|
| | Plasmodium vivax Genome Project |
| TIGR Home | TIGR Database | Genome Home | Introduction | Related Links | Help | ||
|
Download |
Introduction - The Plasmodium vivax Genome DatabaseThe P. vivax genome The P. vivax nuclear genome is estimated to be 30 Mb in size and distributed among 14 chromosomes [1]. Both these estimates were deduced from separations of P. vivax chromosomes by pulsed-field gel electrophoresis, a technique which can be inaccurate especially as regards determination of genome size. Current estimates of the (G+C) content of the P. vivax genome put it at approximately 45%, in comparison to the (G+C) content of P. falciparum which is 19%. Sequencing methodology The P. vivax genome is being sequenced using a whole genome shotgun strategy [3]. This involves 5 basic steps as follows: library construction, random sequencing, assembly of the sequences, gap closure, and annotation of the finished sequence. Small and medium insert size libraries have been constructed in a plasmid vector, and the ends of inserts are being sequenced. The use of paired forward and reverse sequences will greatly simplify gap closure. In addition, the construction of a medium sized insert library will enable the construction of long "scaffolds", groups of contigs determined to be physically linked through paired reads. The Salvador I strain The strain of P. vivax being sequenced is Salvador I, first isolated in from a human infection in the area of Cangrejera, Department of La Paz, El Salvador in the 1960s [4]. The parasite has been passaged in human volunteers and in Aotus and Saimiri monkeys. Eight naive splenectomized Saimiri boliviensis boliviensis monkeys were infected with the Salvador I strain, the parasites extracted and DNA purified. Purification of the parasites from host nuclear material was attempted by a variety of means, although some monkey sequences are likely to be found among the P. vivax sequences. We are grateful to Drs. John Barnwell and William Collins at the Centers for Disease Control for the supply of P. vivax genomic DNA. References [1] Carlton JM, Galinski MR, Barnwell JW, Dame JB. "Karyotype and synteny among the chromosomes of all four species of human malaria parasite." Mol Biochem Parasitol. 1999 Jun 25;101(1-2):23-32. [2] Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM et al. "Genome sequence of the human malaria parasite Plasmodium falciparum." Nature. 2002 Oct 3;419(6906):498-511.[3] Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, Flanigan MJ, Kravitz SA, Mobarry CM,Reinert KH, Remington KA, Anson EL, Bolanos RA, Chou HH, Jordan CM, Halpern AL, Lonardi S,Beasley EM, Brandon RC, Chen L, Dunn PJ, Lai Z, Liang Y, Nusskern DR, Zhan M, Zhang Q, Zheng X, Rubin GM, Adams MD, Venter JC. "A whole-genome assembly of Drosophila." Science. 2000 Mar 24;287(5461):2196-204. [4] Collins WE, Contacos PG, Krotoski WA, Howard WA. "Transmission of four Central American strains of Plasmodium vivax from monkey to man." J Parasitol. 1972 Apr;58(2):332-5. For Comments/Questions send mail to py@tigr.org.
|