Advancing European Aquaculture by Genome Functional Annotation

Rezultaty

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

Publikacje

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

Autorzy: M.-O. Baudement, G. B. Gillard, T. Podgorniak, L. Grønvold, S. Lien and M. P. Kent
Opublikowane w: Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP), 2022, Strona(/y) 3364, ISBN 978-90-8686-940-4
Wydawca: 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.

Autorzy: 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
Opublikowane w: Genome Biology 21 (2020) 1, Numer 10, 2020, ISSN 1474-7596
Wydawca: BioMed Central
DOI: 10.1186/s13059-020-02197-8

Zebrafish regulatory genomic resources for disease modelling and regeneration

Autorzy: Ada Jimenez Gonzalez, Damir Baranasic and Ferenc Müller
Opublikowane w: Disease Models and Mechanisms, Numer Vol 16, Numer 8, 2023, ISSN 1754-8403
Wydawca: The Company of Biologists Ltd.

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

Autorzy: Elise Parey; Alexandra Louis; Jérôme Montfort; Yann Guiguen; Hugues Roest Crollius; Camille Berthelot
Opublikowane w: Genome Research, 2022, ISSN 1088-9051
Wydawca: 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."

Autorzy: Peter W. Harrison, Alexey Sokolov, Akshatha Nayak, Jun Fan, Daniel Zerbino, Guy Cochrane and Paul Flicek
Opublikowane w: Frontiers in Genetics, Numer vol12, 2021, ISSN 1664-8021
Wydawca: 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)

Autorzy: 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.
Opublikowane w: Genomics, Numer 113 (2021), 2021, Strona(/y) 1705-1718, ISSN 0888-7543
Wydawca: 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

Autorzy: 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
Opublikowane w: Molecular Ecology Resources, 2023, ISSN 1755-0998
Wydawca: 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

Autorzy: Teresa Kaminska-Gibas, Joanna Szczygieł, Annemiek Blasweiler, Łukasz Gajda, Ebru Yilmaz, Patrycja Jurecka, Ludmiła Kolek, Marek Ples, Ilgiz Irnazarow
Opublikowane w: Fish & Shellfish Immunology, Numer Volume 142, November 2023, 109087, 2023, ISSN 1050-4648
Wydawca: 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

Autorzy: 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
Opublikowane w: Genomics, Numer Volume 115, Numer 6, November 2023, 110723, 2023, ISSN 0888-7543
Wydawca: Academic Press
DOI: 10.1016/j.ygeno.2023.110723

Evolution of the IRF Family in Salmonids

Autorzy: Thomas C Clark , Pierre Boudinot , Bertrand Collet
Opublikowane w: Genes (This article belongs to the Special Numer Genetics and Genomics of Salmonid Fishes), Numer 12(2), 2021, Strona(/y) 238, ISSN 2073-4425
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/genes12020238

Ensembl 2022

Autorzy: 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
Opublikowane w: Nucleic Acids Research, Numer 50 D1, 2022, Strona(/y) D988–D995, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkab1049

Ensembl 2021

Autorzy: 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
Opublikowane w: Nucleic Acids Research, Numer 49/D1, 2020, Strona(/y) D884-D891, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkaa942

The European Nucleotide Archive in 2020

Autorzy: 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
Opublikowane w: Nucleic Acids Research, 2020, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkaa1028

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

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

Ensembl 2023

Autorzy: 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
Opublikowane w: Nucleic Acids Research, Numer Volume 51, Numer D1, 2023, Strona(/y) D933–D941, ISSN 1362-4962
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkac958

The European Nucleotide Archive in 2019

Autorzy: 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
Opublikowane w: Nucleic Acids Research, 2019, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkz1063

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

Autorzy: 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
Opublikowane w: Nature Genetics, Numer Vol. 55, No. 7, 2022, Strona(/y) 1037–1050, ISSN 1061-4036
Wydawca: 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

Autorzy: Isabel García-Pérez, Anna Molsosa-Solanas, Miquel Perelló-Amorós, Elena Sarropoulou, Josefina Blasco, Joaquim Gutiérrez, and Daniel Garcia de la serrana
Opublikowane w: Cells, Numer 11(3), 2022, Strona(/y) 428, ISSN 2073-4409
Wydawca: MDPI
DOI: 10.3390/cells11030428

Evolution of T cell receptor beta loci in salmonids

Autorzy: Pierre Boudinot , Samuel Novas, Luc Jouneau , Stanislas Mondot , Marie-Paule Lefranc , Unni Grimholt , Susana Magadán
Opublikowane w: Frontiers in immunology, Numer Vol 14 Aug 2023, 2023, ISSN 1664-3224
Wydawca: Frontiers
DOI: 10.3389/fimmu.2023.1238321

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

Autorzy: Oscar Aramburu,Andrés Blanco,Carmen Bouza, Paulino Martínez
Opublikowane w: Aquaculture, Numer Vol. 564, 2023, ISSN 0044-8486
Wydawca: Elsevier BV
DOI: 10.1016/j.aquaculture.2022.739067

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

Autorzy: Carola E Dehler , Pierre Boudinot , Bertrand Collet , SamuelA M Martin
Opublikowane w: Developmental Comparative Immunology, Numer Volume 146, Sept 2023, 104735, 2023, ISSN 0145-305X
Wydawca: Pergamon Press Ltd.
DOI: 10.1016/j.dci.2023.104735

Rezultaty

Publikacje

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