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The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics [PDF]
npj Biodiversity, 2023 A genomic database of all Earth’s eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available.Ann M. Mc Cartney, Giulio Formenti, Alice Mouton, Diego De Panis, Luísa S. Marins, Henrique G. Leitão, Genevieve Diedericks, Joseph Kirangwa, Marco Morselli, Judit Salces-Ortiz, Nuria Escudero, Alessio Iannucci, Chiara Natali, Hannes Svardal, Rosa Fernández, Tim De Pooter, Geert Joris, Mojca Strazisar, Jonathan M. D. Wood, Katie E. Herron, Ole Seehausen, Phillip C. Watts, Felix Shaw, Robert P. Davey, Alice Minotto, José M. Fernández, Astrid Böhne, Carla Alegria, Tyler Alioto, Paulo C. Alves, Isabel R. Amorim, Jean-Marc Aury, Niclas Backstrom, Petr Baldrian, Laima Baltrunaite, Endre Barta, Bertrand BedHom, Caroline Belser, Johannes Bergsten, Laurie Bertrand, Helena Bilandija, Mahesh Binzer-Panchal, Iliana Bista, Mark Blaxter, Paulo A. V. Borges, Guilherme Borges Dias, Mirte Bosse, Tom Brown, Rémy Bruggmann, Elena Buena-Atienza, Josephine Burgin, Elena Buzan, Alessia Cariani, Nicolas Casadei, Matteo Chiara, Sergio Chozas, Fedor Čiampor, Angelica Crottini, Corinne Cruaud, Fernando Cruz, Love Dalen, Alessio De Biase, Javier del Campo, Teo Delic, Alice B. Dennis, Martijn F. L. Derks, Maria Angela Diroma, Mihajla Djan, Simone Duprat, Klara Eleftheriadi, Philine G. D. Feulner, Jean-François Flot, Giobbe Forni, Bruno Fosso, Pascal Fournier, Christine Fournier-Chambrillon, Toni Gabaldon, Shilpa Garg, Carmela Gissi, Luca Giupponi, Jessica Gomez-Garrido, Josefa González, Miguel L. Grilo, Björn Grüning, Thomas Guerin, Nadege Guiglielmoni, Marta Gut, Marcel P. Haesler, Christoph Hahn, Balint Halpern, Peter W. Harrison, Julia Heintz, Maris Hindrikson, Jacob Höglund, Kerstin Howe, Graham M. Hughes, Benjamin Istace, Mark J. Cock, Franc Janžekovič, Zophonias O. Jonsson, Sagane Joye-Dind, Janne J. Koskimäki, Boris Krystufek, Justyna Kubacka, Heiner Kuhl, Szilvia Kusza, Karine Labadie, Meri Lähteenaro, Henrik Lantz, Anton Lavrinienko, Lucas Leclère, Ricardo Jorge Lopes, Ole Madsen, Ghislaine Magdelenat, Giulia Magoga, Tereza Manousaki, Tapio Mappes, Joao Pedro Marques, Gemma I. Martinez Redondo, Florian Maumus, Shane A. McCarthy, Hendrik-Jan Megens, Jose Melo-Ferreira, Sofia L. Mendes, Matteo Montagna, Joao Moreno, Mai-Britt Mosbech, Mónica Moura, Zuzana Musilova, Eugene Myers, Will J. Nash, Alexander Nater, Pamela Nicholson, Manuel Niell, Reindert Nijland, Benjamin Noel, Karin Noren, Pedro H. Oliveira, Remi-Andre Olsen, Lino Ometto, Rebekah A. Oomen, Stephan Ossowski, Vaidas Palinauskas, Snaebjorn Palsson, Jerome P. Panibe, Joana Pauperio, Martina Pavlek, Emilie Payen, Julia Pawlowska, Jaume Pellicer, Graziano Pesole, Joao Pimenta, Martin Pippel, Anna Maria Pirttilä, Nikos Poulakakis, Jeena Rajan, Rúben M.C. Rego, Roberto Resendes, Philipp Resl, Ana Riesgo, Patrik Rodin-Morch, Andre E. R. Soares, Carlos Rodriguez Fernandes, Maria M. Romeiras, Guilherme Roxo, Lukas Rüber, Maria Jose Ruiz-Lopez, Urmas Saarma, Luis P. da Silva, Manuela Sim-Sim, Lucile Soler, Vitor C. Sousa, Carla Sousa Santos, Alberto Spada, Milomir Stefanovic, Viktor Steger, Josefin Stiller, Matthias Stöck, Torsten H. Struck, Hiranya Sudasinghe, Riikka Tapanainen, Christian Tellgren-Roth, Helena Trindade, Yevhen Tukalenko, Ilenia Urso, Benoit Vacherie, Steven M. Van Belleghem, Kees Van Oers, Carlos Vargas-Chavez, Nevena Velickovic, Noel Vella, Adriana Vella, Cristiano Vernesi, Sara Vicente, Sara Villa, Olga Vinnere Pettersson, Filip A. M. Volckaert, Judit Voros, Patrick Wincker, Sylke Winkler, Claudio Ciofi, Robert M. Waterhouse, Camila J. Mazzoni +202 moredoaj +42 more sourcesAuthor Correction: The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics [PDF]
npj BiodiversityCorrection to: npj Biodiversityhttps://doi.org/10.1038/s44185-024-00054-6, published online 17 September 2024 In the orginial version of this Article, the wrong affiliation was given for Maria Angela Diroma. It should be Department of Biology, University of Florence, Sesto Fiorentino, Italy.Ann M. Mc Cartney, Giulio Formenti, Alice Mouton, Diego De Panis, Luísa S. Marins, Henrique G. Leitão, Genevieve Diedericks, Joseph Kirangwa, Marco Morselli, Judit Salces-Ortiz, Nuria Escudero, Alessio Iannucci, Chiara Natali, Hannes Svardal, Rosa Fernández, Tim De Pooter, Geert Joris, Mojca Strazisar, Jonathan M. D. Wood, Katie E. Herron, Ole Seehausen, Phillip C. Watts, Felix Shaw, Robert P. Davey, Alice Minotto, José M. Fernández, Astrid Böhne, Carla Alegria, Tyler Alioto, Paulo C. Alves, Isabel R. Amorim, Jean-Marc Aury, Niclas Backstrom, Petr Baldrian, Laima Baltrunaite, Endre Barta, Bertrand BedHom, Caroline Belser, Johannes Bergsten, Laurie Bertrand, Helena Bilandija, Mahesh Binzer-Panchal, Iliana Bista, Mark Blaxter, Paulo A. V. Borges, Guilherme Borges Dias, Mirte Bosse, Tom Brown, Rémy Bruggmann, Elena Buena-Atienza, Josephine Burgin, Elena Buzan, Alessia Cariani, Nicolas Casadei, Matteo Chiara, Sergio Chozas, Fedor Čiampor, Angelica Crottini, Corinne Cruaud, Fernando Cruz, Love Dalen, Alessio De Biase, Javier del Campo, Teo Delic, Alice B. Dennis, Martijn F. L. Derks, Maria Angela Diroma, Mihajla Djan, Simone Duprat, Klara Eleftheriadi, Philine G. D. Feulner, Jean-François Flot, Giobbe Forni, Bruno Fosso, Pascal Fournier, Christine Fournier-Chambrillon, Toni Gabaldon, Shilpa Garg, Carmela Gissi, Luca Giupponi, Jessica Gomez-Garrido, Josefa González, Miguel L. Grilo, Björn Grüning, Thomas Guerin, Nadege Guiglielmoni, Marta Gut, Marcel P. Haesler, Christoph Hahn, Balint Halpern, Peter W. Harrison, Julia Heintz, Maris Hindrikson, Jacob Höglund, Kerstin Howe, Graham M. Hughes, Benjamin Istace, Mark J. Cock, Franc Janžekovič, Zophonias O. Jonsson, Sagane Joye-Dind, Janne J. Koskimäki, Boris Krystufek, Justyna Kubacka, Heiner Kuhl, Szilvia Kusza, Karine Labadie, Meri Lähteenaro, Henrik Lantz, Anton Lavrinienko, Lucas Leclère, Ricardo Jorge Lopes, Ole Madsen, Ghislaine Magdelenat, Giulia Magoga, Tereza Manousaki, Tapio Mappes, Joao Pedro Marques, Gemma I. Martinez Redondo, Florian Maumus, Shane A. McCarthy, Hendrik-Jan Megens, Jose Melo-Ferreira, Sofia L. Mendes, Matteo Montagna, Joao Moreno, Mai-Britt Mosbech, Mónica Moura, Zuzana Musilova, Eugene Myers, Will J. Nash, Alexander Nater, Pamela Nicholson, Manuel Niell, Reindert Nijland, Benjamin Noel, Karin Noren, Pedro H. Oliveira, Remi-Andre Olsen, Lino Ometto, Rebekah A. Oomen, Stephan Ossowski, Vaidas Palinauskas, Snaebjorn Palsson, Jerome P. Panibe, Joana Pauperio, Martina Pavlek, Emilie Payen, Julia Pawlowska, Jaume Pellicer, Graziano Pesole, Joao Pimenta, Martin Pippel, Anna Maria Pirttilä, Nikos Poulakakis, Jeena Rajan, Rúben M.C. Rego, Roberto Resendes, Philipp Resl, Ana Riesgo, Patrik Rodin-Morch, Andre E. R. Soares, Carlos Rodriguez Fernandes, Maria M. Romeiras, Guilherme Roxo, Lukas Rüber, Maria Jose Ruiz-Lopez, Urmas Saarma, Luis P. da Silva, Manuela Sim-Sim, Lucile Soler, Vitor C. Sousa, Carla Sousa Santos, Alberto Spada, Milomir Stefanovic, Viktor Steger, Josefin Stiller, Matthias Stöck, Torsten H. Struck, Hiranya Sudasinghe, Riikka Tapanainen, Christian Tellgren-Roth, Helena Trindade, Yevhen Tukalenko, Ilenia Urso, Benoit Vacherie, Steven M. Van Belleghem, Kees Van Oers, Carlos Vargas-Chavez, Nevena Velickovic, Noel Vella, Adriana Vella, Cristiano Vernesi, Sara Vicente, Sara Villa, Olga Vinnere Pettersson, Filip A. M. Volckaert, Judit Voros, Patrick Wincker, Sylke Winkler, Claudio Ciofi, Robert M. Waterhouse, Camila J. Mazzoni +202 moredoaj +9 more sourcesA High-quality Reference Genome and Tissue Expression Atlas for the European Lobster (
Homarus gammarus
) [PDF]
Genome Biology and EvolutionAbstract Homarid lobsters are notable for their remarkable immunity and longevity, with lifespans reaching up to 80 years in the wild. A reference genome is available for the American lobster (Homarus americanus), but not for the European lobster (H.Paris JR, Jenkins TL, Ferrer Obiol J, Gundappa MK, Regan T, Campbell L, Maslen GL, Alvarez-Jarreta J, Dyer S, Jeffries AR, Murray G, Farbos A, Bickley LK, Verbruggen B, Bateman KS, Daniels CL, Ellis CD, Ashton TJ, Tyler CR, Stentiford GD, Houston RD, Bean TP, van Aerle R, Macqueen DJ, Stevens JR, Santos EM. +25 moreexaly +4 more sourcesERGA-BGE reference genome of Diadema setosum: the Black Longspine Urchin invading the Mediterranean sea [version 1; peer review: 1 approved, 2 approved with reservations] [PDF]
Open Research EuropeThe Diadema setosum reference genome is important for understanding the species adaptation to the Mediterranean marine environment, where it has been newly introduced.Patrick Wincker, Corinne Cruaud, Alice Moussy, Lola Demirdjian, Karine Labadie, Pedro H. Oliveira, Nuria Escudero, Rosa Fernández, Katerina Vasileiadou, Astrid Böhne, Jean-Marc Aury, Arnaud Couloux, Benjamin Istace, Rita Monteiro, Tereza Manousaki +14 moredoaj +2 more sourcesERGA-BGE reference genome of Xylophaga dorsalis - a common deep-sea wood-boring bivalve with Atlantic-Mediterranean distribution [version 2; peer review: 1 approved, 3 approved with reservations] [PDF]
Open Research EuropeXylophaga dorsalis is a common Atlantic-Mediterranean mollusc that plays a crucial role in deep-sea habitats, where it digests wood that reaches the seabed through a unique symbiosis with specialised bacteria. The reference genome of X.Jèssica Gómez-Garrido, Fernando Cruz, Fergal Martin, Leanne Haggerty, Tyler S. Alioto, Carlota Gracia-Sancha, Sergi Taboada, Carles Galià-Camps, Rebekah A. Oomen, Anna Lazar, Thomas Marcussen, Torsten H. Struck, Astrid Böhne, Chiara Bortoluzzi, Marta Gut, Laura Aguilera, Rita Monteiro, Francisco Câmara Ferreira +17 moredoaj +2 more sourcesERGA-CBP chromosome-level genome assembly of the blind scorpion Belisarius xambeui Simon, 1879 (Belisariidae, Scorpiones), a singular scorpion in Europe [version 2; peer review: 3 approved, 1 approved with reservations] [PDF]
Open Research EuropeWe present a chromosome-level reference genome for the blind scorpion Belisarius xambeui Simon, 1879 (Belisariidae, Scorpiones). The genome size estimated by flow cytometry (4.32 Gb) closely matches the final assembly size (3.98 Gb).Vadim A. Pisarenco, Sara Guirao-Rico, Pau Balart-García, Paula Escuer, Adrià Bellvert, Marc Domènech, Alejandro Sánchez-Gracia, Silvia Adrián-Serrano, Julio Rozas, Miquel A. Arnedo +9 moredoaj +2 more sourcesERGA-BGE reference genome of Gambusia holbrooki, a globally invasive freshwater fish [version 2; peer review: 2 approved] [PDF]
Open Research EuropeThe Gambusia holbrooki (eastern mosquitofish) reference genome will offer a crucial resource for understanding the evolution and adaptation of invasive freshwater fish species. The genome of G. holbrooki was assembled into two haplotypes through a phased Jonathan M.D. Wood, Shane McCarthy, Fergal Martin, Leanne Haggerty, Bonnie Fraser, Francesco Santi, Clelia Gasparini, Amy Denton, Swati Sinha, Rebekah A. Oomen, Thomas Marcussen, Torsten H. Struck, Astrid Böhne, Chiara Bortoluzzi, Caroline Howard, Rita Monteiro, Mark Blaxter, Kerstin Howe +17 moredoaj +2 more sourcesBiodiversity Genomics Europe (BGE) Project – Abridged Grant Proposal [PDF]
Research Ideas and OutcomesThe Biodiversity Genomics Europe (BGE) Project has the overarching aim of accelerating the use of genomic science to enhance understanding of biodiversity, monitor biodiversity change, and guide interventions to address its decline.Dimitris Koureas, Pedro Beja, Mark Blaxter, Astrid Böhne, Sarah Bourlat, Torbjørn Ekrem, Brent Emerson, Katharina Heil, José Melo-Ferreira, Ben Price, Rutger Vos, Wouter Addink, Tyler Alioto, Filippos Aravanopoulos, Jonas Astrin, Jean-Marc Aury, Ian Barnes, Claudia Bruschini, Elena Buzan, Guy Cochrane, Tamás Cserkész, Thanos Dailianis, Elza Duijm, Glenn Dunshea, Rosa Fernández, Sónia Ferreira, Giulio Formenti, Sara Fratini, Konstantinos Gkagkavouzis, Carole Goble, Michal Grabowski, Bjorn Grüning, Ivo Gut, Marta Gut, Peter Harrison, Axel Hausmann, Jacob Höglund, Laura Iacolina, Alessio Iannucci, Kjetill Jakobsen, Urmas Kõljalg, Henrik Lantz, Harris Lewin, Jan Macher, Tereza Manousaki, Fergal Martin, Ximo Mengual, Pedro Oliveira, Rebekah Oomen, Michael Raupach, Ana Riesgo, Hugues Roest Crollius, Anna Somogyi, Torsten Struck, Hannes Svardal, Ave Tooming-Klunderud, Alexandros Triantafyllidis, Olga Vinnere Pettersson, Maximilian Wagner, Patrick Wincker, Ni Yan, Jose Alonso, Ana Casino, Claudio Ciofi, Gabriela Daňková, Peter Hollingsworth, Mara Lawniczak, Camila Mazzoni, Robert Waterhouse +68 moredoaj +3 more sourcesERGA-BGE-CBP chromosome-level genome assembly of the blind scorpion Belisarius xambeui Simon, 1879 (Belisariidae, Scorpiones), the most singular scorpion in Europe [version 1; peer review: 2 approved]
Open Research EuropeWe present a chromosome-level reference genome for the blind scorpion Belisarius xambeui Simon, 1879 (Belisariidae, Scorpiones). The genome size estimated by flow cytometry (4.32 Gb) closely matches the final assembly size (3.98 Gb).Vadim A. Pisarenco, Sara Guirao-Rico, Pau Balart-García, Paula Escuer, Adrià Bellvert, Marc Domènech, Alejandro Sánchez-Gracia, Silvia Adrián-Serrano, Julio Rozas, Miquel A. Arnedo +9 moredoaj +1 more source
