"1000" Drosophila Genomes - DPGP3
Identifiers: SRA: SRP006733
UC Davis: DPGP3
UC Davis: DPGP3
Whole Genome Sequencing
The primary broad resource goal (deliverable to the community) in the next phase of DPGP is a proposed 600 high quality Drosophila melanogaster resequenced genomes and associated stocks. Such deep sampling from populations in Africa (species origin) and Eurasia (the ancient diaspora) will give a complete view of genomic variation in this species including vast numbers of rare variants of many different kinds (e.g. structural variants) throughout the genome. This resource will, of course, be available for the creative and powerful functional studies possible in this model organism. Like rare variants, less frequent (perhaps larger scale) haplotypes will become discernible in these larger samples and can be important in the investigation of natural selection and historical breeding structure. More generally, the large data set will drive the development of ideas, tools and talent that can augment the value and impact of such approaches in other species, especially in the ongoing large-scale human population genomic project. The second aim of the proposed resource will be the systematic description of genomic differentiation between temperate and tropical populations of D. melanogaster on several continents (effectively 300 high quality genome sequences). The goal here is to identify genomic regions that are candidates for selective adaptation on environmental gradients associated with latitude. The main impact of this resource will be detailed annotation of the D. melanogaster genome and the fostering of experimental population genomic approaches to the systematic identification of adaptations. The third aim of the proposed resource would enable population genomic research in seven non-model Drosophila species pairs, pseudoobscura-persimilis, yakuba-santomea, virilis-americana, pseudoobscura-miranda, ananassae-bipectinata and simulans-sechellia/mauritiana. In each case there is a reference sequence upon which a syntenic assembly can be founded. Five to 30 resequenced genomes (effectively 100X D. melanogaster genomes) are proposed for each of these smaller research communities to address their well-focused questions that include speciation, neo-sex chromosome evolution, recent evolution to a specialized (e.g. toxic) host, and sexual selection. The consideration and decisions about the specific genomes to be sequenced in all these project will be vetted with an advisory committee of the interested colleagues, which will be assembled once the project is initiated.
Illumina Paired End Genomic Resequencing - Siavonga (Zambia)