Cattle

Cattle are one of the most populous farmed animals worldwide, with their global population of almost one billion second only to chickens. They provide a significant source of nutrition and livelihood to over 6 billion people. Hundreds of distinct cattle breeds have been established, displaying a diverse range of heritable phenotypes, from differences in production phenotypes such as milk yield, to environmental adaptation, disease tolerance and altered physical characteristics such as horn shape and skin pigmentation.

BOmA Cattle Browser presents data in Talenti et al., with five cattle reference genomes, the expanded ARS-UCD1.2+ genome augmented with sections of the pan-genome not present in the Hereford assembly and the results of various downstream analyses.

The genomes Angus, Hereford, Ankole, N’Dama and Brahman have the following tracks:

ATAC-seq peaks called using the Genrich pipeline on four libraries (B-cell libraries for 1 Holstein-Friesian, 1 N’Dama and 1 Nelore and 1 Holstein-Friesian nucleosome-free library).
Heatmaps of the presence of alignments to genomic segments in the other assemblies (four tracks for each genome) with values of -1 (no alignment) and 1 (alignment).

The genome Hereford (ARS-UCD1.2) and ARS-UCD1.2+ have the following tracks:

Bionano optical mapping structural variant (SV) calls for two N’Dama samples
Variants called on the VG5p graph for nine short-read samples (3 Angus, 3 N’Dama and 3 Sahiwal)
ATAC-seq peaks as described above.
Heatmaps of the presence of alignments to the other assemblies (four tracks) with values of -1 (no alignment) and 1 (alignment).