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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 >>

Are you interested to assemble an animal, plant, or fungal genome? Do you already have HiFi, Hi-C, Bionano or parental Illumina data but don’t know where to start? The new VGP-Galaxy assembly pipeline, just published in the nature biotechnology journal, is your answer to these questions! This pipeline, the result of a collaboration between the Vertebrate Genomes Project (VGP) and ERGA, can help you integrate complementary sequencing technologies to generate the most complete and accurate reference genome of your species of interest with just a few clicks. Click here for more information on the pipeline workflows, description and instructions on how to use them. Publication: https://doi.org/10.1038/s41587-023-02100-3

Join us for the first ERGA BioGenome Analyis & Applications Seminar of 2024 featuring a talk by Stein Aerts Wednesday, January 24th - 11:00 CET Link to the Livestream: Modeling and design of cell type specific enhancers using single-cell multi-omics and deep learning Stein Aerts, Professor at University of Leuven; VIB Scientific Director & Group Leader Single-cell transcriptomics and single-cell epigenomics allow building cell atlases of any tissue and species, providing new opportunities to predict gene regulatory networks that control the identity of cell types and cell states. I will present new computational strategies that take advantage of the joint analysis of scRNA-seq and scATAC-seq data, and that derive “enhancer-GRNs” (eGRN) with key transcription factors, genomic enhancers, and predicted target genes per cell type. In parallel, we use deep learning on the scATAC-seq topics to prioritize enhancers and decipher their regulatory grammar. I will discuss the results of several case studies where we applied these computational strategies, including the Drosophila brain and the mouse liver, and I will illustrate how evolutionary comparisons contribute to learning the gene regulatory code in the vertebrate brain. Finally, I will discuss how enhancer models based on deep learning can be exploited to design synthetic enhancers for Drosophila and human cell types.

Join us for the 4th session of the ERGA BioGenome Analyis & Applications Seminars! Wednesday, December 20th - 12:00 CEST Abstracts Speakers Vitor C. Sousa I conducted my Ph.D. at the Gulbenkian Science Institute (IGC, Oeiras, Portugal) and received my degree from the University of Lisbon in 2010, supervised by Lounès Chikhi and Manuela Coelho. I was then a postdoctoral researcher in Jody Hey’s lab (Rutgers University, New Jersey, USA) from 2010 to 2013, and in Laurent Excoffier’s lab (University of Bern and Swiss Institute of Bioinformatics, Switzerland) from 2013 to 2016. Since 2016 I have been a researcher at cE3c, first as an invited researcher, and from 2017 to 2018 as a Marie Sklodowska-Curie fellow. Since 2020 I am an Assistant Professor at the Department of Animal Biology, University of Lisbon. My research aims at characterising the interplay between demographic processes (e.g. gene flow, bottlenecks, population expansions) and natural selection in the structure and divergence of populations. I am the group leader of the Evolutionary Genetics group at cE3c, working on population genomics, and its applications to speciation, conservation, molecular ecology, and human genetics. João Carvalho I am a master in Evolutionary and Developmental Biology from the University of Lisbon and I am currently finishing a PhD in Biodiversity, Genetics & Evolution, supervised by Vítor C. Sousa of the Evolutionary Genetics group at cE3c and co-supervised by Dr Rui Faria and Dr. Roger Butlin. During my PhD I developed new tools to model and simulate Pool-seq data and combined those tools with an approximate Bayesian computation framework to investigate scenarios of ecotype formation.

The ERGA BioGenome Analysis and Applications Seminars represent a joint endeavor of the ERGA Data Analysis Committee (DAC) and the Biodiversity Genomics Europe Work Package 11 - Genome Applications. The purpose of this seminar series is to promote knowledge exchange on state-of-the-art genomic analyses and applications and to create a space for connection and analysis-oriented discussion for ERGA members and the broader genomics research community. These seminars provide opportunities for interdisciplinary interactions that explore emerging scientific trends, providing a platform for cutting-edge research, novel ideas, and insightful discussions. The series will promote an exciting agenda of talks and hands-on sessions on phylogenomics, comparative genomics, population genomics, and functional genomics. When? The seminars happen every month. Check the ERGA Calendar for more information on the upcoming sessions! All seminars will be broadcast on the ERGA YouTube channel. Watch previous sessions:

The new executive board has been elected by the Council! The team brings together six highly engaged researchers that have been active in various ERGA committees and initiatives. We congratulate each one and wish them the best for their new roles and a term full of exciting achievements and opportunities. We look forward to working together under their leadership and vision so that ERGA can advance and accomplish even more! The second ever iteration of "ERGA elections" has been successfully concluded, representing a major step in the efforts to formalise our community. As Camila Mazzoni, ERGA’s founding chair, puts it: “The Phase 1 of ERGA has established the foundation of the network and is currently undergoing consolidation with the support of the BGE Project until its completion. It is now time to initiate Phase 2, during which ERGA will actively promote the scaling up of reference genome sequencing for European Biodiversity.” The electoral procedure was approved and followed closely by the ERGA Council, in accordance with the guidelines established by the ERGA governance Document. The process also received crucial support and oversight from the Nominations Working Group chaired by Alice Mouton, the Elections Supporting Team (Christian de Guttry, Diego de Panis and João Pimenta) and the JEDI Subcommittee. The expanded structure of the executive board draws upon lessons learned during ERGA's first phase. “The newly expanded Executive Board will play a pivotal role in 1) expanding the network of partnerships and projects under the ERGA umbrella, and 2) expanding ERGA’s role as a knowledge hub that supports capacity building across Europe and ensures that genomes sequenced throughout Europe meet the required standards of the Earth BioGenome Project”, explains former chair Camila Mazzoni, “I am delighted to see the ongoing enthusiasm of our members and extend my best wishes to the new Executive Board for success in their mission to steer ERGA into Phase 2.” Learn more about each of the Executive Board roles: Playlist - ERGA Executive Board Phase 2

We are happy to invite you to the ERGA session during the Biodiversity Genomics Conference 2023! BG23 is an online, open conference and free to attend. This year the conference is organized by the Wellcome Sanger Institute Tree of Life programme and Biodiversity Genomics Europe. ERGA will be hosting a session on Friday, October 6th from 14:00 to 16:00 CEST. 📅 Add the session to your calendar! The first hour will be focused on the ERGA community, and some of the committees will give brief presentations about the innovations and resources they are developing; The second hour will include invited scientific talks by ERGA members showcasing the importance of reference genomes to enhance our understanding of European biodiversity. Check the programme below: Check the Abstracts! Watch all the talks: