Short communication, Note
https://doi.org/10.5513/JCEA01/20.4.2679
The new bovine reference genome assembly provides new insight into genomic organization of the bovine major histocompatibility complex
Minja Zorc
; University of Ljubljana, Biotechnical Faculty, Department of Animal Science, Jamnikarjeva 101 SI-1000 Ljubljana, Slovenia
Jernej Ogorevc
; University of Ljubljana, Biotechnical Faculty, Department of Animal Science, Jamnikarjeva 101 SI-1000 Ljubljana, Slovenia
Peter Dovc
orcid.org/0000-0002-7418-0054
; University of Ljubljana, Biotechnical Faculty, Department of Animal Science, Jamnikarjeva 101 SI-1000 Ljubljana, Slovenia
Abstract
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.
Keywords
BoLA; Bos taurus; genome assembly; optical map; reference genome
Hrčak ID:
230871
URI
Publication date:
19.12.2019.
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