Genomics

Dataset Information

0

Natural selection shapes genome wide patterns of copy number polymorphism in D. melanogaster


ABSTRACT: 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, deletion

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE11326 | GEO | 2008/06/06

SECONDARY ACCESSION(S): PRJNA106647

REPOSITORIES: GEO

Similar Datasets

2008-03-20 | GSE9639 | GEO
2011-02-01 | GSE26450 | GEO
2011-09-01 | GSE29260 | GEO
2006-02-16 | GSE4240 | GEO
| E-GEOD-29260 | biostudies-arrayexpress
2015-04-15 | GSE67871 | GEO
2011-03-03 | GSE27632 | GEO
| E-GEOD-35418 | biostudies-arrayexpress
2012-01-11 | GSE26607 | GEO
| E-GEOD-67871 | biostudies-arrayexpress