Better together: Scientists from 33 European countries join forces to generate reference genomes for the continent’s rich biodiversity

Release: 17 September 2024 

Link to the collection: https://www.nature.com/collections/european-reference-genome-atlas

The European Reference Genome Atlas (ERGA) Pilot Project reports its success in uniting researchers from across Europe to produce high-quality reference genomes for 98 species. This continental effort is setting the stage for a new, inclusive and equitable model for biodiversity genomics.

Strength in (bio)diversity: Some of the European species selected for the ERGA Pilot Project. 

Photos by ©Mantonature, ©Cucu Remus, ©dadalia, ©scubaluna, ©Kristian_Nilsson,  ©AlbyDeTweede, ©Carine Carnier,  ©Daniel Jara from Getty Images via Canva.com

Introduction to the Pilot Project Collection:

In a new publication, the European Reference Genome Atlas (ERGA) announces the success of its Pilot Project. This pioneering initiative assembled a large collaborative network of researchers and institutions across 33 countries to produce high-quality reference genomes of 98 European species. This marks a significant milestone in the quest to create a high-quality reference genome database for all European animals, plants, and fungi. The Pilot Project has provided valuable lessons and highlighted key challenges, positioning ERGA as a model for decentralised, inclusive, and equitable biodiversity genomics initiatives around the world, as reported in a new collection of research articles published today in npj Biodiversity. This collection provides a broad overview of the Pilot Project, the sample collection and processing procedures and insights into national node developments that resulted from the Pilot Project. The collection will continue to be added to as papers associated with the Pilot Project become available over time.

Key Highlights of the Flagship Paper:

Among many of the project’s milestones are the first chromosome-level genome assemblies of species from Greece, one of Europe’s most biodiverse countries. Species such as the Cretan wall lizard and Aristotle’s catfish were sampled by local researchers in Greece to produce genomes that are now openly available for anyone across the world to access and study. This is a great example of what can be achieved by uniting an international community of biodiversity researchers, fostering collaboration between and within countries. The ERGA Pilot emphasised equity and inclusion, with the goal that genomic research and resources are accessible to all, regardless of geographical boundaries. For many of the participating researchers and countries, the project offered the first opportunity to actively engage in the generation of state-of-the art reference genomic resources for their native biodiversity.

The ERGA Pilot was also successful in building momentum and bringing visibility to the growing importance of biodiversity genomics in Europe and beyond. Genomic data hold immense potential to inform conservation actions for endangered species and unlock discoveries in the fields of human health, bioeconomy, biosecurity and many other applications. Among the species sequenced by the project is for example the greater argentine – a commercially important fish species from the northern Atlantic. This new reference genome will enable scientists to make more accurate assessments of the genetic status of the species’ populations, ultimately guiding management decisions to ensure that fishing practices are sustainable and responsible.

As the global scientific community strives to unlock the full potential of genomic data, the establishment of a Europe-wide collaborative network under the ERGA umbrella accelerates scientific progress and facilitates its translation into tangible benefits for biodiversity and society. Additionally, the network helps researchers at all career stages to find and share opportunities for training, partnerships, and funding.

Representatives of ERGA in Lithuania, scientists of Nature Research Centre

The members of the ERGA council representing Lithuania are scientists of the Nature Research Centre, dr. Laima Baltrūnaitė and dr. Vaidas Palinauskas. The scientists contributed to the pilot genomic project, together with their colleagues from Poland offering to sequence the genome of one of the most protected bird species in Europe, aquatic warbler Acrocephalus paludicola. This species is included in the Lithuanian Red Book and in the list of strictly protected animal, plant and mushroom species of the Republic of Lithuania. Sequencing of genome is extremely important for population studies and will serve for conservation and recovery of vulnerable aquatic warbler populations. Currently, genomic data is being analyzed and prepared for deposition.

Addressing Challenges:

ERGA is the European node of the global Earth BioGenome Project (EBP). In order to achieve its ambitious goal – to sequence all eukaryotic life on Earth – the EBP crucially needs worldwide participation and new, decentralised models of genome production. The ERGA Pilot was able to show that a fully distributed, collaborative, and coordinated genome production model is not only feasible, but effective – even at a continental scale and without a central source of funding available. In fact, most of the project budget came from grassroots efforts by individual members and partnering institutions, with additional support from sequencing partners and commercial sequencing companies providing grants, discounts and in-kind contributions.

The ERGA Pilot project helped to identify and address the many challenges of working at the international scale. These challenges include dealing with the legal and logistical hurdles of shipping biological samples across borders, resource disparities between countries, and the search for balance between decentralisation and the need for standardisation to guarantee that only the highest possible quality reference genome assemblies, that met EBP metrics, were produced by the project.

Future Directions:

ERGA’s decentralised approach holds great promise for the future of biodiversity genomics. The Pilot Project’s success in building momentum and uniting researchers illustrates the power of this model. By fostering international collaboration and focusing on inclusivity and equity, ERGA is setting new standards for biodiversity genomics. The lessons learned and challenges addressed in the Pilot Project will guide future efforts, promoting robust and standardised workflows and a comprehensive genomic database for species in Europe and beyond.

Quotes:

“The ERGA Pilot Project attempted to scale the generation of high-quality reference genomes across an entire continent. An endeavour of such magnitude was made possible only through its commitment to the principles of inclusion, equity and collaboration as well  as the dedication of its diverse, transdisciplinary and cross sectoral participants. I feel incredibly lucky to have worked alongside such an amazing group of colleagues to help kickstart the construction of a genomics encyclopaedia of European species.”  Ann McCartney, Member of the ERGA Pilot Committee – Assistant Researcher University of California Santa Cruz, and adjunct Ass. Prof at University College Dublin.

“When we took on the leadership of this project, we didn’t anticipate the extent of the work ahead. It was a challenging endeavour, but through perseverance and teamwork, we succeeded. We also had the invaluable support of sequencing centres, universities, and commercial companies who contributed to the ERGA Pilot Project, offering human resources for library creation, free sequencing, and in-kind products. This experience was truly one of a kind.”  Alice Mouton, Member of the ERGA Pilot Committee – former FNRS postdoctoral researcher, and scientific collaborator at the University of Liege, Belgium.

“ERGA was all a dream, until it wasn’t. Through this pilot project the prospect of uniting Europe under the flag of biodiversity genomics is now reality. We can be proud to have first established the process by which the genomes of many species will become available to the scientific community for conservation and beyond.” Giulio Formenti, Member of the ERGA Pilot Committee – Research Assistant Professor at the Rockefeller University.

“The ERGA Pilot project is a radical step forward for the continent as it links researchers who need genomes sequenced with sequencing hubs ready to do just that. This exchange promotes sharing of tools, approaches, and understanding and has led to the successful bid for Europe-wide Horizon 2020 Biodiversity Genomics Europe funding. The pilot teams’ enthusiasm has carried through to the wider project, and I am excited to see what they will accomplish in the future.” – Mark Blaxter, Head of the Tree of Life Programme, Wellcome Sanger Institute.

“The ERGA pilot demonstrated the importance of a well-connected scientific community that is willing to cooperate to achieve a major common goal. This success marks a significant milestone for ERGA, illustrating that such an initiative can be highly inclusive while still maintaining the high standards set by the Earth BioGenome Project (EBP) for reference genome production. This ERGA pilot provides both an example and a roadmap for distributed efforts to build Biogenomes across Europe and potentially beyond.” Camila Mazzoni, former ERGA Chair and senior author of the article published and group leader at the Leibniz Institute for Zoo and Wildlife Research.

“The ERGA Pilot project is a significant milestone in the Earth BioGenome Project (EBP) and a major step forward for biodiversity genomics in Europe. As the first biodiversity genomics project coordinated at a continental scale, ERGA has demonstrated two fundamental principles on which the EBP was built  — the first being that sequencing capacity will be geographically distributed, and the second being that any benefits derived from sequenced genomes would be shared equitably. ERGA is now poised to expand its goals to sequence thousands of genomes for conserving European biodiversity and the growth of a sustainable bioeconomy.” Harris Lewin, Chair of the EBP Executive Council and Research Professor at ASU.

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For more information about the European Reference Genome Atlas (ERGA) and its Pilot Project, please visit erga-biodiversity.eu and follow the initiative on social media (X and LinkedIn). Join us in advancing the frontiers of biodiversity genomics and contributing to make the field more inclusive.

Contact Information (press release)
Luísa Marins

media@erga-biodiversity.eu , marins@izw-berlin.de
erga-biodiversity.eu

This article, “The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics” and published in npj Biodiversity, will be free to access and can be read here: https://www.nature.com/articles/s44185-024-00054-6

Reference:

Mc Cartney AM., Formenti G., Mouton A., et al. The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics. npj Biodiversity, 2024. DOI: https://doi.org/10.1038/s44185-024-00054-6

Link to the collection: https://www.nature.com/collections/european-reference-genome-atlas

Website: https://www.erga-biodiversity.eu/

Social media Information: please tag the following accounts in your posts and use the #ERGAPilot hashtag 🙂

• X: https://x.com/erga_biodiv
• LinkedIn: https://www.linkedin.com/company/erga-european-reference-genome-atlas
• Youtube Channel: ERGA – European Reference Genome Atlas – YouTube
• Introductory video:  What is ERGA? – European Reference Genome Atlas

More information about the pilot project: https://www.erga-biodiversity.eu/pilot-project

On August 26, 2024, postdoctoral fellow Michal Šujan from the Laboratory of Quaternary Research at the Nature Research Centre, Vilnius, received the IUGS Early Career Scientist Medal during the opening ceremony of the 37th International Geological Congress in Busan, South Korea. The nomination for this prestigious award was submitted to the IUGS Executive Committee by the leadership of the Slovak National Geological Committee, based on the nominee’s outstanding research and application of cosmogenic nuclides in geochronology and sedimentological research.

The IUGS Early Career Scientist Medal is awarded once every four years to a young researcher who has achieved exceptional results in original research in geology. The selection of the laureate is conducted by a vote of the Executive Committee of the International Union of Geological Sciences (IUGS), which represents national geological organizations from 121 countries and represents more than one million geoscientists.

Biologists Agnė Bučaitė and Vita Žvynakytė from Laboratory of Ecotoxicology participated in the “Our Common Baltic” training organized by “Coalition Clean Baltic” (CCB) in Denmark on August 26-30. In the picturesque city of Kerteminde, together with young scientists, environmental enthusiasts and specialists from 7 countries, researchers deepened their knowledge about the ecological state of the Baltic Sea and its protection. They visited The Marine Biological Research Center (University of Southern Denmark), listened to lectures that covered not only environmental protection, pollution and changes in biodiversity, but also the importance of communication and citizen science. During workshops, the CoastWatch initiative was introduced and plastic monitoring was carried out on the sea coast in order to determine the purpose of plastic waste (food packaging, fishing waste, etc.) and waste producers. Researchers also discussed the infrastructure projects around the Baltic Sea, analyzed the Baltic Sea Action Plan (HELCOM), and were introduced to maritime territorial planning.

More information about “Coalition Clean Baltic”: www.ccb.se/

IN MEMORIAM

Dr. Brigita Čapukoitienė

 

 

 

 

We have lost our colleague Brigita Čapukoitienė, PhD in Biomedical Sciences, researcher at the Laboratory of Ecotoxicology.

Dr. Brigita Čapukoitienė obtained Bachelor’s degree in Biology in 2002, and Master’s degree in Genetics in 2004 from Vilnius University.

In 2005-2009, she studied for a PhD at the Nature Research Centre and in 2011 defended her doctoral thesis “The expression of Saccharomyces cerevisiae K2 preprotoxin gene in plant Nicotiana tabacum L. and the search of toxins producing microorganisms and analysis of their use”.

In 2004–2012, she worked at the Laboratory of Genetics of the Institute of Botany of Nature Research Centre.

In 2017–2021, she worked at the Laboratory of Geotoxicology of the Institute of Ecology of Nature Research Centre.

In 2021–2024, she worked at the Laboratory of Ecotoxicology of Nature Research Centre.

Dr. B. Čapukoitienė’s research interests: genetic toxicology, ecotoxicology, genetic engineering, killer yeast research.

She co-authored peer-reviewed scientific papers with colleagues, supervised the final theses of university students and participated in various research projects.

Brigita will be remembered by her colleagues as an enthusiastic, positive personality, full of love for life and respect for every person.

Farewell to Dr. Brigita Čapukoitienė on Monday (26 August, from 16:00 to 21:00) and Tuesday (27 August, from 9:00 to 12:00) at the Vilnius Funeral Home at Sietyno St. 14, Vilnius. The funeral will take place on the second farewell day at Liepynė cemetery.

In summer, as the weather and water warms up, life processes in water bodies become more active. We asked Dr. Judita Koreivienė, Chief Researcher, and Dr. Jūratė Karosienė, Senior Researcher at Nature Research Centre, to comment on the video made the owner of a water body, Aliaus Mazaliauskas from Alytus.

What can we see on the surface of the water? Under what circumstances can this be formed? Is it harmful for humans and fish or not? What measures should be taken by the owner of the body of water?

The material captures water blooms caused by cyanobacteria. During the bloom, cyanobacteria multiply rapidly forming aggregations and turning the water a bluish-green colour. In calm weather, they float to the surface of the water and form films. Water blooms are the most visible consequence of eutrophication in water bodies. Excess nitrogen and phosphorus compounds entering water bodies from the catchment due to intensive farming activities, unsuitable wastewater treatment systems, household chemicals and temperature are among the most important factors for the intensive growth of cyanobacteria and the formation of aquatic blooms. Therefore, water blooms are a common phenomenon in summer.

Studies have shown that up to 75% of bloom water bodies are harmful for humans and animals. Cyanobacteria synthesise and release toxic compounds such as cyanotoxins into the environment. Depending on their composition and concentration in the water body, cyanotoxins can cause allergic skin reactions, shortness of breath or digestive problems. Bathing in bloom water can cause signs of poisoning, such as general weakness, dizziness, difficult breathing, and tingling in hands and feet.  Some cyanotoxins accumulate in the body and cause various chronic diseases (cancer, multiple sclerosis, accelerated Alzheimer’s disease, etc.). In addition, these toxins accumulate in fish and other aquatic organisms and can enter the human body through food.

Please note that the greatest risk to human and animal health comes after the end of the bloom, when cyanobacteria decompose and cyanotoxins enter the water. This is when cyanotoxin amounts are the highest and can persist for weeks to months.

Care should be taken in bloom water, as cyanotoxins can enter the body: do not dive, avoid swallowing water when swimming or playing water sports, do not allow animals bark at the water, and do not water gardens with bloom water. Allergy sufferers, young children and the elderly should be particularly careful.

To cope with the problem of water bloom, the first step is to find out and eliminate the cause – potential sources of nitrogen and phosphorus pollution. Subsequently, different measures can be taken to improve water quality, which should be chosen depending on the size of the water body, flow rate, as well as the intensity and nature of the bloom.

Lithuania’s bloom water bodies can be seen on an interactive map. You can also mark the water blooms you see yourself.

Mark bloom water body here: https://arcg.is/0jqvCn or

The map with bloom water bodies can be found here: https://arcg.is/1v5faT or

 

An additional competition for dissertation topics and supervisors in the fields of Biology, Physical Geography, Geology, Ecology and Environmental Science, and Zoology is offered at Nature Research Centre.

The following documents should be submitted for the competition:

1. dissertation topic application (applications vary depending on the field of science (Biology and Physical Geography have their own application forms)) signed by the head of the laboratory;
2. list of scientific publications and other activities of the potential supervisor;
3. application for participation in the competition.

Documents must be submitted to the Studies Department or by email studijos@gamtc.lt by 16 August. Dissertation topics must be in line with the Centre’s research trends.

The PhD supervisor must meet at least the requirements of the senior researcher. A scientist may supervise a maximum of five doctoral students at a time (including those on sabbatical leave).

In mid-May 2024, a pilot plantation of fast-growing poplar clones (40 different clones planted in total) was established at the NRC Field Research Station (Vilnius) in collaboration with scientists from the Natural Resources Research Institute (NRRI) at the University of Minnesota and specialists from UAB “Euromediena”. The plantation is testing 32 American (NRRI selected) clones of high-yielding poplar hybrids (Populus deltoides × P. maximow iczii; P. deltoides × P. nigra; P. deltoides × (P. trichocarpa × P. deltoides)), as well as 8 Swedish-bred clones of P. trichocarpa and hybrid clones of P. maximow ichii × P. trichocarp.

The plantation was established randomly in square ‘blocks’, each with 9 poplars of the same clone (3 x 3 plants per ‘block’; row to row spacing 4.0 m). The poplars were planted in three replications of clonal (‘block’) sets in order to control the effect of slightly varying soil conditions on tree growth performance. A total of 1080 poplars were planted on an area of approximately 2 ha; the plantation is surrounded by a single row of untested clones of poplars of the same origin, forming a buffer zone to reduce the adverse effects of environmental conditions.

This plantation is a unique, carefully introduced and responsibly managed object which is open to research by NRC scientists. Under a contract with the University of Minnesota, the poplar plantation will be used for annual monitoring of tree growth (biometric measurements, viability, phytosanitary assessment) and for a wide range of studies – from plant physiology to the overall health of the newly formed ecosystem. All are welcome to take advantage of this new opportunity!

For more information about the plantation and its research prospects please contact Dr Vaidotas Lygis (NRC Laboratory of Plant Pathology), e-mail: vaidotas.lygis@gamtc.lt .

We are delighted to share the news that the Laboratory of Chemical and Behavioural Ecology of the Nature Research Centre actively participated at the conference of The International Society of Chemical Ecology in Prague!

Five poster presentations were prepared and presented by our team:
– Laima Blažytė-Čereškienė,
– Rasa Čepulytė,
– Sandra Radžiutė,
– PhD students Deimantė Tiškevičiūtė and Gabrielė Bumbulytė.

Congratulations to PhD student Gabriele Bumbulytė, who was awarded the ISCE Student Travel Award for her outstanding scientific contribution to the conference.