Global Diversity Lines-A Five-Continent Reference Panel of Sequenced Drosophila melanogaster Strains.

Details

Serval ID
serval:BIB_FD38B0C5BD2F
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Global Diversity Lines-A Five-Continent Reference Panel of Sequenced Drosophila melanogaster Strains.
Journal
G3 Genes Genomes Genetics
Author(s)
Grenier J.K., Arguello J.R., Moreira M.C., Gottipati S., Mohammed J., Hackett S.R., Boughton R., Greenberg A.J., Clark A.G.
ISSN
2160-1836 (Electronic)
ISSN-L
2160-1836
Publication state
Published
Issued date
2015
Volume
5
Number
4
Pages
593-603
Language
english
Abstract
Reference collections of multiple Drosophila lines with accumulating collections of "omics" data have proven especially valuable for the study of population genetics and complex trait genetics. Here we present a description of a resource collection of 84 strains of Drosophila melanogaster whose genome sequences were obtained after 12 generations of full-sib inbreeding. The initial rationale for this resource was to foster development of a systems biology platform for modeling metabolic regulation by the use of natural polymorphisms as perturbations. As reference lines, they are amenable to repeated phenotypic measurements, and already a large collection of metabolic traits have been assayed. Another key feature of these strains is their widespread geographic origin, coming from Beijing, Ithaca, Netherlands, Tasmania, and Zimbabwe. After obtaining 12.5× coverage of paired-end Illumina sequence reads, SNP and indel calls were made with the GATK platform. Thorough quality control was enabled by deep sequencing one line to >100×, and single-nucleotide polymorphisms and indels were validated using ddRAD-sequencing as an orthogonal platform. In addition, a series of preliminary population genetic tests were performed with these single-nucleotide polymorphism data for assessment of data quality. We found 83 segregating inversions among the lines, and as expected these were especially abundant in the African sample. We anticipate that this will make a useful addition to the set of reference D. melanogaster strains, thanks to its geographic structuring and unusually high level of genetic diversity.
Keywords
D. melanogaster, global diversity lines, whole-genome sequences, inversion polymorphism, residual heterozygosity
Pubmed
Web of science
Open Access
Yes
Create date
01/05/2015 17:42
Last modification date
20/08/2019 17:28
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