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The reference genome sequence represents a key resource for genetic studies of the target species. In 2009, two reference assemblies of the cattle (Bos taurus) genome, were published (Btau 4.0 and UMD 2.0). Both assemblies were upgraded several times since then. Highly polymorphic major histocompatibility complex (MHC) encodes proteins crucial for immune recognition and regulation of immune response in vertebrates. It is characterised by extensive nucleotide diversity, copy number variation of paralogous genes, and long repetitive sequences. In cattle, MHC is designated as BoLA (bovine leucocyte antigen), located on the chromosome 23. Its organisation differs from typical mammalian MHCs. The structural complexity makes it difficult to assemble a reliable reference sequence of this genomic region. Therefore, this region represents a good genomic model region to compare the accuracy of different assembly strategies. Recent advances in long-read sequence technology, combined with new scaffolding technologies, enabled issuing of the new bovine reference genome assembly build ARS-UCD 1.2, which is significantly improved over previous bovine genome assembly releases. In the current study the software tool Mauve for multiple alignment of conserved genomic sequences with rearrangements was used to identify the differences of genomic organization in the BoLA region assembled in three bovine reference genomes, Btau 5.0.1, UMD 3.1.1, and ARS-UCD 1.2. Multiple alignment of the bovine chromosome 23 sequences extracted from three genome assemblies revealed differences in the structure of the BoLA region. Segments encoding genes BOLA-DMA and BOLA-DQB are rearranged and inverted in the new assembly relative to the previous builds.

While mitochondriopathies, mitochondrial diseases, caused by mutations in mitochondrial DNA (mtDNA), are well documented in humans, single pathogenic mtDNA mutation or disorders are unknown in livestock populations. In a survey of 799 complete cattle mtDNAs belonging to more than 120 breeds two mutations, one in ND1 (C4171T) and the other in ND4L (T10663C) gene were identified, that are confirmed to be pathogenic in humans causing Leber's hereditary optic neuropathy (LHON). In one Cika cow with T10663C mutation, which was in humans reported to cause an acute onset of visual loss or/and many other LHON associated clinical manifestations, an exophthalmia of the right eye that might fit to the pathogenesis of LHON was observed. This work supports the existence of potentially detrimental mtDNA mutations in cattle, while aetiology and pathogenesis need to be further documented.