Bioinformatic strategies to provide functional clues to the unknown genes in Plasmodium falciparum genome

Abstract

The fight against Plasmodium falciparum, the species responsible for 90 % of the lethal forms of human malaria, took a new direction with the publication of its genome in 2002. However, the hopes that the genome should help bringing to the foreground the expected new “vaccines candidates” or “targets of new medicines” were disappointed by the low number of genes that could be functionally annotated – less than 40 % upon the genome publication, just over 50 % eight years later. This 10 % gain of knowledge was made possible by the efforts of the entire scientific community in many directions which include: the production of transcriptomic and proteomic profiles at various stages of the parasite development and in response to drug or stress treatments; the proteomic study of subcellular compartments; the sequencing of numerous Plasmodium related species (allowing whole genome comparisons) and the sequencing of numerous P. falciparum strains (allowing investigations of gene polymorphism). In parallel with this production of experimental biological data, the development of original mining tools adapted to the P. falciparum specificities quickly appeared as a priority, as the performances of “classical” bioinformatic tools, used successfully for other genomes, had limited efficacy. This was the aim of the PlasmoExplore project launched in 2007. This brief review does not cover all efforts made by the international community to decipher the P. falciparum genome but focuses on improvements and novel mining methods investigated by the PlasmoExplore consortium, and some of the lessons we could learn from these efforts.

Keywords

• Plasmodium
• genome
• bioinformatics
• annotations
• novel mining methods