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To further the understanding of the evolution of transcriptional regulation, we profiled genome-wide transcriptional start sites ( TSSs ) in two sub-species,  Bos taurus taurus  and  Bos taurus indicus , that diverged approximately 500,000 years ago. Evolutionary and developmental-stage differences in TSSs were detected across the sub-species, including translocation of dominant TSS and changes in TSS distribution. The 16% of all SNPs located in significant differentially used TSS clusters across sub-species had significant shifts in allele frequency (472 SNPs), indicating they may have been subject to selection. In spleen and muscle, a higher relative TSS expression was observed in  Bos indicus  than  Bos taurus  for all heat shock protein genes, which may be responsible for the tropical adaptation of  Bos indicus .

Evolution of tissue and developmental specificity of transcription start sites in Bos taurus indicus