Abstract
BackgroundIn eukaryotic genomes, deletion or amplification rates have been estimated to be a thousand more frequent than single nucleotide variation. In Plasmodium falciparum, relatively few transcription factors have been identified, and the regulation of transcription is seemingly largely influenced by gene amplification events. Thus copy number variation (CNV) is a major mechanism enabling parasite genomes to adapt to new environmental changes.MethodsCurrently, the detection of CNVs is based on quantitative PCR (qPCR), which is significantly limited by the relatively small number of genes that can be analysed at any one time. Technological advances that facilitate whole-genome sequencing, such as next generation sequencing (NGS) enable deeper analyses of the genomic variation to be performed. Because the characteristics of Plasmodium CNVs need special consideration in algorithms and strategies for which classical CNV detection programs are not suited a dedicated algorithm to detect CNVs across the entire exome of P. falciparum was developed. This algorithm is based on a custom read depth strategy through NGS data and called PlasmoCNVScan.ResultsThe analysis of CNV identification on three genes known to have different levels of amplification and which are located either in the nuclear, apicoplast or mitochondrial genomes is presented. The results are correlated with the qPCR experiments, usually used for identification of locus specific amplification/deletion.ConclusionsThis tool will facilitate the study of P. falciparum genomic adaptation in response to ecological changes: drug pressure, decreased transmission, reduction of the parasite population size (transition to pre-elimination endemic area).
Highlights
In eukaryotic genomes, deletion or amplification rates have been estimated to be a thousand more frequent than single nucleotide variation
According to the results of the copy number obtained for 19 isolates, 21 isolates and 42 isolates with realtime PCR, a correlation line was established with the results from PlasmoCNVScan tool on illumina FASTq files
PlasmoCNVScan vs copy number variation (CNV)‐seq and CNVnator CNV‐seq As CNV-seq method is conceptually derived from array comparative genomic hybridization, two sets of reads mapped onto the same reference genome from the same flow cell is needed
Summary
Deletion or amplification rates have been estimated to be a thousand more frequent than single nucleotide variation. In Plasmodium falciparum, relatively few transcription factors have been identified, and the regulation of transcription is seemingly largely influenced by gene amplification events. Copy number variation (CNV) is a major mechanism enabling parasite genomes to adapt to new environmental changes. Natural evolution of malaria parasites generates an enormous amount of genetic diversity either linked with copy number variations (CNVs), or acquisition of new single nucleotide variations (SNVs) and their accumulation over time [2]. This allows parasites to acquire a high capacity of adaptation to the environmental shifts and develop anti-malarial drug resistance. CNV is a major mechanism enabling parasite genomes to adapt to new environmental changes
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