In this application, the principal investigator proposes to use a shotgun sequencing strategy of isolated chromosomes to determine the entire sequence of chromosomes 9 and 10 of P. falciparum. The investigator plans to isolate the two chromosomes from the remainder of the genome by pulsed-field gel electrophoresis and make plasmid libraries from the isolated DNA. These clones will then be sequenced from each chromosome in a shotgun approach at about 8-fold redundancy, and the sequences will be assembled on a chromosome basis, Based on random distribution of clones a number of gaps, single-stranded regions, and regions of low quality will be present, and these will be fixed by using a number of strategies, including gap-filling, resequencing with additional sequence chemistries, and editing. Following assembly, the sequence will be annotated by applying several gene finding programs, comparing the genomic sequences that are currently being determined and identifying repeat sequences and other interesting structural features.
