Project name: Drosophila melanogaster

Description: The role natural selection plays in governing the locations and early evolution of copy number mutations remains largely unexplored. Here we employ high-density full-genome tiling arrays to create a fine-scale genomic map of copy number polymorphisms (CNPs) in Drosophila melanogaster. We inferred a total of 2,658 independent CNPs, 56% of which overlap genes. These include CNPs likely to be under positive selection, most notably high frequency duplications encompassing toxin-response genes. The locations and frequencies of CNPs are strongly shaped by purifying selection with deletions under stronger purifying selection than duplications. Among duplications, those overlapping exons or introns and those falling on the X-chromosome seem to be subject to the strongest purifying selection.In order to characterize copy number polymorphisms (CNPs) in Drosophila malanogaster, we applied comparative genome hybridization (CGH) using tiling arrays covering the full euchromatic genome of Drosophila melanogaster. We inferred copy number changes with a Hidden Markov Model (HMM) that returned the posterior probabilities for copy number by comparing DNA hybridization intensities between natural isolates and the reference genome strain. Training data for copy number changes were obtained via hybridization with a line known to contain a ~200kb homozygous duplication and from a set of 52 validated homozygous deletions. The probabilities of mutation were parsed to make CNP calls.Key words: comparative genomic hybridization, CGH, copy number polymorphism, CNP, copy number variation, CNV, duplication, deletionOverall design: In all, 17 lines were used in this study: 15 natural isolates derived from throughout sub-Saharan Africa; and 2 laboratory strains representing the reference genome for the tiling arrays and a line containing probes known to be duplicated and deleted. Each line was represented by 3 array hybridizations, for a total of 51 hybridizations. Normalization and subsequent analysis was conducted independently on 15 sets of 9 arrays. Each set was composed of the 6 lab strains and the three replicates from one natural isolate.

Data type: Variation

Sample scope: Multiisolate

Relevance: ModelOrganism

Last updated: 2008-05-02