Fig. 5: Selection signatures for domestication.
From: Telomere-to-telomere genome assembly of a male goat reveals variants associated with cashmere traits
a Geographic distributions of domestic and wild (including bezoars) goats all over the world whose whole genome sequencing datasets are used in this study. b Genome-wide selective signals based on SNPs and FST between bezoars and the domestic goats. A horizontal dash line is used to show the top 1% selective signals. The selective signals in the PURs are highlighted in blue bars. The gene symbols are shown in black for the ones identified by both T2T-goat1.0 and ARS1, and the ones only by T2T-goat1.0 in purple. NKG2D in red uniquely identified by T2T-goat1.0 is selected to be demonstrated as followed. c Venn plot of selective regions based on SNPs and top 1% FST values between T2T-goat1.0 and ARS1 as references. d Selective region with tandem NKG2D genes on chromosome 9 (Chr09) based on the FST and π ratio of bezoars and domestic goats. e Syntenic plotting of the region with NKG2D genes on Chr09 between T2T-goat1.0 and ARS1. The selective region highlighted in blue is exactly located inside the region where tandem NKG2D genes are not assembled well in ARS1. f Collinearity of the region with tandem NKG2D genes on Chr09 between T2T-goat1.0 and ARS1. The tandem NKG2D genes in T2T-goat1.0 were found to correspond to the homologous genes not only on Chr09 of ARS1, but also on the three unplaced contigs. g Tandem NKG2D genes are in accordance with SDs and show their expressions in blood and spleen. h Selective signals based on SVs and FST between bezoars and the domestic goats. The plot is made based on the same method to that of Fig. 5b. i Venn plot of selective genes that overlapped with selective regions based on top 1% FST values of SVs identified by T2T-goat1.0 and ARS1. j A deletion was confirmed within ABCC4 (IMCG12g00097) of bezoars in IGV.
