Composite genome map and recombination parameters derived from three archetypal lineages of Toxoplasma gondii

Asis Khan; Sonya Taylor; Chunlei Su; Aaron J. Mackey; Jon Boyle; Robert Cole; Darius Glover; Keliang Tang; Ian T. Paulsen; Matt Berriman; John C. Boothroyd; Elmer R. Pfefferkorn; J. P. Dubey; James W. Ajioka; David S. Roos; John C. Wootton; L. David Sibley

doi:10.1093/nar/gki604

Composite genome map and recombination parameters derived from three archetypal lineages of Toxoplasma gondii

Asis Khan, Sonya Taylor, Chunlei Su, Aaron J. Mackey, Jon Boyle, Robert Cole, Darius Glover, Keliang Tang, Ian T. Paulsen, Matt Berriman, John C. Boothroyd, Elmer R. Pfefferkorn, J. P. Dubey, James W. Ajioka, David S. Roos, John C. Wootton, L. David Sibley^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

147 Citations (Scopus)

Abstract

Toxoplasma gondii is a highly successful protozoan parasite in the phylum Apicomplexa, which contains numerous animal and human pathogens. T.gondii is amenable to cellular, biochemical, molecular and genetic studies, making it a model for the biology of this important group of parasites. To facilitate forward genetic analysis, we have developed a high-resolution genetic linkage map for T.gondii. The genetic map was used to assemble the scaffolds from a 10X shotgun whole genome sequence, thus defining 14 chromosomes with markers spaced at ∼300 kb intervals across the genome. Fourteen chromosomes were identified comprising a total genetic size of ∼592 cM and an average map unit of ∼104 kb/cM. Analysis of the genetic parameters in T.gondii revealed a high frequency of closely adjacent, apparent double crossover events that may represent gene conversions. In addition, we detected large regions of genetic homogeneity among the archetypal clonal lineages, reflecting the relatively few genetic outbreeding events that have occurred since their recent origin. Despite these unusual features, linkage analysis proved to be effective in mapping the loci determining several drug resistances. The resulting genome map provides a framework for analysis of complex traits such as virulence and transmission, and for comparative population genetic studies.

Original language	English
Pages (from-to)	2980-2992
Number of pages	13
Journal	Nucleic Acids Research
Volume	33
Issue number	9
DOIs	https://doi.org/10.1093/nar/gki604
Publication status	Published - 2005
Externally published	Yes

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Khan, A., Taylor, S., Su, C., Mackey, A. J., Boyle, J., Cole, R., Glover, D., Tang, K., Paulsen, I. T., Berriman, M., Boothroyd, J. C., Pfefferkorn, E. R., Dubey, J. P., Ajioka, J. W., Roos, D. S., Wootton, J. C., & Sibley, L. D. (2005). Composite genome map and recombination parameters derived from three archetypal lineages of Toxoplasma gondii. Nucleic Acids Research, 33(9), 2980-2992. https://doi.org/10.1093/nar/gki604

@article{11a309b05a9b4c43be31160c1810eb6e,

title = "Composite genome map and recombination parameters derived from three archetypal lineages of Toxoplasma gondii",

abstract = "Toxoplasma gondii is a highly successful protozoan parasite in the phylum Apicomplexa, which contains numerous animal and human pathogens. T.gondii is amenable to cellular, biochemical, molecular and genetic studies, making it a model for the biology of this important group of parasites. To facilitate forward genetic analysis, we have developed a high-resolution genetic linkage map for T.gondii. The genetic map was used to assemble the scaffolds from a 10X shotgun whole genome sequence, thus defining 14 chromosomes with markers spaced at ∼300 kb intervals across the genome. Fourteen chromosomes were identified comprising a total genetic size of ∼592 cM and an average map unit of ∼104 kb/cM. Analysis of the genetic parameters in T.gondii revealed a high frequency of closely adjacent, apparent double crossover events that may represent gene conversions. In addition, we detected large regions of genetic homogeneity among the archetypal clonal lineages, reflecting the relatively few genetic outbreeding events that have occurred since their recent origin. Despite these unusual features, linkage analysis proved to be effective in mapping the loci determining several drug resistances. The resulting genome map provides a framework for analysis of complex traits such as virulence and transmission, and for comparative population genetic studies.",

author = "Asis Khan and Sonya Taylor and Chunlei Su and Mackey, {Aaron J.} and Jon Boyle and Robert Cole and Darius Glover and Keliang Tang and Paulsen, {Ian T.} and Matt Berriman and Boothroyd, {John C.} and Pfefferkorn, {Elmer R.} and Dubey, {J. P.} and Ajioka, {James W.} and Roos, {David S.} and Wootton, {John C.} and Sibley, {L. David}",

year = "2005",

doi = "10.1093/nar/gki604",

language = "English",

volume = "33",

pages = "2980--2992",

journal = "Nucleic Acids Research",

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publisher = "Oxford University Press",

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Khan, A, Taylor, S, Su, C, Mackey, AJ, Boyle, J, Cole, R, Glover, D, Tang, K, Paulsen, IT, Berriman, M, Boothroyd, JC, Pfefferkorn, ER, Dubey, JP, Ajioka, JW, Roos, DS, Wootton, JC & Sibley, LD 2005, 'Composite genome map and recombination parameters derived from three archetypal lineages of Toxoplasma gondii', Nucleic Acids Research, vol. 33, no. 9, pp. 2980-2992. https://doi.org/10.1093/nar/gki604

TY - JOUR

T1 - Composite genome map and recombination parameters derived from three archetypal lineages of Toxoplasma gondii

AU - Khan, Asis

AU - Taylor, Sonya

AU - Su, Chunlei

AU - Mackey, Aaron J.

AU - Boyle, Jon

AU - Cole, Robert

AU - Glover, Darius

AU - Tang, Keliang

AU - Paulsen, Ian T.

AU - Berriman, Matt

AU - Boothroyd, John C.

AU - Pfefferkorn, Elmer R.

AU - Dubey, J. P.

AU - Ajioka, James W.

AU - Roos, David S.

AU - Wootton, John C.

AU - Sibley, L. David

PY - 2005

Y1 - 2005

N2 - Toxoplasma gondii is a highly successful protozoan parasite in the phylum Apicomplexa, which contains numerous animal and human pathogens. T.gondii is amenable to cellular, biochemical, molecular and genetic studies, making it a model for the biology of this important group of parasites. To facilitate forward genetic analysis, we have developed a high-resolution genetic linkage map for T.gondii. The genetic map was used to assemble the scaffolds from a 10X shotgun whole genome sequence, thus defining 14 chromosomes with markers spaced at ∼300 kb intervals across the genome. Fourteen chromosomes were identified comprising a total genetic size of ∼592 cM and an average map unit of ∼104 kb/cM. Analysis of the genetic parameters in T.gondii revealed a high frequency of closely adjacent, apparent double crossover events that may represent gene conversions. In addition, we detected large regions of genetic homogeneity among the archetypal clonal lineages, reflecting the relatively few genetic outbreeding events that have occurred since their recent origin. Despite these unusual features, linkage analysis proved to be effective in mapping the loci determining several drug resistances. The resulting genome map provides a framework for analysis of complex traits such as virulence and transmission, and for comparative population genetic studies.

AB - Toxoplasma gondii is a highly successful protozoan parasite in the phylum Apicomplexa, which contains numerous animal and human pathogens. T.gondii is amenable to cellular, biochemical, molecular and genetic studies, making it a model for the biology of this important group of parasites. To facilitate forward genetic analysis, we have developed a high-resolution genetic linkage map for T.gondii. The genetic map was used to assemble the scaffolds from a 10X shotgun whole genome sequence, thus defining 14 chromosomes with markers spaced at ∼300 kb intervals across the genome. Fourteen chromosomes were identified comprising a total genetic size of ∼592 cM and an average map unit of ∼104 kb/cM. Analysis of the genetic parameters in T.gondii revealed a high frequency of closely adjacent, apparent double crossover events that may represent gene conversions. In addition, we detected large regions of genetic homogeneity among the archetypal clonal lineages, reflecting the relatively few genetic outbreeding events that have occurred since their recent origin. Despite these unusual features, linkage analysis proved to be effective in mapping the loci determining several drug resistances. The resulting genome map provides a framework for analysis of complex traits such as virulence and transmission, and for comparative population genetic studies.

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U2 - 10.1093/nar/gki604

DO - 10.1093/nar/gki604

M3 - Article

C2 - 15911631

AN - SCOPUS:21144455796

SN - 0305-1048

VL - 33

SP - 2980

EP - 2992

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - 9

ER -

Composite genome map and recombination parameters derived from three archetypal lineages of Toxoplasma gondii

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