(A) Read depth ratio of male and female Pachón genomic pools showing a strong coverage bias in a single scaffold, Hi_scaffold_28 (enlarged in A’ inset showing male and female read coverage).
(B) Karyoplots of the A chromosome regions duplicated on the Pachón cavefish B (Chr B) showing that the Pachón B is made from a complex mosaic of duplicated A chromosomal fragments.
(C and D) Comparison of the repeat landscapes of the Pachón B (C) and whole genome including the B (D), showing that the Pachón B has a very different repeat element (color code provided in inset of D) content compared to A chromosomes. Short interspersed repeated sequences, SINEs; long interspersed nuclear elements, LINEs; long terminal repeats, LTRs; DNA repeat elements, DNAs; terminal inverted repeat sequences, TIRs.
See also Figures S2A and S2B and Data S1D for additional details.