Abstract

Toxoplasma gondii is among the most prevalent parasites worldwide, infecting many wild and domestic animals and causing zoonotic infections in humans. T. gondii differs substantially in its broad distribution from closely related parasites that typically have narrow, specialized host ranges. To elucidate the genetic basis for these differences, we compared the genomes of 62 globally distributed T. gondii isolates to several closely related coccidian parasites. Our findings reveal that tandem amplification and diversification of secretory pathogenesis determinants is the primary feature that distinguishes the closely related genomes of these biologically diverse parasites. We further show that the unusual population structure of T. gondii is characterized by clade-specific inheritance of large conserved haploblocks that are significantly enriched in tandemly clustered secretory pathogenesis determinants. The shared inheritance of these conserved haploblocks, which show a different ancestry than the genome as a whole, may thus influence transmission, host range and pathogenicity.

Document Type

Article

Publication Date

1-7-2016

Notes/Citation Information

Published in Nature Communications, v. 7, article no. 10147, p. 1-13.

This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

Due to the large number of authors, only the first 30 and the authors affiliated with the University of Kentucky are listed in the author section above. For the complete list of authors, please download this article.

Digital Object Identifier (DOI)

https://doi.org/10.1038/ncomms10147

Funding Information

Sequencing, assembly and annotation for the Tg and Hh genomes reported here were supported by the National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Department of Health and Human Services under contract number HHSN272200900007C. Additional analyses were provided by community-based efforts and included support from NIH grants AI059176 and AI036629 (L.D.S.) and the Canadian Institutes for Health Research grant MOP 84556 (J.P.).

Related Content

Assembled and annotated sequences for the genomes of the T. gondii reference strains have been deposited in GenBank at NCBI under accession codes GT1 (GCA_000149715.2), VEG (GCA_000150015.2), ME49 (GCA_000006565.2), MAS (GCA_000224865.2), RUB (GCA_000224805.2), CAST (GCA_000256705.1), TgCtBr5 (GCA_000259835.1), P89 (GCA_000224885.2), VAND (GCA_000224845.2), COUG (GCA_000338675.1), ARI (GCA_000250965.1), TgCtPRC2 (GCA_000256725.1), GAB2-2007-GAL-DOM2 (GCA_000325525.2), TgCtCo5 (GCA_000278365.1), FOU (GCA_000224905.2) and TgCtBr9 (GCA_000224825.1). Assembled and annotated sequences for the genomes of the H. hammondi reference strains have been deposited in GenBank at NCBI under accession code GCA_000258005.2. The annotation of reference genomes are also available at ToxoDB (http://toxodb.org/common/downloads/WhitePaperProvisionalGenomes/): RNA-Seq reads for T. gondii strains have been deposited in the Sequence Read Archive at NCBI under accession codes GT1 (SRX099798) and ME49 (SRX099799). Sequence reads from the remaining T. gondii strains have been deposited in the Sequence Read Archive at NCBI under the following accession codes RH-88 (SRX160127, SRX160126), RH-JSR (SRX159850, SRX159851), TgCkCr1 (SRX160807), SOU (SRX160119), TgCkGy2 (SRX099785), CASTELLS (SRX099789), TgCatBr1 (SRX099790), TgCatBr18 (SRX099794), TgCatBr34 (SRX160051), BRC TgH 18002 GUY-KOE (SRX099796), BRC TgH 18003 GUY-MAT (SRX099783), GUY-2003-MEL (SRX160131), GUY-2004-ABE (SRX160132), TgRsCr1 (SRX160143), TgCkBr141 (SRX160124), TgCatBr25 (SRX160134), TgCatBr10 (SRX099791), TgCatBr64 (SRX160743), BRC TgH 18001 GUY-DOS (SRX099782), TgCkCr10 (SRX099784), B41 (SRX099774), RAY (SRX099793), TgCatBr44 (SRX160141), GAB1-2007-GAL-DOM10 (SRX159841, SRX159839), GAB3-2007-GAL-DOM9 (SRX160125), GAB5-2007-GAL-DOM6 (SRX159842, SRX159840), TgCatPRC3 (SRX09979), BRC TgH 18009 (SRX171132), BRC TgH 18021 (SRX160041), BRC TgH 20005 (SRX157499, SRX157465), BRC TgH 21016 (SRX099775), GUY-2004-JAG1 (SRX099776), B73 (SRX159844, SRX159843), PRU (SRX099792), M7741 (SRX159890, SRX159849), ROD (SRX160129, SRX160128), TgShUS28 (SRX160130), BOF (SRX099774), GAB5-2007-GAL-DOM1 (SRX160069), TgCatBr26 (SRX099780), TgCatBr72 (SRX160049), TgDogCo17 (SRX099787), TgCatBr15 (SRX099779), G662M (SRX160052), GAB3-2007-GAL-DOM2 (SRX160123), TgCatBr3 (SRX160142) and TgH26044 (SRX160050).

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Supplementary Information: Supplementary Figures 1-17, Supplementary Tables 1-2, Supplementary Methods and Supplementary References
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