(A) Short read alignments of Ler against the reference sequence at position 13,957,178 on chromosome 1. Individual reads are shown as blue lines, while mismatches between reference sequence and short reads are colored according to mismatch types. Three distinct Ler haplotypes align to this region, indicating that this sequence is present in triplicate in the Ler genome. As Ler is homozygous, at least two haplotypes were not aligned to their respective origin. (B) The genomic landscape of the two insertion sites of an ∼80 kb transposition between Ler and Col. Blue and red boxes mark sequences that are unique to Ler and Col respectively. Green boxes highlight the transposed (and inverted) DNA. Genes annotated in Col are shown in grey. (C) Graphical genotypes of chromosome 3 of the four genomes of tetrad 58 (Col-derived genomic regions are shown in red, Ler regions in blue). Cvi sequences are not shown. Grey arrows indicate the insertion sites of the transposition illustrated in B. Tetrad 58_1 and tetrad 58_2 formed a crossover between these insertion sites. As a result, tetrad 58_1 lost all transposed sequences, whereas in tetrad 58_2 the transposed DNA is duplicated. (D) Short read alignments of all four genomes of tetrad 58 to chromosome 3 at positions 22,565,274 to 22,565,374, which overlap the transposed DNA. This region includes two closely linked SNPs that can distinguish all three parental alleles (black dots indicate mismatches to the reference sequence). The reads that can be assigned to one of the three parents are shown by different colors. Tetrad 58_1, which lost the transposed DNA, shows the absence of Col and Ler derived reads, whereas tetrad 58_2, which inherited both transposed regions, shows the presence of both Col and Ler alleles in this region. (E) Redrawing of the graphical genotypes of six Col-Ler F2 offspring, as presented in the appendix of Yang et al. (2012). These offspring experienced a putative double CO, co-localizing with the Col insertion site of above-mentioned transposition. Note that in all six F2 offspring, at least one of the recombinant chromosomes features a CO between the transposition sites. This suggests that the annotated double recombinations are not real, but that the observed patterns originate from copy number variation due to transposed DNA.