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Fig. 6 | Genome Biology

Fig. 6

From: Graph construction method impacts variation representation and analyses in a bovine super-pangenome

Fig. 6

A polymorphic eVNTR discovered from the pangenomes. a VNTR repeat motif and b number of repeat units in the twelve input assemblies. c Bandage plots of a VNTR upstream SPACA7. BLAST hits for the top 5 most common VNTR motifs are coloured per motif. d Genes (black) and (long) non-coding RNAs (dark grey) nearby the VNTR. Blue colour indicates the position of the VNTR. Arrows indicate the orientation of genes and lncRNA. Red colour indicates two genes and five lncRNAs whose expression is associated with the VNTR. e–k Expression (quantified in transcripts per million (TPM)) of the associated genes and ncRNAs in testis tissues of 83 Brown Swiss bulls that are either homozygous for hap1 (H1/H1), homozygous for hap2 (H2/H2) or heterozygous (H1/H2). The number of animals per diplotype is below the boxplots. l Cis-expression QTL mapping for LOC112449094. Different colours indicate the pairwise linkage disequilibrium (r2) between the VNTR haplotype (violet) and all other variants. m Correlation between the abundance of mRNA and lncRNA for the associated genes and lncRNA. n Allelic imbalance of nine heterozygous exonic SNPs in LOC112449094 in testis tissue from a Nellore x Brown Swiss crossbred bull. Orange and blue colours represent paternal (Nellore) and maternal alleles (Brown Swiss)

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