Biodiversity - Biodiversity Genomics Europe (BGE)

• Manzano-Marín, Alejandro; Böhne, Astrid; Monteiro, Rita; Marcussen, Thomas; Struck, Torsten H. & Oomen, Rebekah Alice [Show all 15 contributors for this article] (2026). ERGA-BGE reference genome of Hirudo verbana, a once neglected freshwater haematophagous European medicinal leech. Open Research Europe. 5. doi: 10.12688/openreseurope.21672.2. Full text in Research Archive Show summary

  Hirudo verbana Carena, 1820, commonly known as the southern medicinal leech, is one of several European medicinal leeches, whose full diversity has just recently started to be uncovered. Historically, it has been widely used as a medicinal leech and for centuries it was treated erroneously under the specific name of Hirudo medicinalis L. 1758. Recent molecular and taxonomic analyses have revealed subspecific diversity within the morphospecies H. verbana . Hirudo verbana is a blood-feeding species sucking blood from amphibians, fish, and mammals. It occupies freshwater habitats, typically shallow ponds and lakes. Studies show that this leech species has a "naturally limited microbiome", suggesting it may serve as a powerful model system for the study of gut microbiota. We expect this chromosome-level assembly of H. verbana to serve as a high-quality genomic resource for this most famous leech genus and to serve as a foundation to the study of the diversification and biodiversity of European medicinal leeches, as well as their gut-associated symbionts. The genome of H. verbana was assembled into two haplotypes through a phased assembly approach; however, only the primary haplotype was designated as the reference genome for annotation and downstream analyses. The entirety of the primary haplotype was assembled into 14 contiguous chromosomal pseudomolecules, including the mitogenome. This chromosome-level assembly encompasses 0.18 Gb, composed of 277 contigs and 27 scaffolds, with contig and scaffold N50 values of 1.3 Mb and 13.4 Mb, respectively.

• Lavergne, Sébastien; Rosa, Zoé; Peng, Chuan; Monteiro, Rita; Böhne, Astrid & Marcussen, Thomas [Show all 20 contributors for this article] (2026). ERGA-BGE genome of Androsace saussurei Dentant, Lavergne, F. C. Boucher & S. Ibanez, a recently described plant from the rooftops of Europe. Open Research Europe. 5. doi: 10.12688/openreseurope.21922.1. Full text in Research Archive Show summary

  The reference genome of Androsace saussurei (Ericales: Primulaceae: Primuloideae) provides a valuable resource for understanding the mechanisms of plant adaptations to the highest altitudes where flowering plants can thrive and the speciation mechanisms of plants dwelling on high alpine sky islands. The entirety of the genome sequence was assembled into 20 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 413 Mb, composed of 253 contigs and 101 scaffolds, with contig and scaffold N50 values of 4.95 Mb and 21.2 Mb, respectively.

• Tomasello, Salvatore; Manzo, Eleonora; Monteiro, Rita; Böhne, Astrid; Marcussen, Thomas & Struck, Torsten H [Show all 19 contributors for this article] (2026). ERGA-BGE genome of Xanthium orientale subsp. italicum (Moretti) Greuter. A plant of American origin, now widespread and, in some cases, invasive in Europe. Open Research Europe. 5, p. 367–367. doi: 10.12688/openreseurope.21891.1. Full text in Research Archive Show summary

  The Xanthium orientale subsp. italicum (Asterales: Asteraceae: Asteroideae) reference genome offers a valuable resource for understanding the genetic basis of invasiveness and fitness differences among congeneric species. The entirety of the genome sequence was assembled into 18 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 2.26 Gb, composed of 46 contigs and 32 scaffolds, with contig and scaffold N50 values of 98.8 Mb and 124 Mb, respectively.

• Aguado-Ramsay, Pablo; Lara, Francisco; Draper, Isabel; Conejero, Maria; Böhne, Astrid & Monteiro, Rita [Show all 18 contributors for this article] (2026). ERGA-BGE reference genome of Lewinskya acuminata, a common epiphytic Mediterranean moss with disjunct populations in California and Ethiopia. Open Research Europe. 5. doi: 10.12688/openreseurope.21670.1. Full text in Research Archive Show summary

  The reference genome of Lewinskya acuminata (H. Philib.) F. Lara, Garilleti & Goffinet will enable phylogenomic, biogeographic, and evolutionary studies within the Orthotrichaceae and related bryophyte lineages at a depth previously inaccessible. This species of moss is among the most representative of the Mediterranean epiphytic communities and can be readily identified by its long-acuminate leaves, fusiform capsules with a vestigial exostome, a well-developed endostome of six broad segments, and a dark, puckered peristome mouth when dry. The entirety of the genome sequence was assembled into 6 contiguous chromosomal pseudomolecules, 1 mitochondrial genome, and 2 plastid genomes. This chromosome-level assembly encompasses 0.25 Gb, composed of 51 contigs and 13 scaffolds, with contig and scaffold N50 values of 11.5 Mb and 40.8 Mb, respectively.

• Faria, Rui; Vilela, Rocío Nieto; Lima, Fernando P; Monteiro, Rita; Böhne, Astrid & Marcussen, Thomas [Show all 18 contributors for this article] (2026). ERGA-BGE genome of Patella rustica Linnaeus, 1758: a resource to investigate responses to global warming in the intertidal. Open Research Europe. 5. doi: 10.12688/openreseurope.21608.2. Full text in Research Archive Show summary

  The reference genome of Patella rustica Linnaeus, 1758 will offer a unique opportunity to understand how intertidal organisms respond to the effects of global warming, contributing to improve our predictions about the impact of climate change on the maintenance and diversification of marine biodiversity. A total of 9 contiguous chromosomal pseudomolecules were assembled from the genome sequence. This chromosome-level assembly encompasses 719 Mb, composed of 157 contigs and 24 scaffolds, with contig and scaffold N50 values of 8.52 Mb and 83.6 Mb, respectively.

• Hausdorf, Bernhard; Tapia, Elicio; Monteiro, Rita; Böhne, Astrid; Marcussen, Thomas & Struck, Torsten H [Show all 10 contributors for this article] (2026). ERGA-BGE genome of Anisus vorticulus (Troschel, 1834): the Lesser Ramshorn Snail, an endangered freshwater snail protected under the EU's Habitats and Species Directive. Open Research Europe. 5. doi: 10.12688/openreseurope.20499.1. Full text in Research Archive Show summary

  We have generated a high-quality reference genome for Anisus vorticulus to support monitoring of the genetic diversity of populations of this declining freshwater species. The chromosome-level genome assembly encompasses 1.04 Gb, composed of 835 contigs and 77 scaffolds, with contig and scaffold N50 values of 2.35 Mb and 59.2 Mb, respectively. The genome was assembled into 18 chromosomal pseudomolecules.

• Lopes, Ricardo Jorge; Böhne, Astrid; Marcussen, Thomas; Oomen, Rebekah Alice; Struck, Torsten H & Aguilera, Laura [Show all 12 contributors for this article] (2026). ERGA-BGE reference genome of the Azores Bullfinch - Pyrrhula murina Godman, 1866: an IUCN Vulnerable Species endemic to a single island in the Azores Archipelago (Portugal). Open Research Europe. 5, p. 1–16. doi: 10.12688/openreseurope.20666.3. Full text in Research Archive Show summary

  The reference genome of Pyrrhula murina’s reference genome will substantially enhance the current monitoring of genetic diversity and population viability and will allow us to understand the effective population size trends throughout time and recent bottlenecks and population expansions. A total of 42 contiguous chromosomal pseudomolecules were assembled from the genome sequence, using ONT, HI-C and Illumina data. This chromosome-level assembly encompasses 1.2 Gb, composed of 65 contigs and 60 scaffolds, with contig and scaffold N50 values of 65 Mb and 76 Mb, respectively.

• Aurelle, Didier; Guillemain, Dorian; Zuberer, Frédéric; Malengros, Denys; Böhne, Astrid & Monteiro, Rita [Show all 19 contributors for this article] (2025). ERGA-BGE reference genome of Eunicella cavolini, an IUCN Near Threatened Gorgonian of the Mediterranean Sea. Open Research Europe. 5. doi: 10.12688/openreseurope.21514.1. Full text in Research Archive Show summary

  The Eunicella cavolini reference genome provides an important resource to study the adaptation of this species to different environments and anthropic pressures. This species is impacted by human activities, including climate change, and this reference genome will be useful to study the genomic evolution of this species. The entirety of the genome sequence was assembled into 17 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 0.49 Gb, composed of 159 contigs and 46 scaffolds, with contig and scaffold N50 values of 7.7 Mb and 51.1 Mb, respectively.

• Corrales, Carolina; Bacela‐Spychalska, Karolina; Buzan, Elena; Ekrem, Torbjørn; Ferreira, Sónia & Goodall‐Copestake, William [Show all 9 contributors for this article] (2025). The Role of Community Science in DNA‐Based Biodiversity Monitoring. Molecular Ecology. ISSN 0962-1083. 34(19). doi: 10.1111/mec.70100. Full text in Research Archive Show summary

  The mutual interest in nature by the general public and scientists has led to many collaborations, past and present. Community science shows great potential for monitoring species occurrences and distributions, especially in combination with scalable and (semi)‐automated methods such as DNA‐based monitoring, helping to obtain data from a broader geographic and temporal range than would be possible by the scientific community alone. Here, we present an overview of the complementarity between community science and DNA‐based biomonitoring through examples from ongoing projects. The involvement of hobby experts is particularly crucial for building up the necessary species reference databases that enable DNA‐based monitoring. Based on this overview, we identify some key points related to learning opportunities and participant recognition to maximise the success, impact and benefit of community participants in DNA‐based monitoring.

• Vila, Marta; Marí-Mena, Neus; Vila, Roger; Riesgo, Ana; García-Souto, Daniel & Lopez-Vaamonde, Carlos [Show all 20 contributors for this article] (2025). ERGA-BGE genome of the Spanish moon moth Actias isabellae Graells, 1849: a nocturnal lepidopteran protected by the Habitats Directive. Open Research Europe. 5. doi: 10.12688/openreseurope.20658.2. Full text in Research Archive Show summary

  High-quality reference genomes are critical resources for understanding biodiversity and supporting conservation efforts. We present the chromosome-level assembly of the Spanish moon moth, Actias isabellae (Graells, 1849), a nocturnal lepidopteran protected under the EU Habitats Directive. The assembly spans 0.56 Gb across 31 pseudomolecules, including the Z chromosome, with a contig N50 of 18.9 Mb and a scaffold N50 of 20.4 Mb. The mitochondrial genome was also assembled into a 15,247 bp circular sequence. Annotation identified 11,805 protein-coding genes and 2,238 non-coding genes, with a BUSCO completeness of over 94%. Notably, no W chromosome was detected, suggesting a ZZ/Z0 sex determination system. This reference genome provides an essential foundation for studying sex chromosome evolution in Lepidoptera and enables advanced population genomics monitoring of this protected species. More broadly, it contributes to ongoing efforts within the European Reference Genome Atlas and the Earth BioGenome Project to harness genomics for biodiversity conservation.

• Pešić, Vladimir; Konopleva, Ekaterina S.; Iannucci, Alessio; Ferreira, Sónia & Stur, Elisabeth (2025). Molecular phylogeny reveals three new water mite species of the genus Teutonia Koenike, 1889, from Portugal (Acari, Hydrachnidia, Teutoniidae). Systematic and Applied Acarology. ISSN 1362-1971. 30, p. 381–401. doi: 10.11158/saa.30.2.14. Full text in Research Archive
• Pešić, Vladimir; Smit, Harry; Girão, Dinis; Iannucci, Alessio; Stur, Elisabeth & Ferreira, Sónia (2024). New records of aturid water mites from Portugal, with the integrative description of one new species (Acari, Hydrachnidia, Aturidae). Ecologica Montenegrina. ISSN 2337-0173. 80, p. 209–219. doi: 10.37828/em.2024.80.19. Full text in Research Archive Show summary

  In this paper, three species of the water mite family Aturidae collected in Portugal were identified using an integrative approach that combines morphology and DNA barcodes. Parabrachypoda lusitanica sp. nov. is described as new for science. Two species, Hexaxonopsis romijni (K. Viets, 1923) and Woolastookia rotundifrons (K. Viets, 1922) are reported for the first time for the water mite fauna of Portugal.

• Pešić, Vladimir; Zawal, Andrzej; Ferreira, Sónia; Benitez-Bosco, Laura; Cruz-Oliveira, Ana & Girão, Dinis [Show all 16 contributors for this article] (2024). DNA barcode library of Portuguese water mites, with the descriptions of two new species (Acari, Hydrachnidia). ZooKeys. ISSN 1313-2989. 1217, p. 119–171. doi: 10.3897/zookeys.1217.131730. Full text in Research Archive Show summary

  This study presents the first results from the analysis of water mites collected in Portugal as part of the Biodiversity Genomics Europe project. 307 COI DNA barcodes clustered into 75 BINs are provided, with 38 BINs being unique and deposited for the first time in the Barcode of Life Data Systems (BOLD). 65 species have been identified, of which 36 are new to the water mite fauna of Portugal. Two species, Torrenticola soniae Pešić, sp. nov. and T. elisabethae Pešić, sp. nov. (Torrenticolidae), are described as new to science. 47% of the water mite species currently known from Portugal now have reference barcodes in BOLD. High intraspecific distances were recorded for some species, suggesting the presence of cryptic diversity and species complexes that needs further study. Our results improve the DNA barcode reference database for Portuguese water mites, enhancing species identification accuracy and stimulating future investigation.

• Böhne, Astrid; Fernández, Rosa; Leonard, Jennifer A.; McCartney, Ann M.; McTaggart, Seanna & Melo-Ferreira, José [Show all 10 contributors for this article] (2024). Contextualising samples: supporting reference genomes of European biodiversity through sample and associated metadata collection. npj biodiversity. 3(1), p. 1–11. doi: 10.1038/s44185-024-00053-7. Full text in Research Archive Show summary

  The European Reference Genome Atlas (ERGA) consortium aims to generate a reference genome catalogue for all of Europe's eukaryotic biodiversity. The biological material underlying this mission, the specimens and their derived samples, are provided through ERGA’s pan-European network. To demonstrate the community’s capability and capacity to realise ERGA’s ambitious mission, the ERGA Pilot project was initiated. In support of the ERGA Pilot effort to generate reference genomes for European biodiversity, the ERGA Sampling and Sample Processing committee (SSP) was formed by volunteer experts from ERGA’s member base. SSP aims to aid participating researchers through (i) establishing standards for and collecting of sample/specimen metadata; (ii) prioritisation of species for genome sequencing; and (iii) development of taxon-specific collection guidelines including logistics support. SSP serves as the entry point for sample providers to the ERGA genomic resource production infrastructure and guarantees that ERGA’s high-quality standards are upheld throughout sample collection and processing. With the volume of researchers, projects, consortia, and organisations with interests in genomics resources expanding, this manuscript shares important experiences and lessons learned during the development of standardised operational procedures and sample provider support. The manuscript details our experiences in incorporating the FAIR and CARE principles, species prioritisation, and workflow development, which could be useful to individuals as well as other initiatives.

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• PEŠIĆ, VLADIMIR; BANKOWSKA, ALEKSANDRA; GOLDSCHMIDT, TOM; Hårsaker, Karstein; JOVANOVIĆ, MILICA & KAITETZIDOU, ELISAVET [Show all 21 contributors for this article] (2025). Checklist of water mites from the Balkan Peninsula: second supplement, new DNA barcodes and description of a new species. Magnolia Press. ISBN 9781779734426. 74 p. doi: 10.11646/zootaxa.5676.1.1. Full text in Research Archive Show summary

  Knowledge of the water mite fauna in the Balkans is still very heterogeneous and far from complete. A compilation of published data is considered the first step in creating an up-to-date comprehensive checklist of water mites of the Balkans. In this supplement, we list all species reported from the Balkans from November 2017 to date and provide an updated checklist of water mites that inhabit the Balkan countries. With the additions in this study, the number of water mite species inhabiting the Balkan Peninsula has increased to 426 species and subspecies. One species, Sperchon balcanicus Pešić, sp. nov. (Sperchontidae), is described as new to science. This study adds 299 new barcodes to the existing DNA barcode reference library that now includes 1032 COI DNA barcodes from the Balkans publicly available through the Barcode of Life Data Systems (BOLD). Still, only one-third of the currently known species of water mites in the Balkans now have reference barcodes in BOLD, indicating the need for future integrative research on the morphological and genetic diversity of Balkan water mites.  

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• Struck, Torsten H (2025). Door 12: Is AI the solution to overcome the challenges in sequencing genomes? doi: https:/blog.annelida.de/2025/12/12/door-12-ai-genomes/. Full text in Research Archive
• Ekrem, Torbjørn; Stur, Elisabeth & Aspaas, Aina Mærk (2025). Biologisk mangfold, DNA og insekter. Full text in Research Archive
• Ekrem, Torbjørn; Hartop, Emily Anne & Aspaas, Aina Mærk (2025). Finn arten med DNA-strekkoding. Full text in Research Archive
• Struck, Torsten H (2025). Successfully served the European biodiversity genomic community – Blogs of the CEG research group. doi: https:/blog.annelida.de/2025/03/14/served-biodiversity-community/. Full text in Research Archive
• Struck, Torsten H (2024). Genomics in Norwegian and European biodiversity research. Full text in Research Archive
• Struck, Torsten H (2024). Species selection for large-scale genome projects – an automated process based on explicityly bottom-up defined criteria. Full text in Research Archive
• Struck, Torsten H (2024). Better together: Scientists from 33 European countries join forces to generate reference genomes for the continent’s rich biodiversity. – Blogs of the CEG research group. doi: https:/blog.annelida.de/2024/09/17/erga-better-together/. Full text in Research Archive
• Struck, Torsten H (2024). CEG with an even stronger commitment to Norwegian Biosystematics – Blogs of the CEG research group. doi: https:/blog.annelida.de/2024/11/05/ceg-norwegian-biosystematics/. Full text in Research Archive
• Struck, Torsten H (2024). Door 1: Quo vadis biodiversity genomic research? – Blogs of the CEG research group. doi: https:/blog.annelida.de/2024/12/01/quo-vadis/. Full text in Research Archive
• Struck, Torsten H (2024). CEG with a strong commitment to Norwegian Biodiversity Genomics – Blogs of the CEG research group. doi: https:/blog.annelida.de/2024/04/15/ceg-biodiversity-genomics/. Full text in Research Archive
• Stur, Elisabeth; Ekrem, Torbjørn; Sivell, Duncan; Cristóvão, Joana, P.; Powell, Owain & Price, Benjamin, W. (2024). Mining for the gold standard: Genome skimming of historical Chironomidae (Diptera) types to solve inconsistencies in the barcode reference library. Full text in Research Archive Show summary

  Introduction The family Chironomidae is one of the most species rich groups of Diptera with more than 3600 described species worldwide. Additionally, many species remain unknown to science, and DNA barcode data gathered over the last 15 years have revealed cryptic species in numerous genera. In this setting, DNA barcoding of available primary and other types is particularly valuable to clarify which genetic cluster should be correctly associated with a species name. However, modern Chironomidae primary types are typically cleared and slide mounted in Euparal or Canada balsam, making DNA unavailable for analysis. Some older, historical collections are exceptions, such as the pinned type specimens described by Francis Walker, Frederick W. Edwards and Paul Freeman present in the Natural History Museum, London (NHMUK). Methods We sampled 183 specimens of 182 species from the NHMUK type collection, photographed and dissected off wings from small specimens to prevent them being damaged during whole-body lysis. DNA was extracted from the remaining parts of the specimens (or legs if sufficiently large) using a protocol developed for historical specimens in which DNA content is low and fragmented. The DNA was then subject to low coverage shotgun sequencing (genome skimming) on Illumina NovaSeq XPlus PE150 lanes following protocols developed within the BGE project. Results We will present results from these analyses, focusing on success rates of the actual genome skimming and give examples of how inconsistencies in the barcode reference library could be solved by providing DNA barcodes from historical Chironomidae types.

• Ekrem, Torbjørn; Stavnes, Lars Olav & Karlsen, Morten Børre (2024). NTNU og insektfeller. [Radio]. NRK P1 God ettermiddag Trøndelag. Full text in Research Archive
• Ekrem, Torbjørn; Stavnes, Lars Olav & Karlsen, Morten Børre (2024). Insektfeller. [TV]. NRK Norge i dag. Full text in Research Archive
• Struck, Torsten H (2024). Tror de kan gjen­opplive mammuten i 2028: – Nesten motsatt av «Jurassic Park». [Journal]. NRK. Full text in Research Archive

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