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Join the last ERGA BioGenome Analysis & Applications Seminar of the year! This time with a focus on functional genomics, featuring talks by Susana Coelho and Jaruwatana Sodai Lotharukpong. Don't miss it! 🕚 Wednesday, December 11th 2024 - 11:00 AM CET 📅 Add the seminar to your calendar Join us live on YouTube: Abstract Brown algae independently evolved sexual systems, complex multicellularity and (embryo) development, offering a unique perspective for exploring the general principles underlying the origin and evolution of these processes. Along with dozens of new reference genomes, the ongoing drive to generate transcriptomic data in brown algae have yielded new insights into shared developmental and evolutionary patterns across the tree of life, particularly the hourglass model. The hourglass model describes a recurring pattern in embryogenesis, where the evolutionarily divergent early and late embryonic stages are bridged by a conserved mid-embryonic period. In this talk, we present our recent findings of a transcriptomic hourglass in brown algae and discuss the bioinformatic challenges/solutions when working on non-model organisms. About the speakers Susana Coelho was born in Portugal and completed her PhD at the Marine Biological Association in the laboratory of Colin Brownlee (Plymouth, UK). She worked at the Centre National de la Recherche Scientifique (CNRS) in Roscoff (France) from 2006 where her lab focused in life cycle and reproduction of brown algae, and she had a key role in the establishment of the brown algae  Ectocarpus  as a model organism in evolutionary research. Between 2010 and 2020, she co-led the Algae Genetics Group in Roscoff, and was appointed Research Director at the CNRS in 2015. In 2020, she moved to Tubingen, Germany, where she is Director of the Algal Development and Evolution Department at the Max Planck Institute for Biology. Susana has led a number of large-scale research projects on the evolution and development of brown algae, including two ERC grants (SEXSEA and TETHYS), and she was awarded several prizes including the bronze medal of the CNRS (2015), the Trogoboff Prize of the French National Academy of Sciences (2017) and the Bettencourt Prize Coup d’Elan (2020).  Jaruwatana Sodai Lotharukpong is a PhD student at the Max Planck Institute for Biology in Tübingen. He was born in Japan, grew up in Thailand and completed his undergraduate and masters in London and Cambridge, respectively. Related publication Lotharukpong, J.S., Zheng, M., Luthringer, R. et al.  A transcriptomic hourglass in brown algae. Nature   635 , 129–135 (2024). https://doi.org/10.1038/s41586-024-08059-8

We are happy to invite you to the ERGA session during the Biodiversity Genomics Conference 2024! BG24 is an online, open conference and free to attend. ERGA will host a session on Monday, October 28th at 13:00 CET. Recorded talks: Session slide deck: https://zenodo.org/records/14008438 Check the programme below:

An ongoing project on ecological genomics of common thyme ( Thymus vulgaris ), ERGA-BGE was selected on April 2024 to support the assembly of a chromosome-level genome for T. vulgaris  under the call “Enhancing Biodiversity Genomics Applications for Ongoing Case Studies”. This study is led by researchers from Aarhus University in collaboration with researchers from the Center for Evolutionary and Functional Ecology (CNRS and Montpellier University), and builds upon decades of study of the ecological and evolutionary importance of common thyme chemotype diversity. Close-up view of a flowering thyme plant with the landscape in the background. Photo by Thomas Bataillon Thyme’s aromatic compounds not only have made it an important culinary and medicinal herb across human cultures, but these compounds also have multiple ecological roles, including defence against herbivore predation, resistance to abiotic stresses such as droughts and freezing and even influencing the species composition of surrounding plant communities. Something that is often not known is that there are multiple thyme scents. Thyme plants exhibit a huge diversity in the aromatic compounds they produce, giving rise to multiple chemotypes. For example, in Mediterranean common thyme it is possible to find up to 7 different chemotypes (scents). These different chemotypes can be broadly classified in two different ecotypes, the phenolic and non-phenolic, which provide adaptation to different habitats. Recent studies in Southern France have shown that the phenolic ecotype, which is better adapted to warm and dry conditions, has been expanding its habitat as a response to on-going climate change. The current project has produced a genetic dataset of exome sequencing capture of around 1000 thyme plants across different populations in Southern France. Within each population, a transect that captures a gradient of environmental conditions was sampled making sure that samples from both ecotypes were represented within each of the population. Moreover, for each sampling site along the transect, different environmental variables were measured. This design gives the optimal conditions to identify both the genetic variation responsible for ecotype formation and the genetic and environmental drivers of local adaptation. However, genomic analyses have already shown thyme has high genetic diversity, including structural variation involved in ecotype formation. The reference genome will allow better characterisation of thyme genomic landscape and identification of the relevant functional genetic variation and its genomic context . Ultimately, this will improve the management of thyme populations to ensure all of its chemotype diversity can be maintained, thus improving also the health of the Mediterranean ecosystems where thyme is a dominant plant, and help to better understand a so far successful adaptive response to climate change.   Bodil Ehlers with a thyme plant during field work and sampling, view of the landscape of the thyme ecosystem in Southern France. ( Photos by Thomas Bataillon) This work is part of the AromAdapt project funded by an Independent Research Fund Denmark grant awarded to Bodil Ehlers (Principal Investigator) from the Department of Ecoscience, Aarhus University, and Thomas Bataillon (co-PI) from the Bioinformatics Research Center, Aarhus University. The work is done in collaboration with John Thompson and Perrine Gauthier from the Center for Evolutionary and Functional Ecology at CNRS in Montpellier, Sylvain Santoni from the AGAP Institute (INRAE) and Marc Palmada-Flores from Universitat de Girona. This project is funded by the Horizon Europe research and innovation programme, co-funded by the Swiss Government and the British government. About the Author Genís Garcia-Erill is a bioinformatician and evolutionary biologist. He is a postdoctoral researcher in Thomas Bataillon´s group in the Bioinformatics Research Center, Aarhus University, Denmark, and he is an ERGA member working in the assembly of the common thyme reference genome.

ERGA  (European Reference Genome Atlas) and iBOL (International Barcode of Life) Europe  are pleased to announce the signature of a Memorandum of Understanding (MoU) to officialise their strategic alignment and shared aspirations for the future.  Both iBOL Europe and ERGA address biodiversity loss in Europe by accelerating the application of genomic science to enhance understanding of biodiversity, monitor biodiversity change, and guide interventions to address its decline.   iBOL Europe applies DNA barcoding, while ERGA advances the generation of reference genomes for European Biodiversity. The MoU includes concrete agreements on crucial strategic alignment aspects, especially cross-collaboration, knowledge exchange and network building. With both research-oriented initiatives focused on applying genomic science to better understand biodiversity, there are many natural synergies and complementary approaches to building shared knowledge. The MoU was signed on 10 October 2024 in Thessaloniki (Greece) by the representatives of each initiative.  We look forward to taking our collaboration forward.

In June 2024, researchers from the Centre for Ecology, Evolution, and Environmental Changes  (CE3C) at the Faculty of Sciences, University of Lisbon, Portugal, in partnership with Biodiversity Genomics Europe  (BGE), launched a groundbreaking project to improve the genomic annotation of the white crowberry ( Corema album ). This initiative seeks to deepen our understanding of this essential coastal plant species and address its conservation needs amid changing environmental conditions. Corema album  ssp. album  is an Iberian Peninsula endemic species with a recognised ecological value in its natural habitat. This dioecious perennial woody shrub is a key structural species of the dune systems and is only found in the Iberian Peninsula’s coastal dunes and pine tree forests. Its habitat holds a priority conservation status under Council Directive 92/43/EEC. Due to anthropogenic pressures and climate change, C. album  populations are declining, particularly populations inhabiting the southern limit of the distribution range, and the species is listed as a conservation concern in PROGEN by ICNF. Corema album population over the cliffs of Vila Nova de Milfontes, Portugal. (Photo credit: João Jacinto) The main target of this project is to produce a high-quality reference genome for Corema album , included in the ERGA Pilot Project, by conducting RNA sequencing (RNA-seq) on multiple tissues from both male and female plants. This effort will help annotate the reference genome, providing comprehensive insights into the species’ genetic diversity and adaptation mechanisms. Studying both male and female C. album  plants is crucial due to its dioecious nature, which is essential for understanding sex-based genetic diversity. A well-annotated reference genome will enable researchers to better understand the genetic basis of Corema album ’s adaptation to its coastal habitat, particularly aridity. By enhancing the genomic understanding of Corema album , this project aims to contribute significantly to the conservation of coastal dune ecosystems, ensuring their resilience and sustainability for future generations. This project also highlights the broader importance of genomics in biodiversity conservation, potentially guiding conservation strategies for other species in similar habitats. Close-up of a female Corema album plant bearing fruits. (Photo credit: Carla Alegria) Leading this endeavour is Manuela Sim-Sim and a dedicated team of researchers, including Helena Trindade, Vítor Sousa, Bruno Nevado, Carla Alegria and João Jacinto, combining expertise in systematics, taxonomy, genetics, molecular biology, bioinformatics, and ecology, actively participating in both ERGA and the Genome Team of the pilot project. By bringing together a diverse team and leveraging cutting-edge genomic techniques, this initiative represents a significant step toward integrating genomic data into effective conservation strategies, safeguarding the biodiversity of coastal dune ecosystems. This project has received funding from the European Union under the European Union’s Horizon Europe research and innovation programme, co-funded by the Swiss Government and the British Government, with additional support from CE3C’s FCT Unit funding UIDB/00329/2020 ( https://doi.org/10.54499/UIDB/00329/2020 ). By integrating genomic data into conservation efforts, this project aims to pave the way for more informed and effective strategies to protect and sustain biodiversity in coastal ecosystems. About the Author Manuela Sim-Sim , Helena Trindade , Vítor Sousa , Carla Alegria  and João Jacinto  are members of the Corema genome team for the ERGA pilot project. Additionally, Vítor Sousa participates in the Data Analysis Committee  and is also a member of the ERGA Council of Country Representatives . Manuela Sim-Sim, Vítor Sousa and Bruno Nevado are leaders of CE3C’s research groups Natural History Collections & Systematics  (NHC&S), Evolutionary Genomics and Bioinformatics  (EGB), and Speciation Genomics  (SG), respectively, and Helena Trindade, Carla Alegria and João Jacinto (PhD student) are members of CE3C’s Plant Functional Ecology  research group.

We are excited to announce the upcoming Genome Application Symposium , which will be held on September 30 and October 1, 2024. This two-day online  event promises to be an enriching experience, bringing together leading experts and enthusiasts in the field of genomics and promoting knowledge exchange. Focusing on the development of genome applications for the protection of biodiversity and stakeholder engagement , this symposium will provide opportunities for interdisciplinary interactions from basic to applied science.   Event Details: 📅 September 30 and October 1, 2024 ( click to add to your agenda! ) 🕘 9:00 to 16:45 CEST | ▶️ Venue: Zoom   A playlist with all recorded sessions is now available on Youtube: Participation is open to everyone. No registration is required, the event will be openly transmitted via Zoom   Overview of the program:

Imagine it’s June again – flowering time for Arnica! Except this year, June also saw the beginning of a pioneering research project on this well-known medicinal plant, which is currently disappearing from large parts of its native range in Europe. At the invitation of Dr Katja Reichel from FU Berlin, Arnica specialists from several European countries will join forces in the new BGE ERGA case study ArnicaSNP  and develop a scheme for monitoring diversity and changes in the species’ genome – through time and space. Quo vadis, Arnica? As populations decline and disappear in large parts of its range, the species faces an uncertain future. Photo by Katja Reichel. In the BGE project, Arnica serves as an example to show how the availability of reference genomes impacts the way conservation geneticists work. Currently, wild stands of the charismatic yellow-flowering herb are highly protected in some European countries, yet heavily exploited in others, since large-scale cultivation has so far failed. Populations in different parts of the species’ range thus face a variety of threats, from overharvesting to the abandonment of hay meadows, which used to be an important Arnica habitat type especially in the lowlands, but whose existence depends on mowing. These direct factors in the decline are overlaid by more complex effects of climate change, which may also impact the higher-up growth sites that gave Arnica its Latin name, Arnica montana , and Arnica’s composite reproductive system, including both sexual offspring from seeds and clonal “daughter” plants connected underground to their parent. The need to understand Arnica’s evolution to ensure the species’ effective protection has motivated a number of previous local conservation genetic studies, yet so far, no range-wide comparison exists. Arnica habitats at a glance. Photos by Katja Reichel, Aaron Pérez Haase and G. Mansion / A. Guggisberg. ArnicaSNP now takes Arnica conservation research to a new level: By jointly analysing genomic data from across Europe, based on DNA samples collected in previous studies and over a period of more than ten years, it will provide essential information to allow the repeated, range-wide measuring of the species’ natural diversity. This includes testing methodological questions, such as which sections of the genome evolve locally vs. in different parts of the plant’s range, or on which time scale to expect detectable changes. The Arnica reference genome, which is also being generated as part of the ERGA BGE project, will hereby serve as a “map” for smaller stretches of DNA (RADtags, SSR loci) sequenced in a total of over 400 samples. Moreover, the project will give future conservation scientists an opportunity to get their first experience with genomic data in the project’s equally important training and dissemination part. By bringing the European Arnica community together,  we hope that ArnicaSNP will be a hotbed of further ideas on the plants’ sustainable protection and equitable use, and inspire similar networks for other disappearing species.  This project is made possible by the support of the ERGA community, and receives funding from the European Union under the European Union’s Horizon Europe research and innovation programme, co-funded by the Swiss Government and the British Government, as well as from FU Berlin. About the Author Katja Reichel works at Freie Universität Berlin , doing research  on the population and conservation genetics of partially clonal (and other) plants, often – as for ArnicaSNP – in collaboration with the Berlin Botanic Garden and Botanical Museum . She is also the current co-chair of the ERGA Sampling and Sample Processing Committee.

The “Enhancing Biodiversity Genomics Applications for Ongoing Case Studies” call of BGE has triggered much of our interest at the beginning of 2024. We study an endangered small mammal species in Hungary, and we had already produced a short-read dataset, but long-reads and Hi-C data were missing to achieve a high-quality genome. So, we rapidly nominated our target species, the Hungarian birch mouse ( Sicista trizona ) of the Sminthidae family of Rodentia, arguably one of the rarest mammals in Europe. The nominal subspecies, S. trizona trizona , is extinct in Austria and Slovakia, most probably in Serbia, and has almost gone extinct in Hungary, where only a single population is known. Our research team formed by the researchers of the HUN-REN–UD Conservation Biology Research Group, the Evolutionary Genomics Research Group of the University of Debrecen, and the Hungarian Natural History Museum has won the opportunity to undertake this research under the umbrella of the HUN-REN Office for Supported Research Groups (Budapest, Hungary). The study will provide a high-quality reference genome for the Hungarian birch mouse, which will assist a population genomic study at the single locality, representing the only known population of the subspecies, managed by the Bükk National Park Directorate at the protected territory “Borsodi-Mezőség” Landscape Protection Area (Hungary). The Hungarian Birch-mouse ( Sicista trizona trizona) . Photo by Gábor Sramkó. During the annual monitoring survey of this species, we managed to collect enough blood samples from two animals for high-molecular-weight DNA extraction. One sample of individuals, coded as ST65, provided enough clear DNA samples with fragment size > 30kb. This will first be subject to Pac-Bio HiFi sequence data generation using a commercially available service provider based in the EU that should yield approximately 40× long-read coverage of the Hungarian birch mouse’s genome. Furthermore, we will also produce Hi-C data from samples collected during the second round of monitoring surveys at the known locality this autumn. All these data will make a perfect use for analysing genomic data originating from a reduced-representation genomic library technique RADseq. The latter data were collected from across the currently known range of the habitat of the subspecies, and thus we hope to deliver readily usable results for the effective preservation of the Hungarian birch-mouse on its last known site. Furthermore, this reference genome will be the first to represent the family Sminthidae, the basal clade of the mice suborder, Myomorpha. Therefore, we also expect our birch mouse genome to become a valuable resource in evolutionary research targeting research questions in mice (in a broad taxonomic sense). Photos by Gábor Sramkó. In summary, we feel privileged by the opportunity the BGE project provided to us: our favourite birch mouse, on the brink of extinction, can enormously benefit from a genomic resource that will lay down the genetic basis of a well-established management plan for this critically endangered taxon. We extend our gratitude to the Bükk National Park Directorate and personally to Péter Balázsi, for their invaluable help during the fieldwork and the project. We are highly indebted to the two PhD students of the PI, Virág Nyíri and Lajos Szatmári, for the high-quality work during the laboratory work. This project is funded by the Horizon Europe research and innovation programme, co-funded by the Swiss Government and the British government, with additional support from a national research grant awarded to the PI (NKFIH FK137962); and fieldwork supported by the GRASSLAND-HU LIFE IP. We also thank BGE-ERGA for providing a collaborative platform that made this research possible. About the Author Gábor Sramkó is part of the ERGA community from Hungary. He is contributing to the WP11 action in BGE, where he helps an ongoing ERGA case study  on the common hamster ( Cricetus cricetus ) as an evolutionary geneticist expert.  Gábor’s main interest lays in phylogenetics, phylogeography and conservation genetics at the genomic level among plants and animals. He is the head of the Evolutionary Genomics Research Group at the University of Debrecen, Hungary . Tamás Cserkész is part of the ERGA community from Hungary. He is contributing to the WP4 and WP11 action in BGE, where he coordinates an ongoing ERGA case study on the common hamster ( Cricetus cricetus ) as an mammalogist expert.  Tamás’s main interest lays in phylogenetics, phylogeography and conservation of mammals. He is the project coordinator at the Hungarian Natural History Museum, Hungary .

The Phycology Research Group at Ghent University contributes with a case study to the BioGenEurope "Enhancing Biodiversity Genomics Applications" program with a project started in June 2024. Within the project, we aim to establish reference genomes for two red macroalgae Porphyra dioica  and Porphyra linearis  to support ongoing research.  Porphyra dioica  and Porphyra linearis belong to an ancient red algae group, commonly known as bladed Bangiales. This order includes many fascinating species, some of which are well known, such as Nori sheets - an essential ingredient in sushi - but there are also others with a complex physiology that permits them to survive in the stressful intertidal environment. Besides tolerating quick changes in temperature and light intensity, they can also survive desiccation and freezing.  Porphyra dioica  and Porphyra linearis belong to an ancient red algae group, sequencing their genomes will help researchers to better understand their complex physiology and evolution.   Photo by By Emile Wuitner - Wuitner, Emile (1921) Algues Marines des Cotes de France (Manche et Ocean), Encyclopedie Pratique du Naturaliste. v.VII, Paris: Paul Lechevalier, Public Domain. With the help of these two genomes, we will be able to gain a better understanding of underlying fundamental processes in red macroalgal evolution, adaptation, and specific life cycle variation. In addition to providing fundamental knowledge about this ancient lineage of red algae, this new genomic data can assist in overcoming hurdles associated with the valorisation of European Porphyra. This project received funding from the European Union under the European Union’s Horizon Europe research and innovation programme, co-funded by the Swiss Government and the British Government, with additional support from national research grants. We also thank BGE-ERGA for providing a collaborative platform that made this research possible. Porphyra linearis  growing in its natural habitat. Photo by Jessica Knoop About the Author Prof. Olivier De Clerck and Dr. Jessica Knoop are from the Phycology Research Group at Ghent University, BE. The working group focuses on genetics, diversity, life cycle control of marine macroalgae. We address questions ranging from descriptive taxonomy over ecological studies forecasting the distribution of species in relation to environmental change to genomics. These fundamental biological questions are also used to solve more applied aspects - advancing seaweed cultivation in Europe. You can find more information about the research at https://phycology.ugent.be/