The genome assembly and RefSeq gene annotation data were downloaded from the NCBI ftp site:
https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/
For BovineMine and JBrowse we converted chromosome identifiers in the assembly file to numbers and letters (1-29, MT, X, Y), but kept RefSeq accessions for unassigned scaffolds:
Assembly file:
GCF_002263795.3_ARS-UCD2.0_genome_refseq_chrids.fa.gz
We reformatted gff3 files to meet our requirements for BovineMine and JBrowse. We separated the genes into three files: protein coding, noncoding and pseudogenes. For the RefSeq gff3 files, we renumbered the chromosomes as described above. For the Ensembl gff3 files, we changed the ids of the unassigned scaffolds from GenBank ids to RefSeq ids.
RefSeq gff3 files:
GCF_002263795.3-RS_2024_12_refseq_noncoding.gff3.gz
GCF_002263795.3-RS_2024_12_refseq_proteincoding.gff3.gz
GCF_002263795.3-RS_2024_12_refseq_pseudogenes.gff3.gz
Ensembl GFF3 files:
Bos_taurus.ARS-UCD2.0.114_ensembl_noncoding.gff3.gz
Bos_taurus.ARS-UCD2.0.114_ensembl_proteincoding.gff3.gz
Bos_taurus.ARS-UCD2.0.114_ensembl_pseudogenes.gff3.gz
Curated Bovine Selective Sweeps: