Genome variation and evolution of the malaria parasite Plasmodium falciparum

Nature Genetics - Tập 39 Số 1 - Trang 120-125 - 2007
Daniel Jeffares1, Arnab Pain2, Andrew Berry2, Anthony V. Cox3, James Stalker3, Catherine Ingle3, Alan W. Thomas4, Michael A. Quail2, Kyle Siebenthall5,3, Anne‐Catrin Uhlemann6, Sue Kyes7, Sanjeev Krishna6, Chris Newbold7, Emmanouil T. Dermitzakis3, Matthew Berriman2
1Informatics Division, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, CB10 1SA Hinxton, UK.
2Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
3Informatics Division, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
4Biomedical Primate Research Centre, Lange Kleiweg 139, Rijswijk, Postbus 3306, Rijswijk, The Netherlands
5Department of Molecular Biology and Genetics, Cornell University, Ithaca, USA
6St George’s University of London, Cranmer Terrace, London, UK
7The Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK

Tóm tắt

Từ khóa


Tài liệu tham khảo

Korenromp, E., Miller, J., Nahlen, B., Wardlaw, T. & Young, M. World Malaria Report 2005 (Roll Back Malaria Partnership, Geneva, 2005).

Mu, J. et al. Chromosome-wide SNPs reveal an ancient origin for Plasmodium falciparum. Nature 418, 323–326 (2002).

Anderson, T.J. Mapping drug resistance genes in Plasmodium falciparum by genome-wide association. Curr. Drug Targets Infect. Disord. 4, 65–78 (2004).

Gardner, M.J. et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419, 498–511 (2002).

Ning, Z., Cox, A.J. & Mullikin, J.C. SSAHA: a fast search method for large DNA databases. Genome Res. 11, 1725–1729 (2001).

Anderson, T.J. et al. Microsatellite markers reveal a spectrum of population structures in the malaria parasite Plasmodium falciparum. Mol. Biol. Evol. 17, 1467–1482 (2000).

Volkman, S.K. et al. Excess polymorphisms in genes for membrane proteins in Plasmodium falciparum. Science 298, 216–218 (2002).

Carret, C.K. et al. Microarray-based comparative genomic analyses of the human malaria parasite Plasmodium falciparum using Affymetrix arrays. Mol. Biochem. Parasitol. 144, 177–186 (2005).

Yang, Z. & Bielawski, J.P. Statistical methods for detecting molecular adaptation. Trends Ecol. Evol. 15, 496–503 (2000).

McDonald, J.H. & Kreitman, M. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351, 652–654 (1991).

Rocha, E.P. The quest for the universals of protein evolution. Trends Genet. 22, 412–416 (2006).

Florens, L. et al. A proteomic view of the Plasmodium falciparum life cycle. Nature 419, 520–526 (2002).

Le Roch, K.G. et al. Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. Genome Res. 14, 2308–2318 (2004).

Bozdech, Z. et al. The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol. 1, E5 (2003).

Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25–29 (2000).

Marti, M., Good, R.T., Rug, M., Knuepfer, E. & Cowman, A.F. Targeting malaria virulence and remodeling proteins to the host erythrocyte. Science 306, 1930–1933 (2004).

Hall, N. et al. A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses. Science 307, 82–86 (2005).

Nielsen, R. et al. A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol. 3, e170 (2005).

Garnham, P.C.C. & Duggan, A.J. Malaria Parasites and Other Haemosporidia (Blackwell Scientific, Oxford, 1996).

Martin, M.J., Rayner, J.C., Gagneux, P., Barnwell, J.W. & Varki, A. Evolution of human-chimpanzee differences in malaria susceptibility: relationship to human genetic loss of N-glycolylneuraminic acid. Proc. Natl. Acad. Sci. USA 102, 12819–12824 (2005).

Winter, G. et al. SURFIN is a polymorphic antigen expressed on Plasmodium falciparum merozoites and infected erythrocytes. J. Exp. Med. 201, 1853–1863 (2005).

Li, F. et al. Plasmodium ookinete-secreted proteins secreted through a common micronemal pathway are targets of blocking malaria transmission. J. Biol. Chem. 279, 26635–26644 (2004).

Mu, J. et al. Genome-wide variation and identification of vaccine targets in the Plasmodium falciparum genome. Nat. Genet. advance online publication 10 December 2006 (doi:10.1038/ng1924).

Volkman, S.K. et al. A genome-wide map of diversity in Plasmodium falciparum. Nat. Genet. advance online publication 10 December 2006 (doi:10.1038/ng1930).

Horrocks, P., Kyes, S., Pinches, R., Christodoulou, Z. & Newbold, C. Transcription of subtelomerically located var gene variant in Plasmodium falciparum appears to require the truncation of an adjacent var gene. Mol. Biochem. Parasitol. 134, 193–199 (2004).

Bowman, S. et al. The complete nucleotide sequence of chromosome 3 of Plasmodium falciparum. Nature 400, 532–538 (1999).

Altshuler, D. et al. An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407, 513–516 (2000).

Yang, Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555–556 (1997).

Rand, D.M. & Kann, L.M. Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans. Mol. Biol. Evol. 13, 735–748 (1996).

Young, J.A. et al. The Plasmodium falciparum sexual development transcriptome: a microarray analysis using ontology-based pattern identification. Mol. Biochem. Parasitol. 143, 67–79 (2005).