Reevaluation of the Toxoplasma gondii and Neospora caninum genomes reveals misassembly, karyotype differences, and chromosomal rearrangements

Abstract

Neosporacaninum primarily infects cattle, causing abortions, with an estimated impact of a billion dollars on the worldwide economy annually. However, the study of its biology has been unheeded by the established paradigm that it is virtually identical to its close relative, the widely studied human pathogen Toxoplasma gondii. By revisiting the genome sequence, assembly, and annotation using third-generation sequencing technologies, here we show that the N. caninum genome was originally incorrectly assembled under the presumption of synteny with T. gondii. We show that major chromosomal rearrangements have occurred between these species. Importantly, we show that chromosomes originally named Chr VIIb and VIII are indeed fused, reducing the karyotype of both N. caninum and T. gondii to 13 chromosomes. We reannotate the N. caninum genome, revealing more than 500 new genes. We sequence and annotate the nonphotosynthetic plastid and mitochondrial genomes and show that although apicoplast genomes are virtually identical, high levels of gene fragmentation and reshuffling exist between species and strains. Our results correct assembly artifacts that are currently widely distributed in the genome database of N. caninum and T. gondii and, more importantly, highlight the mitochondria as a previously oversighted source of variability and pave the way for a change in the paradigm of synteny, encouraging rethinking the genome as basis of the comparative unique biology of these pathogens.

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

“…This karyotype that is robustly supported by our assemblies are consistent with existing Hi-C data (Bunnik et al 2019) and existing genetic linkage maps from F1 progeny derived from type IxII and IxIII crosses (Khan et al 2005;Khan et al 2014). Similar results were obtained in a cosubmitted manuscript appearing in this same issue (Berná et al 2021).…”

“…8B). Similar chromosomal rearrangement patterns were observed in other N. caninum strains (as described in the cosubmitted paper [Berná et al 2021]).…”

Compilation of parasitic immunogenic proteins from 30 years of published research using machine learning and natural language processing

“…Most parasite sequences are predicted from poor quality genomes. For example, a recent study 79 reveals misassembly, karyotype differences, and chromosomal rearrangements of the T. gondii and Neospora caninum genomes following a re-evaluation. These genomes were originally sequenced using conventional Sanger sequencing technology 80 i.e., first generation sequencing.…”

“…TGS potentially provides this solution but has a higher sequencing error rate and systematic error than NGS 83 . Nevertheless, the recent combination of NGS and TGS data with the advances in assembly technologies has resulted in greatly improved genome sequence quality, which is epitomised by the new TGS-derived T. gondii and N. caninum genomes 79 . An increase in quality parasite genomes ultimately equates to reverse vaccinology progressing towards its full potential.…”

Paving the Way: Contributions of Big Data to Apicomplexan and Kinetoplastid Research

“…T. gondii is the only species of the Toxoplasma genus ( Tenter et al., 2000 ; Dubey, 2010 ). T. gondii’s genome is 65 Mb, encoding ~8,000 genes throughout 13 chromosomes [previously annotated chromosomes VIIb and VIII are now a single chromosome ( Lorenzi et al., 2016 ; Berná et al., 2021 )]. The T. gondii genome contains multiple repetitive and low-complex regions evenly distributed across chromosomes ( Berná et al., 2021 ).…”