BovReg

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The BovReg consortium aims to provide a comprehensive map of functionally active genomic features in cattle and how their (epi)genetic variation in beef and dairy breeds translates into phenotypes. This constitutes key knowledge for biology-driven genomic prediction needed by scientific and industry livestock communities.

BovReg brings together a critical mass of experts in ruminant research and beyond encompassing bioinformatics, molecular and quantitative genetics, animal breeding, reproductive physiology, ethics and social science. 20 partners from the EU, Canada and Australia form a global interdisciplinary team, which builds on previous and running national and EU-funded projects and many established industry cooperations. Datasets will be shared and coordinated with other FAANG initiatives via the FAANG data coordination centre.

Ensembl is a partner in the BovReg 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
Bos taurus GCA_002263795.2 USDA ARS GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Bos gaurus GCA_014182915.1 USDA, ARS, USMARC GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org
Bos grunniens GCA_005887515.1 Lanzhou University GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Bos indicus x Bos taurus GCA_003369695.2 University of Adelaide GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Bos mutus GCA_000298355.1 BGI-shenzhen GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org
Bos mutus (Datong Yak) GCA_007646595.3 Lanzhou University GTF, GFF3 FASTA FASTA FASTA FTP dumps rapid.ensembl.org
Bos indicus x Bos taurus GCA_003369685.2 University of Adelaide GTF, GFF3 FASTA FASTA FASTA FTP dumps ensembl.org