GENE-SWitCH
GENE-SWitCH aims to deliver new underpinning knowledge on the functional genomes of two main monogastric farm species (pig and chicken) and to enable immediate translation to the pig and poultry sectors.
The GENE-SWitCH consortium brings together partners representing pan-European excellence (including the academic institutions which pioneered FAANG) and world-leading animal breeding and biotech industry in a true co-creation effort. Overall, GENE-SWitCH will contribute to the global FAANG effort considerably, demonstrate how functional annotation of genomes can foster the advancement of genomic selection for immediate benefit to the breeding industry, and produce cutting-edge research paving the way to new studies and strategies for sustainable productions. Datasets will be shared and coordinated with other FAANG initiatives via the FAANG data coordination centre.
Ensembl is a partner in the GENE-SWitCH project, and we annotate the protein-coding and non-coding RNA gene structures using a re-engineered version of our Gene Annotation System (Aken et al, 2017). After QC, genomes and annotations are made available via our FTP site (see table below) before subsequently being made available in the Ensembl Genome Browser.
| Species | Accession | Assembly submitted by | Annotation | Proteins | Transcripts | Softmasked genome | Repeat library | Other data | View in browser |
|---|---|---|---|---|---|---|---|---|---|
| Sus scrofa (pig - e102) | GCA_000003025.6 | The Swine Genome Sequencing Consortium (SGSC) | GTF, GFF3 | FASTA | FASTA | FASTA | Repeatmodeler | FTP dumps | ensembl.org |
| Sus scrofa (pig - e107) | GCA_000003025.6 | The Swine Genome Sequencing Consortium (SGSC) | GTF, GFF3 | FASTA | FASTA | FASTA | Repeatmodeler | FTP dumps | rapid.ensembl.org |
| Gallus gallus (jungle fowl - e102) | GCA_000002315.5 | Genome Reference Consortium | GTF, GFF3 | FASTA | FASTA | FASTA | Repeatmodeler | FTP dumps | ensembl.org |
| Gallus gallus (jungle fowl - e107) | GCA_000002315.5 | Genome Reference Consortium | GTF, GFF3 | FASTA | FASTA | FASTA | Repeatmodeler | FTP dumps | rapid.ensembl.org |
| Gallus gallus (broiler - e107) | GCA_016699485.1 | Vertebrate Genomes Project | GTF, GFF3 | FASTA | FASTA | FASTA | Repeatmodeler | FTP dumps | rapid.ensembl.org |
| Gallus gallus (layer - e107) | GCA_016700215.2 | Vertebrate Genomes Project | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | rapid.ensembl.org |
| Sus scrofa (bamei - e102) | GCA_001700235.1 | Novogene | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | ensembl.org |
| Sus scrofa (berkshire - e102) | GCA_001700575.1 | Novogene | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | ensembl.org |
| Sus scrofa (hampshire - e102) | GCA_001700165.1 | Novogene | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | ensembl.org |
| Sus scrofa (jinhua - e102) | GCA_001700295.1 | Novogene | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | ensembl.org |
| Sus scrofa (landrace - e102) | GCA_001700215.1 | Novogene | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | ensembl.org |
| Sus scrofa (largewhite - e102) | GCA_001700135.1 | Novogene | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | ensembl.org |
| Sus scrofa (meishan - e102) | GCA_001700195.1 | Novogene | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | ensembl.org |
| Sus scrofa (pietrain - e102) | GCA_001700255.1 | Novogene | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | ensembl.org |
| Sus scrofa (rongchang - e102) | GCA_001700155.1 | Novogene | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | ensembl.org |
| Sus scrofa (tibetan - e102) | GCA_000472085.2 | Novogene | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | ensembl.org |
| Sus scrofa (usmarc - e102) | GCA_002844635.1 | USDA ARS | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | ensembl.org |
| Sus scrofa (wuzhishan - e102) | GCA_000325925.2 | BGI-shenzhen | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | ensembl.org |