Volkman et al (2) sequenced high-quality draft genomes of three

Volkman et al. (2) sequenced high-quality draft genomes of three parasite laboratory clones (the reference sequenced as 3D7, HB3 and Dd2) isolated from different parts of

the world. Their work alone identified 26845 single-nucleotide polymorphisms (SNPs) at a frequency of one SNP every 780 bases between the three clones and an additional 37 039 insertion–deletions (indels) between 3D7 and HB3. They further extended their genotyping to 12 P. falciparum strains and 20 genomic regions from 54 worldwide P. falciparum isolates. Results were consistent with initial genetic diversity studies that Opaganib were performed using whole-genome microarray analysis (5). All together, they identified more than 46937 SNPs (one every 446 bases in average) across the whole genome. High levels of SNPs were detected in genes involved in antigenic variation as well as genes involved in drug resistance. These data were further confirmed by the survey of approximately 60% CH5424802 chemical structure of P. falciparum predicted genes (3)

and a shotgun sequencing strategy of a Ghanaian clinical isolate (4). Taken together, these reports identified a high number of rare SNP variants and suggested that most SNPs have yet to be discovered. As a whole, these results underscore the importance of creating comprehensive maps of genetic diversity in P. falciparum field isolates. These SNPs are strongly suspected to be markers for various phenotypic traits such as virulence or resistance to drugs.

Recent advances in next-generation sequencing (NGS) technologies are enabling fast and affordable production of large amounts of genome sequence information. These technologies are already opening new perspectives of functional genomics in the field of primary, applied and clinical malaria research. After 30 years of dominance of first-generation ‘Sanger’ dideoxy sequencing, the past 5 years PJ34 HCl have seen the explosion of NGS methods. Next-generation sequencing has transformed the field of whole-genome sequencing and analysis. Unlike Sanger sequencing, NGS avoids the need for bacterial cloning and therefore bypasses associated biases. For example, AT- or GC-rich regions are often toxic to bacteria and difficult to reliably read with cloning-based sequencing. This issue is of major importance in the case of the P. falciparum’s extremely AT-rich genome. The major leap forward from NGS is the ability to produce an enormous amount of data within small volumes; a tremendous number of DNA fragments, up to 2 billion short reads per instrument run, can be sequenced in parallel. Three main NGS platforms have been commercialized over the past 5 years: the Roche 454 (Roche Life Sciences, Branford, CT, USA), the Applied Biosystems SOLiD (Applied Biosystems , Carlsbad, CA, USA) and finally the Illumina® (formally known as Solexa) Genome Analyzer and Hi-Seq platforms.

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