Fig. 7: Identification of structural variation in coding sequences of QRICH2, TAS2R46 and PRDM9 through the HiFi-based pangenome. | Nature Communications

Fig. 7: Identification of structural variation in coding sequences of QRICH2, TAS2R46 and PRDM9 through the HiFi-based pangenome.

From: Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies

Fig. 7

a Pangenome topology in the fifth exon of bovine QRICH2 revealed tandem repeats of 30 bp sequence. b Nucleotide (upper) and protein (lower) sequence logo plot of the repeat motif. c While the ARS-UCD1.2 reference sequence contains 15 copies of the repeat motif, the pangenome revealed 1, 5, and 6 additional copies in the five haplotype-resolved assemblies (A—ARS-UCD1.2, B—Brown Swiss, O—Original Braunvieh, P—Piedmontese, N—Nellore, G—gaur). d Representation of a 17 kb deletion on BTA5 encompassing TAS2R46 and ENSBTAG00000001761. e Coverage of binned HiFi (above horizontal line) and ONT (below horizontal line) long read alignments in gaur indicate a large deletion between 98,587,384 and 98,604,401 bp. f Pangenome topology at the eleventh exon of PRDM9 indicating paths with gain and loss of 84 bp sequence. g Representation of the domains of PRDM9 in the haplotype-resolved assemblies including a variable number of zinc fingers (ZF) in the different assemblies, where Om and Op are the maternal and paternal haplotypes of the OxO.

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