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https://eurofaang.eu/about

EuroFAANG is a concept development and conceptualization project for a European Functional Annotation of ANimal Genomes infrastructure to realise the full potential of genotype to phenotype (G2P) research across species, breeds and populations of farmed animal species in Europe. To achieve accurate G2P predictions, it is necessary to be able to refine and characterise highly complex traits as sets of intermediate informative phenotypes along the entire cascade from genome to cell, organism, environment, population and across different environments. The goal of the EuroFAANG infrastructure project is to develop concepts for streamlining the use of interdisciplinary capabilities for G2P research in terrestrial and aquatic farmed animals and to establish models for transnational access to the required wide portfolio of relevant facilities, expertise and knowledge to European stakeholders. This will address the need to bring together national facilities at the pan-European level in the field of animal genetic resources, phenotyping and breeding, and animal health, which was identified as a gap in the infrastructure landscape by the 2021 ESFRI Roadmap. The proposal builds on the foundation provided by the six current H2020 EuroFAANG projects, AQUA-FAANG, BovReg, GENE-SWitCH, GEroIMO, HOLORUMINANT and RUMIGEN, and connects with existing infrastructures for data management and animal agriculture in the European research infrastructure landscape. The six institutions and organisations currently developing the EuroFAANG infrastructure concept have comprehensive expertise in fundamental and applied farmed animal science and consolidated established connections to European stakeholders in farmed animal science. The outcomes of this project will lead to better alignment of the development of the research infrastructures landscape for the advancement of excellent farmed animal science and frontier G2P research in Europe and globally.
EuroFAANG
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Ensembl Rapid Release associated with GENE-SWitCH, AQUA-FAANG, BovReg, GEroNIMO, RUMIGEN

Species
Accession
Assembly submitted by
Annotation Proteins Transcripts Softmasked genome Repeat library Other data View in browser
Project
Bos gaurus GCA_014182915.1 USDA, ARS, USMARC GTF, GFF3FASTAFASTAFASTAFTP dumpsrapid.ensembl.org BovReg
Bos grunniens GCA_005887515.1 Lanzhou University GTF, GFF3FASTAFASTAFASTAFTP dumpsensembl.org BovReg
Bos indicus x Bos taurus GCA_003369695.2 University of Adelaide GTF, GFF3FASTAFASTAFASTAFTP dumpsensembl.org BovReg
Bos indicus x Bos taurus GCA_003369685.2 University of Adelaide GTF, GFF3FASTAFASTAFASTAFTP dumpsensembl.org BovReg
Bos mutus GCA_000298355.1 BGI-shenzhen GTF, GFF3FASTAFASTAFASTARepeatmodelerFTP dumpsensembl.org BovReg
Bos mutus (Datong Yak) GCA_007646595.3 Lanzhou University GTF, GFF3FASTAFASTAFASTAFTP dumpsrapid.ensembl.org BovReg
Bos taurus GCA_002263795.2 USDA ARS GTF, GFF3FASTAFASTAFASTARepeatmodelerFTP dumpsensembl.org BovReg
Cyprinus carpio carpio GCA_905221575.1 WAGENINGEN UR GTF, GFF3FASTAFASTAFASTAFTP dumpsensembl.org AQUA-FAANG
Danio rerio GCA_000002035.4 Genome Reference Consortium GTF, GFF3FASTAFASTAFASTARepeatmodelerFTP dumpsensembl.org AQUA-FAANG
Dicentrarchus labrax GCA_905237075.1 Hellenic Centre for Marine Research, Institute for Marine Biology, Biotechnology and Aquaculture, Heraklion, Crete, Greece GTF, GFF3FASTAFASTAFASTARepeatmodelerFTP dumpsensembl.org AQUA-FAANG
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Related Publications associated with GENE-SWitCH, AQUA-FAANG, BovReg, GEroNIMO, RUMIGEN

Title
Year
Journal
Secondary Project
Allele-biased expression of the bovine APOB gene associated with the cholesterol deficiency defect suggests cis-regulatory enhancer effects of the LTR retrotransposon insertion. 2022 Sci Rep BovReg
Biological Network Approach for the Identification of Regulatory Long Non-Coding RNAs Associated With Metabolic Efficiency in Cattle. 2019 Front Genet BovReg
Comparative Analysis of the Circular Transcriptome in Muscle, Liver, and Testis in Three Livestock Species. 2021 Front Genet BovReg
Genome-wide detection of selection signatures in Jianli pigs reveals novel cis-regulatory haplotype in EDNRB associated with two-end black coat color. 2024 BMC Genomics GENE-SWitCH
Identification and Annotation of Potential Function of Regulatory Antisense Long Non-Coding RNAs Related to Feed Efficiency in <i>Bos taurus</i> Bulls. 2020 Int J Mol Sci BovReg
Imprinting at the KBTBD6 locus involves species-specific maternal methylation and monoallelic expression in livestock animals. 2023 J Anim Sci Biotechnol GENE-SWitCH
Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using CAGE sequencing 2023 BovReg
Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing. 2023 G3 (Bethesda) BovReg
Integrated functional genomic analysis identifies the regulatory variants underlying a major QTL for disease resistance in European sea bass 2024 AQUA-FAANG
Loss of Monoallelic Expression of <i>IGF2</i> in the Adult Liver <i>Via</i> Alternative Promoter Usage and Chromatin Reorganization. 2022 Front Genet GENE-SWitCH
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Related Datasets associated with GENE-SWitCH, AQUA-FAANG, BovReg, GEroNIMO, RUMIGEN

Study name
Species
Archive
Assay type
Secondary Project
PRJEB34570 Bos taurus ENA RNA-seq of total RNA BovReg
PRJEB41576 Bos taurus ENA RNA-seq of coding RNA BovReg
PRJEB41822 Sus scrofa ENA methylation profiling by high throughput sequencing GENE-SWitCH
PRJEB41829 Gallus gallus ENA methylation profiling by high throughput sequencing GENE-SWitCH
PRJEB41970 Sus scrofa ENA RNA-seq of total RNA GENE-SWitCH
PRJEB42001 Sus scrofa ENA microRNA profiling by high throughput sequencing GENE-SWitCH
PRJEB42025 Gallus gallus ENA RNA-seq of total RNA GENE-SWitCH
PRJEB42041 Gallus gallus ENA microRNA profiling by high throughput sequencing GENE-SWitCH
PRJEB42772 Sus scrofa ENA methylation profiling by high throughput sequencing GENE-SWitCH
PRJEB42775 Gallus gallus ENA methylation profiling by high throughput sequencing GENE-SWitCH
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Related Files associated with GENE-SWitCH, AQUA-FAANG, BovReg, GEroNIMO, RUMIGEN

File name
Assay type
Experiment target
File size
Secondary Project
Download
ERR10003184_1.fastq.gz 4.48GB AQUA-FAANG
ERR10003184_2.fastq.gz 4.7GB AQUA-FAANG
ERR10003185_1.fastq.gz 4.52GB AQUA-FAANG
ERR10003185_2.fastq.gz 4.67GB AQUA-FAANG
ERR10003186_1.fastq.gz 3.59GB AQUA-FAANG
ERR10003186_2.fastq.gz 3.82GB AQUA-FAANG
ERR10003187_1.fastq.gz 3.35GB AQUA-FAANG
ERR10003187_2.fastq.gz 3.43GB AQUA-FAANG
ERR10003188_1.fastq.gz 3.77GB AQUA-FAANG
ERR10003188_2.fastq.gz 3.93GB AQUA-FAANG
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Related Organisms associated with GENE-SWitCH, AQUA-FAANG, BovReg, GEroNIMO, RUMIGEN

BioSamples ID
Species
Sex
Breed
Secondary Project
SAMEA10256251 TN60 GENE-SWitCH
SAMEA10256252 TN60 GENE-SWitCH
SAMEA10256253 TN60 GENE-SWitCH
SAMEA10256254 TN60 GENE-SWitCH
SAMEA10256255 TN60 GENE-SWitCH
SAMEA10256256 TN60 GENE-SWitCH
SAMEA10256257 TN60 GENE-SWitCH
SAMEA10256258 TN60 GENE-SWitCH
SAMEA10256259 TN60 GENE-SWitCH
SAMEA10256260 TN60 GENE-SWitCH
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Related Specimens associated with GENE-SWitCH, AQUA-FAANG, BovReg, GEroNIMO, RUMIGEN

BioSamples ID
Material
Organism part/Cell type
Sex
Species
Breed
Secondary Project
SAMEA10256411 specimen from organism liver Male Sus scrofa TN60 GENE-SWitCH
SAMEA10256412 specimen from organism liver Female Sus scrofa TN60 GENE-SWitCH
SAMEA10256413 specimen from organism liver Male Sus scrofa TN60 GENE-SWitCH
SAMEA10256414 specimen from organism liver Female Sus scrofa TN60 GENE-SWitCH
SAMEA10256415 specimen from organism liver Male Sus scrofa TN60 GENE-SWitCH
SAMEA10256416 specimen from organism liver Male Sus scrofa TN60 GENE-SWitCH
SAMEA10256417 specimen from organism liver Male Sus scrofa TN60 GENE-SWitCH
SAMEA10256418 specimen from organism liver Female Sus scrofa TN60 GENE-SWitCH
SAMEA10256419 specimen from organism liver Male Sus scrofa TN60 GENE-SWitCH
SAMEA10256420 specimen from organism liver Male Sus scrofa TN60 GENE-SWitCH
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Related Protocol Analysis associated with GENE-SWitCH, AQUA-FAANG, BovReg, GEroNIMO, RUMIGEN

Protocol Name
University Name
Protocol Year
Secondary Project
GENE SWitCH RRBS analysis WU 2021 GENE-SWitCH
GENE SWitCH WGBS analysis WU 2022 GENE-SWitCH
GENESWITCH WP2 isoseq gene annotation Roslin Institute (Edinburgh, UK) 2021 GENE-SWitCH
GENESWITCH WP2 isoseq gene annotation V2 Roslin Institute (Edinburgh, UK) 2022 GENE-SWitCH
srnaseq-processing INSERM-INRAE 2021 GENE-SWitCH
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