Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster.

ABSTRACT: Short-read sequencing techniques provide the opportunity to capture genome-wide sequence data in a single experiment. A current challenge is to identify questions that shallow-depth genomic data can address successfully and to develop corresponding analytical methods that are statistically sound. Here, we apply the Roche/454 platform to survey natural variation in strains of Drosophila melanogaster from an African (n = 3) and a North American (n = 6) population. Reads were aligned to the reference D. melanogaster genomic assembly, single nucleotide polymorphisms were identified, and nucleotide variation was quantified genome wide. Simulations and empirical results suggest that nucleotide diversity can be accurately estimated from sparse data with as little as 0.2x coverage per line. The un

SUBMITTER: Sackton TB 

PROVIDER: S-EPMC2839279 | biostudies-literature | 2009 Nov

REPOSITORIES: biostudies-literature