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

Primary de novo assembly of TgRH88 genome using Nanopore reads revises T. gondii karyotype. (A) Bivariate plot showing a comparison of the aligned read length with the sequenced read length. (B) Bivariate plot showing a comparison of the aligned–corrected read length (log₁₀-transformed) with the percentage identity. In this case, corrected reads refer to the method deployed by Canu using read overlap. (C) Histogram showing comparison of chromosome size between the ToxoDB-48_TgGT1 genome and TgRH88 initial long-read assembly. (D) Inter-chromosomal Hi-C contact-count heat map plotted using the TgRH88 initial long-read assembly sequence showing 13 chromosomes in the assembly. (E) Intra-chromosomal Hi-C contact-count heat map plotted using the sequence of TgRH88_tig00000001 in TgRH88 initial long-read assembly showing no aberrant signal along the contig.