Contiguity of the goat genome assembly enables comparative analyses and gene discovery within the repetitive immune-related regions

Authors: SCHWARTZ, JOHN - The Pirbright Institute; SANDERSON, NICHOLAS - The Pirbright Institute; PHILP, REBECCA - The Pirbright Institute; Bickhart, Derek; Smith, Timothy - Tim; HAMMOND, JOHN - The Pirbright Institute

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 10/4/2018
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Highly repetitive regions of the genome are notoriously difficult to assemble in whole genome sequencing attempts, resulting in gene complexes that are either heavily disrupted with many sequence gaps, incorrectly assembled, or missing a large amount of sequence. Many such regions encode genes that are integral to immune system functions, are under strong selective pressures, and as such, among the most quickly evolving regions of the genome. In the recent high-quality goat assembly (ARS1), we have characterized six immune-related gene clusters that are largely intact on single contigs: the three antibody loci, the natural killer complex (NKC), and the leukocyte receptor complex (LRC). Comparative analyses have identified a novel immunoglobulin-like receptor gene family across non-primate and non-rodent species, and the independent expansion of the killer cell immunoglobulin-like receptors (KIR) in sheep and goats compared to cattle. These accurate gene models have enabled us to examine transcription, revealing a diverse gene expression profile across different immune and non-immune tissue compartments. These results will help inform future species-specific studies that investigate the role of these receptors in livestock health and disease.