Third-generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants

Long-read assembly reveals previously unknown inversions and the centromere location on Chr IV in T. gondii. (A) Inversion in the RH88 long-read assembly on Chromosome III relative to the ToxoDB-48_TgGT1 assembly. (B) Inversion in the ME49 long-read assembly on Chromosome XII relative to the ToxoDB-44_TgME49 genome. (C) Dot plot comparison of the TgRH88 long-read assembly and the ToxoDB-48_TgGT1 genome showing a 429.3-kb inversion at 2,096,529–2,525,795 bp on Chr IV. (D) Intra-chromosomal Hi-C contact-count heat map plotted using the sequence of tig00000014 in TgRH88 long-read assembly showing a clear centromere signal at position 2.2–2.3 Mb. (E) ChIP-on-chip signal of centromeric histone 3 variant (CenH3) (Brooks et al. 2011) plotted using the TgRH88 long-read assembly as coordinate.