Abstract
BackgroundCopy number is a major source of genome variation with important evolutionary implications. Consequently, it is essential to determine copy number variant (CNV) behavior, distributions and frequencies across genomes to understand their origins in both evolutionary and generational time frames. We use comparative genomic hybridization (CGH) microarray and the resolution provided by a segregating population of cloned progeny lines of the malaria parasite, Plasmodium falciparum, to identify and analyze the inheritance of 170 genome-wide CNVs.ResultsWe describe CNVs in progeny clones derived from both Mendelian (i.e. inherited) and non-Mendelian mechanisms. Forty-five CNVs were present in the parent lines and segregated in the progeny population. Furthermore, extensive variation that did not conform to strict Mendelian inheritance patterns was observed. 124 CNVs were called in one or more progeny but in neither parent: we observed CNVs in more than one progeny clone that were not identified in either parent, located more frequently in the telomeric-subtelomeric regions of chromosomes and singleton de novo CNVs distributed evenly throughout the genome. Linkage analysis of CNVs revealed dynamic copy number fluctuations and suggested mechanisms that could have generated them. Five of 12 previously identified expression quantitative trait loci (eQTL) hotspots coincide with CNVs, demonstrating the potential for broad influence of CNV on the transcriptional program and phenotypic variation.ConclusionsCNVs are a significant source of segregating and de novo genome variation involving hundreds of genes. Examination of progeny genome segments provides a framework to assess the extent and possible origins of CNVs. This segregating genetic system reveals the breadth, distribution and dynamics of CNVs in a surprisingly plastic parasite genome, providing a new perspective on the sources of diversity in parasite populations.
Highlights
Copy number is a major source of genome variation with important evolutionary implications
copy number variant (CNV) are a significant source of segregating and de novo genome variation involving hundreds of genes
Genome-wide frequency of copy number variants We investigated genome wide distribution, frequency and characteristics of CNVs within a segregating population of progeny derived from a genetic cross between a multidrug resistant and a generally drug sensitive parasite [56]
Summary
Copy number is a major source of genome variation with important evolutionary implications. CNVs in P. falciparum have been studied in field isolates and laboratory adapted lines using various CGH platforms [18,19,20,22,23,24] These initially relied on expression microarray designs targeting open reading frames (ORFs), while more recent experiments use densely tiled probe sets across the genome [23]
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