Advancing European Aquaculture by Genome Functional Annotation

Deliverables

Websites, patent fillings, videos etc. (1)

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

Documents, reports (2)

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.

Publications

Peer reviewed articles (9)

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

Author(s): Peter W. Harrison, Alexey Sokolov, Akshatha Nayak, Jun Fan, Daniel Zerbino, Guy Cochrane and Paul Flicek
Published in: Frontiers in Genetics, vol12, 2021, ISSN 1664-8021
Publisher: 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)

Author(s): 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.
Published in: Genomics, 113 (2021), 2021, Page(s) 1705-1718, ISSN 0888-7543
Publisher: Academic Press
DOI: 10.1016/j.ygeno.2021.04.007

Evolution of the IRF Family in Salmonids

Author(s): Thomas C Clark , Pierre Boudinot , Bertrand Collet
Published in: Genes (This article belongs to the Special Issue Genetics and Genomics of Salmonid Fishes), 12(2), 2021, Page(s) 238, ISSN 2073-4425
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/genes12020238

Ensembl 2022

Author(s): 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
Published in: Nucleic Acids Research, 50 D1, 2022, Page(s) D988–D995, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab1049

Ensembl 2021

Author(s): 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
Published in: Nucleic Acids Research, 49/D1, 2020, Page(s) D884-D891, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa942

The European Nucleotide Archive in 2020

Author(s): 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
Published in: Nucleic Acids Research, 2020, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa1028

The European Nucleotide Archive in 2019

Author(s): 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
Published in: Nucleic Acids Research, 2019, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz1063

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

Author(s): Isabel García-Pérez, Anna Molsosa-Solanas, Miquel Perelló-Amorós, Elena Sarropoulou, Josefina Blasco, Joaquim Gutiérrez, and Daniel Garcia de la serrana
Published in: Cells, 11(3), 2022, Page(s) 428, ISSN 2073-4409
Publisher: MDPI
DOI: 10.3390/cells11030428

From FAANG to Fork: Application of Highly Annotated Genomes to Improve Farmed Animal Production

Author(s): Clark, Emily L.; Archibald, Alan L.; Daetwyler, Hans D.; AM, Martien Groenen; Harrison, Peter W.; Houston, Ross D.; Kuehn, Christa; Lien, Sigbjorn; Macqueen, Daniel J.; Reecy, James M.; Robledo, Diego; Watson, Mick; Tuggle, Christopher K.; Giuffra, Elisabetta
Published in: Genome Biology, 21, 2020, Page(s) 285 (2020), ISSN 1465-6906
Publisher: GenomeBiology.com
DOI: 10.20944/preprints202010.0118.v1