Published online 23 May 2005
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Composite genome map and recombination parameters derived from three archetypal lineages of Toxoplasma gondii
Department of Molecular Microbiology, Center for Infectious Diseases, Washington University School of Medicine St Louis, MO 63110, USA 1Department of Biology and Penn Genomics Institute, University of Pennsylvania Philadelphia, PA 19104, USA 2Department of Microbiology and Immunology, Stanford University School of Medicine Stanford, CA 94305, USA 3The Institute for Genomic Research Rockville, MD 20850, USA 4The Wellcome Trust Sanger Institute Hinxton, UK CB10 1SA 5Department of Microbiology and Immunology, Dartmouth Medical School Hanover, NH 03755, USA 6Animal Parasitic Disease Laboratory, ARS, ANRI, USDA Beltsville, MD 20705, USA 7Department of Pathology, Cambridge University Cambridge, UK CB2 1QP 8Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health Bethesda, MD 20894, USA
*To whom correspondence should be addressed. Tel: +1 314 362 8873; Fax: +1 314 286 0060; Email: sibley{at}borcim.wustl.edu
Received March 2, 2005. Revised May 2, 2005. Accepted May 2, 2005.
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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