A genetic map and recombination parameters of the human malaria parasite Plasmodium falciparum

Science

Volumn 286, Issue 5443, 1999, Pages 1351-1353

  Su, Xin Zhuan ^a   Ferdig, Michael T ^a   Huang, Yarning ^b   Huynh, Chuong Q ^c   Liu, Anna ^a   You, Jingtao ^a   Wootton, John C ^c   Wellems, Thomas E ^a  

^a NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES   (United States)

^b Guangxi Inst Parasitic Dis Contr   (China)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELISM; ARTICLE; CROSS LINKING; GENE CONVERSION; GENE LOCATION; GENE MAPPING; GENE SEQUENCE; GENETIC RECOMBINATION; GENETIC VARIABILITY; MALARIA; NONHUMAN; PLASMODIUM FALCIPARUM; PRIORITY JOURNAL; VIRULENCE;

ANIMALS; CHROMOSOME MAPPING; CROSSES, GENETIC; CROSSING OVER, GENETIC; GENE CONVERSION; GENETIC MARKERS; GENOME, PROTOZOAN; HAPLOTYPES; HUMANS; MEIOSIS; MICROSATELLITE REPEATS; MUTATION; PLASMODIUM FALCIPARUM; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RECOMBINATION, GENETIC;

EID: 0032698219     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.286.5443.1351     Document Type: Article

References (28)

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12. 19 oligonucleotides [X. Su and T. E. Wellems, Genomics 33, 430 (1996)]. Simple sequence repeats were also obtained from GenBank deposits and from the P. falciparum genome project, including data from recently reported sequences of chromosomes 2 and 3 [M. J. Gardner et al., Science 282, 1126 (1998); S. Bowman et al., Nature 400, 532 (1999); www.tigr.org/tdb/mdb/pfdb/pfdb.html; www.sanger.ac.uk/Projects/P_falciparum/; sequence-www.stanford.edu/group/malaria/index.html]. Fluorescent detection of microsatellites was according to X. Su, D. J. Carucci, and T. E. Wetlems [Exp. Parasitol. 89, 262 (1998)].
13. 19 oligonucleotides [X. Su and T. E. Wellems, Genomics 33, 430 (1996)]. Simple sequence repeats were also obtained from GenBank deposits and from the P. falciparum genome project, including data from recently reported sequences of chromosomes 2 and 3 [M. J. Gardner et al., Science 282, 1126 (1998); S. Bowman et al., Nature 400, 532 (1999); www.tigr.org/tdb/mdb/pfdb/pfdb.html; www.sanger.ac.uk/Projects/P_falciparum/; sequence-www.stanford.edu/group/malaria/index.html]. Fluorescent detection of microsatellites was according to X. Su, D. J. Carucci, and T. E. Wetlems [Exp. Parasitol. 89, 262 (1998)].
14. 19 oligonucleotides [X. Su and T. E. Wellems, Genomics 33, 430 (1996)]. Simple sequence repeats were also obtained from GenBank deposits and from the P. falciparum genome project, including data from recently reported sequences of chromosomes 2 and 3 [M. J. Gardner et al., Science 282, 1126 (1998); S. Bowman et al., Nature 400, 532 (1999); www.tigr.org/tdb/mdb/pfdb/pfdb.html; www.sanger.ac.uk/Projects/P_falciparum/; sequence-www.stanford.edu/group/malaria/index.html]. Fluorescent detection of microsatellites was according to X. Su, D. J. Carucci, and T. E. Wetlems [Exp. Parasitol. 89, 262 (1998)].
15. 19 oligonucleotides [X. Su and T. E. Wellems, Genomics 33, 430 (1996)]. Simple sequence repeats were also obtained from GenBank deposits and from the P. falciparum genome project, including data from recently reported sequences of chromosomes 2 and 3 [M. J. Gardner et al., Science 282, 1126 (1998); S. Bowman et al., Nature 400, 532 (1999); www.tigr.org/tdb/mdb/pfdb/pfdb.html; www.sanger.ac.uk/Projects/P_falciparum/; sequence-www.stanford.edu/group/malaria/index.html]. Fluorescent detection of microsatellites was according to X. Su, D. J. Carucci, and T. E. Wetlems [Exp. Parasitol. 89, 262 (1998)].
16. A. Walker-Jonah et al., Mol. Biochem. Parasitol. 51, 313 (1992). The 35 independent progeny were isolated from the set of HB3 × Dd2 clones described by L. A. Kirkman, X. Su, and T. E. Wellems [Exp. Parasitol. 83, 147 (1996)].
17. A. Walker-Jonah et al., Mol. Biochem. Parasitol. 51, 313 (1992). The 35 independent progeny were isolated from the set of HB3 × Dd2 clones described by L. A. Kirkman, X. Su, and T. E. Wellems [Exp. Parasitol. 83, 147 (1996)].
18. Assignments and relative order of the markers were determined by the Mapmaker program [S. E. Lincoln and E. S. Lander, Genomics 14, 604 (1992); E. S. Lander et al., Genomics 1, 174 (1987)]. Physical assignments of 154 markers were also established with chromosome DNAs separated by pulsed-field gradient electrophoresis.
19. Assignments and relative order of the markers were determined by the Mapmaker program [S. E. Lincoln and E. S. Lander, Genomics 14, 604 (1992); E. S. Lander et al., Genomics 1, 174 (1987)]. Physical assignments of 154 markers were also established with chromosome DNAs separated by pulsed-field gradient electrophoresis.
20. The full segregation data set, marker data, and mapping information are available at www.ncbi. nlm.nih.gov/Malaria/index.html.
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22. S. Karlin and U. Liberman, Adv. Appl. Probab. 11, 479 (1979); U. Liberman, J. Math. Biol. 21, 1 (1984). Poisson parameters were fitted to individual chromosomes as well as genome-wide crossover count distributions. Results were found to be consistent with a single count-location process, and generalized interference functions were not necessary to model the data.
23. Significant spikes of crossover activity were observed in chromosomes 12 and 9, whereas the elevation of counts seen near the RNA polymerase III gene in chromosome 13 (Fig. 3) is of marginal statistical significance (P = 0.06). A table comparing recombination frequencies in eukaryotic organisms is available at the National Center for Biotechnology Information web site (11).
24. The theoretical line was calculated from the distributions of the distances between pairs of random points occurring uniformly within a bounded interval. Fourteen individual computations were performed on the basis of the numbers of intermarker spaces in the 14 linkage groups. The model and its expected variance were confirmed by simulations. For the purpose of calculating map parameters, all single-marker events (n = 1; Fig. 4) were classified as gene conversion candidates and were excluded from counts of crossovers. All other events (n ≥ 2; Fig. 4) were classified as pairs of crossovers. Assignment errors in this classification scheme would have produced negligible consequence on the overall analysis, as they are few and tend to cancel out.
25. P. J. Hastings, Mutat. Res. 284, 97 (1992).
26. The eight markers with noncanonical alleles in multiple progeny are C3M29, TA101, C4M41, BM83, P11_1, CH12M29, C14M56, and C14M92; the other five markers are C4M76, C3M63, Y357M3, Y357M2.2, and TA88.
27. K. Hinterberg, D. Mattei, T. E. Wellems, A. Scherf, EMBO J. 13, 4174 (1994).
28. We thank T. Tatusov for graphical display software; D. Severson and A. A. Schärfer for discussions on linkage analysis; and K. Pruitt, J. Ostell, and D. Lipman for advice and support. Y. Huang gratefully acknowledges sabbatical support from the China Scholarship Council.