Sequenced Breakpoints of Crossover Suppressor/Inversion qC1

Abstract

We used whole-genome sequencing (WGS) data from a number of balanced lethal strains in Caenorhabditis elegans to show that the crossover suppressor qC1 is an inversion. The rearrangement is complex, with a large primary inversion that contains several other smaller inverted regions. The graphical representation below depicts these various qC1 rearrangements for ease of conceptualization. It is the simplest chromosomal structure compatible with the data currently available, but even then it is worth noting that the complexity of the qC1 chromosome can make the graphical reconstruction difficult to understand, and it may seem a bit like relativity theory or artwork from M.C. Escher (https://moa.byu.edu/m-c-eschers-relativity/).

Figure 1. Chromosome III in the qC1 balancer

(A) Breakpoint connections deduced by aligning split reads at the breakpoints. Identical strands indicates that the sequence on the left is connected directly to the sequence on the right, while different strands denotes a change of strand (inversion). Genes affected by the breakpoints are listed in the third column. (B) A schematic representation of chromosome III deduced for qC1 is shown. Each arrow represents the chromosomal segment of the reference sequence with the corresponding coordinates listed. The direction and color of each arrow represent the strand/direction of the sequence within the original reference chromosome. For simplicity of visualization, the complex rearrangement around 6.6Mb is shown separately. (C) A further simplified schematic representation of the chromosome rearrangements in qC1. Only the genomic segment represented in red is inverted relative to the wild-type chromosome III. Genes at breakpoints are indicated and the asterisks linked with the black wavy arrow represent the complex structural variation near 6.6Mb.