andar cerca de 40 minutos, galochas são recomendadas e mesmo assim não me safei de ficar molhado. Zona das Lombadas e os seus depósitos hidrotermais que vamos encontrando ao longo do caminho. Trata-se de um local de extrema beleza, ao longo da ribeira encontramos locais onde a água é quente e o solo encontra-se pintado de laranja, a estes locais chamamos de depósitos hidrotermais. Esta cor alaranjada é adquirida, pois por baixo dos nossos pés existe magma que aquece água, esta água é extremamente rica em minerais e quando sobe à superfície a água arrefece e os minerais precipitam voltando ao seu estado sólido e pintado as rochas de laranja. Ao chegar ao local, onde esta espécie ocorre, comecei a colheita. Para tal levei uma pequena pá que me permitiu tirar a planta com as raízes intactas e colocá-la num vaso, de seguida esse vaso é colocado num frasco com água da ribeira e fechado de modo a ficar protegida. Na viagem a mesma foi comigo na mochila e chegou em segurança ao laboratório em Inglaterra, onde é feita a sequenciação desta planta, nomeadamente em Norwich que conta com um laboratório com o qual temos parceria. Na chegada foram colhidas algumas folhas e congeladas em nitrogénio líquido - um método eficiente para preservar o tecido vegetal. Os resultados ainda estão a ser gerados, mas mal posso esperar para ver os mistérios que esta espécie esconde e como podemos utilizá-los para a construção de um futuro mais sustentável e onde esta espécie ainda possa existir. Agrião dos Açores colhido e colocado nos contentores para transportar para Inglaterra (à esquerda). As amostras foram então transportadas até o Instituto Earlham, em Norwich, onde estão sendo sequenciadas. (Mapa fora de escala) Referências Schäefer, H.  (2021) Flora of the Azores—A Field Guide. Margraf Verlag, Weikersheim Seubert, M. (1844): Flora Azorica. Adolph Marcus, Bonn. 50 pp. Trelease, W. (1897) Botanical observations on the Azores. Missouri Botanical Garden Annual Report 1897, 177. Para mais informações sobre outros projetos a ser desenvolvidos pelo grupo de investigação DIVERGE ou vontade em juntares-te a nós contacta a Professora Mónica Moura através do email. 🇵🇹 Gostaria de interagir com outros cientistas interessados na geração de genomas de referência para a biodiversidade portuguesa? Entre em contato com os representantes do ERGA em Portugal! Leia mais sobre o projeto Biogenome Portugal Imagens: Guilherme Roxo Read the English translation of this text >>

Guilherme Roxo, CIBIO-Azores, Universidade dos Açores The Azores archipelago is one of Portugal's best kept secrets. The volcanic soil of the islands allows various types of food to be cultivated, from your grandma's favorite tea to the pineapple devoured by children. However, it is not just agriculture that characterizes the archipelago, in fact, one of its best kept secrets is its native flora. Among the green pastures and cities with unique architecture are forests that have existed here long before human settlement. It is exactly in these forests where unique and extremely beautiful plants occur. One of these plants is the Azorean Bittercress (Cardamine caldeirarum). Landscapes acoss the Azores. This cress species, endemic to the Azores, belongs to the Brassicaceae family, a group that includes species of extreme importance as a food source, including cabbage, turnips, broccoli, among others. What differentiates this cress from others is that this species only grows in this archipelago, with the exception of Graciosa Island. One of the main characteristics of this cress is that it only grows in places that are permanently humid (Schäefer, 2021). In 1838, the Swiss scientist Heinrich J. Guthnick collected a sample of the species during his visit to the archipelago, and it was described for the first time by the German botanist Moritz August Seubert in 1844 (Seubert, 1844). In 1897, the American botanist William Trelease described the species he found on the island of São Miguel, which differs from the others due to its larger flowers (Trelease, 1897). Genetic studies on this species, carried out by the DIVERGE team from the University of the Azores and led by Professor Mónica Moura, have already indicated the possibility of the existence of several cryptic species throughout the archipelago. Cryptic species are two or more species that, despite their similar (external) appearance, are considerably different at a genetic level. Azorean bittercress in its natural habitat (right) and detail of its flowers with a potential pollinator (left). ERGA (European Reference Genome Atlas) is a pan-European initiative that aims to sequence quality reference genomes for all European species. The genome is the set of all the genetic information of an individual or a species. Sequencing it means determining the order of the nucleotides (the building blocks of DNA) of a DNA molecule. Sequencing species requires extremely expensive machines that do not exist in the Azores. In order to build high-quality reference genomes, it is necessary to keep the plant as healthy as possible until the moment of DNA extraction. And why is it important to sequence a species? Since the genome is all of  the genetic information of a given individual, sequencing a representative of a species can bring several discoveries that can be applied to conservation, human health, economic development, food sources, biosecurity, among many others. An example could be the transfer of genes from this cress species to, for example, watercress, making it more resistant to certain stresses, increasing its production or even increasing its nutritional value. The Azorean bittercress was one of the species chosen for sequencing as part of the ERGA pilot project. The habitats where the Azores Bittercress occurs are degraded and the presence of this species is increasingly rare. Therefore, I traveled to the Lombadas valley in São Miguel in order to collect the necessary samples. It was a rainy day and to get to the place I had to drive through an old and skiddy stone road. When you arrive at the place, you need to enter the river and walk for about 40 minutes, galoshes are recommended and even then I couldn’t help getting wet. The Lombadas Valley and the hydrothermal deposits found along the way. It is a place of extreme beauty, along the river we find spots where the water is warm and the soil is orange, these are hydrothermal deposits. This orange color is acquired because beneath our feet there is magma that heats the water, this water is extremely rich in minerals and when it rises to the surface the water cools and the minerals precipitate returning to their solid state and painting the rocks orange. Upon arriving at the spot where this Bittercress occurs, I started sampling. To do this, I took a small shovel that allowed me to remove the plant with its roots intact and place it in a vase, then this vase is placed inside a jar with water from the river and closed to keep it protected. The next step was to bring the plants to our partner laboratory in Norwich, England, where the sequencing would happen. I carried the plants in my backpack and they arrived safely at the laboratory. Upon arrival, some leaves were collected and frozen in liquid nitrogen - an efficient method for preserving them. The results of this effort are still being generated, but I can't wait to discover the mysteries that this species hides and how they can help us to create a more sustainable future in which the Azorean Bittercress can still exist. Azorean Bittercress harvested and placed in containers for transport to England (left). The samples were then transported to the Earlham Institute in Norwich, where they are being sequenced. References Schäefer, H.  (2021) Flora of the Azores—A Field Guide. Margraf Verlag, Weikersheim Seubert, M. (1844): Flora Azorica. Adolph Marcus, Bonn. 50 pp. Trelease, W. (1897) Botanical observations on the Azores. Missouri Botanical Garden Annual Report 1897, 177. For more information about other projects being developed by the DIVERGE research group or if you want to join us, contact Professor Mónica Moura via email. 🇵🇹 Would you like to interact with other scientists interested in generating reference genomes for Portuguese biodiversity? Contact ERGA representatives in Portugal! Read more about the Biogenome Portugal project. Read more about the participation of the Earlham Institute in the ERGA Pilot Project Images: Guilherme Roxo Leia esse texto na versão original em português >>