Fig. 2: Detection of polymorphic ERVs and de novo ERV mobilization events in the Damona pedigree.
a ERVK elements - including the ERVK[2-1-LTR] clade - are overrepresented amongst polymorphic ERVs detected with LocaTER when compared to their abundance (relative to other ERV elements) in the bovine genome, supporting their youth. b ERVs are overrepresented in intergenic regions, or – when genic – in antisense (as opposed to sense) orientation, when compared to the corresponding genome space, supporting purifying selection. Two-sided p-values (< 10−6) were determined from the outcome of > 106 random samples with probabilities of success corresponding to the genomic expectations (sample() function in R). c The Damona pedigree comprises 743 whole genome sequenced animals constituting 127 pedigrees with at least three generations: parents, offspring and (≥ 5) grand-offspring. De novo mutations (including ERV mobilization events; blue triangle) are detected by their absence in the parents, presence in the offspring, and transmission to some grand-offspring. Linkage with a grand-parental chromosome (sire’s blue chromosome in the example) allows assignment of the de novo event to the sire’s or the dam’s germline. d Description of the five de novo ERVK[2-1-LTR] insertions, with, from left to right: (i) chromosomal position (ARS-UCD1.2 genome assembly), (ii) genome compartment, (iii) when genic, orientation with respect to the affected gene, (iv) when genic, gene symbol of the affected gene, (v) parental germline in which the insertion occurred: Dam (blue) or Sire (red) with numbers identifying individuals according to Supplementary Fig. 3 (three de novo insertions occurred in Sire 1; the * identifies the two insertions that were co-transmitted in the same gamete, (vi) Mendelian transmission to “x” (2 or 3) out of five grand-offspring (G-off). Source data are provided as a Source Data file.
