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

Xia, Jing; Venkat, Aarthi; Bainbridge, Rachel E.; Reese, Michael L.; Roch, Karine G. Le; Ay, Ferhat; Boyle, Jon P.

doi:10.1101/gr.262816.120

Cited by 25 publications

(23 citation statements)

References 66 publications

(83 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…3 A). CenH3 localized to 13 different loci and was absent from Chromosome VIIb, consistent with the revised genome of T. gondii containing 13 chromosomes [ 26 ]. Further work is required to determine whether CenH3 and H3.3 are part of the same nucleosome within a double variant heterodimer of CenH3 and H3.3, or if T. gondii centromeres consist of interspersed CenH3 and H3.3-containing nucleosomes that may in turn be enriched at different phases of the cell cycle [ 27 ].…”

Section: Resultssupporting

confidence: 68%

Genome-wide localization of histone variants in Toxoplasma gondii implicates variant exchange in stage-specific gene expression

et al. 2022

View full text Add to dashboard Cite

Background Toxoplasma gondii is a protozoan parasite that differentiates from acute tachyzoite stages to latent bradyzoite forms in response to environmental cues that modify the epigenome. We studied the distribution of the histone variants CenH3, H3.3, H2A.X, H2A.Z and H2B.Z, by genome-wide chromatin immunoprecipitation to understand the role of variant histones in developmental transitions of T. gondii parasites. Results H3.3 and H2A.X were detected in telomere and telomere associated sequences, whereas H3.3, H2A.X and CenH3 were enriched in centromeres. Histones H2A.Z and H2B.Z colocalize with the transcriptional activation mark H3K4me3 in promoter regions surrounding the nucleosome-free region upstream of the transcription start site. The H2B.Z/H2A.Z histone pair also localizes to the gene bodies of genes that are silent but poised for activation, including bradyzoite stage-specific genes. The majority of H2A.X and H2A.Z/H2B.Z loci do not overlap, consistent with variant histones demarcating specific functional regions of chromatin. The extent of enrichment of H2A.Z/H2B.Z (and H3.3 and H2A.X) within the entire gene (5’UTR and gene body) reflects the timing of gene expression during the cell cycle, suggesting that dynamic turnover of H2B.Z/H2A.Z occurs during the tachyzoite cell cycle. Thus, the distribution of the variant histone H2A.Z/H2B.Z dimer defines active and developmentally silenced regions of the T. gondii epigenome including genes that are poised for expression. Conclusions Histone variants mark functional regions of parasite genomes with the dynamic placement of the H2A.Z/H2B.Z dimer implicated as an evolutionarily conserved regulator of parasite and eukaryotic differentiation.

show abstract

Section: Resultssupporting

confidence: 68%

Genome-wide localization of histone variants in Toxoplasma gondii implicates variant exchange in stage-specific gene expression

et al. 2022

View full text Add to dashboard Cite

show abstract

“…The total haploid genome of T. gondii contains 13 chromosomes, with a total genome size of about 65 million base pairs (Mbp) and more than 8300 protein coding genes identified ( Lorenzi et al., 2016 ; Xia et al., 2021 ). The genome-wide polymorphism rate between the three archetypal clonal lineages has been estimated to be approximately 1%, characterized by an extensive bi-allelism falling into type I, II and III single nucleotide polymorphisms (SNP) ( Grigg et al., 2001 ; Khan et al., 2005 ; Boyle et al., 2006 ; Sibley and Ajioka, 2008 ).…”

Section: Toxoplasma Gondii a Complex Organism With Complex ...mentioning

confidence: 99%

Toxoplasma gondii Genotyping: A Closer Look Into Europe

Fernández‐Escobar

Schares

Maksimov

et al. 2022

Front. Cell. Infect. Microbiol.

View full text Add to dashboard Cite

Toxoplasma gondii is a major zoonotic agent which may cause harmful effects mainly in pregnant and immunocompromised hosts. Despite many efforts on its genetic characterization, an entirely clear picture of the population structure in Europe has not been achieved yet. The present study aimed to summarize the available genotyping information and to map the distribution of circulating strains. There is consensus on type II T. gondii genotypes prevailing in Europe, but the absence of harmonization in the use of typing methods limits detailed knowledge. Standardized, high-end typing tools and integrative strategies are needed to fill the gaps and complete an accurate image of the T. gondii genetic population in Europe.

show abstract

“…However, there are notable exceptions; the mitochondrial genome of coccidians being a beautifully illustrative example. From PacBio and ONT sequencing the number of nuclear chromosomes of both T. gondii and N. caninum was reduced from 14 to 13, and important chromosomal rearrangements between both species were described (Berná et al, 2021;Xia et al, 2021). However, none of the mitochondrial genomes could be completely resolved; neither have been conclusively resolved the level at which the diversity exists nor the mechanisms underlying this diversity.…”

Section: Cox1 Cox3 and Cobmentioning

confidence: 99%

The Elusive Mitochondrial Genomes of Apicomplexa: Where Are We Now?

2021

View full text Add to dashboard Cite

Mitochondria are vital organelles of eukaryotic cells, participating in key metabolic pathways such as cellular respiration, thermogenesis, maintenance of cellular redox potential, calcium homeostasis, cell signaling, and cell death. The phylum Apicomplexa is entirely composed of obligate intracellular parasites, causing a plethora of severe diseases in humans, wild and domestic animals. These pathogens include the causative agents of malaria, cryptosporidiosis, neosporosis, East Coast fever and toxoplasmosis, among others. The mitochondria in Apicomplexa has been put forward as a promising source of undiscovered drug targets, and it has been validated as the target of atovaquone, a drug currently used in the clinic to counter malaria. Apicomplexans present a single tubular mitochondria that varies widely both in structure and in genomic content across the phylum. The organelle is characterized by massive gene migrations to the nucleus, sequence rearrangements and drastic functional reductions in some species. Recent third generation sequencing studies have reignited an interest for elucidating the extensive diversity displayed by the mitochondrial genomes of apicomplexans and their intriguing genomic features. The underlying mechanisms of gene transcription and translation are also ill-understood. In this review, we present the state of the art on mitochondrial genome structure, composition and organization in the apicomplexan phylum revisiting topological and biochemical information gathered through classical techniques. We contextualize this in light of the genomic insight gained by second and, more recently, third generation sequencing technologies. We discuss the mitochondrial genomic and mechanistic features found in evolutionarily related alveolates, and discuss the common and distinct origins of the apicomplexan mitochondria peculiarities.

show abstract

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

Cited by 25 publications

References 66 publications

Genome-wide localization of histone variants in Toxoplasma gondii implicates variant exchange in stage-specific gene expression

Genome-wide localization of histone variants in Toxoplasma gondii implicates variant exchange in stage-specific gene expression

Toxoplasma gondii Genotyping: A Closer Look Into Europe

The Elusive Mitochondrial Genomes of Apicomplexa: Where Are We Now?

Contact Info

Product

Resources

About