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. 2019 Apr 26;212(2):469–487. doi: 10.1534/genetics.119.302232

Figure 9.

Figure 9

Abundant copy-number variation at the pseudoautosomal boundary in wild house mice. (A) Copy number in the distal X chromosome, estimated from whole-genome sequencing read depth in 1-kb bins, for representative individuals of M. m. domesticus (dom, blue), M. m. musculus (mus, red), and M. m. castaneus (cas, green). Inferred sex-chromosome karyotype is shown for each individual. Dashed lines show the boundaries of the CAST/EiJ extended and canonical pseudoautosomal regions (PARs), respectively. Canonical PAR is shaded gray. Deletions adjacent to the PAR boundary in M. m. castaneus are indicated with red arrowheads. (B) Distinct copy-number alleles ascertained from breakpoint-spanning reads in 67 wild mice. Each allele is represented as a rectangle extending from the proximal breakpoint up to the pseudoautosomal boundary, and is shown in proportion to the number of times it is observed in our sample. (C) Transcripts of the Mid1 gene from Ensembl release 96. (D) Repeat elements annotated in the mm10 reference by the University of California Santa Cruz Genome Browser. (E) Recombination hotspots ascertained in C57BL/6J (B6), CAST/EiJ (CAST), and F1 males (Baker et al. 2015).