Biodiversity Genomics Europe

Livrables

Species prioritisation for genome sequencing

Priority lists of species selected for sampling in WP5 and WP12 based on a gap analysis of available reference genomes for European biodiversity and a feasibility evaluation, serves as guideline for general prioritisation in genome sequencing consortia.

Metadata collection standards

Produce standard metadata collection sheets to be used by participants in the Project.

Biobanking standards

Definition of biobanking standards and guidelines for the Project, with option for central biobank storage.

SOPs karyotyping, genome size, cell culturing

SOPs for karyotyping, genome size estimation and cell culturing and maintenance of frozen archives.

Genome assembly/quality control tools

State-of-the-art genome assembly and quality control tools packaged in openly accessible computational workflows for use by in-Project partners and the wider genomics community.

Aquatic field sampling

Report documenting samples collected for reference library barcoding and eDNA samples collected from marine ports for biomonitoring.

Instance of BOLD Europe

Set-up an operational instance of BOLD in Europe.

Prioritisation guidelines for the wider community

This report will detail plans that guide species selection for the duration of the project and other consortia in the wider biodiversity genomics (BioGenomes) community.

Material for genome sequencing critical European biodiversity

150-200 species submitted to sequencing centres, vouchered in biobanks and museums and metadata completed.

BOLD Europe design study

A consensus report on the future architecture and implementation steps of the BOLD Europe instance.

Material for genome sequencing European biodiversity hotspots

150-200 species (providing ca. 200Gbp genome assembly span, further material for future extension) submitted to sequencing centres, vouchered in biobanks and museums and metadata completed.

Terrestrial field sampling

Report documenting the sampling for barcoding and metabarcoding, proposing methodological guidelines for standardisation of field sampling for biomonitoring of terrestrial habitats using DNA metabarcoding.

Population-level sample collection

Report summarising all population-level ollinator sampling efforts and delivered samples.

Online Barcode Information Portal

Full release of content-rich online platform providing a nexus for the DNA barcoding community in Europe.

Publications

The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered

Auteurs: Kessy Abarenkov, R Henrik Nilsson, Karl-Henrik Larsson, Andy F S Taylor, Tom W May, Tobias Guldberg Frøslev, Julia Pawlowska, Björn Lindahl, Kadri Põldmaa, Camille Truong, Duong Vu, Tsuyoshi Hosoya, Tuula Niskanen, Timo Piirmann, Filipp Ivanov, Allan Zirk
Publié dans: Nucleic Acids Research, Numéro 52, 2023, ISSN 1362-4962
Éditeur: Nucleic Acids Research
DOI: 10.1093/nar/gkad1039

Building a Portuguese coalition for biodiversity genomics

Auteurs: João P. Marques, Paulo C. Alves, Isabel R. Amorim, Ricardo J. Lopes, Monica Moura, Eugene Myers, Manuela Sim-sim, Carla Sousa-Santos, M. Judite Alves, Paulo A. V. Borges, Thomas Brown, Miguel Carneiro, Carlos Carrapato, Luís M. P. Ceríaco, Claúdio Ciofi, Luís P. da Silva, Genevieve Diedericks, Maria Angela Diroma, Liliana Farelo, Giulio Formenti, Fátima Gil, Miguel Grilo, Alessio Iannucci, Henrique G. Leitão, Cristina Máguas, Ann M. Mc Cartney, Sofia L. Mendes, João M. Moreno, Marco Morselli, Alice Mouton, Chiara Natali, Fernando Pereira, Rúben M. C. Rego, Roberto Resendes, Guilherme Roxo, Hannes Svardal, Helena Trindade, Sara Vicente, Sylke Winkler, Marcela Alvarenga, Andreia J. Amaral, Agostinho Antunes, Paula F. Campos, Adelino V. M. Canário, Rita Castilho, L. Filipe C. Castro, Angelica Crottini, Mónica V. Cunha, Gonçalo Espregueira Themudo, Pedro J. Esteves, Rui Faria, Carlos Rodríguez Fernandes, Jean-Baptiste Ledoux, Bruno Louro, Sara Magalhaes, Octávio S. Paulo, Gareth Pearson, João Pimenta, Francisco Pina-Martins, Teresa L. Santos, Ester Serrão, José Melo-Ferreira, Vítor C. Sousa
Publié dans: npj Biodiversity, Numéro 3, 2024, ISSN 2731-4243
Éditeur: Springer Science and Business Media LLC
DOI: 10.1038/S44185-024-00061-7

ERGA-BGE genome of Acomys minous (Bate, 1906): the Crete spiny mouse, endemic to the island of Crete, Greece

Auteurs: Petros Lymberakis, Danae Karakasi, Manolis Papadimitrakis, Rita Monteiro, Astrid Böhne, Rosa Fernández, Nuria Escudero, Jean-Marc Aury, Alice Moussy, Corinne Cruaud, Karine Labadie, Sophie Mangenot, Caroline Belser, Lola Demirdjian, Swati Sinha, Leanne Haggerty, Fergal Martin, Patrick Wincker, Pedro H. Oliveira, Tom Brown
Publié dans: 2025
Éditeur: Pensoft Publishers
DOI: 10.3897/ARPHAPREPRINTS.E153920

ERGA-BGE Reference Genome of the Northern chamois (Rupicapra rupicapra): Europe’s most abundant mountain ungulate

Auteurs: Elena Buzan, Aja Bončina, Boštjan Pokorny, Nuria Escudero, Rosa Fernández, Astrid Böhne, Rita Monteiro, Marta Gut, Francisco Câmara Ferreira, Fernando Cruz, Jèssica Gómez-Garrido, Tyler S. Alioto, Leanne Haggerty, Fergal Martin, Diego De Panis
Publié dans: 2024
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.11.20.624344

Taxonomic position of Tetrops peterkai Skořepa, 2020 (Сoleoptera: Сerambycidae) and its cryptic distribution.

Auteurs: Zamoroka, A., & Zinenko, O.
Publié dans: Journal of Vasyl Stefanyk Precarpathian National University. Biology,, Numéro 11, 2024, ISSN 2413-2349
Éditeur: Vasyl Stefanyk Precarpathian National University
DOI: 10.15330/JPNUBIO.11.6-19

Ensembl 2025

Auteurs: Sarah C Dyer, Olanrewaju Austine-Orimoloye, Andrey G Azov, Matthieu Barba, If Barnes, Vianey Paola Barrera-Enriquez, Arne Becker, Ruth Bennett, Martin Beracochea, Andrew Berry, Jyothish Bhai, Simarpreet Kaur Bhurji, Sanjay Boddu, Paulo R Branco Lins, Lucy Brooks, Shashank Budhanuru Ramaraju, Lahcen I Campbell, Manuel Carbajo Martinez, Mehrnaz Charkhchi, Lucas A Cortes, Claire Davidson, Sukanya Denni, Kamalkumar Dodiya, Sarah Donaldson, Bilal El Houdaigui, Tamara El Naboulsi, Oluwadamilare Falola, Reham Fatima, Thiago Genez, Jose Gonzalez Martinez, Tatiana Gurbich, Matthew Hardy, Zoe Hollis, Toby Hunt, Mike Kay, Vinay Kaykala, Diana Lemos, Disha Lodha, Nourhen Mathlouthi, Gabriela Alejandra Merino, Ryan Merritt, Louisse Paola Mirabueno, Aleena Mushtaq, Syed Nakib Hossain, José G Pérez-Silva, Malcolm Perry, Ivana Piližota, Daniel Poppleton, Irina Prosovetskaia, Shriya Raj, Ahamed Imran Abdul Salam, Shradha Saraf, Nuno Saraiva-Agostinho, Swati Sinha, Botond Sipos, Vasily Sitnik, Emily Steed, Marie-Marthe Suner, Likhitha Surapaneni, Kyösti Sutinen, Francesca Floriana Tricomi, Ian Tsang, David Urbina-Gómez, Andres Veidenberg, Thomas A Walsh, Natalie L Willhoft, Jamie Allen, Jorge Alvarez-Jarreta, Marc Chakiachvili, Jitender Cheema, Jorge Batista da Rocha, Nishadi H De Silva, Stefano Giorgetti, Leanne Haggerty, Garth R Ilsley, Jon Keatley, Jane E Loveland, Benjamin Moore, Jonathan M Mudge, Guy Naamati, John Tate, Stephen J Trevanion, Andrea Winterbottom, Bethany Flint, Adam Frankish, Sarah E Hunt, Robert D Finn, Mallory A Freeberg, Peter W Harrison, Fergal J Martin, Andrew D Yates
Publié dans: Nucleic Acids Research, Numéro 53, 2025, ISSN 0305-1048
Éditeur: Oxford University Press (OUP)
DOI: 10.1093/NAR/GKAE1071

The role of community science in DNA-based biodiversity monitoring

Auteurs: Corrales, C., Bacela-Spychalska, K., Buzan, E., Ekrem, T., Ferreira, S., Goodall-Copestake, W., van Ommen Kloeke, E., Hollingsworth, P., Bourlat, S. J.
Publié dans: Molecular Ecology (in review), 2025
Éditeur: NA
DOI: 10.22541/au.174238571.18077669/v1

Contextualising samples: Supporting reference genomes of European biodiversity through sample and associated metadata collection

Auteurs: Astrid Böhne, Rosa Fernández, Jennifer A. Leonard, Ann M. McCartney, Seanna McTaggart, José Melo-Ferreira, Rita Monteiro, Rebekah A. Oomen, Olga Vinnere Pettersson, Torsten H. Struck
Publié dans: Contextualising samples: Supporting reference genomes of European biodiversity through sample and associated metadata collection, 2024, ISSN 2692-8205
Éditeur: npj Biodiversity
DOI: 10.1038/S44185-024-00053-7

ERGA-BGE genome of Valencia hispanica (Valenciennes, 1826): a critically endangered Iberian toothcarp

Auteurs: Marc Ventura, Nati Franch, Rosa Fernández, Javier Palma-Guerrero, Astrid Böhne, Rita Monteiro, Laura Aguilera, Marta Gut, Tyler S Alioto, Francisco Câmara Ferreira, Fernando Cruz, Jèssica Gómez-Garrido, Leanne Haggerty, Fergal Martin, Tom Brown
Publié dans: 2025
Éditeur: Pensoft Publishers
DOI: 10.3897/ARPHAPREPRINTS.E152862

ERGA-BGE genome of Noah`s Ark shell (Arca noae Linnaeus, 1758), a Mediterranean bivalve species

Auteurs: Katerina Vasileiadou, Tereza Manousaki, Thanos Dailianis, Grigorios Skouradakis, Emmanouela Vernadou, Danae Karakasi, Astrid Böhne, Rita Monteiro, Rosa Fernández, Nuria Escudero, Genoscope Sequencing Team, Alice Moussy, Corinne Cruaud, Karine Labadie, Lola Demirdjian, Emilie Téodori, Simone Duprat, Patrick Wincker, Pedro H Oliveira, Jean-Marc Aury, Leanne Haggerty, Swati Sinha, Fergal Martin, Chiara Bortoluzzi
Publié dans: 2025
Éditeur: Pensoft Publishers
DOI: 10.3897/ARPHAPREPRINTS.E154439

ERGA-BGE Reference Genome of the Striped Field Mouse (Apodemus agrarius), a Widespread and Abundant Species in Central and Eastern Europe

Auteurs: Franc Janžekovič, Elena Buzan, Aja Bončina, Nuria Escudero, Rosa Fernández, Astrid Böhne, Rita Monteiro, Laura Aguilera, Marta Gut, Francisco Câmara Ferreira, Fernando Cruz, Jèssica Gómez-Garrido, Tyler Alioto, Leanne Haggerty, Fergal Martin, Diego De Pan
Publié dans: 2025
Éditeur: ARPHA Preprints
DOI: 10.3897/ARPHAPREPRINTS.E154773

Ensembl 2024

Auteurs: Peter W Harrison et. al.
Publié dans: Nucleic Acids Research, 2023, ISSN 1362-4962
Éditeur: Oxford University Press
DOI: 10.1093/NAR/GKAD1049

ERGA-BGE genome ofCoenonympha oedippus: an IUCN endangered European butterfly species occurring in two ecotypes

Auteurs: Tatjana Čelik, Tjaša Lokovšek, Elena Bužan, Astrid Böhne, Rita Monteiro, Rosa Fernández, Nuria Escudero, Marta Gut, Laura Aguilera, Francisco Câmara Ferreira, Fernando Cruz, Jèssica Gómez-Garrido, Tyler S. Alioto, Chiara Bortoluzzi
Publié dans: 2025
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.02.10.637396

ERGA-BGE genome ofErebia palaricaChapman, 1905: a montane butterfly endemic to North-West Iberia

Auteurs: Marta Vila, Laura Torrado-Blanco, Nils Ryrholm, David Romero-Pedreira, María Conejero, Astrid Böhne, Rita Monteiro, Thomas Marcussen, Rebekah Oomen, Torsten Hugo Struck, Laura Aguilera, Marta Gut, Francisco Câmara Ferreira, Fernando Cruz Rodriguez, Jèssica Gómez-Garrido, Tyler S. Alioto, Chiara Bortoluzzi
Publié dans: 2025
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.01.08.631636

A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses

Auteurs: Ali Hakimzadeh, Alejandro Abdala Asbun, Davide Albanese, Maria Bernard, Dominik Buchner, Benjamin Callahan, J. Gregory Caporaso, Emily Curd, Christophe Djemiel, Mikael Brandström Durling, Vasco Elbrecht, Zachary Gold, Hyun S. Gweon, Mehrdad Hajibabaei, Falk Hildebrand, Vladimir Mikryukov, Eric Normandeau, Ezgi Özkurt, Jonathan M. Palmer, Géraldine Pascal, Teresita M. Porter, Daniel Straub, Martti Vasar, Tomáš Větrovský, Haris Zafeiropoulos, Sten Anslan
Publié dans: Molecular Ecology Resources, Numéro 24, 2024, ISSN 1755-098X
Éditeur: Wiley
DOI: 10.1111/1755-0998.13847

Molecular phylogeny reveals three new water mite species of the genus Teutonia Koenike, 1889, from Portugal (Acari, Hydrachnidia, Teutoniidae)

Auteurs: Vladimir Pešić, Ekaterina S. Konopleva, Alessio Iannucci, Sónia Ferreira, Elisabeth Stur
Publié dans: Systematic and Applied Acarology, 2025, ISSN 2056-6069
Éditeur: Systematic and Applied Acarology Society
DOI: 10.11158/SAA.30.2.14

Under pressure: the Critically Endangered common hamster in Hungary reached an all-time demographic low in 2024

Auteurs: Lajos Szatmári, Gábor Sramkó, Virág Nyíri, Tamás Cserkész
Publié dans: Oryx, Numéro 58, 2024, ISSN 0030-6053
Éditeur: Cambridge University Press (CUP)
DOI: 10.1017/S003060532400070X

The InBIO Barcoding Initiative Database: DNA barcodes of Iberian Bees

Auteurs: Wood T, Gaspar H, Divelec RL, Penado A, Silva TL, Mata V, Veríssimo J, Michez D, Castro S, Loureiro J, Beja P, Ferreira S
Publié dans: Biodiversity Data Journal, 2024, ISSN 1314-2828
Éditeur: 10.3897/BDJ.12.e117172
DOI: 10.3897/BDJ.12.E117172

Delimiting Species—Prospects and Challenges for <scp>DNA</scp> Barcoding

Auteurs: Brent C. Emerson
Publié dans: Molecular Ecology, Numéro 34, 2025, ISSN 0962-1083
Éditeur: Wiley
DOI: 10.1111/MEC.17677

DNA barcode library of Portuguese water mites, with the descriptions of two new species (Acari, Hydrachnidia)

Auteurs: Vladimir Pešić, Andrzej Zawal, Sónia Ferreira, Laura Benitez-Bosco, Ana Cruz-Oliveira, Dinis Girão, Adriana Padilha, Paolo Turaccio, Samantha Rossini, Lorenzo Ballini, Giorgia Staffoni, Sara Fratini, Claudio Ciofi, Alessio Iannucci, Torbjørn Ekrem, Elisabeth Stur
Publié dans: ZooKeys, Numéro 1217, 2024, ISSN 1313-2970
Éditeur: Pensoft Publishers
DOI: 10.3897/ZOOKEYS.1217.131730

New records of aturid water mites from Portugal, with the integrative description of one new species (Acari, Hydrachnidia, Aturidae)

Auteurs: Vladimir Pešić, Harry Smit, Dinis Girão, Alessio Iannucci, Elisabeth Stur, Sónia Ferreira
Publié dans: Ecologica Montenegrina, Numéro 80, 2024, ISSN 2336-9744
Éditeur: Institute for Biodiversity and Ecology
DOI: 10.37828/EM.2024.80.19

ERGA-BGE genome of the Spanish Moon MothGraellsia isabellaeGraells, 1849: a nocturnal lepidopteran protected by the Habitats Directive

Auteurs: Marta Vila, Neus Marí-Mena, Roger Vila, Ana Riesgo, Daniel García-Souto, Carlos Lopez-Vaamonde, Astrid Böhne, Rita Monteiro, Thomas Marcussen, Rebekah Oomen, Torsten Hugo Struck, Marta Gut, Laura Aguilera, Francisco Câmara Ferreira, Fernando Cruz Rodriguez, Jèssica Gómez-Garrido, Tyler S. Alioto, Chiara Bortoluzzi
Publié dans: 2025
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.01.08.631683

How Fish Population Genomics Can Promote Sustainable Fisheries: A Road Map

Auteurs: Andersson, L., Bekkevold, D., Berg, F., Farrell, E.D., Felkel, S., Ferreira, M., Fuentes-Pardo, A.P., Goodall, J., Pettersson, M.
Publié dans: Annual Review in Animal Biosciences, 2024, ISSN 2165-8102
Éditeur: Annual Reviews Inc.
DOI: 10.1146/ANNUREV-ANIMAL-021122-102933

ERGA-BGE genome of Cheirolophus tagananensis: an IUCN endangered shrub endemic to the Canary Islands

Auteurs: Jaume Pellicer, Teresa Garnatje, Daniel Vitales, Oriane Hidalgo, Joan Valles, Alfredo Garcia-Fernandez, Arnoldo Santos-Guerra, Astrid Bohne, Rita Monteiro, Rosa Fernandez, Nuria Escudero, null null, null null, null null, Abitha Thomas, Benjamin Jackson, Jonathan MD Wood, Kerstin Howe, Mark Blaxter, Shane McCarthy, Chiara Bortoluzzi
Publié dans: 2025
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.01.24.634661

The InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of cuckoo wasps, with the description of new species from the Iberian Peninsula (Hymenoptera, Chrysididae)

Auteurs: Paolo Rosa, Thomas Wood, Teresa Luísa L. Silva, Joana Veríssimo, Vanessa A. Mata, Denis Michez, Pedro Beja, Sónia Ferreira
Publié dans: The InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of cuckoo wasps, with the description of new species from the Iberian Peninsula (Hymenoptera, Chrysididae), 2023, ISSN 1314-2828
Éditeur: Biodiversity Data Journal
DOI: 10.3897/BDJ.8.e55137FreePMCarticle

ERGA-BGE genome of Pinctada radiata (Leach, 1814): one of the first Lessepsian migrants

Auteurs: Katerina Vasileiadou, Tereza Manousaki, Thanos Dailianis, Grigorios Skouradakis, Emmanouela Vernadou, Danae Karakasi, Astrid Böhne, Rita Monteiro, Rosa Fernández, Nuria Escudero, Genoscope Sequencing Team, Alice Moussy, Corinne Cruaud, Karine Labadie, Lola Demirdjian, Benjamin Istace, Arnaud Couloux, Patrick Wincker, Pedro H Oliveira, Jean-Marc Aury, Leanne Haggerty, Swati Sinha, Fergal Martin, Chiara Bortoluzzi
Publié dans: 2025
Éditeur: Pensoft Publishers
DOI: 10.3897/ARPHAPREPRINTS.E154462

ERGA-BGE genome ofValencia hispanica(Valenciennes, 1826): a critically endangered Iberian toothcarp

Auteurs: Marc Ventura, Nati Franch, Rosa Fernández, Javier Palma-Guerrero, Astrid Böhne, Rita Monteiro, Laura Aguilera, Marta Gut, Tyler S. Alioto, Francisco Câmara Ferreira, Fernando Cruz, Jèssica Gómez-Garrido, Leanne Haggerty, Fergal Martin, Thomas Brown
Publié dans: 2024
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.07.31.604920

Harmonising genomics research excellence and stakeholder needs in conservation management

Auteurs: Elena Buzan, Christian de Guttry, Chiara Bortoluzzi, Nathaniel Street, Kay Lucek, Anna Rosling, Lino Ometto, Alice Mouton, Luísa Marins, María José Ruiz-López, José Melo-Ferreira, Elisabet Ottosson, Camila Mazzoni, Robert Waterhouse
Publié dans: 2024
Éditeur: Authorea, Inc.
DOI: 10.22541/au.172510123.38206942/v1

ERGA-BGE genome ofStigmatoteuthis arcturiRobson, 1948: the jewelled squid

Auteurs: Fernando Ángel Fernández-Álvarez, Ainhoa Bernal-Bajo, Nuria Escudero, María Conejero, Ana Riesgo, Rosa Fernández, Rita Monteiro, Astrid Böhne, Laura Aguilera, Marta Gut, Tyler S. Alioto, Francisco Câmara Ferreira, Fernando Cruz, Jèssica Gómez-Garrido, Tom Brown
Publié dans: 2025
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.01.13.632676

ERGA-BGE genome ofAndrosace saussureiDentant, Lavergne, F. C. Boucher & S. Ibanez, a recently described plant from the rooftops of Europe

Auteurs: Sébastien Lavergne, Alexy Rosa, Chuan Peng, Rita Monteiro, Astrid Böhne, Thomas Marcussen, Torsten Struck, Rebekah A. Oomen, null null, Alice Moussy, Corinne Cruaud, Karine Labadie, Emilie Téodori, Lola Demirdjian, Patrick Wincker, Pedro H. Oliveira, Jean-Marc Aury, Tom Brown
Publié dans: 2025
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.01.21.634019

ERGA-BGE Reference Genome ofLoboptera subterranea: a cave adapted cockroach endemic to the Canary Islands

Auteurs: Heriberto López, Pedro Oromí, Xavier Belles, Guillem Ylla, Nuria Escudero, Rosa Fernández, Astrid Böhne, Marta Gut, Laura Aguilera, Tyler Alioto, Francisco Câmara Ferreira, Jèssica Gómez-Garrido, Fernando Cruz, Rita Monteiro
Publié dans: 2025, ISSN 2692-8205
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.02.06.636782

Genome Annotation and Other Post-Assembly Workflows for the Tree of Life

Auteurs: Tom Brown, Kathleen A. Collier, Fernando Cruz, Anestis Gkanogiannis, Sagane Joye-Dind, Yannis Nevers, Stepan Saenko, Tyler Alioto, Anthony Bretaudeau, Michael Charleston, Phuong Duy Doan, Christoph Hahn, Thomas W. Harrop, Katie E Herron, Fredrick Kebaso,
Publié dans: BioHackrXiv Preprints, 2024
Éditeur: BioHackrXiv.org
DOI: 10.37044/OSF.IO/FY49G

Livrables

Publications

Partager cette page Partager cette page sur les réseaux sociaux

Télécharger Télécharger le contenu de la page