Advancing European Aquaculture by Genome Functional Annotation

Risultati finali

Best-practices guidelines for sample collection and data curation

D12 Bestpractices guidelines for sample collection and data curation written protocols describing biological sampling and standard requirements for metadata recording in the AQUAFAANG project M9 Can be used to measure achievement of objective 12

Project Brochure

D7.3. Project Brochure; document (EFFAB: M8). Can be used to measure achievement of objective 7.3

Development of standardized, optimized and processing efficient lab protocols

D1.1. Development of standardized, optimized and processing efficient lab protocols; written lab protocols describing in detail how to perform library preparation for ATAC-Seq, ChIP-Seq, RNA-Seq and sRNA-Seq (M9). Can be used to measure achievement of objective 1.1.

Industrial whitepaper; peer-reviewed publication

D7.9. Industrial whitepaper; peer-reviewed publication (XELECT: M45). Can be used to measure achievement of objective 7.1

Results Brochures

D7.8. Results Brochures; document (EFFAB: M42). Can be used to measure achievement of sub-goal 7.3

AQUA-FAANG website launched

D7.1. AQUA-FAANG website launched, link to website (EFFAB: M3). Can be used to measure achievement of objective 7.3

AQUA-FAANG YouTube video

D76 AQUAFAANG YouTube video link to website EFFAB M24 Can be used to measure achievement of objective 73

Three E-learning series to enhance industry-specific exploitation

D7.10. Report from three E-learning series to enhance industry-specific exploitation; link to websites and report of attendance and feedback results (EFFAB, M48). Can be used to measure achievement of objective 7.1

Six newsletters

D7.11 Six newsletters; documents and link to website (EFFAB: M48). Can be used to measure achievement of sub-goal 7.3

Pubblicazioni

European project AQUA-FAANG: the epigenetic landscape of the Atlantic Salmon; focus on liver tissue

Autori: M.-O. Baudement, G. B. Gillard, T. Podgorniak, L. Grønvold, S. Lien and M. P. Kent
Pubblicato in: Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP), 2022, Pagina/e 3364, ISBN 978-90-8686-940-4
Editore: Wageningen Academic Publishers
DOI: 10.3920/978-90-8686-940-4

From FAANG to fork: application of highly annotated genomes to improve farmed animal production.

Autori: Emily L. Clark; Alan Archibald; Hans D. Daetwyler; Martien A. M. Groenen; Peter W. Harrison; Ross D. Houston; Christa Kühn; Christa Kühn; Sigbjørn Lien; Daniel J. Macqueen; James M. Reecy; Diego Robledo; Mick Watson; Christopher K. Tuggle; Elisabetta Giuffra
Pubblicato in: Genome Biology 21 (2020) 1, Numero 10, 2020, ISSN 1474-7596
Editore: BioMed Central
DOI: 10.1186/s13059-020-02197-8

Zebrafish regulatory genomic resources for disease modelling and regeneration

Autori: Ada Jimenez Gonzalez, Damir Baranasic and Ferenc Müller
Pubblicato in: Disease Models and Mechanisms, Numero Vol 16, Numero 8, 2023, ISSN 1754-8403
Editore: The Company of Biologists Ltd.

An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication

Autori: Elise Parey; Alexandra Louis; Jérôme Montfort; Yann Guiguen; Hugues Roest Crollius; Camille Berthelot
Pubblicato in: Genome Research, 2022, ISSN 1088-9051
Editore: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.276953.122

"The FAANG Data Portal: Global, Open-Access, ""FAIR"", and Richly Validated Genotype to Phenotype Data for High-Quality Functional Annotation of Animal Genomes."

Autori: Peter W. Harrison, Alexey Sokolov, Akshatha Nayak, Jun Fan, Daniel Zerbino, Guy Cochrane and Paul Flicek
Pubblicato in: Frontiers in Genetics, Numero vol12, 2021, ISSN 1664-8021
Editore: Frontiers Media
DOI: 10.3389/fgene.2021.639238

A genome-wide association study, supported by a new chromosome-level genome assembly, suggests sox2 as a main driver of the undifferentiatiated ZZ/ZW sex determination of turbot (Scophthalmus maximus)

Autori: Paulino Martínez., Diego Robledo., Xoana Taboada., Andrés Blanco., Michel Moser., Francesco Maroso., Miguel Hermida., Antonio Gómez-Tato., Blanca Álvarez-Blázquez., Santiago Cabaleiro., Francesc Piferrer., Carmen Bouza., Sigbjørn Lien., Ana M. Viñas.
Pubblicato in: Genomics, Numero 113 (2021), 2021, Pagina/e 1705-1718, ISSN 0888-7543
Editore: Academic Press
DOI: 10.1016/j.ygeno.2021.04.007

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

Autori: Roberto de la Herrán, Miguel Hermida, Juan Andres Rubiolo, Jèssica Gómez-Garrido, Fernando Cruz, Francisca Robles, Rafael Navajas-Pérez, Andres Blanco, Paula Rodriguez Villamayor, Dorinda Torres, Pablo Sánchez-Quinteiro, Daniel Ramirez, Maria Esther Rodríguez, Alberto Arias-Pérez, Ismael Cross, Neil Duncan, Teresa Martínez-Peña, Ana Riaza, Adrian Millán, M. Cristina De Rosa, Davide Pirol
Pubblicato in: Molecular Ecology Resources, 2023, ISSN 1755-0998
Editore: John Wiley & Sons Ltd.
DOI: 10.1111/1755-0998.13750

New reports on iron related proteins: Molecular characterization of two ferroportin genes in common carp (Cyprinus carpio L.) and its expression pattern

Autori: Teresa Kaminska-Gibas, Joanna Szczygieł, Annemiek Blasweiler, Łukasz Gajda, Ebru Yilmaz, Patrycja Jurecka, Ludmiła Kolek, Marek Ples, Ilgiz Irnazarow
Pubblicato in: Fish & Shellfish Immunology, Numero Volume 142, November 2023, 109087, 2023, ISSN 1050-4648
Editore: Academic Press
DOI: 10.1016/j.fsi.2023.109087

Symmetric expression of ohnologs encoding conserved antiviral responses in tetraploid common carp suggest absence of subgenome dominance after whole genome duplication

Autori: A. Blasweiler, H.-J. Megens, M.R.G. Goldman, R. Tadmor-Levi, J. Lighten, M.A.M. Groenen, R.P. Dirks, H.J. Jansen, H.P. Spaink, L. David, P. Boudinot, G.F. Wiegertjes
Pubblicato in: Genomics, Numero Volume 115, Numero 6, November 2023, 110723, 2023, ISSN 0888-7543
Editore: Academic Press
DOI: 10.1016/j.ygeno.2023.110723

Evolution of the IRF Family in Salmonids

Autori: Thomas C Clark , Pierre Boudinot , Bertrand Collet
Pubblicato in: Genes (This article belongs to the Special Numero Genetics and Genomics of Salmonid Fishes), Numero 12(2), 2021, Pagina/e 238, ISSN 2073-4425
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/genes12020238

Ensembl 2022

Autori: 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, Tama
Pubblicato in: Nucleic Acids Research, Numero 50 D1, 2022, Pagina/e D988–D995, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkab1049

Ensembl 2021

Autori: Kevin L Howe, Premanand Achuthan, James Allen, Jamie Allen, Jorge Alvarez-Jarreta, M Ridwan Amode, Irina M Armean, Andrey G Azov, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu, Mehrnaz Charkhchi, Carla Cummins, Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Dodiya, Bilal El Houdaigui, Reham Fatima, Astrid Gall, Carlos Garcia Giron, Tiago Grego, Cristina Guijarro-Clarke, Lea
Pubblicato in: Nucleic Acids Research, Numero 49/D1, 2020, Pagina/e D884-D891, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkaa942

The European Nucleotide Archive in 2020

Autori: Peter W Harrison, Alisha Ahamed, Raheela Aslam, Blaise T F Alako, Josephine Burgin, Nicola Buso, Mélanie Courtot, Jun Fan, Dipayan Gupta, Muhammad Haseeb, Sam Holt, Talal Ibrahim, Eugene Ivanov, Suran Jayathilaka, Vishnukumar Balavenkataraman Kadhirvelu, Manish Kumar, Rodrigo Lopez, Simon Kay, Rasko Leinonen, Xin Liu, Colman O’Cathail, Amir Pakseresht, Youngmi Park, Stephane Pesant, Nadim Rahm
Pubblicato in: Nucleic Acids Research, 2020, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkaa1028

Conserved and divergent arms of the antiviral response in the duplicated genomes of salmonid fishes

Autori: Thomas C. Clark; Shahmir Naseer; Manu Kumar Gundappa; Audrey Laurent; Aline Perquis; Bertrand Collet; Daniel J. Macqueen; Samuel A.M. Martin; Pierre Boudinot
Pubblicato in: Genomics, Numero Volume 115, Numero 4, July 2023, 110663, 2023, ISSN 0888-7543
Editore: Academic Press
DOI: 10.1016/j.ygeno.2023.110663

Ensembl 2023

Autori: 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
Pubblicato in: Nucleic Acids Research, Numero Volume 51, Numero D1, 2023, Pagina/e D933–D941, ISSN 1362-4962
Editore: Oxford University Press
DOI: 10.1093/nar/gkac958

The European Nucleotide Archive in 2019

Autori: Clara Amid, Blaise T F Alako, Vishnukumar Balavenkataraman Kadhirvelu, Tony Burdett, Josephine Burgin, Jun Fan, Peter W Harrison, Sam Holt, Abdulrahman Hussein, Eugene Ivanov, Suran Jayathilaka, Simon Kay, Thomas Keane, Rasko Leinonen, Xin Liu, Josue Martinez-Villacorta, Annalisa Milano, Amir Pakseresht, Nadim Rahman, Jeena Rajan, Kethi Reddy, Edward Richards, Dmitriy Smirnov, Alexey Sokolov, Sen
Pubblicato in: Nucleic Acids Research, 2019, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkz1063

Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements

Autori: Damir Baranasic; Matthias Hörtenhuber; Piotr J. Balwierz; Tobias Zehnder; Abdul Kadir Mukarram; Chirag Nepal; Csilla Várnai; Yavor Hadzhiev; Ada Jimenez-Gonzalez; Nan Li; Joseph Wragg; Fabio M. D’Orazio; Dorde Relic; Mikhail Pachkov; Noelia Díaz; Benjamín Hernández-Rodríguez; Zelin Chen; Marcus Stoiber; Michaël Dong; Irene Stevens; Samuel E. Ross; Anne Eagle; Ryan Martin; Oluwapelumi Obas
Pubblicato in: Nature Genetics, Numero Vol. 55, No. 7, 2022, Pagina/e 1037–1050, ISSN 1061-4036
Editore: Nature Publishing Group
DOI: 10.5445/ir/1000148259

The Emerging Role of Long Non-Coding RNAs in Development and Function of Gilthead Sea Bream (Sparus aurata) Fast Skeletal Muscle

Autori: Isabel García-Pérez, Anna Molsosa-Solanas, Miquel Perelló-Amorós, Elena Sarropoulou, Josefina Blasco, Joaquim Gutiérrez, and Daniel Garcia de la serrana
Pubblicato in: Cells, Numero 11(3), 2022, Pagina/e 428, ISSN 2073-4409
Editore: MDPI
DOI: 10.3390/cells11030428

Evolution of T cell receptor beta loci in salmonids

Autori: Pierre Boudinot , Samuel Novas, Luc Jouneau , Stanislas Mondot , Marie-Paule Lefranc , Unni Grimholt , Susana Magadán
Pubblicato in: Frontiers in immunology, Numero Vol 14 Aug 2023, 2023, ISSN 1664-3224
Editore: Frontiers
DOI: 10.3389/fimmu.2023.1238321

Integration of host-pathogen functional genomics data into the chromosome-level genome assembly of turbot (Scophthalmus maximus)

Autori: Oscar Aramburu,Andrés Blanco,Carmen Bouza, Paulino Martínez
Pubblicato in: Aquaculture, Numero Vol. 564, 2023, ISSN 0044-8486
Editore: Elsevier BV
DOI: 10.1016/j.aquaculture.2022.739067

Phylogeny and expression of tetraspanin CD9 paralogues in rainbow trout (Oncorhynchus mykiss)

Autori: Carola E Dehler , Pierre Boudinot , Bertrand Collet , SamuelA M Martin
Pubblicato in: Developmental Comparative Immunology, Numero Volume 146, Sept 2023, 104735, 2023, ISSN 0145-305X
Editore: Pergamon Press Ltd.
DOI: 10.1016/j.dci.2023.104735

Risultati finali

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