Figure 2.

Evidence of Meiotic Irregularities and Homoeologous Exchange in the Synthetic Allopolyploid.

Examples of individual dosage plots. Sequencing reads were aligned to the reference genome and sorted into consecutive bins along the 13 chromosomes of the allopolyploid genome. For ease of visualization, relative read coverage is normalized such that dosage plots of fragments present in two copies fluctuated around 2.0. Changes up or down in relative coverage of consecutive bins indicates variation in dosage and correspond to the addition or deletion of a particular chromosome or chromosomal fragment, respectively. Relative coverage around the centromeric repeats consistently appears noisy most likely because of mis-mapping, quality of reference sequence, and changes in repeated elements. Gray arrows indicate aneuploidy of a whole or segment of a chromosome. The black arrow indicates an example of a complex dosage variation (part of a chromosome is present in one copy and another part is present in three copies). Compensating dosage variants, in which one chromosome fragment is missing and the corresponding homoeologous fragment from the other genome is present in three copies, are indicated by circles.