Long-read assembly identifies 13 chromosomes in the T. gondii genome from multiple strains. (A) Dot plot showing the comparison of the TgME49 long-read assembly and the ToxoDB-48_TgME49 genome. Red box shows that the Chromosomes VIIb and VIII in the ToxoDB-48_TgME49 genome are fused in a single contig, TgME49_tig00000001_ChrVIII, in the TgME49 long-read assembly. (B) Coverage of the “breakpoint” (TgME49_tig00000001_ChrVIII: 5,090,422 bp, indicated by a vertical red line) of Chromosomes VIIb and VIII with 37 Nanopore reads in the TgME49 long-read assembly. (C) Coverage of the edges (indicated by a vertical red line) of Chromosomes VIIb and VIII with 105 Nanopore reads mapped to the ToxoDB-48_TgME49 genome. (D) Nanopore reads mapping to the end of Chromosomes IX and X in the ToxoDB-48_TgME49 genome assembly, showing that Nanopore reads only map to the end of each chromosome and do not span the junction between these chromosomes (indicated by a vertical red line). (E) Inter-chromosomal Hi-C contact-count heat map plotted using the TgME49 initial long-read assembly sequence showing 13 chromosomes in the assembly. (F) Intra-chromosomal Hi-C contact-count heat map plotted using the sequence of TgME49_tig00000001 in the TgME49 initial long-read assembly showing no aberrant signal along the contig.