Open access articles affiliated with AQUA-FAANG

AQUAFAANG White Paper
Advancing fish breeding in aquaculture through genome
functional annotation - January 2024

Ian A. Johnston, Matthew P. Kent, Pierre Boudinot, Mark Looseley, Luca Bargelloni, Sara Faggion, Gabriela A. Merino, Garth R. Ilsley, Julien Bobe, Costas S. Tsigenopoulos, Joseph Robertson, Peter W. Harrison, Paulino Martinez, Diego Robledo,
Daniel J. Macqueen, Sigbjørn Lien
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New reports on iron related proteins: Molecular characterization of two ferroportin genes in common carp (Cyprinus carpio L.) and its expression pattern - November 2023

Teresa Kami´nska-Gibas, Joanna Szczygieł, Annemiek Blasweiler, Łukasz Gajda, Ebru Yilmaz, Patrycja Jurecka, Ludmiła Kolek, Marek Ples, Ilgiz Irnazarow 
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Evolution of T cell receptor beta loci in salmonids - August 2023

Pierre Boudinot, Samuel Novas, Luc Jouneau,
Stanislas Mondot, Marie-Paule Lefranc, Unni Grimholt,
Susana Magada´
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Zebrafish regulatory genomic resources for disease modelling and regeneration - August 2023

Ada Jimenez Gonzalez, Damir Baranasic, Ferenc Müller
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Phylogeny and expression of tetraspanin CD9 paralogues in rainbow trout (Oncorhynchus mykiss) - September 2023

Carola E. Dehler, Pierre Boudinot, Bertrand Collet, Samuel A.M. Martin 
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A genome-wide association study, supported by a new chromosome-level genome assembly, suggests sox2 as a main driver of the undifferentiated ZZ/ZW sex determination of turbot (Scophthalmus maximus) - April 2021

Martínez P, Robledo D, Taboada X, Blanco A, Moser M, Maroso F, Hermida M, Gómez-Tato, Álvarez-Blázquez B, Cabaleiro S, Piferrer F, Bouza C, Lien S, Viñas AM. A genome-wide association study, supported by a new chromosome-level genome assembly, suggests sox2 as a main driver of the undifferentiated ZZ/ZW sex determination of turbot (Scophthalmus maximus). Genomics 113 (2021) 1705-1718
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The European Nucleotide Archive in 2019
- November 2019

Amid C, Alako BTF, Kadhirvelu VB, Burdett T, Burgin J, Fan J, Harrison PW, Holt S, Hussein A, Ivanov E, Jayathilaka S, Kay S, Keane T, Leinonen R, Liu X, Martinez-Villacorta J, Milano A, Pakseresht A, Rahman N, Rajan J, Reddy K, Richards E, Smirnov D, Sokolov A, Vijayaraja S, Cochrane G. The European Nucleotide Archive in 2019. Nucleic Acids Research 2020; Volume 48, Issue D1, 08 January 2020, Pages D70–D76​
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The FAANG Data Portal: Global, Open-Access, "FAIR", and Richly Validated Genotype to Phenotype Data for High-Quality Functional Annotation of Animal Genomes – June 2021

Peter W. Harrison, Alexey Sokolov, Akshatha Nayak, Jun Fan, Daniel Zerbino, Guy Cochrane and Paul Flicek.The FAANG Data Portal: Global, Open-Access, "FAIR", and Richly Validated Genotype to Phenotype Data for High-Quality Functional Annotation of Animal Genomes, published in 2021 in Front. Genet. Volume 12 – 2021.
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Evolution of the IRF Family in Salmonids –February 2021

Thomas C. Clark, Pierre Boudinot and bertrand Collet – Evolution of the IRF Family in Salmonids, Genes 2021, 12, 238.
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Ensembl 2022 – November 2021

Fiona Cunningham, James E Allen, Jamie Allen, Jorge Alvarez-Jarreta, M Ridwan Amode, Irina M Armean, Olanrewaju Austine-Orimoloye, Andrey G Azov, If Barnes, Ruth Bennett, Andrew Berry, Jyothish Bhai, Alexandra Bignell, Konstantinos Billis, Sanjay Boddu, Lucy Brooks, Mehrnaz Charkhchi, Carla Cummins, Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Dodiya, Sarah Donaldson, Bilal El Houdaigui, Tamara El Naboulsi, Reham Fatima, Carlos Garcia Giron, Thiago Genez, Jose Gonzalez Martinez, Cristina Guijarro-Clarke, Arthur Gymer, Matthew Hardy, Zoe Hollis, Thibaut Hourlier, Toby Hunt, Thomas Juettemann, Vinay Kaikala, Mike Kay, Ilias Lavidas, Tuan Le, Diana Lemos, José Carlos Marugán, Shamika Mohanan, Aleena Mushtaq, Marc Naven, Denye N Ogeh, Anne Parker, Andrew Parton, Malcolm Perry, Ivana Piližota, Irina Prosovetskaia, Manoj Pandian Sakthivel, Ahamed Imran Abdul Salam, Bianca M Schmitt, Helen Schuilenburg, Dan Sheppard, José G Pérez-Silva, William Stark, Emily Steed, Kyösti Sutinen, Ranjit Sukumaran, Dulika Sumathipala, Marie-Marthe Suner, Michal Szpak, Anja Thormann, Francesca Floriana Tricomi, David Urbina-Gómez, Andres Veidenberg, Thomas A Walsh, Brandon Walts, Natalie Willhoft, Andrea Winterbottom, Elizabeth Wass, Marc Chakiachvili, Bethany Flint, Adam Frankish, Stefano Giorgetti, Leanne Haggerty, Sarah E Hunt, Garth R IIsley, Jane E Loveland, Fergal J Martin, Benjamin Moore, Jonathan M Mudge, Matthieu Muffato, Emily Perry, Magali Ruffier, John Tate, David Thybert, Stephen J Trevanion, Sarah Dyer, Peter W Harrison, Kevin L Howe, Andrew D Yates, Daniel R Zerbino, Paul Flicek, Ensembl 2022, Nucleic Acids Research, Volume 50, Issue D1, 7 January 2022, Pages D988–D995
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Integration of host-pathogen functional genomics data into the chromosome-level genome assembly of turbot (Scophthalmus maximus) – February 2023

Oscar Aramburu, Andrés Blanco, Carmen Bouza, Paulino Martínez, Integration of host-pathogen functional genomics data into the chromosome-level genome assembly of turbot (Scophthalmus maximus), Aquaculture, Volume 564, 2023.
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Ensembl 2023 – November 2022

Fergal J Martin, M Ridwan Amode, Alisha Aneja, Olanrewaju Austine-Orimoloye, Andrey G Azov, If Barnes, Arne Becker, Ruth Bennett, Andrew Berry, Jyothish Bhai, Simarpreet Kaur Bhurji, Alexandra Bignell, Sanjay Boddu, Paulo R Branco Lins, Lucy Brooks, Shashank Budhanuru Ramaraju, Mehrnaz Charkhchi, Alexander Cockburn, Luca Da Rin Fiorretto, Claire Davidson, Kamalkumar Dodiya, Sarah Donaldson, Bilal El Houdaigui, Tamara El Naboulsi, Reham Fatima, Carlos Garcia Giron, Thiago Genez, Gurpreet S Ghattaoraya, Jose Gonzalez Martinez, Cristi Guijarro, Matthew Hardy, Zoe Hollis, Thibaut Hourlier, Toby Hunt, Mike Kay, Vinay Kaykala, Tuan Le, Diana Lemos, Diego Marques-Coelho, José Carlos Marugán, Gabriela Alejandra Merino, Louisse Paola Mirabueno, Aleena Mushtaq, Syed Nakib Hossain, Denye N Ogeh, Manoj Pandian Sakthivel, Anne Parker, Malcolm Perry, Ivana Piližota, Irina Prosovetskaia, José G Pérez-Silva, Ahamed Imran Abdul Salam, Nuno Saraiva-Agostinho, Helen Schuilenburg, Dan Sheppard, Swati Sinha, Botond Sipos, William Stark, Emily Steed, Ranjit Sukumaran, Dulika Sumathipala, Marie-Marthe Suner, Likhitha Surapaneni, Kyösti Sutinen, Michal Szpak, Francesca Floriana Tricomi, David Urbina-Gómez, Andres Veidenberg, Thomas A Walsh, Brandon Walts, Elizabeth Wass, Natalie Willhoft, Jamie Allen, Jorge Alvarez-Jarreta, Marc Chakiachvili, Bethany Flint, Stefano Giorgetti, Leanne Haggerty, Garth R Ilsley, Jane E Loveland, Benjamin Moore, Jonathan M Mudge, John Tate, David Thybert, Stephen J Trevanion, Andrea Winterbottom, Adam Frankish, Sarah E Hunt, Magali Ruffier, Fiona Cunningham, Sarah Dyer, Robert D Finn, Kevin L Howe, Peter W Harrison, Andrew D Yates, Paul Flicek, Ensembl 2023, Nucleic Acids Research, Volume 51, Issue D1, 6 January 2023, Pages D933–D941
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 Conserved and divergent arms of the antiviral response in the duplicated genomes of salmonid fishes - July 2023

Thomas C. Clark, Shahmir Naseer, Manu Kumar Gundappa, Audrey Laurent, Aline Perquis, Bertrand Collet, Daniel J. Macqueen, Samuel A.M. Martin, Pierre Boudinot 
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European project AQUA-FAANG: the epigenetic landscape of the Atlantic Salmon; focus on liver tissue - February 2023

M.-O. Baudement, G. B. Gillard, T. Podgorniak, L. Grønvold, S. Lien and M. P. Kent
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The European Nucleotide Archive in 2020
​- November 2020

Harrison PW, Ahamed A, Aslam R, Alako BTF, Burgin J, Buso N, Courtot M, Fan J, Gupta D, Haseeb M, Holt S, Ibrahim T, Ivanov E, Jayathilaka S, Kadhirvelu VB, Kumar M, Lopez R, Kay S, Leinonen R, Liu X, O’Cathail C, Pakseresht A, Park Y, Pesant S, Rahman N, Rajan J, Sokolov A, Vijayaraja S, Waheed Z, Zyoud A, Burdett, Cochrane G. The European Nucleotide Archive in 2020. Nucleic Acids Research 2021; Volume 49, Issue D1, 8 January 2021, Pages D82–D85. 
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Ensembl 2021 - November 2020

Howe KL, Achuthan P, Allen J, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Azov AG, Bennett R, Bhai J, Billis K, Boddu S, Charkhchi M, Cummins C, Fioretto, LDR, Davidson C, Dodiya K, Houdaigui BE, Fatima R, Gall A, Giron CG, Grego T, Guijarro-Clarke C, Haggerty L, Hemrom A, Hourlier T, Izuogu OG, Juettemann T, Kaikala V, Kay M, Lavidas I, Le T, Lemos D, Martinez JG, Marugán JC, Maurel T, McMahon AC, MohananS, Moore B, Muffato M, Oheh DN, Paraschas D, Parker A, Parton A, Prosovetskaia I, Sakthivel MP, Salam AIA, Schmitt BM, Schuilenburg H, Sheppard D, Steed E, Szpak M, Szuba M, Taylor K, Thormann A, Threadgold G, Walts B, Winterbottom A, Chakiachvili M, Chaubal A, Silva ND, Flint B, Frankish A, Hunt SE, Ilsley GR, Langridge N, Loveland JE, Martin FJ, Mudge JM, Morales J, Perry E, Ruffier M, Tate J, Thybert D, Trevanion S, Cunningham F, Yates AD, Zerbino DR, Flicek P. Ensembl 2021. Nucleic Acids Research 2021; Volume 49, Issue D1, 8 January 2021, Pages D884–D891. 
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From FAANG to fork: application of highly annotated genomes to improve farmed animal production - November 2020

Clark EL, Archibald AL, Daetwyler HD, Groenen MAM, Harrison PW, Houston RD, Kühn C, Lien S, Macqueen DJ, Reecy JM, Robledo D, Watson M, Tuggle CK, Giuffra E. From FAANG to fork: application of highly annotated genomes to improve farmed animal production. Genome Biol. 2020; 21:285. 
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The Emerging Role of Long Non-Coding RNAs in Development and Function of Gilthead Sea Bream (Sparus aurata) Fast Skeletal Muscle – January 2022

García-Pérez, I.; Molsosa-Solanas, A.; Perelló-Amorós, M.; Sarropoulou, E.; Blasco, J.; Gutiérrez, J.; Garcia de la serrana, D. The Emerging Role of Long Non-Coding RNAs in Development and Function of Gilthead Sea Bream (Sparus aurata) Fast Skeletal Muscle. Cells 2022,11,428.
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Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements – July 2022

Baranasic, D., Hörtenhuber, M., Balwierz, P.J. et al. Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. Nat Genet 54, 1037–1050 (2022).
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A chromosome-level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex-determining gene in the flatfish Solea senegalensis – January 2023

de la Herrán, R.,  Hermida, M.,  Rubiolo, J. A.,  Gómez-Garrido, J.,  Cruz, F.,  Robles, F.,  Navajas-Pérez, R., Blanco, A.,  Villamayor, P. R.,  Torres, D.,  Sánchez-Quinteiro, P.,  Ramirez, D.,  Rodríguez, M. E.,  Arias-Pérez, A., Cross, I.,  Duncan, N.,  Martínez-Peña, T.,  Riaza, A.,  Millán, A. …  Martínez, P. (2023).  A chromosome-level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex-determining gene in the flatfish Solea senegalensis. Molecular Ecology Resources,  00,  1– 19.
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An atlas of fish genome evolution reveals delayedrediploidization following the teleost whole-genome duplication

Elise Parey, Alexandra Louis, Jérôme Montfort, Yann Guiguen, Hugues Roest Crollius, and Camille Berthelot. Genome Res. 2022. 32: 1685-1697
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Non-open access articles affiliated with AQUA-FAANG

Genome structures resolve the early diversification of teleost fishes